Index

A

A() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) A0 (PYME.DSView.modules.blobMeasure.DataBlock property) A1 (PYME.DSView.modules.blobMeasure.DataBlock property) A2 (PYME.DSView.modules.blobMeasure.DataBlock property) aberations (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) abort() (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Acquire.xyztc.XYZTCAcquisition method) (PYME.IO.Spooler.Spooler method) acquire_focus_lock() (PYME.Acquire.stage_leveling.StageLeveler method) AcquireClient (class in PYME.Acquire.acquire_client) AcquireHTTPServer (class in PYME.Acquire.acquire_server) AcquireHTTPServerMixin (class in PYME.Acquire.acquire_server) AcquireWxHTTPServer (class in PYME.Acquire.acquirewx) acquisition_cls (PYME.Acquire.SpoolController.SpoolController property) AcquisitionBase (class in PYME.Acquire.acquisition_base) Action (class in PYME.Acquire.actions) action_from_dict() (in module PYME.Acquire.actions) ACTION_POSITION (PYME.DSView.displayOptions.DisplayOpts attribute) ACTION_SELECT_OBJECT (PYME.DSView.displayOptions.DisplayOpts attribute) ACTION_SELECTION (PYME.DSView.displayOptions.DisplayOpts attribute) ActionManager (class in PYME.Acquire.ActionManager) ActionManagerServer (class in PYME.Acquire.ActionManager) ActionManagerWebWrapper (class in PYME.Acquire.ActionManager) actions (PYME.Acquire.htsms.tweeter.LazyScopeTweeter property) activate() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) active (PYME.ui.manualFoldPanel.CaptionButton property) adapt_numarray() (in module PYME.IO.FileUtils.thumbnailDatabase) (in module PYME.misc.sqlitendarray) add() (PYME.DSView.modules.annotation.AnnotationList method) add_96wp_positions() (PYME.Acquire.stage_leveling.StageLeveler method) add_common_menu_items() (PYME.ui.AUIFrame.AUIFrame method) add_curve() (PYME.DSView.modules.annotation.AnnotationList method) add_curved_line() (PYME.DSView.modules.annotation.AnnotateBase method) add_endpoints() (in module PYME.Acquire.webui) (PYME.util.webframework.APIHTTPServer method) add_filled_polygon() (PYME.DSView.modules.annotation.AnnotateBase method) add_grid() (PYME.Acquire.stage_leveling.StageLeveler method) add_ibidi8wellslide_positions() (PYME.Acquire.stage_leveling.StageLeveler method) add_integer_id_rule() (PYME.cluster.ruleserver.RuleServer method) add_layer() (PYME.LMVis.layer_panel.LayerPane method) (PYME.LMVis.visCore.VisGUICore method) add_layers() (PYME.LMVis.visCore.VisGUICore method) add_line() (PYME.DSView.modules.annotation.AnnotationList method) add_menu_item() (PYME.LMVis.Extras.dockedPanel.DockedPanel static method) add_mesh_layer() (PYME.LMVis.visCore.VisGUICore method) add_octree_layer() (in module PYME.LMVis.Extras.extra_layers) add_overlay() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) add_pointcloud_layer() (PYME.LMVis.visCore.VisGUICore method) add_polygon() (PYME.DSView.modules.annotation.AnnotationList method) add_position() (PYME.Acquire.stage_leveling.StageLeveler method) add_quiver_layer() (PYME.LMVis.visCore.VisGUICore method) add_rectangle() (PYME.DSView.modules.annotation.AnnotationList method) add_roi (PYME.tileviewer.tileviewer.TileServer attribute) add_service() (PYME.misc.pyme_zeroconf.ZCListener method) add_shader() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) add_shortcut() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) add_snapshot() (PYME.LMVis.Extras.animation.VideoPanel method) add_snapshot_to_list() (PYME.LMVis.Extras.animation.VideoPanel method) add_static_handler() (PYME.util.webframework.APIHTTPServer method) add_tesselation() (in module PYME.LMVis.Extras.extra_layers) add_tesselation_layer() (in module PYME.LMVis.Extras.extra_layers) add_tweet_condition() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) add_user() (in module PYME.util.authenticate) AddAqTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) AddCamTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) addChild() (PYME.cluster.webdav.Tag method) addColumn() (PYME.IO.tabular.DictSource method) (PYME.IO.tabular.MappingFilter method) addEdges() (in module PYME.Analysis.points.EdgeDB.edgeDB) AddElement() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) addEntries() (in module PYME.misc.tempDB) (PYME.ui.MetadataTree.MetadataPanel method) addEntry() (in module PYME.misc.tempDB) addEvents() (PYME.IO.h5rFile.H5RFile method) addFrame() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) additionalDims (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource property) AddMenuItem() (PYME.LMVis.visCore.VisGUICore method) (PYME.ui.AUIFrame.AUIFrame method) AddNewElement() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) AddPage() (PYME.ui.AUIFrame.AUIFrame method) AddPane() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) AddRecord() (PYME.Analysis.processLogger.BackendBase method) (PYME.Analysis.processLogger.ContextLayer method) (PYME.Analysis.processLogger.ContextManager method) (PYME.Analysis.processLogger.TablesBackend method) address (PYME.misc.sqlite_ns.NSInfo attribute) AddSlice() (PYME.IO.FileUtils.saveTiffStack.TiffMP method) AddTool() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) addVariable() (PYME.IO.tabular.MappingFilter method) AddVoxelSizeSetting() (PYME.Acquire.microscope.Microscope method) advert (PYME.cluster.ruleserver.IntegerIDRule property) af() (PYME.Acquire.autofocus.AutoFocus method) afterPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) Afunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method)

aggregate_dirlisting() (in module PYME.IO.clusterListing) aggregateMean() (in module PYME.Analysis.points.DeClump.deClump) aggregateMin() (in module PYME.Analysis.points.DeClump.deClump) aggregateSum() (in module PYME.Analysis.points.DeClump.deClump) aggregateWeightedMean() (in module PYME.Analysis.points.DeClump.deClump) Ahfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) all (PYME.Analysis.Tracking.trackUtils.ClumpManager property) (PYME.Analysis.Tracking.trackUtils.TrackManager property) all_props (PYME.cluster.webdav.DAVRequestHandler attribute) allmodules() (in module PYME.DSView.modules) alpha (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute) AnalysisDetailsPanel (class in PYME.Acquire.ui.AnalysisSettingsUI) analysisMDH (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisDetailsPanel property) (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettingsPanel property) AnalysisSettings (class in PYME.Acquire.ui.AnalysisSettingsUI) AnalysisSettingsPanel (class in PYME.Acquire.ui.AnalysisSettingsUI) angHist() (in module PYME.Analysis.angleFilter) angHist2() (in module PYME.Analysis.angleFilter) angle_filter() (in module PYME.Analysis.angleFilter) angle_filter_m() (in module PYME.Analysis.angleFilter) angularDist() (PYME.DSView.modules.blobMeasure.BlobObject method) aniso() (in module PYME.misc.aniso) anisodiff() (in module PYME.contrib.aniso.aniso) anisodiff3() (in module PYME.contrib.aniso.aniso) AnndataSource (class in PYME.IO.tabular) annealThresh() (in module PYME.Analysis.annealThresh) annealThresh2() (in module PYME.Analysis.annealThresh) annealThresh2D() (in module PYME.Analysis.annealThresh) AnnotateBase (class in PYME.DSView.modules.annotation) Annotater (class in PYME.DSView.modules.annotation) AnnotationList (class in PYME.DSView.modules.annotation) AnnotationOverlayLayer (class in PYME.LMVis.Extras.annotation) Annotator (class in PYME.LMVis.Extras.annotation) Any (in module PYME.misc.mock_traits) APIHTTPServer (class in PYME.util.webframework) apodization (PYME.DSView.modules.psfTools.PSFTools attribute) (PYME.DSView.modules.pupilTools.PupilTools attribute) append() (PYME.DSView.displayOptions.MyWeakSet method) Append() (PYME.DSView.modules.composite.ImageList method) appendToTable() (PYME.IO.h5rFile.H5RFile method) apply_labels_to_points() (PYME.LMVis.Extras.annotation.Annotator method) apply_mask() (PYME.DSView.modules.annotation.Annotater method) apply_shifts_to_points() (in module PYME.Analysis.points.multiview) applyByChannel() (in module PYME.Analysis.BleachProfile.kinModels) applyLUT() (in module PYME.DSView.LUT) applyLUTf() (in module PYME.DSView.LUT.lut) applyLUTu16() (in module PYME.DSView.LUT.lut) applyLUTu8() (in module PYME.DSView.LUT.lut) approximate_image_bounds() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) approximate_normal() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) approximate_zernikes() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) arcmf() (in module PYME.Analysis.points.arcfit.arcmf) arcmft() (in module PYME.Analysis.points.arcfit.arcmf) arrangeNodes() (in module PYME.misc.depGraph) arrangeNodes_() (in module PYME.misc.depGraph) ArrayDataSource (class in PYME.IO.DataSources.ArrayDataSource) ArrayFrame (class in PYME.ui.recArrayView) ArrayPanel (class in PYME.ui.recArrayView) ArrayViewPanel (class in PYME.DSView.arrayViewPanel) asarray() (PYME.contrib.gohlke.czifile.CziFile method) (PYME.contrib.gohlke.fcsfiles.ConfoCor2Raw method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) (PYME.contrib.gohlke.tifffile.TIFFfile method) ASF() (in module PYME.misc.snells) assemble_tiles() (in module PYME.Analysis.deTile) assemble_tiles_xyztc() (in module PYME.Analysis.deTile) assert_name_ok() (in module PYME.IO.unifiedIO) assert_path_ok() (in module PYME.IO.unifiedIO) assert_uri_ok() (in module PYME.IO.unifiedIO) assert_uri_path_ok() (in module PYME.IO.unifiedIO) astig_lookup() (in module PYME.Analysis.points.astigmatism.astiglookup) astigmatic_gaussian() (in module PYME.localization.FitFactories.AstigGaussGPUFitFR) atleast_nd() (in module PYME.Analysis.tile_pyramid) (in module PYME.IO.DataSources.ArrayDataSource) attachment_directory (PYME.contrib.gohlke.czifile.CziFile attribute) attachments() (PYME.contrib.gohlke.czifile.CziFile method) AUIFrame (class in PYME.ui.AUIFrame) Auserlist (PYME.cluster.webdav.DAVRequestHandler attribute) auth_enable (PYME.cluster.webdav.DAVRequestHandler attribute) auth_file (PYME.cluster.webdav.DAVRequestHandler attribute) authenticate() (in module PYME.util.authenticate) authenticate_hash() (in module PYME.util.authenticate) auto_promote() (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper class method) AutoFocus (class in PYME.Acquire.autofocus) autostart_analysis (PYME.Acquire.SpoolController.SpoolController property) AutoWidthListCtrl (class in PYME.Acquire.sampleInformation) available_spool_methods (PYME.Acquire.SpoolController.SpoolController property) averageNormals() (in module PYME.Analysis.points.gen3DTriangs) averageNormalsF() (in module PYME.Analysis.points.gen3DTriangs) axes (PYME.contrib.gohlke.czifile.CziFile attribute) AxesOverlayLayer (class in PYME.LMVis.layers.AxesOverlayLayer) axis_scaling (PYME.simulation.pointsets.SHNucleusSource attribute) axis_sigmas (PYME.simulation.pointsets.SHNucleusSource attribute)

B

Backend (class in PYME.Analysis.points.features.metal) (class in PYME.IO.acquisition_backends) BackendBase (class in PYME.Analysis.processLogger) background() (in module PYME.Analysis.PSFEst.psfQuality) (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) backgroundBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) backgroundBufferM (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) backgroundBufferMC (class in PYME.IO.buffers) backgroundCorrectPSFWF() (in module PYME.Analysis.PSFEst.extractImages) backgroundIntensity (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) BACKWARDS (PYME.Acquire.stackSettings.StackSettings attribute) bandwidthTesting (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) bareDNA() (in module PYME.simulation.wormlike) (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) base64_image() (in module PYME.IO.rgb_image) baseconvert() (in module PYME.IO.FileUtils.nameUtils) BaseDataSource (class in PYME.IO.DataSources.BaseDataSource) BaseEngine (class in PYME.LMVis.layers.base) BaseEnum (class in PYME.misc.mock_traits) BaseFloat (in module PYME.misc.mock_traits) BaseHDFSource (class in PYME.IO.tabular) BaseLayer (class in PYME.LMVis.layers.base) basePupil (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) basic_props (PYME.cluster.webdav.DAVRequestHandler attribute) bbox (PYME.DSView.modules.blobMeasure.DataBlock property) (PYME.LMVis.layers.base.BaseLayer property) (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.labels.LabelLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) bead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) bf_int() (in module PYME.Analysis.BleachProfile.intensProf) bgFrameBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) bgFrameBufferC (class in PYME.IO.buffers) BGInitTask (class in PYME.Acquire.ExecTools) Bid (class in PYME.cluster.ruleserver) bid() (PYME.cluster.ruleserver.IntegerIDRule method)

bid_on_tasks() (PYME.cluster.ruleserver.RuleServer method) bidder_id (PYME.cluster.ruleserver.Bid attribute) BigGouraudFlatpointsShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) BigGouraudSphereShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) BigOpaquePointShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) BigPointSpriteShaderProgram (class in PYME.LMVis.shader_programs.PointSpriteShaderProgram) BigTransparentPointShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) binAvg() (in module PYME.Analysis.binAvg) bind_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) BindMixin (class in PYME.LMVis.layers.base) binMedian() (in module PYME.Analysis.binAvg) binned_average() (in module PYME.Analysis.binAvg) binned_median() (in module PYME.Analysis.binAvg) BitmapFromImage() (in module PYME.ui.wx_compat) BitPacker (class in PYME.contrib.lzw) bitstobytes() (in module PYME.contrib.lzw) BitUnpacker (class in PYME.contrib.lzw) BlankResult() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) blob() (in module PYME.Analysis.tile_pyramid) blobColourKey (PYME.LMVis.triBlobs.BlobSettings attribute) BlobFinder (class in PYME.DSView.modules.blobFinding) (class in PYME.DSView.modules.shiftfield_estimation) blobify() (in module PYME.Analysis.points.gen3DTriangs) blobify2D() (in module PYME.Analysis.points.gen3DTriangs) BlobObject (class in PYME.DSView.modules.blobMeasure) BlobSettings (class in PYME.LMVis.triBlobs) BlobSettingsPanel (class in PYME.LMVis.triBlobs) Blue() (in module PYME.misc.colormaps) Bool (in module PYME.misc.mock_traits) bool_map_between_events() (in module PYME.Analysis.piecewiseMapping) BoolFloatParam (class in PYME.localization.MetaDataEdit) BoolParam (class in PYME.localization.MetaDataEdit) bounds (PYME.IO.image.ImageBounds property) BufferManager (class in PYME.localization.remFitBuf) BufWriter (class in PYME.cluster.webdav) build_call_tree_threads() (in module PYME.util.fProfile.convertProfile) builddict() (in module PYME.cluster.webdav) (PYME.cluster.webdav.XMLDict_Parser method) ByteDecoder (class in PYME.contrib.lzw) ByteEncoder (class in PYME.contrib.lzw) bytestobits() (in module PYME.contrib.lzw)

C

C (in module PYME.Acquire.protocol) c_mul() (in module PYME.misc.hash32) CacheEntry (class in PYME.Analysis.tile_pyramid) CachingMDHandler (class in PYME.IO.MetaDataHandler) CachingResultsFilter (class in PYME.IO.tabular) cachingResultsFilter() (in module PYME.IO.tabular) calc_gauss_weights() (in module PYME.localization.ofind) (in module PYME.localization.ofind_pri) (in module PYME.localization.ofind_split) calc_shifts_for_points() (in module PYME.Analysis.points.multiview) calcCenteredMoments() (in module PYME.Analysis.points.moments) calcCoeffs() (in module PYME.misc.zernike) calcCoeffs_rays() (in module PYME.misc.zernike) calcCorrections() (in module PYME.Analysis.points.twoColour) calcCorrShift() (in module PYME.Analysis.deTile) CalcCramerRao() (in module PYME.Analysis.cramerRao) CalcCramerReoZ() (in module PYME.Analysis.cramerRao) calcCRB() (PYME.DSView.modules.psfTools.CRBViewPanel method) calcDistances() (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) calcDistCorr() (in module PYME.Analysis.Colocalisation.distColoc) calcEdgeDists() (in module PYME.Analysis.points.objectMeasure) calcEdgeLengths() (in module PYME.Analysis.points.EdgeDB.edgeDB) CalcFisherInfoModel() (in module PYME.Analysis.cramerRao) CalcFisherInform2D() (in module PYME.Analysis.cramerRao) CalcFisherInformZ() (in module PYME.Analysis.cramerRao) CalcFisherInformZn() (in module PYME.Analysis.cramerRao) CalcFisherInformZn2() (in module PYME.Analysis.cramerRao) calcLinkageMatrix() (PYME.Analysis.Tracking.tracking.Tracker method) calcLinkages() (PYME.Analysis.Tracking.tracking.Tracker method) calcMCCenteredMoments() (in module PYME.Analysis.points.moments) calcMeanEdge() (in module PYME.Analysis.points.gen3DTriangs) calcMEs() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) calcNeighbourDistPart() (in module PYME.LMVis.visHelpers) calcNeighbourDists() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) calcProf() (in module PYME.Analysis.BleachProfile.intensProf) calcSigma() (PYME.localization.remFitBuf.fitTask class method) calcTetVolume() (in module PYME.Analysis.points.gen3DTriangs) calcThreshold() (PYME.localization.remFitBuf.fitTask method) calcTrackVelocity() (in module PYME.Analysis.Tracking.trackUtils) calcTs() (in module PYME.Analysis.BleachProfile.intensProf) calcTwist() (in module PYME.localization.twist) calculate_length_with_reversal() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) calculate_path_length() (in module PYME.Analysis.points.traveling_salesperson.two_opt) CalcUnscrolledPosition() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) calibrate() (in module PYME.localization.FitFactories.zEstimators.astigEstimator) (in module PYME.localization.FitFactories.zEstimators.biplaneEstimator) (in module PYME.localization.FitFactories.zEstimators.genericDualEstimator) (in module PYME.localization.FitFactories.zEstimators.genericEstimator) (in module PYME.localization.FitFactories.zEstimators.priEstimator) call_in_main_thread() (in module PYME.ui.mytimer) (PYME.Acquire.event_loop.EventLoop method) CameraChooserPanel (class in PYME.Acquire.ui.selectCameraPanel) CameraInfoManager (class in PYME.localization.remFitBuf) can_fold (PYME.ui.manualFoldPanel.foldingPane property) CaptionButton (class in PYME.ui.manualFoldPanel) cart2sph() (in module PYME.Analysis.points.coordinate_tools) cartesian_to_spherical() (in module PYME.Analysis.points.coordinate_tools) cascading_layout() (PYME.ui.cascading_layout.CascadingLayoutMixin method) (PYME.ui.manualFoldPanel.foldPanel method) CascadingLayoutMixin (class in PYME.ui.cascading_layout) CascadingLayoutPanel (class in PYME.ui.cascading_layout) Cauchy() (in module PYME.misc.glassModel) CDLL (class in PYME.misc.mock_ctypes) center() (PYME.Acquire.zScanner.zScanner method) centre (PYME.simulation.pointsets.WiglyFibreSource attribute) CENTRE_AND_LENGTH (PYME.Acquire.stackSettings.StackSettings attribute) centre_roi_on() (PYME.Acquire.microscope.Microscope method) CentreROIOn (class in PYME.Acquire.actions) centroid (PYME.DSView.modules.blobMeasure.DataBlock property) centroidNM (PYME.DSView.modules.blobMeasure.DataBlock property) cglob() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) chain() (PYME.cluster.rules.RuleFactory method) change_text_flavour() (PYME.LMVis.importTextDialog.ImportTextDialog method) channel (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) channel_rois (PYME.Analysis.splitting.SplittingInfo property) channel_shape (PYME.Analysis.splitting.SplittingInfo property) ChannelFoldingPane (class in PYME.ui.layerFoldPanel) check_for_updates() (in module PYME.misc.check_for_updates) check_inside() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) check_name() (in module PYME.IO.unifiedIO) check_path() (in module PYME.IO.unifiedIO) check_required_names() (in module PYME.IO.csv_flavours) check_uri() (in module PYME.IO.unifiedIO) CheckColNames() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) checkHardware() (PYME.Acquire.frameWrangler.FrameWrangler method) CheckItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) CheckListCtrlMixin (class in PYME.contrib.listctrlMixins) ChecksumFitFactory (class in PYME.localization.FitFactories.ChecksumFR) (class in PYME.localization.FitFactories.ChecksumGPUFR) (class in PYME.localization.FitFactories.ChecksumMultifitSR) checkTQ() (PYME.DSView.modules.deconvolution.Deconvolver method) CheckWxPhoenix() (in module PYME.ui.wx_compat) cherrypy_server() (in module PYME.cluster.dataserver_wsgi) chi2_mse() (in module PYME.Analysis.BleachProfile.kinModels) ChoiceParam (class in PYME.localization.MetaDataEdit) ChunkedHuffmanCompress() (in module PYME.IO.PZFFormat) ChunkedHuffmanCompress_o() (in module PYME.IO.PZFFormat) ChunkedHuffmanDecompress() (in module PYME.IO.PZFFormat) CInt (in module PYME.misc.mock_traits) circGeom (class in PYME.misc.coverslipGeometries) CircularScanner (class in PYME.Acquire.Utils.pointScanner) CircularTilePanel (class in PYME.Acquire.ui.tile_panel) ClassicMappingFFTW (class in PYME.Deconv.dec) ClassicMappingNP (class in PYME.Deconv.dec) classify() (PYME.Analysis.svmSegment.svmClassifier method) cleanup() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) (PYME.cluster.HTTPTaskPusher.HTTPTaskPusher method) (PYME.cluster.rules.Rule method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) clear() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) (PYME.LMVis.Extras.animation.VideoPanel method) Clear() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) clear_all() (PYME.DSView.modules.annotation.AnnotateBase method) clear_positions() (PYME.Acquire.stage_leveling.StageLeveler method) clear_rois (PYME.tileviewer.tileviewer.TileServer attribute) clear_selected() (PYME.DSView.modules.annotation.AnnotateBase method) clear_shader_clipping() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) clear_view() (PYME.LMVis.Extras.animation.VideoPanel method) ClearTrack() (PYME.Acquire.positionTracker.PositionTracker method) click_test() (PYME.ui.manualFoldPanel.CaptionButton method) client_disconnected() (PYME.Acquire.webui.ipy.IPYTermManager method) clim (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.labels.LabelLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) clip_plane_matrix (PYME.LMVis.views.View property) clipped_widefield_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) ClippingPanel (class in PYME.LMVis.view_clipping_pane) CloneSource (class in PYME.IO.tabular) cloneSource() (in module PYME.IO.tabular) close() (PYME.contrib.gohlke.czifile.CziFile method) (PYME.contrib.gohlke.fcsfiles.ConfoCor2Raw method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Fcs method) (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) (PYME.contrib.gohlke.tifffile.TIFFfile method) (PYME.IO.cluster_streaming.Stream method) (PYME.IO.cluster_streaming.Streamer method) (PYME.IO.FileUtils.obf_support.File method) (PYME.IO.FileUtils.saveTiffStack.TiffMP method) (PYME.IO.tabular.BaseHDFSource method) CloseEditor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) Clump (class in PYME.Analysis.Tracking.trackUtils) clump_key (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) ClumpManager (class in PYME.Analysis.Tracking.trackUtils) cluster() (in module PYME.Analysis.points.tCluster) ClusterAnalyser (class in PYME.LMVis.Extras.clusterAnalysis) ClusterBackend (class in PYME.IO.acquisition_backends) ClusterOfOne (class in PYME.cluster.cluster_of_one) ClusterPZFTileCache (class in PYME.Analysis.tile_pyramid) ClusterPZFTileIO (class in PYME.Analysis.tile_pyramid) cmap (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.labels.LabelLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) CMapDict (class in PYME.misc.colormaps) cmapnames (PYME.misc.colormaps.CMapDict property) cmp() (in module PYME.contrib.listctrlMixins)

cnn_filter() (in module PYME.DSView.modules.convnet) coalesce_dict_sorted() (in module PYME.Analysis.points.multiview) coalesceClumps() (in module PYME.Analysis.points.DeClump.pyDeClump) coalesceClumps_() (in module PYME.Analysis.points.DeClump.pyDeClump) code_size() (PYME.contrib.lzw.Decoder method) (PYME.contrib.lzw.Encoder method) coeff (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) COIFitFactory (class in PYME.localization.FitFactories.LatFitCOIR) (class in PYME.localization.FitFactories.SplitterFitCOIR) COIFitResultR() (in module PYME.localization.FitFactories.ConfocCOIR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.SplitterFitCOIR) collapsingPane (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) collectConnected() (in module PYME.Analysis.points.EdgeDB.segment) (in module PYME.Analysis.points.gen3DTriangs) Collection (class in PYME.cluster.webdav) COLLECTION_MIME_TYPE (PYME.cluster.webdav.DirCollection attribute) Colocaliser (class in PYME.DSView.modules.coloc) ColocSettingsDialog (class in PYME.DSView.modules.coloc) (class in PYME.DSView.modules.fourierRingCorrelation) colorize_file() (in module PYME.util.mProfile.colorize_db_t) colour() (in module PYME.Analysis.PSFEst.psfQuality) colour_map (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.labels.LabelLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) colourDataKey (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute) ColourFilter (class in PYME.IO.tabular) colourFilter (PYME.LMVis.renderers.CurrentRenderer property) colourFilter() (in module PYME.IO.tabular) ColourFilterPane (class in PYME.LMVis.colourFilterGUI) ColourFromStyle() (in module PYME.ui.autoFoldPanel) (in module PYME.ui.manualFoldPanel) ColourImageViewPanel (class in PYME.LMVis.imageView) (class in PYME.LMVis.imageView2) ColourRenderer (class in PYME.LMVis.renderers) ColumnMappingDialog (class in PYME.LMVis.importTextDialog) ColumnSorterMixin (class in PYME.contrib.listctrlMixins) ColumnSource (class in PYME.IO.tabular) common_prefix() (in module PYME.Analysis.composite) complete (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.Rule property) complexMode (PYME.DSView.displayOptions.DisplayOpts property) CompositeDialog (class in PYME.DSView.modules.composite) Compositor (class in PYME.DSView.modules.composite) compress() (in module PYME.contrib.lzw) ComputationInProgress (class in PYME.ui.progress) computeLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) ConcatenateFilter (class in PYME.IO.tabular) concatenateFilter() (in module PYME.IO.tabular) configuration() (in module PYME.Acquire.setup) (in module PYME.Analysis.points.arcfit.setup) (in module PYME.Analysis.points.astigmatism.setup) (in module PYME.Analysis.points.DeClump.setup) (in module PYME.Analysis.points.DistHist.setup) (in module PYME.Analysis.points.EdgeDB.setup) (in module PYME.Analysis.points.setup) (in module PYME.Analysis.points.SoftRend.setup) (in module PYME.Analysis.points.traveling_salesperson.setup) (in module PYME.Analysis.PSFGen.setup) (in module PYME.Analysis.setup) (in module PYME.contrib.gohlke.setup) (in module PYME.contrib.setup) (in module PYME.DSView.LUT.setup) (in module PYME.DSView.setup) (in module PYME.IO.countdir.setup) (in module PYME.IO.FileUtils.setup) (in module PYME.IO.setup) (in module PYME.LMVis.setup) (in module PYME.localization.cInterp.setup) (in module PYME.localization.cModels.setup) (in module PYME.localization.setup) (in module PYME.resources.setup) (in module PYME.setup) (in module PYME.setup_exe) confocal_parser (class in PYME.DSView.logparser) ConfocCOI() (in module PYME.localization.FitFactories.ConfocCOIR) ConfoCor2Raw (class in PYME.contrib.gohlke.fcsfiles) ConfoCor3Fcs (class in PYME.contrib.gohlke.fcsfiles) ConfoCor3Raw (class in PYME.contrib.gohlke.fcsfiles) congrid() (in module PYME.contrib.congrid) connect() (PYME.contrib.dispatch.dispatcher.Signal method) ContextLayer (class in PYME.Analysis.processLogger) ContextManager (class in PYME.Analysis.processLogger) Controller() (in module PYME.misc.mock_traitsui) convert() (in module PYME.util.fProfile.convertProfile) convert_numarray() (in module PYME.IO.FileUtils.thumbnailDatabase) (in module PYME.misc.sqlitendarray) convertFile() (in module PYME.IO.FileUtils.h5rToTxt) (in module PYME.IO.FileUtils.RawToHdf5) convertFiles() (in module PYME.IO.FileUtils.TiffSeqToHdf5) copy() (PYME.LMVis.views.View class method) copy_sample_metadata() (in module PYME.LMVis.renderers) copyEntriesFrom() (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.QueueMDHandler method) CopyImage() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) CopyOnWriteMDHandler (class in PYME.IO.MetaDataHandler) correct() (PYME.Analysis.splitting.ShiftCorrector method) correct_target_positions() (in module PYME.Analysis.piezo_movement_correction) correctImage() (PYME.localization.remFitBuf.CameraInfoManager method) correlate() (PYME.localization.ofind_xcorr_fw.fftwWeiner method) correlative_shift() (in module PYME.Analysis.points.multiview) corrScale() (in module PYME.Analysis.Colocalisation.colocScaleDep) cost (PYME.cluster.ruleserver.Bid attribute) COST_THRESHOLD (PYME.cluster.ruleserver.IntegerIDRule attribute) crb3d() (in module PYME.Analysis.PSFEst.psfQuality) CRBViewPanel (class in PYME.DSView.modules.psfTools) create() (in module PYME.Acquire.acquiremainframe) (in module PYME.Acquire.acquirewx) (in module PYME.Acquire.ui.seqdialog) (in module PYME.util.shmarray.shmarray) create_and_set_shader_program() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) create_buttons() (PYME.LMVis.Extras.saved_views.ViewPanel method) create_copy() (in module PYME.util.shmarray.shmarray) create_ctrls() (PYME.DSView.OverlaysPanel.OverlayPanel method) create_distributed_pyramid_from_dataset() (in module PYME.Analysis.distributed_pyramid) create_editor() (PYME.simulation.pointsets.WRDictEnum method) create_gui() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) create_ipy_server() (in module PYME.Acquire.webui.ipy) create_overlay_panel() (PYME.DSView.dsviewer.DSViewFrame method) create_pyramid_from_dataset() (in module PYME.Analysis.tile_pyramid) create_remote_part() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) create_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) create_tool_bar() (PYME.LMVis.visCore.VisGUICore method) CreateColourFilterPane() (in module PYME.LMVis.colourFilterGUI) CreateDisplayPane() (in module PYME.LMVis.displayPane) CreateFilterPane() (in module PYME.DSView.modules.measure.filterPan) (in module PYME.ui.filterPane) createFitTaskFromTaskDef() (in module PYME.localization.remFitBuf) CreateFoldPanel() (PYME.ui.AUIFrame.AUIFrame method) createGUI() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.ParamGroup method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) createImage() (in module PYME.Acquire.sampleInformation) CreateLayerPane() (in module PYME.LMVis.layer_panel) CreateLayerPanel() (in module PYME.LMVis.layer_panel) CreateMenuBar() (PYME.LMVis.visCore.VisGUICore method) CreateModuleMenu() (PYME.DSView.dsviewer.DSViewFrame method) CreatePens() (PYME.DSView.modules.flowView.FlowView method) createQT() (in module PYME.Analysis.points.QuadTree.pointQT) (in module PYME.Analysis.points.QuadTree.pointQTF) CreateToolBar() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) CreateToolPanel() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) creation_time (PYME.misc.sqlite_ns.NSInfo attribute) crop_image() (in module PYME.IO.DataSources.CropDataSource) CropExportData() (in module PYME.ui.crop_dialog) Cropper (class in PYME.DSView.modules.cropping) CrosshairsOverlay (class in PYME.DSView.overlays) CSInterpolator (class in PYME.localization.FitFactories.Interpolators.CSInterpolator) (class in PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP) CStr (class in PYME.misc.mock_traits) CubicSplineInterpolator (class in PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator) cull_triangles_2D() (in module PYME.Analysis.points.gen3DTriangs) cumuexpfit() (in module PYME.LMVis.Extras.QPobjectSegment) (in module PYME.LMVis.objectDarkMeasure) current_scan (PYME.Acquire.stage_leveling.StageLeveler property) CurrentRenderer (class in PYME.LMVis.renderers) Cyan() (in module PYME.misc.colormaps) CziFile (class in PYME.contrib.gohlke.czifile)

D

dark() (in module PYME.DSView.modules.dark_and_flatfield) data (PYME.Analysis.tile_pyramid.CacheEntry attribute) (PYME.IO.image.ImageStack property) (PYME.misc.editgrid.EntryGrid property) data_complete (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.Rule property) (PYME.cluster.rules.SpoolLocalLocalizationRule property) data_limits (PYME.LMVis.view_clipping_pane.ClippingPanel property) data_type (PYME.Analysis.points.spherical_harmonics.ScaledShell attribute) data_xytc (PYME.IO.image.ImageStack property) data_xyztc (PYME.IO.image.ImageStack property) DataBlock (class in PYME.DSView.modules.blobMeasure) dataBuffer (class in PYME.IO.buffers) (class in PYME.IO.DataSources.BGSDataSource) DataChanged() (PYME.DSView.dsviewer.DSViewFrame method) dataserver (class in PYME.cluster.dataserver_wsgi) dataservers (PYME.IO.cluster_directory.DirectoryInfoManager property) DataSource (class in PYME.IO.DataSources.AlignDataSource) (class in PYME.IO.DataSources.BioformatsDataSource) (class in PYME.IO.DataSources.BufferedDataSource) (class in PYME.IO.DataSources.ClusterPZFDataSource) (class in PYME.IO.DataSources.ConcatenatedDataSource) (class in PYME.IO.DataSources.CropDataSource) (class in PYME.IO.DataSources.DcimgDataSource) (class in PYME.IO.DataSources.ElectronsPerSecondDataSource) (class in PYME.IO.DataSources.FlatFieldDataSource) (class in PYME.IO.DataSources.HDFDataSource) (class in PYME.IO.DataSources.HTTPDataSource) (class in PYME.IO.DataSources.ImageSeriesDataSource) (class in PYME.IO.DataSources.MultiviewDataSource) (class in PYME.IO.DataSources.OBFDataSource) (class in PYME.IO.DataSources.RandomDataSource) (class in PYME.IO.DataSources.TiffDataSource) (class in PYME.IO.DataSources.TQDataSource) (class in PYME.IO.DataSources.UnsplitDataSource) (in module PYME.IO.DataSources.BGSDataSource) datasource (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.labels.LabelLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) dataSource (PYME.ui.filterPane.FilterPanel property) DataSource() (in module PYME.IO.DataSources.SupertileDatasource) (in module PYME.IO.DataSources.TileDataSource) DAVRequestHandler (class in PYME.cluster.webdav) DAVServer (class in PYME.cluster.webdav) dBdt() (in module PYME.Analysis.BleachProfile.deMod) DCIMGFile (class in PYME.IO.dcimg) dec (class in PYME.Analysis.PSFEst.dec) dec_4pi (class in PYME.Deconv.dec) dec_4pi_c (class in PYME.Deconv.dec) dec_bead (class in PYME.Deconv.dec) dec_conv (class in PYME.Deconv.dec) (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) dec_conv_slow (class in PYME.Deconv.dec) (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) dec_psf (class in PYME.Analysis.PSFEst.dec) dec_test() (in module PYME.Analysis.PSFEst.psfQuality) dec_wiener (class in PYME.Deconv.wiener) DecayAnalyser (class in PYME.LMVis.Extras.photophysics) deClump() (in module PYME.Analysis.points.DeClump.pyDeClump) deClumpDialog (class in PYME.Analysis.points.DeClump.deClumpGUI) deClumpedDType() (in module PYME.Analysis.points.DeClump.pyDeClump) deClumpf() (in module PYME.Analysis.points.DeClump.pyDeClump) decmod_onestate() (in module PYME.Analysis.BleachProfile.intensProf) decode() (PYME.contrib.lzw.Decoder method) decode_json() (PYME.LMVis.views.View class method) decodefrombytes() (PYME.contrib.lzw.ByteDecoder method) decodepages() (PYME.contrib.lzw.PagingDecoder method) Decoder (class in PYME.contrib.lzw) decompress() (in module PYME.contrib.lzw) decompZar() (in module PYME.misc.zemax) deconv() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) (PYME.Deconv.richardsonLucyMV.MultiviewRichardsonLucy method) (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) (PYME.Deconv.wiener.dec_wiener method) DeconvMappingBase (class in PYME.Deconv.dec) Deconvolver (class in PYME.DSView.modules.deconvolution) deconvp() (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) DeconvProgressDialog (class in PYME.Deconv.deconvDialogs) DeconvProgressPanel (class in PYME.Deconv.deconvDialogs) DeconvSettingsDialog (class in PYME.Deconv.deconvDialogs) decResult (class in PYME.Deconv.decTask) decTask (class in PYME.Deconv.decTask) decThread (class in PYME.Deconv.decThread) default_compression_settings (PYME.IO.acquisition_backends.ClusterBackend attribute) DEFAULT_PARAMS (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisDetailsPanel attribute) default_traits_view() (PYME.DSView.modules.flowView.FlowView method) (PYME.DSView.modules.psfGeneration.PupilGenerator method) (PYME.DSView.modules.psfTools.PSFTools method) (PYME.DSView.modules.pupilTools.PupilTools method) (PYME.LMVis.Extras.pointSetGeneration.Generator method) (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.labels.LabelLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) (PYME.simulation.pointsets.ImageSource method) default_view (PYME.LMVis.layers.image_layer.ImageRenderLayer property) (PYME.LMVis.layers.labels.LabelLayer property) (PYME.LMVis.layers.mesh.TriangleRenderLayer property) (PYME.LMVis.layers.octree.OctreeRenderLayer property) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer property) (PYME.LMVis.layers.quiver.QuiverRenderLayer property) (PYME.LMVis.layers.tracks.TrackRenderLayer property) DefaultGlass (class in PYME.misc.zemax) DefaultList (class in PYME.IO.DataSources.BaseDataSource) DEFAULTS (PYME.Acquire.stackSettings.StackSettings attribute) DefaultShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) defm() (in module PYME.Analysis.BleachProfile.rollins) DelayPanel (class in PYME.Acquire.ui.mpd_picosecond_delay_panel) delete_snapshot() (PYME.LMVis.Extras.animation.VideoPanel method) delete_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) delete_tile() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) deleteFiles() (in module PYME.misc.diskCleanup) DeleteItem() (PYME.DSView.modules.composite.ImageList method) DeletePage() (PYME.ui.AUIFrame.AUIFrame method) denominator (PYME.IO.FileUtils.obf_support.Fraction attribute) density (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) DensityFilter (class in PYME.Analysis.density_filter) DensityFitRenderer (class in PYME.LMVis.renderers) deprecated_name() (in module PYME.IO.tabular) depth (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) depth_dec() (in module PYME.Analysis.PSFEst.psfQuality) depth_loc() (in module PYME.Analysis.PSFEst.psfQuality) descr (PYME.IO.dataExporter.H5Exporter attribute) (PYME.IO.dataExporter.NumpyExporter attribute) (PYME.IO.dataExporter.OMETiffExporter attribute) (PYME.IO.dataExporter.PSFExporter attribute) (PYME.IO.dataExporter.TiffSeriesExporter attribute) (PYME.IO.dataExporter.TiffStackExporter attribute) (PYME.IO.dataExporter.TxtExporter attribute) destroy() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.zScanner.zScanner method) detach() (PYME.Acquire.Utils.fastTiler.fastTiler method) Detach() (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) detailed_version() (in module PYME.version) Detatch() (PYME.Acquire.positionTracker.PositionTracker method) dh5view_cmd (PYME.Acquire.SpoolController.SpoolController property) Dict (in module PYME.misc.mock_traits) DictMDHandler (class in PYME.IO.MetaDataHandler) DictSource (class in PYME.IO.tabular) DictStrAny (in module PYME.misc.mock_traits) DictStrBool (in module PYME.misc.mock_traits) DictStrFloat (in module PYME.misc.mock_traits)

DictStrList (in module PYME.misc.mock_traits) DictStrStr (in module PYME.misc.mock_traits) dictToRecarray() (in module PYME.Analysis.processLogger) dir_lock() (PYME.IO.clusterListing.DirCache method) DirCache (class in PYME.IO.clusterListing) DirCollection (class in PYME.cluster.webdav) direction_to_nearest_n_points() (in module PYME.Analysis.points.coordinate_tools) DirectoryInfoManager (class in PYME.IO.cluster_directory) dirname (PYME.Acquire.SpoolController.SpoolController property) dirname() (in module PYME.IO.unifiedIO) dirsize() (in module PYME.IO.countdir.countdir) disable_texture_2d() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture static method) disconnect() (PYME.contrib.dispatch.dispatcher.Signal method) disk_usage() (in module PYME.IO.FileUtils.freeSpace) dispersion_data() (in module PYME.misc.read_agf) display_dirname (PYME.Acquire.SpoolController.SpoolController property) display_name (PYME.DSView.overlays.Overlay attribute) display_normals (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) DisplayOpts (class in PYME.DSView.displayOptions) DisplayPane (class in PYME.LMVis.displayPane) DisplayPaneHorizontal (class in PYME.LMVis.displayPane) DisplayPaneLight (class in PYME.LMVis.displayPane) dispRatio() (in module PYME.Analysis.points.twoColour) dispSettingsFrame (class in PYME.DSView.displaySettingsPanel) dispSettingsPanel (class in PYME.DSView.displaySettingsPanel) dispSettingsPanel2 (class in PYME.DSView.displaySettingsPanel) dist_along_vector() (in module PYME.simulation.wormlike2) distance (PYME.Analysis.Tracking.trackUtils.Track property) distance_to_image_mask() (in module PYME.Analysis.points.coordinate_tools) distance_to_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) distance_to_shell_along_vector_from_point() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) distance_to_surface() (in module PYME.LMVis.Extras.extra_layers) distanceHistogram() (in module PYME.Analysis.points.DistHist.distHist) distanceHistogram3D() (in module PYME.Analysis.points.DistHist.distHist) distanceHistogram3DThreaded() (in module PYME.Analysis.points.DistHist.distHistThreaded) distanceHistogramThreaded() (in module PYME.Analysis.points.DistHist.distHistThreaded) distanceProduct() (in module PYME.Analysis.points.DistHist.distHist) distfcn_oidic() (in module PYME.IO.acquisition_backends) distfcn_random() (in module PYME.IO.acquisition_backends) distributed_pyramid() (in module PYME.Analysis.distributed_pyramid) DistributedImagePyramid (class in PYME.Analysis.distributed_pyramid) distribution_function_round_robin() (in module PYME.IO.cluster_streaming) distributor_url (PYME.cluster.rulenodeserver.NodeServer property) distThreshold (PYME.LMVis.triBlobs.BlobSettings attribute) dlHd() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) dlHd2() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) dNdfcn() (in module PYME.Analysis.BleachProfile.intensProf) dNofcn() (in module PYME.Analysis.BleachProfile.intensProf) do (PYME.Acquire.ui.intensity_trace.IntensityTracePanel property) do_COPY() (PYME.cluster.webdav.DAVRequestHandler method) do_DELETE() (PYME.cluster.webdav.DAVRequestHandler method) do_GET() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) (PYME.util.webframework.JSONAPIRequestHandler method) do_HEAD() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.webdav.DAVRequestHandler method) do_LOCK() (PYME.cluster.webdav.DAVRequestHandler method) do_login() (PYME.Acquire.acquire_server.AcquireHTTPServerMixin method) do_MKCOL() (PYME.cluster.webdav.DAVRequestHandler method) do_MOVE() (PYME.cluster.webdav.DAVRequestHandler method) do_OPTIONS() (PYME.cluster.webdav.DAVRequestHandler method) do_POST() (PYME.util.webframework.JSONAPIRequestHandler method) do_PROPFIND() (PYME.cluster.webdav.DAVRequestHandler method) do_PROPPATCH() (PYME.cluster.webdav.DAVRequestHandler method) do_PUT() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) do_radial_anal() (in module PYME.Analysis.points.rings) do_summary_plots() (in module PYME.Analysis.points.rings) do_UNLOCK() (PYME.cluster.webdav.DAVRequestHandler method) DockedPanel (class in PYME.LMVis.Extras.dockedPanel) DoGetBestSize() (PYME.ui.MetadataTree.MyTreeListCtrl method) DoNix() (PYME.DSView.scrolledImagePanel.ImagePanel method) doNothing() (in module PYME.misc.mock_ctypes) DoPaint() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.splashScreen.SplashPanel method) (PYME.LMVis.imageView.ColourImageViewPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ColourImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) doPostInit() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) doStartLog() (PYME.Acquire.stackSettings.StackSettings method) doStopLog() (PYME.Acquire.stackSettings.StackSettings method) doTraceDisp() (in module PYME.Analysis.BleachProfile.intensProf) doTraceDispdl() (in module PYME.Analysis.BleachProfile.intensProf) doTraceDispdl2() (in module PYME.Analysis.BleachProfile.intensProf) draw() (PYME.Acquire.positionTracker.TrackerPanel method) (PYME.Acquire.positionTracker.TrackerPlotPanel method) (PYME.contrib.wxPlotPanel.PlotPanel method) (PYME.DSView.fitInfo.fitDispPanel method) (PYME.DSView.modules.fastGraphPanel.GraphViewPanel method) (PYME.DSView.modules.psfTools.CRBViewPanel method) (PYME.LMVis.progGraph.progPanel method) draw_box_pixel_coords() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) draw_cross_pixel_coords() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) drawGraph() (in module PYME.misc.depGraph) drawNode() (PYME.Analysis.points.QuadTree.QTrend.QTRendererNode method) drawNodeDL() (PYME.Analysis.points.QuadTree.QTrend.QTRendererNode method) drawOverlay() (PYME.DSView.modules.blobMeasure.BlobObject method) DrawOverlays() (PYME.DSView.fitInfo.FitInfoPanel method) (PYME.DSView.modules.annotation.AnnotateBase method) (PYME.DSView.modules.blobMeasure.Measurements method) (PYME.DSView.modules.flowView.FlowView method) (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) DrawOverlays_() (PYME.DSView.modules.flowView.FlowView method) drawProgBar() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.splashScreen.SplashPanel method) drawProjection() (PYME.misc.VolProj.Isosurf method) drawTetrahedra() (in module PYME.Analysis.points.SoftRend.triRend) drawTree() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) drawTriang() (in module PYME.Analysis.points.SoftRend.triRend) drawTriangles() (in module PYME.Analysis.points.SoftRend.triRend) dsa (PYME.Acquire.frameWrangler.FrameWrangler property) dsname (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.labels.LabelLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) dsRefresh() (PYME.DSView.dsviewer.DSViewFrame method) DSViewFrame (class in PYME.DSView.dsviewer) dtype (PYME.Analysis.tile_pyramid.PyramidLayer attribute) (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.TileDataSource.TileDataSource property) (PYME.IO.dataWrap.ListWrapper property) dtypes (PYME.Analysis.Tracking.trackUtils.Clump property) Dumbell3DFitFactory (class in PYME.localization.FitFactories.Dumbell3DFitR) Dumbell3DFitResultR() (in module PYME.localization.FitFactories.Dumbell3DFitR) DumbellFitFactory (class in PYME.localization.FitFactories.DumbellFitR) dummy (class in PYME.localization.FitFactories.Interpolators.baseInterpolator) DummyFileMember (class in PYME.cluster.webdav) DummyFramewrangler (class in PYME.IO.testClusterSpooling) dumps() (in module PYME.IO.PZFFormat) duplicateFiles() (in module PYME.IO.clusterDuplication) duration (PYME.LMVis.Extras.animation.EditPanel property) (PYME.LMVis.views.VideoView property) dyedyemod() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemod2() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemod3() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemoda() (in module PYME.Analysis.BleachProfile.rawIntensity) dyedyemodt() (in module PYME.Analysis.BleachProfile.rawIntensity)

E

e2mod() (in module PYME.Analysis.BleachProfile.kinModels) e3mod() (in module PYME.Analysis.BleachProfile.kinModels) e4mod() (in module PYME.Analysis.BleachProfile.kinModels) e_field() (PYME.Analysis.PSFGen.fourierHNA.FourierPSF method) E_field_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) edge_cutoff (PYME.LMVis.Extras.objectMeasurements.OMDialog property) EdgeDB (class in PYME.Analysis.points.EdgeDB.edges) EditableTreeList (class in PYME.ui.MetadataTree) EditDialog (class in PYME.LMVis.Extras.animation) editorBgColour (PYME.contrib.listctrlMixins.TextEditMixin attribute) (PYME.ui.MetadataTree.TextEditMixin attribute) editorFgColour (PYME.contrib.listctrlMixins.TextEditMixin attribute) (PYME.ui.MetadataTree.TextEditMixin attribute) EditPanel (class in PYME.LMVis.Extras.animation) EField_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) efunc() (in module PYME.misc.kdFit) ei2mod() (in module PYME.Analysis.BleachProfile.kinModels) ei3mod() (in module PYME.Analysis.BleachProfile.kinModels) eimod() (in module PYME.Analysis.BleachProfile.kinModels) emg() (in module PYME.localization.Test.fitTestJig) (in module PYME.localization.Test.fitTestJigSCMOS) (in module PYME.localization.Test.fitTestJigWC) eMod() (in module PYME.Analysis.BleachProfile.intensProf) emod() (in module PYME.Analysis.BleachProfile.kinModels) eMod2() (in module PYME.Analysis.BleachProfile.intensProf) eMod3() (in module PYME.Analysis.BleachProfile.intensProf) eMod4() (in module PYME.Analysis.BleachProfile.intensProf) eMod5() (in module PYME.Analysis.BleachProfile.intensProf) EmptyBitmap() (in module PYME.ui.wx_compat) EmptyImage() (in module PYME.ui.wx_compat) emptyListDict (class in PYME.Analysis.points.gen3DTriangs) enable_texture_2d() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture static method) EnableJoystick() (PYME.Acquire.microscope.Microscope method) encode() (PYME.contrib.lzw.Encoder method) encodepages() (PYME.contrib.lzw.PagingEncoder method) Encoder (class in PYME.contrib.lzw) encodetobytes() (PYME.contrib.lzw.ByteEncoder method) encoding (PYME.Acquire.webui.ipy.TTYDummy attribute) EndSelection() (PYME.DSView.displayOptions.DisplayOpts method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) engine (PYME.LMVis.layers.base.EngineLayer attribute) EngineLayer (class in PYME.LMVis.layers.base) ensure_VM() (in module PYME.IO.DataSources.BioformatsDataSource) EntryGrid (class in PYME.misc.editgrid) Enum (in module PYME.misc.mock_traits) EnumEditor() (in module PYME.misc.mock_traitsui) errFunc() (PYME.misc.coverslipGeometries.circGeom method) error() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) errorPlot() (in module PYME.Analysis.binAvg) errors (PYME.Acquire.webui.ipy.TTYDummy attribute) estimate_circumcentre_densities() (in module PYME.LMVis.Extras.extra_layers) estimate_density() (in module PYME.LMVis.Extras.extra_layers) estimate_spool_time() (PYME.Acquire.SpoolController.SpoolController method) estimated_duration() (PYME.Acquire.actions.Action method) estimateFromSource() (PYME.IO.image.ImageBounds class method) (PYME.LMVis.visHelpersMin.ImageBounds class method) eth_mod2() (in module PYME.Analysis.BleachProfile.intensProf) eth_mod3() (in module PYME.Analysis.BleachProfile.intensProf) ethet3() (in module PYME.Analysis.BleachProfile.intensProf) ev() (PYME.Analysis.points.twoColour.lin2Model method) (PYME.Analysis.points.twoColour.lin3Model method) (PYME.Analysis.points.twoColour.lin3zModel method) (PYME.Analysis.points.twoColour.linModel method) (PYME.Analysis.points.twoColour.sffake method) (PYME.misc.sffake.sffake method) evalModel() (PYME.localization.FitFactories.AstigGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.BeadConvolvedAstigGaussFit.GaussianFitFactory class method) (PYME.localization.FitFactories.Dumbell3DFitR.Dumbell3DFitFactory class method) (PYME.localization.FitFactories.DumbellFitR.DumbellFitFactory class method) (PYME.localization.FitFactories.GaussFitConstrR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory class method) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory class method) (PYME.localization.FitFactories.InterpFitR.PSFFitFactory class method) (PYME.localization.FitFactories.LatGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.MultiviewFitInterpNR.InterpFitFactory class method) (PYME.localization.FitFactories.PRInterpFitQR.PSFFitFactory class method) (PYME.localization.FitFactories.PRInterpFitR.PSFFitFactory class method) (PYME.localization.FitFactories.SpecGaussFitFR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitFNR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitFusionR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterFitInterpBNR.InterpFitFactory class method) (PYME.localization.FitFactories.SplitterFitInterpNR.InterpFitFactory class method) (PYME.localization.FitFactories.SplitterFitScavNR.GaussianFitFactory class method) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory class method)

evalParams() (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) eventFileName (PYME.IO.DataSources.ClusterPZFDataSource.DataSource property) eventify() (in module PYME.simulation.locify) eventify2() (in module PYME.simulation.locify) eventInfo (class in PYME.misc.eventSpy) EventLogger (class in PYME.IO.events) eventLogPanel (class in PYME.DSView.eventLogViewer) eventLogTPanel (class in PYME.DSView.eventLogViewer) EventLoop (class in PYME.Acquire.event_loop) events (PYME.IO.events.MemoryEventLogger property) (PYME.IO.h5rFile.H5RFile property) Ex() (in module PYME.Acquire.protocol) excepthook() (in module PYME.misc.pyro_tracebacks) execBG() (in module PYME.Acquire.ExecTools) execFile() (in module PYME.Acquire.ExecTools) execFileBG() (in module PYME.Acquire.ExecTools) exists() (in module PYME.IO.clusterIO) (in module PYME.IO.HTTPSpooler_v2) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.IO.cluster_directory.DirectoryInfoManager method) expired (PYME.cluster.ruleserver.IntegerIDRule property) Export() (PYME.IO.dataExporter.Exporter method) (PYME.IO.dataExporter.H5Exporter method) (PYME.IO.dataExporter.NumpyExporter method) (PYME.IO.dataExporter.OMETiffExporter method) (PYME.IO.dataExporter.PSFExporter method) (PYME.IO.dataExporter.TiffSeriesExporter method) (PYME.IO.dataExporter.TiffStackExporter method) (PYME.IO.dataExporter.TxtExporter method) ExportData() (in module PYME.IO.dataExporter) ExportDialog (class in PYME.ui.crop_dialog) Exporter (class in PYME.IO.dataExporter) exporter() (in module PYME.IO.dataExporter) ExportImageToCluster() (in module PYME.IO.clusterExport) ExportStackToPNG() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) ExtendContext() (PYME.Analysis.processLogger.ContextManager method) extension (PYME.IO.dataExporter.H5Exporter attribute) (PYME.IO.dataExporter.NumpyExporter attribute) (PYME.IO.dataExporter.OMETiffExporter attribute) (PYME.IO.dataExporter.PSFExporter attribute) (PYME.IO.dataExporter.TiffSeriesExporter attribute) (PYME.IO.dataExporter.TiffStackExporter attribute) (PYME.IO.dataExporter.TxtExporter attribute) extensions_map (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.util.webframework.StaticFileHandler attribute) extent (PYME.IO.image.ImageBounds property) extra_template_kwargs() (PYME.cluster.taskWorkerHTTP.RecipeTaskError method) (PYME.cluster.taskWorkerHTTP.TaskError method) extract_profile() (in module PYME.Analysis.profile_extraction) extractAverageTrajectory() (in module PYME.Analysis.points.fiducials) extractBlobs() (in module PYME.DSView.modules.extractBlobs) extractFeatures() (in module PYME.Analysis.svmSegment) extractFeatures2() (in module PYME.Analysis.svmSegment) extractFrames() (in module PYME.IO.FileUtils.h5ExFrames) extractFramesF() (in module PYME.IO.FileUtils.h5ExFrames) extractFromMetadata() (PYME.IO.image.ImageBounds class method) extractIms() (in module PYME.Analysis.PSFEst.extractImages) ExtractPupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2)

F

f() (in module PYME.Analysis.points.surfit) f_dumbell() (in module PYME.localization.FitFactories.DumbellFitR) f_dumbell3d() (in module PYME.localization.FitFactories.Dumbell3DFitR) f_gauss1d() (in module PYME.localization.FitFactories.SpecGaussFitFR) f_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_gauss2d2c() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) f_gauss2d2cA() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) f_gauss2d2ccb() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) f_gauss2d_no_bg() (in module PYME.localization.FitFactories.LatGaussFitFR) f_gauss2dF() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_gauss2dSlow() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_Gauss3d() (in module PYME.localization.FitFactories.Gauss3DFitR) f_gaussAstigBead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) f_gaussAstigSlow() (in module PYME.localization.FitFactories.AstigGaussFitFR) f_Interp3d() (in module PYME.localization.autopsf.roifit) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) f_Interp3d2c() (in module PYME.localization.FitFactories.SplitterFitInterpNR) f_Interp3d2cr() (in module PYME.localization.autopsf.roifit) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) f_Interp3Dmultiview() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) f_J_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) f_j_gauss2d() (in module PYME.localization.FitFactories.GaussFitConstrR) f_J_gauss2d() (in module PYME.localization.FitFactories.GaussMultifitR) f_j_gauss2d() (in module PYME.localization.FitFactories.GaussMultifitR) f_J_gauss2d() (in module PYME.localization.FitFactories.LatGaussFitFR) f_j_gauss2d() (in module PYME.localization.FitFactories.LatGaussFitFR) f_J_gauss2d() (in module PYME.localization.FitFactories.SplitterMultifitSR) f_j_gauss2d() (in module PYME.localization.FitFactories.SplitterMultifitSR) f_J_Interp3d2c() (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) f_J_Interp3Dmultiview() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) f_multiGauss() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_multiGaussJ() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_multiGaussS() (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.SplitterMultifitSR) f_PSF3d() (in module PYME.localization.FitFactories.LatPSFFitR) f_rotGaussAstigBead() (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) facsPlotContour() (in module PYME.misc.facsPlot) facsPlotScatter() (in module PYME.misc.facsPlot) facsPlotScatter2() (in module PYME.misc.facsPlot) facsPlotScatterLog() (in module PYME.misc.facsPlot) Failsafe (class in PYME.Acquire.Utils.failsafe) FailsafeClient (class in PYME.Acquire.Utils.failsafe) FailsafeServer (class in PYME.Acquire.Utils.failsafe) FakeAPI (class in PYME.Acquire.htsms.tweeter) fast_grey() (in module PYME.DSView.displayOptions) fast_validate (PYME.recipes.traits.Input attribute) (PYME.recipes.traits.Output attribute) FastGraphPanel (class in PYME.ui.fastGraph) fastRectTiler (class in PYME.Acquire.Utils.fastTiler) fastTiler (class in PYME.Acquire.Utils.fastTiler) FatLineShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) FeatureMean (class in PYME.Analysis.Tracking.trackUtils) FeaturePlot (class in PYME.Analysis.Tracking.trackUtils) FeatureStd (class in PYME.Analysis.Tracking.trackUtils) FFBase (class in PYME.localization.FitFactories.FFBase) fftwWeiner (class in PYME.localization.ofind_xcorr_fw) fibre10nm() (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) fibre30nm() (in module PYME.simulation.wormlike) (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3) (in module PYME.simulation.wormlike_curled) FIkz() (in module PYME.Analysis.cramerRao) File (class in PYME.IO.FileUtils.obf_support) (in module PYME.misc.mock_traits) file (PYME.simulation.pointsets.FileSource attribute) FILE_EXTENSION (PYME.Acquire.Utils.tiler.TileAcquisition attribute) file_header_unpack() (in module PYME.IO.FileUtils.obf_support) file_info() (in module PYME.IO.countdir.countdir) filebytes() (in module PYME.contrib.lzw) fileFitResult() (PYME.IO.h5rFile.H5RFile method) fileFormattedResults() (in module PYME.IO.clusterResults) FileInfo (class in PYME.IO.clusterListing) FileMember (class in PYME.cluster.webdav) filename() (PYME.contrib.gohlke.fcsfiles.ConfoCor3Raw method) FilenameParam (class in PYME.localization.MetaDataEdit) fileno() (PYME.Acquire.webui.ipy.TTYDummy method) FileOrURI (class in PYME.recipes.traits) fileResults() (in module PYME.IO.clusterResults) FileSelectionError FileSource (class in PYME.simulation.pointsets) fileTasksForFrames() (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) (PYME.cluster.HTTPTaskPusher.HTTPTaskPusher method) fileTasksForInputs() (PYME.cluster.HTTPRulePusher.RecipePusher method) (PYME.cluster.HTTPTaskPusher.RecipePusher method) fileType (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) (PYME.LMVis.importTextDialog.ImportMatlabDialog attribute) (PYME.LMVis.importTextDialog.ImportTextDialog attribute) FILETYPE_SERIES_COMPLETE (in module PYME.IO.clusterListing) FillGrid() (PYME.DSView.modules.psfTools.PSFQualityPanel method) fillInBlanks() (in module PYME.Analysis.MetaData) filter() (PYME.Analysis.density_filter.DensityFilter method) (PYME.localization.ofind_xcorr_fw.fftwWeiner method) filter_quad_results() (in module PYME.Analysis.points.surfit) filtered (PYME.Analysis.Tracking.trackUtils.TrackManager property) filtered_subblock_directory (PYME.contrib.gohlke.czifile.CziFile attribute) FilterEditDialog (class in PYME.ui.editFilterDialog) Filterer (class in PYME.DSView.modules.filtering) filterer (class in PYME.DSView.modules.sparkprepare) filterKeys (PYME.ui.filterPane.FilterPane property) FilterPane (class in PYME.DSView.modules.measure.filterPan) (class in PYME.ui.filterPane) FilterPanel (class in PYME.ui.filterPane) fImod() (in module PYME.Analysis.BleachProfile.kinModels) finalise() (PYME.Acquire.actions.Action method) (PYME.Acquire.actions.RemoteSpoolSeries method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Analysis.distributed_pyramid.PartialPyramid method) (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.HDFBackend method) (PYME.IO.acquisition_backends.MemoryBackend method) (PYME.IO.acquisition_backends.TiffFolderBackend method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) finalize() (PYME.IO.cluster_streaming.Stream method) finalize_c() (PYME.Acquire.xyztc.XYZTCAcquisition method) finalize_t() (PYME.Acquire.xyztc.TiledXYZTCMixin method) (PYME.Acquire.xyztc.XYZTCAcquisition method) finalize_z() (PYME.Acquire.xyztc.XYZTCAcquisition method) find_and_add_zRange() (in module PYME.Analysis.points.astigmatism.astigTools) find_catalog() (in module PYME.misc.read_agf) find_clumps() (in module PYME.Analysis.points.multiview) find_clumps_within_channel() (in module PYME.Analysis.points.multiview) find_glassdict() (in module PYME.misc.read_agf) find_points_within_cone() (in module PYME.Analysis.points.coordinate_tools) find_points_within_cylinder() (in module PYME.Analysis.points.coordinate_tools) find_principle_axes() (in module PYME.Analysis.points.coordinate_tools) find_spec() (PYME.ui.patch_traitsui.MyMetaFinder method) find_stack_by_name() (PYME.IO.FileUtils.obf_support.File method) FindAndFit() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory method) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory method) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory method) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory method) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory method) findClumps() (in module PYME.Analysis.points.DeClump) (in module PYME.Analysis.points.DeClump.deClump) findClumpsN() (in module PYME.Analysis.points.DeClump.deClump) findConnected() (in module PYME.Analysis.points.DeClump.pyDeClump) findMember() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) FindObjects() (PYME.localization.ofind.ObjectIdentifier method) (PYME.localization.ofind3d.ObjectIdentifier method) (PYME.localization.ofind_nofilt.ObjectIdentifier method) (PYME.localization.ofind_pri.ObjectIdentifier method) (PYME.localization.ofind_split.ObjectIdentifier method) (PYME.localization.ofind_xcorr.ObjectIdentifier method) (PYME.localization.ofind_xcorr_fw.ObjectIdentifier method) findRectangularROIs() (in module PYME.Analysis.deTile) findTracks() (in module PYME.Analysis.Tracking.trackUtils) findTracks2() (in module PYME.Analysis.Tracking.trackUtils) findWonkyVectors() (in module PYME.Analysis.points.twoColour) finish (PYME.ui.selection.Selection property) finish_base_tiles() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method) finish_request() (PYME.cluster.webdav.DAVServer method) finished (PYME.cluster.ruleserver.IntegerIDRule property) finished() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.IO.acquisition_backends.Backend method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) fit() (in module PYME.Analysis.points.qpaint) (PYME.Analysis.points.spherical_harmonics.SHShell method) (PYME.Analysis.points.twoColour.lin2Model method) (PYME.Analysis.points.twoColour.lin3Model method) (PYME.Analysis.points.twoColour.lin3zModel method) (PYME.Analysis.points.twoColour.linModel method) (PYME.Analysis.points.twoColour.sffake method) (PYME.localization.autopsf.autopsf.ZernikePSFModel method) Fit() (PYME.misc.coverslipGeometries.geom method) fit_model() (in module PYME.Analysis.autoencoder_classifier) fit_quad_surf() (in module PYME.Analysis.points.surfit) fit_quad_surf_to_neighbourbood() (in module PYME.Analysis.points.surfit) fit_quad_surfaces() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_P() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_Pr() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_t() (in module PYME.Analysis.points.surfit) fit_quad_surfaces_tr() (in module PYME.Analysis.points.surfit) fit_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) fitallA() (in module PYME.localization.autopsf.roifit) fitDarktimes() (in module PYME.LMVis.objectDarkMeasure) fitDecay() (in module PYME.Analysis.BleachProfile.kinModels) fitDispPanel (class in PYME.DSView.fitInfo) FitFactory (in module PYME.localization.FitFactories.AstigGaussFitFR) (in module PYME.localization.FitFactories.AstigGaussGPUFitFR) (in module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) (in module PYME.localization.FitFactories.ChecksumFR) (in module PYME.localization.FitFactories.ChecksumGPUFR) (in module PYME.localization.FitFactories.ChecksumMultifitSR) (in module PYME.localization.FitFactories.Dumbell3DFitR) (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.localization.FitFactories.FFBase) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.GaussMultifitSR) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.InterpFitWFR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.ROIExtractNR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitCOIR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterROIExtractNR) (in module PYME.localization.FitFactories.SplitterShiftEstFR)

FitFactory() (in module PYME.localization.FitFactories.ConfocCOIR) fitFluorBrightness() (in module PYME.Analysis.BleachProfile.kinModels) fitFluorBrightnessT() (in module PYME.Analysis.BleachProfile.kinModels) fitIndep() (in module PYME.Analysis.points.twoColour) FitInfoPanel (class in PYME.DSView.fitInfo) FitJumpSizeDist() (in module PYME.Analysis.Tracking.trackUtils) fitKD() (in module PYME.misc.kdFit) fitMod (PYME.localization.remFitBuf.fitTask property) fITmod() (in module PYME.Analysis.BleachProfile.kinModels) fITmod2() (in module PYME.Analysis.BleachProfile.kinModels) FitModel_N() (in module PYME.Analysis.BleachProfile.rollins) FitModel_NB() (in module PYME.Analysis.BleachProfile.rollins) FitModelG() (in module PYME.Analysis.BleachProfile.kinModels) fitOnTimes() (in module PYME.Analysis.BleachProfile.kinModels) fitPtA() (in module PYME.Analysis.points.surfit) fitPts() (in module PYME.Analysis.points.surfit) fitPtsA() (in module PYME.Analysis.points.surfit) fitPtsAP() (in module PYME.Analysis.points.surfit) fitPtsAt() (in module PYME.Analysis.points.surfit) fitResult (class in PYME.localization.remFitBuf) FitResult() (in module PYME.localization.FitFactories.ConfocCOIR) (in module PYME.localization.FitFactories.Dumbell3DFitR) (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatFitCOIR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitCOIR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) FitResultR() (in module PYME.localization.FitFactories.DumbellFitR) (in module PYME.simulation.locify) FitResultsDType() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) FitResultsSource (class in PYME.IO.tabular) fitResultsSource() (in module PYME.IO.tabular) fitROI() (in module PYME.localization.autopsf.roifit) fitTask (class in PYME.localization.remFitBuf) Fitter (class in PYME.DSView.modules.profileFitting) fitTestJig (class in PYME.localization.Test.fitTestJig) (class in PYME.localization.Test.fitTestJigSCMOS) (class in PYME.localization.Test.fitTestJigWC) FitTrace() (in module PYME.Analysis.BleachProfile.fitRecover) fix_name() (in module PYME.IO.unifiedIO) fixEMGain() (in module PYME.Analysis.MetaData) flag_piezo_movement() (in module PYME.Analysis.piezo_movement_correction) flat() (in module PYME.DSView.modules.dark_and_flatfield) FlatFaceEngine (class in PYME.LMVis.layers.mesh) flatten (PYME.simulation.pointsets.WiglyFibreSource attribute) flF2() (in module PYME.Analysis.BleachProfile.deMod) flF2Mod() (in module PYME.Analysis.BleachProfile.deMod) flFpow() (in module PYME.Analysis.BleachProfile.deMod) flFsq() (in module PYME.Analysis.BleachProfile.deMod) flFsq1() (in module PYME.Analysis.BleachProfile.deMod) flip() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) flip_starts() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) flipSecondaryAxis() (PYME.DSView.modules.blobMeasure.DataBlock method) Float (class in PYME.misc.mock_traits) FloatListParam (class in PYME.localization.MetaDataEdit) FloatParam (class in PYME.localization.MetaDataEdit) flowImage (PYME.DSView.modules.flowView.FlowView property) flowImageName (PYME.DSView.modules.flowView.FlowView attribute) flowMaskName (PYME.DSView.modules.flowView.FlowView attribute) flowVectArrowSize (PYME.DSView.modules.flowView.FlowView attribute) flowVectScale (PYME.DSView.modules.flowView.FlowView attribute) flowVectSpacing (PYME.DSView.modules.flowView.FlowView attribute) flowVectThresh (PYME.DSView.modules.flowView.FlowView attribute) flowVectType (PYME.DSView.modules.flowView.FlowView attribute) flowVectWidth (PYME.DSView.modules.flowView.FlowView attribute) FlowView (class in PYME.DSView.modules.flowView) flush() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.Analysis.tile_pyramid.TileIO method) (PYME.cluster.webdav.BufWriter method) (PYME.contrib.lzw.Encoder method) (PYME.IO.h5rFile.H5RFile method) FLUSH_INTERVAL (PYME.IO.h5rFile.H5RFile attribute) FlushBuffer() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.IO.Spooler.Spooler method) fmfROI() (in module PYME.localization.autopsf.roifit) fmtSlicesUsed() (in module PYME.localization.FitFactories.fitCommon) FocusLockPanel (class in PYME.Acquire.ui.focus_lock_gui) FocusLogPanel (class in PYME.Acquire.ui.focus_lock_gui) fold() (in module PYME.Analysis.angleFilter) Fold() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) fold1() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldPanel method) foldElement (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldingPane (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldPanel (class in PYME.ui.autoFoldPanel) (class in PYME.ui.manualFoldPanel) foldX() (in module PYME.Analysis.points.multiview) font_size (PYME.LMVis.layers.labels.LabelLayer attribute) format() (PYME.util.mProfile.colorize_db_t.Parser method) format_results() (in module PYME.IO.clusterResults) format_string (PYME.LMVis.layers.labels.LabelLayer attribute) format_taskDesc() (PYME.cluster.taskWorkerHTTP.RecipeTaskError method) (PYME.cluster.taskWorkerHTTP.TaskError method) formField() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) formFields() (PYME.localization.MetaDataEdit.MDParam method) (PYME.localization.MetaDataEdit.ParamGroup method) FORWARDS (PYME.Acquire.stackSettings.StackSettings attribute) fourier_ring_correlation() (in module PYME.Analysis.Colocalisation.correlationCoeffs) FourierPropagator (class in PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) FourierPropagatorClipHNA (class in PYME.Analysis.PSFGen.fourierHNA) (class in PYME.Analysis.PSFGen.fourierHNA2) FourierPropagatorHNA (class in PYME.Analysis.PSFGen.fourierHNA) (class in PYME.Analysis.PSFGen.fourierHNA2) FourierPSF (class in PYME.Analysis.PSFGen.fourierHNA) Fraction (class in PYME.IO.FileUtils.obf_support) frame_weights() (PYME.Analysis.tile_pyramid.ImagePyramid class method) frameCOI() (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) frames_to_times() (in module PYME.Analysis.piecewiseMapping) FrameWrangler (class in PYME.Acquire.frameWrangler) fresult_dtype() (in module PYME.localization.FitFactories.MultiviewFitInterpNR) from_filename() (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource static method) (PYME.IO.DataSources.TileDataSource.TileDataSource class method) from_json() (in module PYME.IO.MetaDataHandler) from_md_entry() (PYME.Analysis.points.twoColour.ShiftModel class method) from_raw_tile_series() (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource static method) from_request() (PYME.Analysis.distributed_pyramid.PartialPyramid class method) from_spool_settings() (PYME.Acquire.acquisition_base.AcquisitionBase class method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition class method) (PYME.Acquire.Utils.tiler.TileAcquisition class method) (PYME.Acquire.xyztc.TiledZStackAcquisition class method) (PYME.Acquire.xyztc.XYZTCAcquisition class method) (PYME.Acquire.xyztc.ZStackAcquisition class method) from_tabular() (PYME.Analysis.points.spherical_harmonics.ScaledShell static method) fromMDFile() (PYME.localization.Test.fitTestJig.fitTestJig class method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig class method) (PYME.localization.Test.fitTestJigWC.fitTestJig class method) FromPoint() (PYME.localization.FitFactories.AstigGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.BeadConvolvedAstigGaussFit.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumFR.ChecksumFitFactory method) (PYME.localization.FitFactories.Dumbell3DFitR.Dumbell3DFitFactory method) (PYME.localization.FitFactories.DumbellFitR.DumbellFitFactory method) (PYME.localization.FitFactories.FFBase.FFBase method) (PYME.localization.FitFactories.Gauss3DFitR.Gauss3dFitFactory method) (PYME.localization.FitFactories.GaussFitConstrR.GaussianFitFactory method) (PYME.localization.FitFactories.InterpFitR.PSFFitFactory method) (PYME.localization.FitFactories.InterpFitWFR.WFPSFFitFactory method) (PYME.localization.FitFactories.LatFitCOIR.COIFitFactory method) (PYME.localization.FitFactories.LatGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.LatObjFindFR.GaussianFitFactory method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitFactory method) (PYME.localization.FitFactories.MultiviewFitInterpNR.InterpFitFactory method) (PYME.localization.FitFactories.PRInterpFitQR.PSFFitFactory method) (PYME.localization.FitFactories.PRInterpFitR.PSFFitFactory method) (PYME.localization.FitFactories.ROIExtractNR.GaussianFitFactory method) (PYME.localization.FitFactories.SpecGaussFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitCOIR.COIFitFactory method) (PYME.localization.FitFactories.SplitterFitFNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitFusionR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterFitInterpBNR.InterpFitFactory method) (PYME.localization.FitFactories.SplitterFitInterpNR.InterpFitFactory method) (PYME.localization.FitFactories.SplitterFitScavNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterObjFindR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterROIExtractNR.GaussianFitFactory method) (PYME.localization.FitFactories.SplitterShiftEstFR.GaussianFitFactory method) front() (PYME.LMVis.views.View method) frustrum() (in module PYME.LMVis.mv_math) fstat (PYME.contrib.gohlke.tifffile.TIFFfile attribute) FunctionAction (class in PYME.Acquire.actions) FunctionOverlay (class in PYME.DSView.overlays)

G

g_histfitting() (in module PYME.Analysis.BleachProfile.rollins) Gauss2D() (in module PYME.Analysis.points.segmentLL) (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) Gauss3d() (in module PYME.LMVis.visHelpers) Gauss3dFitFactory (class in PYME.localization.FitFactories.Gauss3DFitR) Gauss3dFitResultR() (in module PYME.localization.FitFactories.Gauss3DFitR) GaussFitResult (class in PYME.localization.FitFactories.Gauss3DFitR) Gaussian3DRenderer (class in PYME.LMVis.renderers) gaussian_blob_paint() (in module PYME.Analysis.points.rings) GaussianFitFactory (class in PYME.localization.FitFactories.AstigGaussFitFR) (class in PYME.localization.FitFactories.AstigGaussGPUFitFR) (class in PYME.localization.FitFactories.BeadConvolvedAstigGaussFit) (class in PYME.localization.FitFactories.GaussFitConstrR) (class in PYME.localization.FitFactories.GaussMultifitLinesR) (class in PYME.localization.FitFactories.GaussMultifitR) (class in PYME.localization.FitFactories.GaussMultifitSR) (class in PYME.localization.FitFactories.LatGaussFitFR) (class in PYME.localization.FitFactories.LatObjFindFR) (class in PYME.localization.FitFactories.ROIExtractNR) (class in PYME.localization.FitFactories.SpecGaussFitFR) (class in PYME.localization.FitFactories.SplitterFitFNR) (class in PYME.localization.FitFactories.SplitterFitFusionR) (class in PYME.localization.FitFactories.SplitterFitScavNR) (class in PYME.localization.FitFactories.SplitterMultifitSR) (class in PYME.localization.FitFactories.SplitterObjFindR) (class in PYME.localization.FitFactories.SplitterROIExtractNR) (class in PYME.localization.FitFactories.SplitterShiftEstFR) GaussianFitResultR() (in module PYME.localization.FitFactories.GaussFitConstrR) (in module PYME.localization.FitFactories.GaussMultifitLinesR) (in module PYME.localization.FitFactories.GaussMultifitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.LatObjFindFR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) GaussianRenderer (class in PYME.LMVis.renderers) gaussKernel() (in module PYME.LMVis.rendGauss) GaussTexture (class in PYME.LMVis.shader_programs.PointSpriteShaderProgram) gen2DMask() (in module PYME.Analysis.annealThresh) gen3DBlobs() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangs() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsT() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsTF() (in module PYME.Analysis.points.gen3DTriangs) gen3DTriangsTFC() (in module PYME.Analysis.points.gen3DTriangs) Gen4PiPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) gen_autoencoder() (in module PYME.Analysis.autoencoder_classifier) gen_features() (in module PYME.Analysis.fiducial_matching) gen_features2() (in module PYME.Analysis.fiducial_matching) gen_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_isosurface_from_tesselation() (in module PYME.LMVis.Extras.extra_layers) gen_mdh() (in module PYME.IO.csv_flavours) gen_nb_testdata() (in module PYME.Analysis.BleachProfile.rollins) gen_octree_from_points() (in module PYME.LMVis.Extras.extra_layers) gen_octree_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_pairwise_distance_features() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) gen_point_dis_isosurface() (in module PYME.LMVis.Extras.extra_layers) gen_quad_rot_surf() (in module PYME.Analysis.points.surfit) gen_sequence_id() (PYME.IO.acquisition_backends.Backend class method) gen_text_image() (PYME.LMVis.layers.text.Text class method) gen_traces_from_speckles() (in module PYME.IO.FileUtils.readSpeckle) gen_training_data() (in module PYME.Analysis.autoencoder_classifier) GenAstigPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genBeadImage() (in module PYME.Deconv.beadGen) GenBesselPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenBiplanePSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenBlobFindingPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) GenBlobFitPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) GenBlobPanel() (in module PYME.LMVis.triBlobs) GenClippedWidefieldPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genClusterDataFilepath() (in module PYME.IO.FileUtils.nameUtils) genClusterResultFileName() (in module PYME.IO.FileUtils.nameUtils) GenColourPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genContents() (PYME.DSView.modules.playback.PlayPanel method) genCoords() (in module PYME.Analysis.angleFilter) (PYME.Acquire.Utils.pointScanner.CircularScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.pointScanner.Scanner method) GenCubicPhasePSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genCurves() (in module PYME.Analysis.PSFGen.genCRBcurves) genDark() (in module PYME.Analysis.deTile) genDataFileID() (in module PYME.IO.FileUtils.fileID) genDataSourceID() (in module PYME.IO.FileUtils.fileID) GenDataSourcePanel() (PYME.LMVis.visCore.VisGUICore method) genDefaultMask() (in module PYME.Analysis.annealThresh) GenDHPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genEdgeDB() (in module PYME.LMVis.visHelpers) Generate() (PYME.LMVis.renderers.ColourRenderer method) (PYME.LMVis.renderers.CurrentRenderer method) generate_a_pyrex_source() (in module PYME.misc.cython_numpy_monkey) generate_icosahedron() (in module PYME.Analysis.points.spherical_harmonics) generate_maps() (in module PYME.Analysis.gen_sCMOS_maps) generate_uniform_map() (in module PYME.Analysis.gen_sCMOS_maps) GenerateBacklashCorrPMFromEventList() (in module PYME.Analysis.piecewiseMapping) GenerateDataGrid() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) GeneratedImage() (in module PYME.IO.image) GenerateGUI() (PYME.LMVis.renderers.ColourRenderer method) (PYME.LMVis.renderers.CurrentRenderer method) GeneratePMFromEventList() (in module PYME.Analysis.piecewiseMapping) GeneratePMFromProtocolEvents() (in module PYME.Analysis.piecewiseMapping) GeneratePupil() (PYME.DSView.modules.psfGeneration.MeasuredPupil method) (PYME.DSView.modules.psfGeneration.PhaseRampPupil method) (PYME.DSView.modules.psfGeneration.WidefieldPupil method) Generator (class in PYME.LMVis.Extras.pointSetGeneration) genFileID() (in module PYME.IO.FileUtils.fileID) genFitImage() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatGaussFitFR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) (in module PYME.localization.FitFactories.SplitterFitScavNR) GenFlowPanel() (PYME.DSView.modules.flowView.FlowView method) genFnl() (in module PYME.IO.FileUtils.fnlGen) genFrameID() (in module PYME.IO.FileUtils.fileID) genGauss() (in module PYME.localization.cModels.gauss_app) genGauss3D() (in module PYME.localization.cModels.gauss_app) genGaussA() (in module PYME.localization.cModels.gauss_app) genGaussInArray() (in module PYME.localization.cModels.gauss_app) genGaussJac() (in module PYME.localization.cModels.gauss_app) genGaussJacW() (in module PYME.localization.cModels.gauss_app) genGaussPhotonStats() (PYME.DSView.fitInfo.FitInfoPanel method) genHDFDataFilepath() (in module PYME.IO.FileUtils.nameUtils) GenHist() (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) GenICPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genIm() (in module PYME.Analysis.Colocalisation.colocScaleDep) (PYME.LMVis.renderers.CurrentRenderer method) (PYME.LMVis.renderers.DensityFitRenderer method) (PYME.LMVis.renderers.Gaussian3DRenderer method) (PYME.LMVis.renderers.GaussianRenderer method) (PYME.LMVis.renderers.Histogram3DRenderer method) (PYME.LMVis.renderers.HistogramRenderer method) (PYME.LMVis.renderers.LHoodRenderer method) (PYME.LMVis.renderers.QuadTreeRenderer method) (PYME.LMVis.renderers.Triangle3DRenderer method) (PYME.LMVis.renderers.TriangleRenderer method) (PYME.LMVis.renderers.TriangleRendererW method) (PYME.LMVis.renderers.VoronoiRenderer method) GenImageDialog (class in PYME.LMVis.genImageDialog) genImageID() (in module PYME.IO.FileUtils.fileID) genImageTime() (in module PYME.IO.FileUtils.fileID) genImR() (in module PYME.Analysis.Colocalisation.colocScaleDep) genImR2() (in module PYME.Analysis.Colocalisation.colocScaleDep) genIndexAndLabels() (in module PYME.Analysis.points.moments) genMetaData() (PYME.simulation.pointsets.FileSource method) (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.RandomSource method) (PYME.simulation.pointsets.WormlikeSource method) genMetaDataFromSourceAndMDH() (in module PYME.Analysis.MetaData) GenMultiChanZernikeDPSF() (in module PYME.localization.autopsf.roifit) genMultiGauss() (in module PYME.localization.cModels.gauss_app) genMultiGaussJac() (in module PYME.localization.cModels.gauss_app) GenPanels() (PYME.LMVis.visCore.VisGUICore method) GenPlayPanel() (PYME.DSView.modules.playback.player method) genPlots() (in module PYME.Analysis.Colocalisation.colocScaleDep) GenPointsPanel() (in module PYME.LMVis.pointSettingsPanel) GenPRIEField() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenPRIPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenPSFPanel() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) GenQuadTreePanel() (in module PYME.LMVis.quadTreeSettings) GenR3PSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genResultDirectoryPath() (in module PYME.IO.FileUtils.nameUtils) genResultFileName() (in module PYME.IO.FileUtils.nameUtils) genResultsFileID() (in module PYME.IO.FileUtils.fileID) genResultsText() (PYME.DSView.fitInfo.FitInfoPanel method) genRGBImage() (in module PYME.Analysis.points.twoColour) GenRunPositions() (PYME.Acquire.Utils.fastTiler.fastRectTiler method) GenSAAstigPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSABesselPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSAPRIPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenSAPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenShiftedPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genShiftFieldDirectoryPath() (in module PYME.IO.FileUtils.nameUtils) GenShiftMapPanel() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) genShiftVectorField() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldLinear() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldMC() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQ() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQuad() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQuadz() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldQz() (in module PYME.Analysis.points.twoColour) genShiftVectorFieldSpline() (in module PYME.Analysis.points.twoColour) genShiftVectors() (in module PYME.Analysis.points.twoColour) genSplitGaussInArray() (in module PYME.localization.cModels.gauss_app) genSplitGaussInArrayPVec() (in module PYME.localization.cModels.gauss_app) GenStartMetadata() (PYME.Acquire.microscope.Microscope method) (PYME.Acquire.sampleInformation.SimpleSampleInfoPanel method) genStartMetadata() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettings method) genStartParams() (PYME.misc.coverslipGeometries.circGeom method) genStatus() (PYME.Acquire.microscope.Microscope method) GenStatusText() (in module PYME.LMVis.statusLog) GenStripePRIPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genTraces() (in module PYME.Analysis.BleachProfile.intensProf) genTracesDE() (in module PYME.Analysis.BleachProfile.intensProf) GenViewClippingPanel() (in module PYME.LMVis.view_clipping_pane) GenWidefieldAP() (in module PYME.Analysis.PSFGen.fourier) GenWidefieldPSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) genWidefieldPSF() (in module PYME.Analysis.PSFGen.ps_app) genWidefieldPSFW() (in module PYME.Analysis.PSFGen.ps_app) GenZernikeDAPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikeDonutPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikeDPSF() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) GenZernikePSF() (in module PYME.Analysis.PSFGen.fourier) (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) geom (class in PYME.misc.coverslipGeometries) geom_depth (PYME.DSView.modules.blobMeasure.DataBlock property) geom_length (PYME.DSView.modules.blobMeasure.DataBlock property) geom_width (PYME.DSView.modules.blobMeasure.DataBlock property) get() (in module PYME.config) (PYME.Acquire.microscope.StateManager method) (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) get3DIsosurf() (PYME.DSView.modules.blobMeasure.BlobObject method) get3DROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) get_advertised_services() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZCListener method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) get_all_glasses() (in module PYME.misc.read_agf) get_analysis_rulechains() (in module PYME.config) get_any() (PYME.cluster.rulenodeserver.Rater method) get_bead_pupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) get_bounds() (PYME.simulation.pointsets.ImageSource method) get_cached_queue_info() (in module PYME.cluster.distribution) get_camera_physical_roi_origin() (in module PYME.IO.MetaDataHandler) get_camera_roi_origin() (in module PYME.IO.MetaDataHandler) get_canvas() (PYME.LMVis.Extras.dockedPanel.DockedPanel method) get_channel() (in module PYME.Analysis.splitting) get_channel_column() (PYME.IO.tabular.ColourFilter method) get_channel_ds() (PYME.IO.tabular.ColourFilter method) get_cluster_dirname() (PYME.Acquire.SpoolController.SpoolController method) get_code() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) get_color_limit() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_color_map() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_colors() (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_colour_chans() (PYME.IO.tabular.ColourFilter class method) get_compression_settings() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) get_custom_protocols() (in module PYME.config) get_custom_recipes() (in module PYME.config) get_dir_manager() (in module PYME.IO.clusterIO) get_dirname() (PYME.Acquire.SpoolController.SpoolController method) get_duration() (PYME.LMVis.Extras.animation.EditDialog method) get_file() (in module PYME.IO.clusterIO) (PYME.IO.h5File.H5File method) (PYME.util.webframework.StaticFileHandler method) get_fitted_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) get_frame() (PYME.IO.dcimg.DCIMGFile method) (PYME.IO.h5File.H5File method) get_frame_png() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) get_frame_png_b64() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) get_frame_pzf() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) get_frame_raw() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) get_free_space() (in module PYME.IO.FileUtils.freeSpace) (PYME.Acquire.SpoolController.SpoolController method) get_free_space_bytes() (in module PYME.IO.FileUtils.freeSpace) get_frozen_settings() (PYME.Acquire.acquisition_base.AcquisitionBase class method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition class method) (PYME.Acquire.Utils.tiler.TileAcquisition class method) (PYME.Acquire.xyztc.TiledZStackAcquisition class method) (PYME.Acquire.xyztc.ZStackAcquisition class method) get_glob() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_h5_part() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_hist_data() (PYME.DSView.displayOptions.DisplayOpts method) get_img_array() (PYME.LMVis.layers.text.Text method) get_index() (in module PYME.misc.read_agf) get_info() (PYME.Acquire.SpoolController.SpoolController method) (PYME.misc.pyme_zeroconf.ZCListener method) get_init_filename() (in module PYME.config) get_json_annotations() (PYME.DSView.modules.annotation.AnnotateBase method) get_k_for_exp_costheta() (in module PYME.simulation.wormlike3) get_label_image() (PYME.DSView.modules.annotation.Annotater method) get_labels() (PYME.DSView.modules.annotation.LabelPanel method) get_labels_from_image() (in module PYME.Analysis.points.cluster_morphology) get_layer_tile_coords() (PYME.Analysis.tile_pyramid.ImagePyramid method) (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) get_listing() (PYME.IO.h5File.H5File method) get_local() (PYME.cluster.rulenodeserver.Rater method) get_local_data_directory() (in module PYME.IO.FileUtils.nameUtils) get_local_path() (in module PYME.IO.clusterIO) get_localip() (in module PYME.cluster.webdav) get_mesh_vertices_faces() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) get_misfit_map() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) get_n_frames() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.IO.acquisition_backends.Backend method) (PYME.IO.Spooler.Spooler method) get_name() (PYME.LMVis.Extras.animation.EditDialog method) get_new_tasks() (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.Rule method) get_normals() (in module PYME.Analysis.points.surfit) (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) get_ns() (in module PYME.IO.cluster_directory) get_num_slices() (PYME.IO.dcimg.DCIMGFile method) get_offset() (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) get_offtime_cdf() (in module PYME.Analysis.points.qpaint) get_oversize_tile() (PYME.Analysis.tile_pyramid.ImagePyramid method) get_package_versions() (in module PYME.ui.progress) get_params() (PYME.DSView.modules.psfTools.PSFFitSettingsDialog method) get_plugin_report_filters() (in module PYME.config) get_plugin_template_dirs() (in module PYME.config) get_plugins() (in module PYME.config) get_polled_status() (in module PYME.cluster.status) get_position_from_events() (in module PYME.Analysis.tile_pyramid) get_profile_stats() (in module PYME.util.mProfile.tProfile) get_program() (PYME.LMVis.shader_programs.ShaderProgramFactory.ShaderProgramFactory static method) get_propagator() (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA class method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA class method) get_protocol() (in module PYME.Acquire.protocol) get_protocol_for_acquisition() (PYME.Acquire.SpoolController.ProtocolAcquisitionSettings method) get_protocol_list() (in module PYME.Acquire.protocol) get_queue_info() (PYME.cluster.ruleserver.RuleServer method) get_queues() (PYME.cluster.ruleserver.RuleServer method) get_ratios() (in module PYME.LMVis.dyeRatios) get_results() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) get_roi_centre() (PYME.Acquire.microscope.Microscope method) get_roi_locations (PYME.tileviewer.tileviewer.TileServer attribute) get_roi_offset() (PYME.Acquire.microscope.Microscope method) get_rule() (PYME.cluster.rules.RuleFactory method) get_salt() (in module PYME.util.authenticate) get_scale_box_layer() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) get_scope_state() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) get_sensor_size() (in module PYME.Analysis.gen_sCMOS_maps) get_service_name() (in module PYME.IO.FileUtils.nameUtils) get_session_yaml() (PYME.LMVis.visCore.VisGUICore method) get_settings() (PYME.Acquire.SpoolController.SpoolController method) (PYME.LMVis.genImageDialog.GenImageDialog method) get_shader_program() (PYME.LMVis.layers.base.ShaderMixin method) (PYME.LMVis.shader_programs.GLProgram.GLProgram method) get_shiftmap() (in module PYME.localization.FitFactories.FFBase) get_shifts() (in module PYME.localization.splitting) get_size_factor() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.PointSpriteShaderProgram method) get_slice_shape() (PYME.IO.dcimg.DCIMGFile method) get_snap() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) get_source() (PYME.reports.UnifiedLoader method) get_specific_shader_program() (PYME.LMVis.layers.base.ShaderMixin method) get_splitter_rois() (in module PYME.localization.splitting) get_spool_subdir() (in module PYME.IO.FileUtils.nameUtils) get_status() (in module PYME.IO.clusterIO) (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_status_msg() (PYME.Acquire.ExecTools.BGInitTask method) get_tabular_part() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) get_terminal() (PYME.Acquire.webui.ipy.IPYTermManager method) get_test_data_dir() (in module PYME.resources) get_tick_distance() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) get_tile (PYME.tileviewer.tileviewer.TileServer attribute) get_tile() (PYME.Analysis.tile_pyramid.ImagePyramid method) (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) get_tiled_area() (PYME.Acquire.Utils.tiler.TileAcquisition class method) get_token() (in module PYME.util.authenticate) get_uniform_location() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) get_vecs() (PYME.LMVis.layers.quiver.QuiverRenderLayer method) get_vertices() (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method)

get_viewport_size() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) get_voxelsize_nm() (in module PYME.IO.MetaDataHandler) get_web_dir() (in module PYME.resources) get_web_static_dir() (in module PYME.resources) get_zernike_psf() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) GetActiveCameraName() (PYME.Acquire.microscope.Microscope method) GetActiveChans() (PYME.DSView.displayOptions.DisplayOpts method) getAll() (PYME.Analysis.points.QuadTree.pointQT.qtNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtNode method) GetBackground() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getBackground() (PYME.IO.buffers.backgroundBuffer method) (PYME.IO.buffers.backgroundBufferM method) (PYME.IO.DataSources.BGSDataSource.backgroundBuffer method) (PYME.IO.DataSources.BGSDataSource.backgroundBufferM method) GetBaseColour() (in module PYME.ui.patch_traitsui) GetBeadRadius() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getBestScanner() (in module PYME.Acquire.zScanner) GetBins() (PYME.DSView.modules.coloc.ColocSettingsDialog method) (PYME.DSView.modules.fourierRingCorrelation.ColocSettingsDialog method) GetBlocking() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetBlockSize() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetBoundingRect() (PYME.Acquire.Utils.fastTiler.fastRectTiler method) getCalibrationDir() (in module PYME.IO.FileUtils.nameUtils) getCentroid() (PYME.Acquire.zScanner.zScanner method) GetChanFilename() (PYME.DSView.modules.composite.ShiftmapSelectionDialog method) GetChannel() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetChans() (PYME.DSView.modules.coloc.ColocSettingsDialog method) (PYME.DSView.modules.fourierRingCorrelation.ColocSettingsDialog method) GetClumpRadiusMultiplier() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetClumpRadiusVariable() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetClumpTimeWindow() (PYME.Analysis.points.DeClump.deClumpGUI.deClumpDialog method) GetCollapsedIconBitmap() (in module PYME.misc.fbpIcons) GetCollapsedIconData() (in module PYME.misc.fbpIcons) GetCollapsedIconImage() (in module PYME.misc.fbpIcons) getColour() (PYME.LMVis.genImageDialog.GenImageDialog method) getColourChans() (PYME.IO.tabular.ColourFilter method) GetColumnSorter() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetColumnWidths() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetComputerName() (in module PYME.misc.computerName) getConn() (in module PYME.misc.tempDB) getCoords() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator.CubicSplineInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP.LinearInterpolator method) getCorrection() (in module PYME.Analysis.points.twoColour) getDarkMap() (PYME.localization.remFitBuf.CameraInfoManager method) getDataErrors() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) getDataSourceForFilename() (in module PYME.IO.DataSources) GetDelim() (PYME.LMVis.importTextDialog.ImportTextDialog method) GetDirection() (PYME.Acquire.stackSettings.StackSettings method) getDirectorySize() (in module PYME.misc.dirSize) getDistributorInfo() (in module PYME.cluster.distribution) GetEndPos() (PYME.Acquire.stackSettings.StackSettings method) getEntries() (in module PYME.misc.tempDB) getEntry() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) getEntryNames() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) getEvents() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetExpandedIconBitmap() (in module PYME.misc.fbpIcons) GetExpandedIconData() (in module PYME.misc.fbpIcons) GetExpandedIconImage() (in module PYME.misc.fbpIcons) getExternalEdges() (in module PYME.Analysis.points.gen3DTriangs) GetFieldNames() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) (PYME.LMVis.importTextDialog.ImportMatDialog method) getFileMetadata() (in module PYME.IO.FileUtils.fileID) getFileTags() (in module PYME.IO.FileUtils.fileID) getFlatfieldMap() (PYME.localization.remFitBuf.CameraInfoManager method) GetFlavour() (PYME.LMVis.importTextDialog.ImportTextDialog method) GetFormat() (PYME.ui.crop_dialog.ExportDialog method) getFPS() (PYME.Acquire.frameWrangler.FrameWrangler method) getFrame() (PYME.Acquire.frameWrangler.FrameWrangler method) getFullExistingFilename() (in module PYME.IO.FileUtils.nameUtils) getFullFilename() (in module PYME.IO.FileUtils.nameUtils) getGeometricMean() (PYME.LMVis.genImageDialog.GenImageDialog method) GetGeometry() (in module PYME.misc.coverslipGeometries) getGraph() (PYME.DSView.modules.blobMeasure.BlobObject method) getIconPath() (in module PYME.resources) GetIgnoreZ() (PYME.DSView.modules.composite.CompositeDialog method) GetImage() (PYME.Acquire.positionTracker.PositionTracker method) getImage() (PYME.DSView.modules.blobMeasure.BlobObject method) getImageTags() (in module PYME.IO.FileUtils.fileID) getInfo() (PYME.IO.tabular.AnndataSource method) (PYME.IO.tabular.FitResultsSource method) (PYME.IO.tabular.H5RDSource method) (PYME.IO.tabular.H5RSource method) (PYME.IO.tabular.HDFSource method) (PYME.IO.tabular.MatfileColumnSource method) (PYME.IO.tabular.MatfileSource method) (PYME.IO.tabular.RandomSource method) (PYME.IO.tabular.RecArraySource method) (PYME.IO.tabular.TextfileSource method) getInRadius() (in module PYME.Analysis.points.QuadTree.pointQT) (in module PYME.Analysis.points.QuadTree.pointQTF) getIntCenter() (in module PYME.Analysis.PSFEst.extractImages) GetInterp() (PYME.DSView.modules.composite.CompositeDialog method) GetItemFullname() (PYME.ui.MetadataTree.MetadataPanel method) getJitterScale() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterScaleZ() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterVariable() (PYME.LMVis.genImageDialog.GenImageDialog method) getJitterVariableZ() (PYME.LMVis.genImageDialog.GenImageDialog method) getLeaves() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) GetLimits() (PYME.ui.histLimits.HistLimitDialog method) getLinkageCandidates() (PYME.Analysis.Tracking.tracking.Tracker method) getListCtrlSelection() (in module PYME.contrib.listctrlMixins) getLUT() (in module PYME.DSView.arrayViewPanel) getMappedResults() (PYME.IO.tabular.MappingFilter method) GetMaster() (PYME.DSView.modules.composite.CompositeDialog method) getMCProbability() (PYME.LMVis.genImageDialog.GenImageDialog method) getMembers() (PYME.cluster.webdav.Collection method) (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) getMetadata() (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) GetMethod() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetMixMatrix() (PYME.DSView.modules.unmixing.UnMixSettingsDlg method) GetMultichannel() (PYME.LMVis.importTextDialog.ImportMatlabDialog method) getMultiviewROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) GetName() (PYME.DSView.modules.composite.ImageList method) getNeighbourDists() (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) getNewID() (in module PYME.DSView.modules.blobMeasure) getnexttag() (PYME.cluster.webdav.XMLDict_Parser method) getNodeInfo() (in module PYME.cluster.distribution) getNS() (in module PYME.misc.hybrid_ns) (in module PYME.misc.pyme_zeroconf) (in module PYME.misc.sqlite_ns) GetNumberComments() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) GetNumIterationss() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getNumSamples() (PYME.LMVis.genImageDialog.GenImageDialog method) getNumSlices() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetOffset() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) (PYME.DSView.modules.unmixing.UnMixSettingsDlg method) getOrDefault() (PYME.IO.MetaDataHandler.MDHandlerBase method) GetPadding() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) GetPadSize() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getPercentile() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) getPerimeter() (in module PYME.Analysis.points.gen3DTriangs) getPhotonNums() (in module PYME.Analysis.BleachProfile.kinModels) GetPixelSize() (PYME.Acquire.microscope.Microscope method) getPixelSize() (PYME.LMVis.genImageDialog.GenImageDialog method) GetPixelSize() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) getPoints() (PYME.simulation.pointsets.FileSource method) (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.RandomSource method) (PYME.simulation.pointsets.SHNucleusSource method) (PYME.simulation.pointsets.WiglyFibreSource method) (PYME.simulation.pointsets.WormlikeSource method) getPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) GetPos() (PYME.Acquire.microscope.Microscope method) GetPosRange() (PYME.Acquire.microscope.Microscope method) GetPrevPos() (PYME.Acquire.stackSettings.StackSettings method) getPrincipalAxis() (in module PYME.Analysis.points.objectMeasure) getProperties() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.DummyFileMember method) (PYME.cluster.webdav.FileMember method) (PYME.cluster.webdav.Member method) (PYME.cluster.webdav.TempDirCollection method) getPSF() (in module PYME.Analysis.PSFEst.extractImages) GetPSF() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getPSF3D() (in module PYME.Analysis.PSFEst.extractImages) GetPSFFilename() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getPSFSlice() (in module PYME.Analysis.PSFEst.extractImages) GetPupil() (PYME.DSView.modules.psfGeneration.PupilGenerator method) getQTLeafSize() (PYME.LMVis.genImageDialog.GenImageDialog method) getQueueInfo() (in module PYME.cluster.distribution) getRatio() (in module PYME.LMVis.dyeRatios) getReducedFilename() (in module PYME.Acquire.protocol_acquisition) (in module PYME.IO.HTTPSpooler_v2) GetRegion() (PYME.DSView.modules.blobMeasure.Measurements method) GetRegularisationLambda() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getRelFilename() (in module PYME.IO.FileUtils.nameUtils) GetRemovePadding() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) getReqMemChans() (PYME.Acquire.frameWrangler.FrameWrangler method) getROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) getSampleData() (in module PYME.Acquire.sampleInformation) getSampleDataFailsafe() (in module PYME.Acquire.sampleInformation) getscalar() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) GetScanChannel() (PYME.Acquire.stackSettings.StackSettings method) getSchematic() (PYME.DSView.modules.blobMeasure.BlobObject method) getSchematic3D() (PYME.DSView.modules.blobMeasure.BlobObject method) GetScrollPixelsPerUnit() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) GetSecondarySortValues() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSelectedPage() (PYME.DSView.dsviewer.DSViewFrame method) getSelection() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) GetSelections() (PYME.DSView.modules.composite.CompositeDialog method) GetSeqLength() (PYME.Acquire.stackSettings.StackSettings method) GetShiftmap() (PYME.DSView.modules.composite.CompositeDialog method) GetSimpleString() (PYME.IO.MetaDataHandler.MDHandlerBase method) getSize() (PYME.cluster.webdav.BufWriter method) getSlice() (PYME.IO.buffers.dataBuffer method) (PYME.IO.buffers.SliceBuffer method) (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.dataBuffer method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.ElectronsPerSecondDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) GetSliceSelection() (PYME.DSView.displayOptions.DisplayOpts method) getSliceShape() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource method) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource method) (PYME.IO.DataSources.BaseDataSource.BaseDataSource method) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper method) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.HTTPDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.RandomDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.TQDataSource.DataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) (PYME.IO.dataWrap.ListWrapper method) getSoftRender() (PYME.LMVis.genImageDialog.GenImageDialog method) GetSortImages() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSortState() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) GetSpeciesDescriptor() (PYME.LMVis.Extras.sequentialSpecies.SpeciesDialog method) getSplitROIAtPoint() (PYME.localization.FitFactories.FFBase.FFBase method) GetStartMode() (PYME.Acquire.stackSettings.StackSettings method) getStartParameters() (in module PYME.localization.FitFactories.zEstimators.astigEstimator) (in module PYME.localization.FitFactories.zEstimators.biplaneEstimator) (in module PYME.localization.FitFactories.zEstimators.genericDualEstimator) (in module PYME.localization.FitFactories.zEstimators.genericEstimator) (in module PYME.localization.FitFactories.zEstimators.priEstimator) GetStartPos() (PYME.Acquire.stackSettings.StackSettings method) GetStepSize() (PYME.Acquire.stackSettings.StackSettings method) getTableData() (PYME.IO.h5rFile.H5RFile method) GetTags() (PYME.Acquire.positionTracker.PositionTracker method) getTextFileLock() (in module PYME.cluster.dataserver_wsgi) (in module PYME.cluster.HTTPDataServer) getThumbnail() (in module PYME.IO.FileUtils.thumbnailDatabase) GetTrack() (PYME.Acquire.positionTracker.PositionTracker method) GetTSlice() (PYME.ui.crop_dialog.ExportDialog method) getURL() (in module PYME.DSView.htmlServe) (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.HDFBackend method) (PYME.IO.acquisition_backends.TiffFolderBackend method) (PYME.IO.HTTPSpooler_v2.Spooler method) GetUseMask() (PYME.DSView.modules.coloc.ColocSettingsDialog method) getUsername() (in module PYME.IO.FileUtils.nameUtils) GetValue() (PYME.ui.histLimits.HistLimitPanel method) GetValues() (PYME.Acquire.ui.positionUI.GOTODialog method) getVarianceMap() (PYME.localization.remFitBuf.CameraInfoManager method) GetVarName() (PYME.LMVis.importTextDialog.ImportMatDialog method) getVertexEdgeLengths() (in module PYME.Analysis.points.EdgeDB.edgeDB) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) getVertexNeighbours() (in module PYME.Analysis.points.EdgeDB.edgeDB) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) GetVoxX() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) GetVoxY() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) GetVoxZ() (PYME.DSView.voxSizeDialog.VoxSizeDialog method) getXML() (PYME.IO.MetaDataHandler.OMEXMLMDHandler method) GetXSlice() (PYME.ui.crop_dialog.ExportDialog method) GetYSlice() (PYME.ui.crop_dialog.ExportDialog method) getZ() (in module PYME.localization.twist) getZBounds() (PYME.LMVis.genImageDialog.GenImageDialog method) GetZrange() (PYME.DSView.modules.coloc.ColocSettingsDialog method) GetZSlice() (PYME.ui.crop_dialog.ExportDialog method) getZSliceThickness() (PYME.LMVis.genImageDialog.GenImageDialog method) gfm() (in module PYME.Analysis.BleachProfile.rollins) Glass (class in PYME.misc.zemax) glob() (in module PYME.IO.clusterGlob) glob_test() (in module PYME.Analysis.PSFEst.psfQuality) globalLHood() (PYME.Analysis.points.segmentLL.segmenter method) GLProgram (class in PYME.LMVis.shader_programs.GLProgram) GLProgramException GLShaderLoadException goalfcn() (in module PYME.Analysis.BleachProfile.kinModels) GOTODialog (class in PYME.Acquire.ui.positionUI) GouraudFlatpointsShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) GouraudShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) GouraudSphereShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) gp() (in module PYME.Analysis.points.surfit) gpn() (in module PYME.Analysis.points.surfit) gpnA() (in module PYME.Analysis.points.surfit) gpnA2() (in module PYME.Analysis.points.surfit) Grab() (PYME.misc.VolProj.Isosurf method) GrabComp() (PYME.misc.VolProj.Isosurf method) GrabImage() (in module PYME.misc.VolProj) (PYME.DSView.arrayViewPanel.ArrayViewPanel method) GrabPNG() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) GrabPNGToBuffer() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) graded_cmaps (PYME.misc.colormaps.CMapDict property) graphs() (PYME.DSView.modules.blobMeasure.Measurements method) GraphViewPanel (class in PYME.DSView.modules.fastGraphPanel) greedy_sort() (in module PYME.Analysis.points.traveling_salesperson.sort) Green() (in module PYME.misc.colormaps) grey_overflow() (in module PYME.misc.colormaps) grff() (in module PYME.Analysis.BleachProfile.rollins) Group() (in module PYME.misc.mock_traitsui) gt() (in module PYME.Analysis.BleachProfile.intensProf) gt_mod() (in module PYME.Analysis.BleachProfile.intensProf) guess_flavour() (in module PYME.IO.csv_flavours) guess_install_type() (in module PYME.misc.check_for_updates) guess_text_options() (in module PYME.IO.csv_flavours) guess_type() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.util.webframework.StaticFileHandler method) guessFlat() (in module PYME.Analysis.deTile) guessH5RImageID() (in module PYME.IO.FileUtils.fileID) guessUserID() (in module PYME.IO.FileUtils.fileID) gui_prompt_once() (in module PYME.misc.check_for_updates) gui_prompt_update() (in module PYME.misc.check_for_updates) GuiGetDirList() (in module PYME.IO.FileUtils.fnlGen) GUIInitTask (class in PYME.Acquire.ExecTools)

H

H5Exporter (class in PYME.IO.dataExporter) H5File (class in PYME.IO.h5File) H5RDSource (class in PYME.IO.tabular) h5rDSource() (in module PYME.IO.tabular) H5RFile (class in PYME.IO.h5rFile) H5RSource (class in PYME.IO.tabular) h5rSource() (in module PYME.IO.tabular) handin() (PYME.cluster.ruleserver.RuleServer method) has_key() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) has_listeners() (PYME.contrib.dispatch.dispatcher.Signal method) hash_password() (in module PYME.util.authenticate) hashString32() (in module PYME.misc.hash32) HasStrictTraits (in module PYME.misc.mock_traits) HasTraits (class in PYME.misc.mock_traits) HDFBackend (class in PYME.IO.acquisition_backends) HDFEventLogger (class in PYME.IO.events) HDFMDHandler (class in PYME.IO.MetaDataHandler) HDFSource (class in PYME.IO.tabular) hdfSource() (in module PYME.IO.tabular) header_dtype_v3 (in module PYME.IO.PZFFormat) height() (PYME.IO.image.ImageBounds method) (PYME.LMVis.visHelpersMin.ImageBounds method) help_url (PYME.misc.exceptions.UserError attribute) helpInfo (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) (PYME.simulation.pointsets.ImageSource attribute)

helpStr() (PYME.LMVis.Extras.pointSetGeneration.Generator method) (PYME.simulation.pointsets.ImageSource method) hide() (PYME.DSView.modules.blobMeasure.Measurements method) HideTextCtrl() (PYME.LMVis.view_clipping_pane.ClippingPanel method) hill() (in module PYME.misc.hillcurve) hist() (in module PYME.Analysis.graphing_filters) histfitting() (in module PYME.Analysis.BleachProfile.rollins) HistLimitDialog (class in PYME.ui.histLimits) HistLimitEditDialog (class in PYME.ui.histLimits) HistLimitPanel (class in PYME.ui.histLimits) Histogram3DRenderer (class in PYME.LMVis.renderers) HistogramRenderer (class in PYME.LMVis.renderers) hls_to_rgb() (in module PYME.misc.colorsys) hmod() (in module PYME.Analysis.BleachProfile.kinModels) hook() (in module PYME.update_version) hsv_to_rgb() (in module PYME.misc.colorsys) html_error_template (PYME.cluster.taskWorkerHTTP.RecipeTaskError attribute) (PYME.cluster.taskWorkerHTTP.TaskError attribute) html_log_url (PYME.cluster.taskWorkerHTTP.TaskError property) HTTPRedirectResponse (class in PYME.util.webframework) HTTPResponse (class in PYME.util.webframework) HTTPRulePusher (class in PYME.cluster.HTTPRulePusher) HTTPTaskPusher (class in PYME.cluster.HTTPTaskPusher) HWNotPresent HybridNS (class in PYME.misc.hybrid_ns)

I

ib16() (in module PYME.misc.TiffImagePlugin) ib32() (in module PYME.misc.TiffImagePlugin) icosahedron_mesh() (in module PYME.Analysis.points.spherical_harmonics) ICTMDeconvolution (class in PYME.Deconv.dec) id (PYME.LMVis.Extras.animation.EditPanel property) IdFilter (class in PYME.IO.tabular) idFilter() (in module PYME.IO.tabular) iGen() (in module PYME.DSView.modules.blobMeasure) iglob() (in module PYME.IO.clusterGlob) il16() (in module PYME.misc.TiffImagePlugin) il32() (in module PYME.misc.TiffImagePlugin) image (PYME.DSView.modules.psfGeneration.MeasuredPupil attribute) (PYME.simulation.pointsets.ImageSource attribute) image_bounds (PYME.IO.image.ImageStack property) (PYME.IO.tabular.TabularBase property) image_data (PYME.IO.h5File.H5File property) image_enrichment_and_fraction_at_distance() (in module PYME.Analysis.Colocalisation.edtColoc) image_to_cmy() (in module PYME.IO.rgb_image) image_to_rgb() (in module PYME.IO.rgb_image) ImageBounds (class in PYME.IO.image) (class in PYME.LMVis.visHelpersMin) imageDensityAtDistance() (in module PYME.Analysis.Colocalisation.edtColoc) ImageEngine (class in PYME.LMVis.layers.image_layer) ImageFileDirectory (class in PYME.misc.TiffImagePlugin) ImageFrameSource (class in PYME.IO.clusterExport) ImageFromBitmap() (in module PYME.ui.wx_compat) ImageFromData() (in module PYME.ui.wx_compat) ImageList (class in PYME.DSView.modules.composite) ImagePanel (class in PYME.DSView.scrolledImagePanel) ImagePyramid (class in PYME.Analysis.tile_pyramid) ImageRenderLayer (class in PYME.LMVis.layers.image_layer) images() (PYME.DSView.modules.blobMeasure.Measurements method) ImageShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) ImageSource (class in PYME.simulation.pointsets) ImageStack (class in PYME.IO.image) ImageViewPanel (class in PYME.LMVis.imageView) (class in PYME.LMVis.imageView2) imgBounds (PYME.IO.image.ImageStack property) impfilt() (in module PYME.Analysis.implicitFilter) impfilt2() (in module PYME.Analysis.implicitFilter) impfilt3() (in module PYME.Analysis.implicitFilter) import_fit_factory() (in module PYME.localization.FitFactories) ImportMatDialog (class in PYME.LMVis.importTextDialog) ImportMatlabDialog (class in PYME.LMVis.importTextDialog) ImportTextDialog (class in PYME.LMVis.importTextDialog) imread() (in module PYME.contrib.gohlke.czifile) (in module PYME.contrib.gohlke.tifffile) imsave() (in module PYME.contrib.gohlke.tifffile) imshow() (in module PYME.contrib.gohlke.tifffile) inactivate() (PYME.cluster.ruleserver.IntegerIDRule method) inactivate_rule() (PYME.cluster.ruleserver.RuleServer method) index (PYME.IO.tabular.ColourFilter property) (PYME.tileviewer.tileviewer.TileServer attribute) index() (PYME.DSView.modules.blobMeasure.Measurements method) index_coeffs() (in module PYME.misc.read_agf) index_data() (in module PYME.misc.read_agf) infer_tileio_backend() (in module PYME.Analysis.tile_pyramid) info() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) (PYME.cluster.ruleserver.IntegerIDRule method) info_longpoll() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) info_text (PYME.recipes.traits.FileOrURI attribute) Init() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) init_gui() (in module PYME.Acquire.ExecTools) init_hardware() (in module PYME.Acquire.ExecTools) init_pane() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) init_renderers() (in module PYME.LMVis.renderers) init_scan() (PYME.Acquire.Utils.pointScanner.Scanner method) InitBG() (in module PYME.Acquire.ExecTools) InitGUI() (in module PYME.Acquire.ExecTools) initialise() (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.TiffFolderBackend method) initialize() (PYME.Acquire.microscope.Microscope method) initialized (PYME.Acquire.microscope.Microscope property) initializeWorkerTimeout() (PYME.misc.taskDef.Task method) InitPlugins() (in module PYME.LMVis.Extras) Input (class in PYME.recipes.traits) INPUT_LIGHT (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute)

insert() (PYME.Analysis.points.QuadTree.pointQT.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQT.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQT.qtNode method) (PYME.Analysis.points.QuadTree.pointQT.qtRoot method) (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtRoot method) insert_dispersion_coeffs() (in module PYME.misc.read_agf) insert_into_full_map() (in module PYME.Analysis.gen_sCMOS_maps) insertRecords() (PYME.Analysis.points.QuadTree.pointQTF.qtBranchNode method) (PYME.Analysis.points.QuadTree.pointQTF.qtLeafNode method) install_map() (in module PYME.Analysis.gen_sCMOS_maps) InstallSpy() (in module PYME.misc.eventSpy) Instance (in module PYME.misc.mock_traits) InstanceEditor() (in module PYME.misc.mock_traitsui) instanceinlist() (in module PYME.IO.MetaDataHandler) Int (in module PYME.misc.mock_traits) IntegerIDRule (class in PYME.cluster.ruleserver) IntegrationSliders (class in PYME.Acquire.ui.intsliders) IntegrationSliders_ (class in PYME.Acquire.ui.intsliders) IntensityTracePanel (class in PYME.Acquire.ui.intensity_trace) intermediateUpdates (PYME.DSView.modules.psfTools.PSFTools attribute) interp() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator.CubicSplineInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP.LinearInterpolator method) InterpFitFactory (class in PYME.localization.FitFactories.MultiviewFitInterpNR) (class in PYME.localization.FitFactories.SplitterFitInterpBNR) (class in PYME.localization.FitFactories.SplitterFitInterpNR) interpG() (PYME.localization.FitFactories.Interpolators.CSInterpolator.CSInterpolator method) (PYME.localization.FitFactories.Interpolators.LinearInterpolator.LinearInterpolator method) Interpolate() (in module PYME.localization.cInterp.cInterp) InterpolateCS() (in module PYME.localization.cInterp.cInterp) InterpolateInplace() (in module PYME.localization.cInterp.cInterp) InterpolateInplaceM() (in module PYME.localization.cInterp.cInterp) intfrombits() (in module PYME.contrib.lzw) IntParam (class in PYME.localization.MetaDataEdit) inttobits() (in module PYME.contrib.lzw) invalidate_directory() (PYME.IO.clusterListing.DirCache method) IPY (class in PYME.Acquire.webui.ipy) IPYTermManager (class in PYME.Acquire.webui.ipy) IPYWithClients (class in PYME.Acquire.webui.ipy) IQR() (in module PYME.localization.Test.fitTestJigSCMOS) (in module PYME.localization.Test.fitTestJigWC) is_bigtiff (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_cluster_uri() (in module PYME.IO.unifiedIO) is_complete (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCWrapper property) (PYME.IO.DataSources.BaseDataSource.XYZTCWrapper property) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource property) (PYME.IO.DataSources.BufferedDataSource.DataSource property) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource property) (PYME.IO.dataWrap.ListWrapper property) is_fluoview (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_local() (in module PYME.IO.clusterIO) is_lsm (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_nih (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_ome (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_palette (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_port_open() (in module PYME.misc.sqlite_ns) is_rgb (PYME.contrib.gohlke.tifffile.TIFFfile attribute) is_splitter_fit (PYME.localization.remFitBuf.fitTask property) is_stk (PYME.contrib.gohlke.tifffile.TIFFfile attribute) isatty() (PYME.Acquire.webui.ipy.TTYDummy method) IsChecked() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) isdir() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) isnumber() (in module PYME.IO.csv_flavours) (in module PYME.LMVis.importTextDialog) isodata() (in module PYME.Analysis.thresholding) isodata_f() (in module PYME.Analysis.thresholding) Isosurf (class in PYME.misc.VolProj) isosurf_builtin() (PYME.DSView.modules.vis3D.Visualiser method) isosurf_coloured() (PYME.DSView.modules.vis3D.Visualiser method) isosurface3D() (PYME.DSView.modules.blobMeasure.Measurements method) isRunning() (PYME.Acquire.frameWrangler.FrameWrangler method) Item() (in module PYME.misc.mock_traitsui) items() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) iterations (PYME.DSView.modules.psfTools.PSFTools attribute)

J

jittering (PYME.LMVis.triBlobs.BlobSettings attribute) join() (PYME.Acquire.ExecTools.BGInitTask method) (PYME.cluster.rules.Rule method) joinBGInit() (in module PYME.Acquire.ExecTools)

JSON_DURATION (PYME.LMVis.views.VideoView attribute) JSON_LIST_NAME (PYME.LMVis.Extras.animation.VideoPanel attribute) JSONAPIRequestHandler (class in PYME.util.webframework) jumpDistModel() (in module PYME.Analysis.Tracking.trackUtils) jumpDistProb() (in module PYME.Analysis.Tracking.trackUtils)

K

kbp (PYME.simulation.pointsets.WormlikeSource attribute) keep_alive() (in module PYME.IO.clusterDuplication) KEEP_ALIVE_TIMEOUT (PYME.IO.h5File.H5File attribute) (PYME.IO.h5rFile.H5RFile attribute) keep_pairs() (in module PYME.Analysis.keep_pairs) keys() (PYME.Acquire.microscope.StateManager method) (PYME.Analysis.Tracking.trackUtils.Clump method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.tabular.AnndataSource method) (PYME.IO.tabular.CachingResultsFilter method) (PYME.IO.tabular.CloneSource method) (PYME.IO.tabular.ColourFilter method) (PYME.IO.tabular.ConcatenateFilter method) (PYME.IO.tabular.DictSource method) (PYME.IO.tabular.FitResultsSource method) (PYME.IO.tabular.HDFSource method) (PYME.IO.tabular.MappingFilter method) (PYME.IO.tabular.MatfileColumnSource method) (PYME.IO.tabular.MatfileSource method) (PYME.IO.tabular.RandomSource method) (PYME.IO.tabular.RecArraySource method) (PYME.IO.tabular.SelectionFilter method) (PYME.IO.tabular.TabularBase method) (PYME.IO.tabular.TextfileSource method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method)

kill() (PYME.Acquire.Utils.failsafe.Failsafe method) (PYME.Acquire.Utils.failsafe.FailsafeClient method) (PYME.Acquire.webui.ipy.IPY method) (PYME.Acquire.webui.ipy.IPYWithClients method) (PYME.Deconv.decThread.decThread method) kill_all (PYME.Acquire.webui.ipy.IPYTermManager attribute) killpg() (PYME.Acquire.webui.ipy.IPYWithClients method)

L

label_key (PYME.LMVis.Extras.objectMeasurements.OMDialog property) label_points() (PYME.DSView.modules.annotation.AnnotationList method) labeled() (in module PYME.DSView.displayOptions) (in module PYME.misc.colormaps) LabelLayer (class in PYME.LMVis.layers.labels) LabelPanel (class in PYME.DSView.modules.annotation) LaserSliders (class in PYME.Acquire.ui.lasersliders) LaserSliders_ (class in PYME.Acquire.ui.lasersliders) LaserToggles (class in PYME.Acquire.ui.lasersliders) launch() (PYME.cluster.cluster_of_one.ClusterOfOne method) launch_analysis() (PYME.Acquire.SpoolController.SpoolController method) launch_browser() (in module PYME.util.fProfile.viewProfile) launch_ipy_server_thread() (in module PYME.Acquire.webui.ipy) launch_localize() (in module PYME.cluster.HTTPRulePusher) (in module PYME.cluster.HTTPTaskPusher) LaunchAnalysis() (PYME.Acquire.SpoolController.SpoolController method) layer_from_session_info() (in module PYME.LMVis.layers) LayerFoldingPane (class in PYME.ui.layerFoldPanel) LayerPane (class in PYME.LMVis.layer_panel) layers (PYME.Analysis.tile_pyramid.ImagePyramid property) (PYME.LMVis.visCore.VisGUICore property) LazyScopeTweeter (class in PYME.Acquire.htsms.tweeter) leafSize (PYME.LMVis.quadTreeSettings.QuadTreeSettings attribute) length (PYME.simulation.pointsets.WiglyFibreSource attribute) length_nm (PYME.DSView.overlays.ScaleBarOverlay attribute) lengthPerKbp (PYME.simulation.pointsets.WormlikeSource attribute) levels (PYME.IO.DataSources.TileDataSource.TileDataSource property) Lfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) Lhfunc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.dec_4pi_c method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) LHoodRenderer (class in PYME.LMVis.renderers) LIGHT_PROPS (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) lights_vector (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) LimitedSizeDict (class in PYME.Acquire.sampleInformation) lin2Model (class in PYME.Analysis.points.twoColour) lin3Model (class in PYME.Analysis.points.twoColour) lin3zModel (class in PYME.Analysis.points.twoColour) line_sdf() (in module PYME.simulation.wormlike2) line_width (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) LinearInterpolator (class in PYME.localization.FitFactories.Interpolators.LinearInterpolator) (class in PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP) link() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) link_route() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) linMod() (in module PYME.Analysis.BleachProfile.rawIntensity) linModel (class in PYME.Analysis.points.twoColour) List (class in PYME.misc.mock_traits) list() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZCListener method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) list_directory() (in module PYME.IO.clusterListing) (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.IO.clusterListing.DirCache method) list_directory_p() (in module PYME.IO.clusterListing) list_h5() (in module PYME.IO.pyme_h5ls) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) list_single_node_dir() (PYME.IO.cluster_directory.DirectoryInfoManager method) list_to_array() (PYME.IO.events.EventLogger class method) listCalibrationDirs() (in module PYME.Analysis.gen_sCMOS_maps) ListCtrlAutoWidthMixin (class in PYME.contrib.listctrlMixins) ListCtrlSelectionManagerMix (class in PYME.contrib.listctrlMixins) listdir() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) listdirectory() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) ListFloat (in module PYME.misc.mock_traits) ListInt (in module PYME.misc.mock_traits) ListRowHighlighter (class in PYME.contrib.listctrlMixins) ListStr (in module PYME.misc.mock_traits) ListWrapper (class in PYME.IO.dataWrap)

lNdfcn() (in module PYME.Analysis.BleachProfile.intensProf) lNdfcnDE() (in module PYME.Analysis.BleachProfile.intensProf) lNofcn() (in module PYME.Analysis.BleachProfile.intensProf) lNofcnDE() (in module PYME.Analysis.BleachProfile.intensProf) load() (in module PYME.IO.FileUtils.SPAD) (PYME.Analysis.tile_pyramid.TileCache method) Load() (PYME.IO.image.ImageStack method) load() (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_byte() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_config() (in module PYME.config) load_dispatch (PYME.misc.TiffImagePlugin.ImageFileDirectory attribute) load_double() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_existing() (PYME.Analysis.tile_pyramid.ImagePyramid class method) load_float() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_header() (in module PYME.IO.PZFFormat) load_json() (in module PYME.IO.MetaDataHandler) load_long() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_ply() (in module PYME.IO.FileUtils.ply) load_psf() (in module PYME.IO.load_psf) load_rational() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_session() (PYME.LMVis.visCore.VisGUICore method) load_shiftmap() (in module PYME.Analysis.points.multiview) load_short() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_stl_binary() (in module PYME.IO.FileUtils.stl) load_string() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_template() (in module PYME.Acquire.webui) load_texture() (PYME.LMVis.shader_programs.PointSpriteShaderProgram.GaussTexture method) load_undefined() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) load_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) load_wisdom() (in module PYME.Deconv.fftwWisdom) loadDark() (in module PYME.IO.FileUtils.SPAD) loadFile() (PYME.Analysis.svmSegment.svmClassifier method) loadMode() (in module PYME.DSView.modules) loadModule() (in module PYME.DSView.modules) LoadModule() (PYME.DSView.dsviewer.DSViewFrame method) LoadPerspective() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) loadRaw() (in module PYME.IO.FileUtils.SPAD) loads() (in module PYME.IO.PZFFormat) LoadShiftField() (in module PYME.Analysis.splitting) loc_test() (in module PYME.Analysis.PSFEst.psfQuality) local_or_temp_filename() (in module PYME.IO.unifiedIO) localisation_origin_nm() (in module PYME.IO.MetaDataHandler) LocalisationRule (class in PYME.cluster.rules) LocalisationRuleFactory (class in PYME.cluster.rules) locate() (in module PYME.misc.locate) locate_file() (in module PYME.IO.clusterIO) (PYME.IO.cluster_directory.DirectoryInfoManager method) Location (class in PYME.tileviewer.tileviewer) locify() (in module PYME.simulation.locify) log_error() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) log_message() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.cluster.webdav.DAVRequestHandler method) log_request() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) (PYME.util.webframework.JSONAPIRequestHandler method) log_stream() (in module PYME.cluster.PYMERuleServer) log_url (PYME.cluster.taskWorkerHTTP.TaskError property) logEvent() (in module PYME.Acquire.eventLog) (PYME.IO.events.EventLogger method) (PYME.IO.events.HDFEventLogger method) (PYME.IO.events.MemoryEventLogger method) logger (in module PYME.IO.dcimg) login() (PYME.Acquire.acquire_server.AcquireHTTPServerMixin method) logout() (PYME.Acquire.acquire_server.AcquireHTTPServerMixin method) logparser (class in PYME.DSView.logparser) logrequests (PYME.cluster.dataserver_wsgi.dataserver attribute) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) (PYME.util.webframework.JSONAPIRequestHandler attribute) logwriter (class in PYME.DSView.logparser) long_unpack() (in module PYME.IO.FileUtils.obf_support) longAxisDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) longAxisOrthDist() (PYME.DSView.modules.blobMeasure.BlobObject method) lookup_astig_z() (in module PYME.Analysis.points.astigmatism.astigTools) lookup_astig_z_dsigma() (in module PYME.Analysis.points.astigmatism.astigTools) lookup_offset() (PYME.Acquire.stage_leveling.StageLeveler method) loop_forever() (in module PYME.ui.mytimer) (PYME.Acquire.event_loop.EventLoop method) (PYME.cluster.taskWorkerHTTP.taskWorker method) lp_poisson() (in module PYME.Analysis.cramerRao) lp_poisson_n() (in module PYME.Analysis.cramerRao) LUTBitmap (class in PYME.ui.layerFoldPanel) LUTOverlayLayer (class in PYME.LMVis.layers.LUTOverlayLayer)

M

M_COLLECTION (PYME.cluster.webdav.Member attribute) M_MEMBER (PYME.cluster.webdav.Member attribute) mad_0 (PYME.DSView.modules.blobMeasure.DataBlock property) mad_1 (PYME.DSView.modules.blobMeasure.DataBlock property) mad_2 (PYME.DSView.modules.blobMeasure.DataBlock property) Magenta() (in module PYME.misc.colormaps) main() (in module PYME.Acquire.acquire_server) (in module PYME.Acquire.PYMEAcquire) (in module PYME.Analysis.gen_sCMOS_maps) (in module PYME.cluster.cluster_of_one) (in module PYME.cluster.dataserver_wsgi) (in module PYME.cluster.HTTPDataServer) (in module PYME.cluster.PYMERuleNodeServer) (in module PYME.cluster.PYMERuleServer) (in module PYME.cluster.webdav) (in module PYME.DSView.dsviewer) (in module PYME.util.authenticate) main_loop() (PYME.Acquire.acquirebase.PYMEAcquireBase method) main_page() (PYME.Acquire.acquire_server.AcquireHTTPServerMixin method) make() (PYME.LMVis.Extras.animation.VideoPanel method) make_composite() (in module PYME.Analysis.composite) make_editor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) make_info() (in module PYME.misc.sqlite_ns) make_range_available() (PYME.cluster.ruleserver.IntegerIDRule method) makeColumnEditable() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) makedirs_safe() (in module PYME.cluster.HTTPDataServer) (in module PYME.cluster.webdav) makeFilter() (in module PYME.Analysis.points.fiducials) makeGraph() (in module PYME.misc.depGraph) makePathUnlessExists() (in module PYME.Analysis.gen_sCMOS_maps) managed() (in module PYME.ui.progress) map_corrected_focus() (in module PYME.Analysis.piezo_movement_correction) map_filename() (in module PYME.Analysis.gen_sCMOS_maps) map_piezo_moving() (in module PYME.Analysis.piezo_movement_correction) map_splitter_coords() (in module PYME.localization.splitting) map_splitter_coords_() (in module PYME.localization.splitting) MappingFilter (class in PYME.IO.tabular) mappingFilter() (in module PYME.IO.tabular) mark_complete() (PYME.cluster.ruleserver.IntegerIDRule method) mark_release_complete() (PYME.cluster.ruleserver.IntegerIDRule method) (PYME.cluster.ruleserver.RuleServer method) maskFractions() (in module PYME.Analysis.Colocalisation.correlationCoeffs) maskManders() (in module PYME.Analysis.Colocalisation.correlationCoeffs) mat3_to_mat4() (in module PYME.LMVis.mv_math) match_points() (in module PYME.Analysis.fiducial_matching) MatfileColumnSource (class in PYME.IO.tabular) matfileColumnSource() (in module PYME.IO.tabular) MatfileMultiColumnSource (class in PYME.IO.tabular) MatfileSource (class in PYME.IO.tabular) matfileSource() (in module PYME.IO.tabular) MAX_ADVERTISEMENTS (PYME.cluster.ruleserver.RuleServer attribute) max_level_changed() (PYME.ui.histLimits.HistLimitDialog method) MAXIDX (PYME.IO.buffers.bgFrameBuffer attribute) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer attribute) MAXSHORT (PYME.IO.buffers.bgFrameBuffer attribute) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer attribute) mc_points_from_mask() (in module PYME.Analysis.points.ripleys) mc_sampling_statistics() (in module PYME.Analysis.points.ripleys) md (PYME.Acquire.protocol_acquisition.ProtocolAcquisition property) (PYME.Acquire.xyztc.XYZTCAcquisition property) (PYME.IO.acquisition_backends.Backend property) md() (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.Acquire.Utils.tiler.TileAcquisition method) mdh (PYME.Analysis.tile_pyramid.ImagePyramid property) (PYME.IO.DataSources.HDFDataSource.DataSource property) (PYME.IO.h5rFile.H5RFile property) (PYME.IO.tabular.CachingResultsFilter property) MDHandlerBase (class in PYME.IO.MetaDataHandler) MDParam (class in PYME.localization.MetaDataEdit) MDSource (class in PYME.IO.clusterExport) meanDuration (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) meanEventNumber (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) meanIntensity (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) meanTime (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) measure() (in module PYME.Analysis.points.objectMeasure) (in module PYME.LMVis.objectDarkMeasure) measure_3d() (in module PYME.Analysis.points.cluster_morphology) measure_offsets() (PYME.Acquire.stage_leveling.StageLeveler method) measureAligned() (in module PYME.Analysis.points.objectMeasure) MeasuredPupil (class in PYME.DSView.modules.psfGeneration) Measurements (class in PYME.DSView.modules.blobMeasure) measureObjects() (in module PYME.Analysis.points.objectMeasure) measureObjectsByID() (in module PYME.Analysis.points.objectMeasure) (in module PYME.LMVis.objectDarkMeasure) Member (class in PYME.cluster.webdav) memmap() (in module PYME.misc.memmap) memory() (in module PYME.misc.memUsage) MemoryBackend (class in PYME.IO.acquisition_backends) MemoryEventLogger (class in PYME.IO.events) merge_clumps() (in module PYME.Analysis.points.multiview) mergeClumps() (in module PYME.Analysis.points.DeClump.pyDeClump) mergeEntriesFrom() (PYME.IO.MetaDataHandler.MDHandlerBase method) MeshViewFrame (class in PYME.DSView.modules.vis3D) metadata (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.IO.image.ImageStack property) MetadataPanel (class in PYME.ui.MetadataTree) method (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) mf() (in module PYME.Analysis.points.surfit) mf2() (in module PYME.Analysis.points.surfit) mfA() (in module PYME.Analysis.points.surfit) mfA1() (in module PYME.Analysis.points.surfit) Microscope (class in PYME.Acquire.microscope) min_level_changed() (PYME.ui.histLimits.HistLimitDialog method) min_points (PYME.LMVis.layers.octree.OctreeRenderLayer attribute) minimum_distance_to_poly() (in module PYME.DSView.modules.annotation) minmax_u16() (in module PYME.DSView.LUT.lut) minSize (PYME.LMVis.triBlobs.BlobSettings attribute) mirror (PYME.misc.zemax.DefaultGlass attribute) mirror_file() (in module PYME.IO.clusterIO) misfallA() (in module PYME.localization.autopsf.roifit) misfallB() (in module PYME.localization.autopsf.roifit) misfallB_MP() (in module PYME.localization.autopsf.roifit) misfitROI() (in module PYME.localization.autopsf.roifit) mkDefaultPath() (in module PYME.Analysis.gen_sCMOS_maps) mkDestPath() (in module PYME.Analysis.gen_sCMOS_maps) mock_decorator() (in module PYME.misc.mock_traits) mod1pk() (in module PYME.Analysis.BleachProfile.intensProf) mode (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) (PYME.LMVis.renderers.CurrentRenderer attribute) (PYME.LMVis.renderers.DensityFitRenderer attribute) (PYME.LMVis.renderers.Gaussian3DRenderer attribute) (PYME.LMVis.renderers.GaussianRenderer attribute) (PYME.LMVis.renderers.Histogram3DRenderer attribute) (PYME.LMVis.renderers.HistogramRenderer attribute) (PYME.LMVis.renderers.LHoodRenderer attribute) (PYME.LMVis.renderers.QuadTreeRenderer attribute) (PYME.LMVis.renderers.Triangle3DRenderer attribute) (PYME.LMVis.renderers.TriangleRenderer attribute) (PYME.LMVis.renderers.TriangleRendererW attribute) (PYME.LMVis.renderers.VoronoiRenderer attribute) module PYME PYME.Acquire PYME.Acquire.acquire_client PYME.Acquire.acquire_server PYME.Acquire.acquirebase PYME.Acquire.acquiremainframe PYME.Acquire.acquirewx PYME.Acquire.acquisition_base PYME.Acquire.ActionManager PYME.Acquire.actions PYME.Acquire.autofocus PYME.Acquire.event_loop PYME.Acquire.eventLog PYME.Acquire.ExecTools PYME.Acquire.frameWrangler PYME.Acquire.htsms PYME.Acquire.htsms.tweeter PYME.Acquire.microscope PYME.Acquire.misc PYME.Acquire.misc.tempLogger PYME.Acquire.misc.tempLoggerDB PYME.Acquire.misc.tempMonitor PYME.Acquire.positionTracker PYME.Acquire.protocol PYME.Acquire.protocol_acquisition PYME.Acquire.PYMEAcquire PYME.Acquire.sampleInformation PYME.Acquire.setup PYME.Acquire.SpoolController PYME.Acquire.stackSettings PYME.Acquire.stage_leveling PYME.Acquire.ui PYME.Acquire.ui.AnalysisSettingsUI PYME.Acquire.ui.focus_lock_gui PYME.Acquire.ui.HDFSpoolFrame PYME.Acquire.ui.intensity_trace PYME.Acquire.ui.intsliders PYME.Acquire.ui.lasersliders PYME.Acquire.ui.mpd_picosecond_delay_panel PYME.Acquire.ui.multiview_select PYME.Acquire.ui.positionUI PYME.Acquire.ui.preflight PYME.Acquire.ui.scanner_panel PYME.Acquire.ui.selectCameraPanel PYME.Acquire.ui.seqdialog PYME.Acquire.ui.splashScreen PYME.Acquire.ui.spool_panel PYME.Acquire.ui.tile_panel PYME.Acquire.ui.tilesettingsui PYME.Acquire.ui.voxelSizeDialog PYME.Acquire.Utils PYME.Acquire.Utils.failsafe PYME.Acquire.Utils.fastTiler PYME.Acquire.Utils.MultiPointScanner PYME.Acquire.Utils.pointScanner PYME.Acquire.Utils.sarcSpacing PYME.Acquire.Utils.strip_tiler PYME.Acquire.Utils.tiler PYME.Acquire.Utils.vibrationAnalysis PYME.Acquire.webui PYME.Acquire.webui.ipy PYME.Acquire.xyztc PYME.Acquire.zScanner PYME.Analysis PYME.Analysis.angleFilter PYME.Analysis.annealThresh PYME.Analysis.autoencoder_classifier PYME.Analysis.binAvg PYME.Analysis.BleachProfile PYME.Analysis.BleachProfile.deMod PYME.Analysis.BleachProfile.fitRecover PYME.Analysis.BleachProfile.intensProf PYME.Analysis.BleachProfile.kinModels PYME.Analysis.BleachProfile.rawIntensity PYME.Analysis.BleachProfile.rollins PYME.Analysis.Colocalisation PYME.Analysis.Colocalisation.colocScaleDep PYME.Analysis.Colocalisation.correlationCoeffs PYME.Analysis.Colocalisation.distColoc PYME.Analysis.Colocalisation.edtColoc PYME.Analysis.composite PYME.Analysis.cramerRao PYME.Analysis.density_filter PYME.Analysis.deTile PYME.Analysis.distributed_pyramid PYME.Analysis.fiducial_matching PYME.Analysis.gen_sCMOS_maps PYME.Analysis.graphing_filters PYME.Analysis.implicitFilter PYME.Analysis.keep_pairs PYME.Analysis.MetaData PYME.Analysis.optic_flow PYME.Analysis.piecewise PYME.Analysis.piecewiseMapping PYME.Analysis.piezo_movement_correction PYME.Analysis.points PYME.Analysis.points.arcfit PYME.Analysis.points.arcfit.arcmf PYME.Analysis.points.arcfit.setup PYME.Analysis.points.astigmatism PYME.Analysis.points.astigmatism.astiglookup PYME.Analysis.points.astigmatism.astigTools PYME.Analysis.points.astigmatism.setup PYME.Analysis.points.cluster_morphology PYME.Analysis.points.coordinate_tools PYME.Analysis.points.DeClump PYME.Analysis.points.DeClump.deClump PYME.Analysis.points.DeClump.deClumpGUI PYME.Analysis.points.DeClump.pyDeClump PYME.Analysis.points.DeClump.setup PYME.Analysis.points.DeClump.testClump PYME.Analysis.points.DistHist PYME.Analysis.points.DistHist.distHist PYME.Analysis.points.DistHist.distHistThreaded PYME.Analysis.points.DistHist.setup PYME.Analysis.points.EdgeDB PYME.Analysis.points.EdgeDB.edgeDB PYME.Analysis.points.EdgeDB.edges PYME.Analysis.points.EdgeDB.edgeTest PYME.Analysis.points.EdgeDB.segment PYME.Analysis.points.EdgeDB.setup PYME.Analysis.points.features PYME.Analysis.points.features.metal PYME.Analysis.points.fiducials PYME.Analysis.points.gen3DTriangs PYME.Analysis.points.moments PYME.Analysis.points.multiview PYME.Analysis.points.objectMeasure PYME.Analysis.points.qpaint PYME.Analysis.points.QuadTree PYME.Analysis.points.QuadTree.pointQT PYME.Analysis.points.QuadTree.pointQTF PYME.Analysis.points.QuadTree.QTrend PYME.Analysis.points.QuadTree.rendQT PYME.Analysis.points.rings PYME.Analysis.points.ripleys PYME.Analysis.points.segmentLL PYME.Analysis.points.setup PYME.Analysis.points.SoftRend PYME.Analysis.points.SoftRend.setup PYME.Analysis.points.SoftRend.testTetrahedra PYME.Analysis.points.SoftRend.triRend PYME.Analysis.points.spherical_harmonics PYME.Analysis.points.surfit PYME.Analysis.points.tCluster PYME.Analysis.points.traveling_salesperson PYME.Analysis.points.traveling_salesperson.queue_opt PYME.Analysis.points.traveling_salesperson.sectioned_two_opt PYME.Analysis.points.traveling_salesperson.setup PYME.Analysis.points.traveling_salesperson.sort PYME.Analysis.points.traveling_salesperson.two_opt PYME.Analysis.points.traveling_salesperson.two_opt_utils PYME.Analysis.points.twoColour PYME.Analysis.points.twoColourPlot PYME.Analysis.processLogger PYME.Analysis.profile_extraction PYME.Analysis.PSFEst PYME.Analysis.PSFEst.dec PYME.Analysis.PSFEst.extractImages PYME.Analysis.PSFEst.fit_psf_zernikes PYME.Analysis.PSFEst.psfQuality PYME.Analysis.PSFGen PYME.Analysis.PSFGen.fourier PYME.Analysis.PSFGen.fourierHNA PYME.Analysis.PSFGen.fourierHNA2 PYME.Analysis.PSFGen.genCRBcurves PYME.Analysis.PSFGen.nijboer_zernike PYME.Analysis.PSFGen.ps_app PYME.Analysis.PSFGen.setup PYME.Analysis.PSFGen.test_ps_app PYME.Analysis.setup PYME.Analysis.splitting PYME.Analysis.svmSegment PYME.Analysis.thresholding PYME.Analysis.tile_pyramid PYME.Analysis.Tracking PYME.Analysis.Tracking.msd PYME.Analysis.Tracking.tracking PYME.Analysis.Tracking.trackUtils PYME.Analysis.widefieldify PYME.cluster PYME.cluster.cluster_of_one PYME.cluster.dataserver_wsgi PYME.cluster.distribution PYME.cluster.HTTPDataServer PYME.cluster.HTTPRulePusher PYME.cluster.HTTPTaskPusher PYME.cluster.PYMERuleNodeServer PYME.cluster.PYMERuleServer PYME.cluster.rulenodeserver PYME.cluster.rules PYME.cluster.ruleserver PYME.cluster.status PYME.cluster.taskWorkerHTTP PYME.cluster.webdav PYME.config PYME.contrib PYME.contrib.aniso PYME.contrib.aniso.aniso PYME.contrib.auiFloatBook PYME.contrib.congrid PYME.contrib.dispatch PYME.contrib.dispatch.dispatcher PYME.contrib.gohlke PYME.contrib.gohlke.czifile PYME.contrib.gohlke.fcsfiles PYME.contrib.gohlke.setup PYME.contrib.gohlke.tifffile PYME.contrib.listctrlMixins PYME.contrib.lzw PYME.contrib.pad PYME.contrib.pad.info_pad PYME.contrib.pad.pad PYME.contrib.setup PYME.contrib.TextCtrlAutoComplete PYME.contrib.wxPlotPanel PYME.Deconv PYME.Deconv.beadGen PYME.Deconv.dec PYME.Deconv.dec_test PYME.Deconv.deconvDialogs PYME.Deconv.decTask PYME.Deconv.decThread PYME.Deconv.fftwWisdom PYME.Deconv.richardsonLucy PYME.Deconv.richardsonLucyMV PYME.Deconv.richardsonLucyMVM PYME.Deconv.test_block_dec PYME.Deconv.wiener PYME.DSView PYME.DSView.arrayViewPanel PYME.DSView.displayOptions PYME.DSView.DisplayOptionsPanel PYME.DSView.displaySettingsPanel PYME.DSView.dsviewer PYME.DSView.eventLogViewer PYME.DSView.fitInfo PYME.DSView.htmlServe PYME.DSView.logparser PYME.DSView.LUT PYME.DSView.LUT.lut PYME.DSView.LUT.setup PYME.DSView.modules PYME.DSView.modules.annotation PYME.DSView.modules.arrayView PYME.DSView.modules.blobFinding PYME.DSView.modules.blobMeasure PYME.DSView.modules.camera_maps PYME.DSView.modules.coloc PYME.DSView.modules.composite PYME.DSView.modules.convnet PYME.DSView.modules.cropping PYME.DSView.modules.dark_and_flatfield PYME.DSView.modules.deconvolution PYME.DSView.modules.eventView PYME.DSView.modules.extractBlobs PYME.DSView.modules.fastGraphPanel PYME.DSView.modules.filtering PYME.DSView.modules.flowView PYME.DSView.modules.fourierRingCorrelation PYME.DSView.modules.gl_image_view PYME.DSView.modules.measure PYME.DSView.modules.measure.filterPan PYME.DSView.modules.metadataView PYME.DSView.modules.multithreshold PYME.DSView.modules.neuroglancer PYME.DSView.modules.object_tagging PYME.DSView.modules.playback PYME.DSView.modules.prebleachExtraction PYME.DSView.modules.profileFitting PYME.DSView.modules.profilePlotting PYME.DSView.modules.projections PYME.DSView.modules.psfExtraction PYME.DSView.modules.psfGeneration PYME.DSView.modules.psfTools PYME.DSView.modules.pupilTools PYME.DSView.modules.redimension PYME.DSView.modules.segmentation PYME.DSView.modules.sheetView PYME.DSView.modules.shell PYME.DSView.modules.shiftfield_estimation PYME.DSView.modules.sparkprepare PYME.DSView.modules.splitter PYME.DSView.modules.synchronise PYME.DSView.modules.tiling PYME.DSView.modules.unmixing PYME.DSView.modules.vis3D PYME.DSView.modules.visgui PYME.DSView.modules.webview PYME.DSView.overlays PYME.DSView.OverlaysPanel PYME.DSView.scrolledImagePanel PYME.DSView.setup PYME.DSView.splashScreen PYME.DSView.voxSizeDialog PYME.IO PYME.IO.acquisition_backends PYME.IO.buffers PYME.IO.cluster_directory PYME.IO.cluster_streaming PYME.IO.clusterDuplication PYME.IO.clusterExport PYME.IO.clusterGlob PYME.IO.clusterIO PYME.IO.clusterListing PYME.IO.clusterResults PYME.IO.clusterUpload PYME.IO.compatibility PYME.IO.countdir PYME.IO.countdir.countdir PYME.IO.countdir.setup PYME.IO.csv_flavours PYME.IO.dataExporter PYME.IO.DataSources PYME.IO.DataSources.AlignDataSource PYME.IO.DataSources.ArrayDataSource PYME.IO.DataSources.BaseDataSource PYME.IO.DataSources.BGSDataSource PYME.IO.DataSources.BioformatsDataSource PYME.IO.DataSources.BufferedDataSource PYME.IO.DataSources.ClusterPZFDataSource PYME.IO.DataSources.ConcatenatedDataSource PYME.IO.DataSources.CropDataSource PYME.IO.DataSources.DcimgDataSource PYME.IO.DataSources.ElectronsPerSecondDataSource PYME.IO.DataSources.FlatFieldDataSource PYME.IO.DataSources.HDFDataSource PYME.IO.DataSources.HTTPDataSource PYME.IO.DataSources.ImageSeriesDataSource PYME.IO.DataSources.MultiviewDataSource PYME.IO.DataSources.OBFDataSource PYME.IO.DataSources.RandomDataSource PYME.IO.DataSources.SupertileDatasource PYME.IO.DataSources.TiffDataSource PYME.IO.DataSources.TileDataSource PYME.IO.DataSources.TQDataSource PYME.IO.DataSources.UnsplitDataSource PYME.IO.dataWrap PYME.IO.dcimg PYME.IO.events PYME.IO.FileUtils PYME.IO.FileUtils.compHdf PYME.IO.FileUtils.fileID PYME.IO.FileUtils.fnlGen PYME.IO.FileUtils.freeSpace PYME.IO.FileUtils.h5ExFrames PYME.IO.FileUtils.h5rFormatDef PYME.IO.FileUtils.h5rToTxt PYME.IO.FileUtils.h5ToTiffSeries PYME.IO.FileUtils.IJLut PYME.IO.FileUtils.nameUtils PYME.IO.FileUtils.obf_support PYME.IO.FileUtils.ply PYME.IO.FileUtils.RawToHdf5 PYME.IO.FileUtils.readSpeckle PYME.IO.FileUtils.readTiff PYME.IO.FileUtils.saveTiffStack PYME.IO.FileUtils.setup PYME.IO.FileUtils.SPAD PYME.IO.FileUtils.stl PYME.IO.FileUtils.thumbnailDatabase PYME.IO.FileUtils.TiffSeqToHdf5 PYME.IO.h5File PYME.IO.h5rFile PYME.IO.HTTPSpooler_v2 PYME.IO.image PYME.IO.load_psf PYME.IO.MetaDataHandler PYME.IO.pyme_h5ls PYME.IO.PZFFormat PYME.IO.ragged PYME.IO.rgb_image PYME.IO.setup PYME.IO.Spooler PYME.IO.tabular PYME.IO.testClusterSpooling PYME.IO.unifiedIO PYME.LMVis PYME.LMVis.colourFilterGUI PYME.LMVis.displayPane PYME.LMVis.dyeRatios PYME.LMVis.Extras PYME.LMVis.Extras.animation PYME.LMVis.Extras.annotation PYME.LMVis.Extras.clusterAnalysis PYME.LMVis.Extras.dockedPanel PYME.LMVis.Extras.extra_layers PYME.LMVis.Extras.flagZMotionArtifacts PYME.LMVis.Extras.fusionUtils PYME.LMVis.Extras.multiColourAnalysis PYME.LMVis.Extras.multiviewMapping PYME.LMVis.Extras.objectMeasurements PYME.LMVis.Extras.particleTracking PYME.LMVis.Extras.perFrameVariable PYME.LMVis.Extras.photophysics PYME.LMVis.Extras.pointSetGeneration PYME.LMVis.Extras.pointwiseColoc PYME.LMVis.Extras.QPobjectSegment PYME.LMVis.Extras.saved_views PYME.LMVis.Extras.scaleBox PYME.LMVis.Extras.sequentialSpecies PYME.LMVis.Extras.setBGImage PYME.LMVis.Extras.shiftmapGenerator PYME.LMVis.Extras.showShortcuts PYME.LMVis.Extras.spherical_harmonics PYME.LMVis.Extras.subsets PYME.LMVis.Extras.surface_fitting PYME.LMVis.Extras.temperaturePlot PYME.LMVis.Extras.vibration PYME.LMVis.genImageDialog PYME.LMVis.gl_offScreenHandler PYME.LMVis.gl_render3D_shaders PYME.LMVis.glcanvas_core PYME.LMVis.imageView PYME.LMVis.imageView2 PYME.LMVis.importTextDialog PYME.LMVis.layer_panel PYME.LMVis.layers PYME.LMVis.layers.AxesOverlayLayer PYME.LMVis.layers.base PYME.LMVis.layers.image_layer PYME.LMVis.layers.labels PYME.LMVis.layers.layer_defaults PYME.LMVis.layers.LUTOverlayLayer PYME.LMVis.layers.mesh PYME.LMVis.layers.octree PYME.LMVis.layers.OverlayLayer PYME.LMVis.layers.pointcloud PYME.LMVis.layers.quiver PYME.LMVis.layers.ScaleBarOverlayLayer PYME.LMVis.layers.ScaleBoxOverlayLayer PYME.LMVis.layers.SelectionOverlayLayer PYME.LMVis.layers.text PYME.LMVis.layers.tracks PYME.LMVis.mv_math PYME.LMVis.objectDarkMeasure PYME.LMVis.pipelineView PYME.LMVis.pointSettingsPanel PYME.LMVis.progGraph PYME.LMVis.quadTreeSettings PYME.LMVis.renderers PYME.LMVis.rendGauss PYME.LMVis.setup PYME.LMVis.setup_exe PYME.LMVis.shader_programs PYME.LMVis.shader_programs.DefaultShaderProgram PYME.LMVis.shader_programs.GLProgram PYME.LMVis.shader_programs.GouraudShaderProgram PYME.LMVis.shader_programs.oit_compositor PYME.LMVis.shader_programs.PointSpriteShaderProgram PYME.LMVis.shader_programs.shader_loader PYME.LMVis.shader_programs.shader_program PYME.LMVis.shader_programs.ShaderProgramFactory PYME.LMVis.shader_programs.TesselShaderProgram PYME.LMVis.shader_programs.WireFrameShaderProgram PYME.LMVis.statusLog PYME.LMVis.tests PYME.LMVis.triBlobs PYME.LMVis.view_clipping_pane PYME.LMVis.views PYME.LMVis.visCore PYME.LMVis.visHelpers PYME.LMVis.visHelpersMin PYME.localization PYME.localization.autopsf PYME.localization.autopsf.autopsf PYME.localization.autopsf.roifit PYME.localization.cInterp PYME.localization.cInterp.cInterp PYME.localization.cInterp.setup PYME.localization.cModels PYME.localization.cModels.gauss_app PYME.localization.cModels.setup PYME.localization.FitFactories PYME.localization.FitFactories.AstigGaussFitFR PYME.localization.FitFactories.AstigGaussGPUFitFR PYME.localization.FitFactories.BeadConvolvedAstigGaussFit PYME.localization.FitFactories.ChecksumFR PYME.localization.FitFactories.ChecksumGPUFR PYME.localization.FitFactories.ChecksumMultifitSR PYME.localization.FitFactories.ConfocCOIR PYME.localization.FitFactories.Dumbell3DFitR PYME.localization.FitFactories.DumbellFitR PYME.localization.FitFactories.FFBase PYME.localization.FitFactories.fitCommon PYME.localization.FitFactories.Gauss3DFitR PYME.localization.FitFactories.GaussFitConstrR PYME.localization.FitFactories.GaussMultifitLinesR PYME.localization.FitFactories.GaussMultifitR PYME.localization.FitFactories.GaussMultifitSR PYME.localization.FitFactories.InterpFitR PYME.localization.FitFactories.InterpFitWFR PYME.localization.FitFactories.Interpolators PYME.localization.FitFactories.Interpolators.baseInterpolator PYME.localization.FitFactories.Interpolators.CSInterpolator PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator PYME.localization.FitFactories.Interpolators.LinearInterpolator PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP PYME.localization.FitFactories.LatFitCOIR PYME.localization.FitFactories.LatGaussFitFR PYME.localization.FitFactories.LatObjFindFR PYME.localization.FitFactories.LatPSFFitR PYME.localization.FitFactories.MultiviewFitInterpNR PYME.localization.FitFactories.PRInterpFitQR PYME.localization.FitFactories.PRInterpFitR PYME.localization.FitFactories.ROIExtractNR PYME.localization.FitFactories.SpecGaussFitFR PYME.localization.FitFactories.SplitterFitCOIR PYME.localization.FitFactories.SplitterFitFNR PYME.localization.FitFactories.SplitterFitFusionR PYME.localization.FitFactories.SplitterFitInterpBNR PYME.localization.FitFactories.SplitterFitInterpNR PYME.localization.FitFactories.SplitterFitScavNR PYME.localization.FitFactories.SplitterMultifitSR PYME.localization.FitFactories.SplitterObjFindR PYME.localization.FitFactories.SplitterROIExtractNR PYME.localization.FitFactories.SplitterShiftEstFR PYME.localization.FitFactories.zEstimators PYME.localization.FitFactories.zEstimators.astigEstimator PYME.localization.FitFactories.zEstimators.biplaneEstimator PYME.localization.FitFactories.zEstimators.genericDualEstimator PYME.localization.FitFactories.zEstimators.genericEstimator PYME.localization.FitFactories.zEstimators.priEstimator PYME.localization.MetaDataEdit PYME.localization.ofind PYME.localization.ofind3d PYME.localization.ofind_nofilt PYME.localization.ofind_pri PYME.localization.ofind_split PYME.localization.ofind_xcorr PYME.localization.ofind_xcorr_fw PYME.localization.remFitBuf PYME.localization.setup PYME.localization.splitting PYME.localization.Test PYME.localization.Test.fitTestJig PYME.localization.Test.fitTestJigSCMOS PYME.localization.Test.fitTestJigWC PYME.localization.twist PYME.misc PYME.misc.aligned_array PYME.misc.aniso PYME.misc.big_sur_fix PYME.misc.check_for_updates PYME.misc.colormaps PYME.misc.colorsys PYME.misc.computerName PYME.misc.coverslipGeometries PYME.misc.cython_numpy_monkey PYME.misc.depGraph PYME.misc.dirSize PYME.misc.diskCleanup PYME.misc.django_widgets PYME.misc.djangoRecarray PYME.misc.editgrid PYME.misc.eventSpy PYME.misc.exceptions PYME.misc.facsPlot PYME.misc.fbpIcons PYME.misc.fftw_compat PYME.misc.findCycles PYME.misc.fortran_interrupt_defeat PYME.misc.glassModel PYME.misc.hash32 PYME.misc.hillcurve PYME.misc.hybrid_ns PYME.misc.kdFit PYME.misc.locate PYME.misc.memmap PYME.misc.memUsage PYME.misc.mock_ctypes PYME.misc.mock_traits PYME.misc.mock_traitsui PYME.misc.pyme_zeroconf PYME.misc.pyro_tracebacks PYME.misc.read_agf PYME.misc.sffake PYME.misc.snells PYME.misc.sqlite_ns PYME.misc.sqlitendarray PYME.misc.taskDef PYME.misc.tempDB PYME.misc.TiffImagePlugin PYME.misc.TiSettings PYME.misc.VolProj PYME.misc.wxThread PYME.misc.zemax PYME.misc.zernike PYME.pyme_warnings PYME.recipes.traits PYME.reports PYME.reports.filters PYME.resources PYME.resources.setup PYME.setup PYME.setup_exe PYME.simulation PYME.simulation.locify PYME.simulation.pointsets PYME.simulation.wormlike PYME.simulation.wormlike2 PYME.simulation.wormlike3 PYME.simulation.wormlike_curled PYME.tileviewer PYME.tileviewer.tileviewer PYME.ui PYME.ui.about_dlg PYME.ui.AUIFrame PYME.ui.autoFoldPanel PYME.ui.cascading_layout PYME.ui.crop_dialog PYME.ui.editFilterDialog PYME.ui.fastGraph PYME.ui.filterPane PYME.ui.histLimits PYME.ui.layerFoldPanel PYME.ui.manualFoldPanel PYME.ui.MetadataTree PYME.ui.mytimer PYME.ui.patch_traitsui PYME.ui.progress PYME.ui.recArrayView PYME.ui.selection PYME.ui.shell PYME.ui.wx_compat PYME.update_version PYME.util PYME.util.authenticate PYME.util.execfile PYME.util.fProfile PYME.util.fProfile.convertProfile PYME.util.fProfile.fProfile PYME.util.fProfile.viewProfile PYME.util.install_dependencies PYME.util.log_verbosity PYME.util.mProfile PYME.util.mProfile.colorize_db_t PYME.util.mProfile.mProfile PYME.util.mProfile.p PYME.util.mProfile.tProfile PYME.util.pymelauncher PYME.util.shmarray PYME.util.shmarray.shmarray PYME.util.shmarray.shmTest PYME.util.webframework PYME.version

moduleName (PYME.IO.DataSources.AlignDataSource.DataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource attribute) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource attribute) (PYME.IO.DataSources.BioformatsDataSource.DataSource attribute) (PYME.IO.DataSources.BufferedDataSource.DataSource attribute) (PYME.IO.DataSources.ClusterPZFDataSource.DataSource attribute) (PYME.IO.DataSources.CropDataSource.DataSource attribute) (PYME.IO.DataSources.DcimgDataSource.DataSource attribute) (PYME.IO.DataSources.ElectronsPerSecondDataSource.DataSource attribute) (PYME.IO.DataSources.FlatFieldDataSource.DataSource attribute) (PYME.IO.DataSources.HDFDataSource.DataSource attribute) (PYME.IO.DataSources.HTTPDataSource.DataSource attribute) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource attribute) (PYME.IO.DataSources.MultiviewDataSource.DataSource attribute) (PYME.IO.DataSources.OBFDataSource.DataSource attribute) (PYME.IO.DataSources.RandomDataSource.DataSource attribute) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource attribute) (PYME.IO.DataSources.TiffDataSource.DataSource attribute) (PYME.IO.DataSources.TileDataSource.TileDataSource attribute) (PYME.IO.DataSources.TQDataSource.DataSource attribute) (PYME.IO.DataSources.UnsplitDataSource.DataSource attribute) MotionCompensatingRichardsonLucy (class in PYME.Deconv.richardsonLucyMVM) motionFlagger (class in PYME.LMVis.Extras.flagZMotionArtifacts) mount() (in module PYME.DSView.htmlServe) MouseEvent() (in module PYME.misc.eventSpy) MoveTo (class in PYME.Acquire.actions) movieplot (PYME.Analysis.Tracking.trackUtils.Track property) movieplot() (in module PYME.Analysis.graphing_filters) movieplot2() (in module PYME.Analysis.graphing_filters) msd() (in module PYME.Analysis.Tracking.msd) msdHistogram() (in module PYME.Analysis.points.DistHist.distHist) msdinfo (PYME.Analysis.Tracking.trackUtils.Track property) msdplot (PYME.Analysis.Tracking.trackUtils.Track property) multichannel (PYME.LMVis.importTextDialog.ImportMatlabDialog attribute) MultiColAnalyzer (class in PYME.LMVis.Extras.multiColourAnalysis) multicolcheck() (in module PYME.LMVis.Extras.multiColourAnalysis) MultiTargetTimer() (PYME.Acquire.event_loop.EventLoop method) MultiThreshold (class in PYME.DSView.modules.multithreshold) MultiviewMapper (class in PYME.LMVis.Extras.multiviewMapping) MultiviewRichardsonLucy (class in PYME.Deconv.richardsonLucyMV) MultiviewSelect (class in PYME.Acquire.ui.multiview_select) MultiwellCircularTiler (class in PYME.Acquire.Utils.tiler) MultiwellProtocolQueuePanel (class in PYME.Acquire.ui.tile_panel) MultiwellTilePanel (class in PYME.Acquire.ui.tile_panel) munge_res() (in module PYME.Analysis.BleachProfile.kinModels) MutablePriorityQueue (class in PYME.Acquire.ActionManager) mutual_information() (in module PYME.Analysis.Colocalisation.correlationCoeffs) mydict (class in PYME.util.mProfile.mProfile) (class in PYME.util.mProfile.p) mydictn (class in PYME.util.mProfile.mProfile) (class in PYME.util.mProfile.p) myListCtrl (class in PYME.DSView.modules.annotation) MyMetaFinder (class in PYME.ui.patch_traitsui) myTask (class in PYME.misc.taskDef) MyTreeListCtrl (class in PYME.ui.MetadataTree) MyWeakSet (class in PYME.DSView.displayOptions)

N

n (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) n() (PYME.misc.zemax.DefaultGlass method) (PYME.misc.zemax.Glass method) n_cluster_servers() (in module PYME.IO.cluster_streaming) n_frames (PYME.IO.h5File.H5File property) n_tiles() (PYME.Acquire.Utils.pointScanner.Scanner class method) NA (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.DSView.modules.psfTools.PSFTools attribute) (PYME.DSView.modules.pupilTools.PupilTools attribute) name (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) (PYME.LMVis.renderers.CurrentRenderer attribute) (PYME.LMVis.renderers.DensityFitRenderer attribute) (PYME.LMVis.renderers.Gaussian3DRenderer attribute) (PYME.LMVis.renderers.GaussianRenderer attribute) (PYME.LMVis.renderers.Histogram3DRenderer attribute) (PYME.LMVis.renderers.HistogramRenderer attribute) (PYME.LMVis.renderers.LHoodRenderer attribute) (PYME.LMVis.renderers.QuadTreeRenderer attribute) (PYME.LMVis.renderers.Triangle3DRenderer attribute) (PYME.LMVis.renderers.TriangleRenderer attribute) (PYME.LMVis.renderers.TriangleRendererW attribute) (PYME.LMVis.renderers.VoronoiRenderer attribute) (PYME.misc.sqlite_ns.NSInfo attribute) names (PYME.IO.image.ImageStack property) nbmf() (in module PYME.Analysis.BleachProfile.rollins) nbrff() (in module PYME.Analysis.BleachProfile.rollins) nbytes (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) ndim (PYME.Analysis.tile_pyramid.ImagePyramid attribute) (PYME.Analysis.tile_pyramid.PyramidLayer attribute) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource property) (PYME.IO.dataWrap.ListWrapper property) neg_binom_histfitting() (in module PYME.Analysis.BleachProfile.rollins) NestedClassMDHandler (class in PYME.IO.MetaDataHandler) Neuroglancer (class in PYME.DSView.modules.neuroglancer)

new_layer_settings() (in module PYME.LMVis.layers.layer_defaults) new_mesh_viewer() (in module PYME.DSView.modules.vis3D) new_terminal() (PYME.Acquire.webui.ipy.IPYTermManager method) next() (PYME.cluster.rulenodeserver.Rater method) next_page() (PYME.contrib.lzw.PagingDecoder method) next_pos() (PYME.Acquire.Utils.pointScanner.Scanner method) ng_viewer (PYME.DSView.modules.neuroglancer.Neuroglancer property) niceVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) NodeServer (class in PYME.cluster.rulenodeserver) noise() (in module PYME.Analysis.PSFEst.psfQuality) non_gui_post_init() (PYME.Acquire.acquirebase.PYMEAcquireBase method) NoNewTasks NoninteractiveContext (class in PYME.pyme_warnings) normal_mode (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) normal_scaling (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) normalize() (PYME.LMVis.views.View static method) normalize_view() (PYME.LMVis.views.View method) normalizeFeatures() (in module PYME.Analysis.svmSegment) NOT_PRESENT (PYME.Acquire.ExecTools.BGInitTask attribute) Notify() (PYME.Acquire.frameWrangler.FrameWrangler method) notify() (PYME.ui.filterPane.FilterPanel method) notimes() (in module PYME.LMVis.objectDarkMeasure) np_load_legacy() (in module PYME.IO.compatibility) NRFilter() (in module PYME.localization.cModels.gauss_app) NSInfo (class in PYME.misc.sqlite_ns) nTrueDims (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) nudge() (PYME.Acquire.ui.positionUI.PositionPanel method) num (PYME.DSView.modules.psfGeneration.ZernikeMode attribute) num_chans (PYME.Analysis.splitting.SplittingInfo property) num_tasks_to_request (PYME.cluster.rulenodeserver.NodeServer property) num_tiles (PYME.Acquire.Utils.pointScanner.Scanner property) numerator (PYME.IO.FileUtils.obf_support.Fraction attribute) numFluors (PYME.simulation.pointsets.WiglyFibreSource attribute) numPoints (PYME.simulation.pointsets.RandomSource attribute) NumpyExporter (class in PYME.IO.dataExporter) NumpyTileIO (class in PYME.Analysis.tile_pyramid) numToAlpha() (in module PYME.IO.FileUtils.nameUtils)

O

ob16() (in module PYME.misc.TiffImagePlugin) ob32() (in module PYME.misc.TiffImagePlugin) OBJECT (PYME.Acquire.stackSettings.StackSettings attribute) ObjectIdentifier (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) objectIndices() (in module PYME.Analysis.points.EdgeDB.edges) ObjectMeasurer (class in PYME.LMVis.Extras.objectMeasurements) ObjectTagger (class in PYME.DSView.modules.object_tagging) observe() (in module PYME.misc.mock_traits) OctreeRenderLayer (class in PYME.LMVis.layers.octree) of() (in module PYME.Analysis.optic_flow) offline_plotting (class in PYME.Analysis.graphing_filters) OffScreenHandler (class in PYME.LMVis.gl_offScreenHandler) OfindPoint (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) OITCompositorProgram (class in PYME.LMVis.shader_programs.oit_compositor) OITGouraudShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) OITShadedFaceEngine (class in PYME.LMVis.layers.mesh) ol16() (in module PYME.misc.TiffImagePlugin) ol32() (in module PYME.misc.TiffImagePlugin) oldData (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) oldSlice (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) OMDialog (class in PYME.LMVis.Extras.objectMeasurements) OMETiffExporter (class in PYME.IO.dataExporter) OMEXMLMDHandler (class in PYME.IO.MetaDataHandler) On3DIsosurf() (PYME.DSView.modules.vis3D.Visualiser method) On3DVolume() (PYME.DSView.modules.vis3D.Visualiser method) on_adjust_snake() (PYME.DSView.modules.annotation.LabelPanel method) on_aq_type_changed() (PYME.Acquire.ui.spool_panel.SpoolingPane method) on_cb_highspeed() (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) on_change_lock_mode() (PYME.DSView.modules.annotation.LabelPanel method) on_copy() (PYME.ui.progress.TracebackDialog method) on_data_complete() (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.Rule method) (PYME.cluster.rules.SpoolLocalLocalizationRule method) on_edit() (PYME.LMVis.Extras.animation.VideoPanel method) on_eof() (PYME.Acquire.webui.ipy.IPYTermManager method) on_frame() (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.tiler.TileAcquisition method) (PYME.Acquire.xyztc.XYZTCAcquisition method) on_idle() (PYME.LMVis.layer_panel.LayerPane method) on_map() (in module PYME.DSView.modules.camera_maps) on_moveto() (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionPanelV2 method) on_select_view() (PYME.LMVis.Extras.animation.VideoPanel method) on_SIGHUP() (in module PYME.cluster.ruleserver) (in module PYME.cluster.taskWorkerHTTP) on_slide() (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) on_toggle() (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.multiview_select.MultiviewSelect method) on_toggle_loc_units() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) on_trait_change() (in module PYME.misc.mock_traits) OnAbout() (PYME.ui.AUIFrame.AUIFrame method) OnAddChan() (PYME.DSView.modules.composite.CompositeDialog method) OnAddSlide() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnAddVSSetting() (PYME.Acquire.ui.voxelSizeDialog.VoxelSizeDialog method) OnAlignChannels() (PYME.DSView.modules.composite.Compositor method) OnApply() (PYME.DSView.modules.composite.ShiftPanel method) (PYME.DSView.modules.segmentation.SegmentationPanel method) OnApplyShiftmap() (PYME.DSView.modules.composite.Compositor method) OnApplyThreshold() (PYME.DSView.modules.filtering.Filterer method) OnAqStart() (PYME.Acquire.zScanner.wavetableZScanner method) (PYME.Acquire.zScanner.zScanner method) OnAqStop() (PYME.Acquire.zScanner.wavetableZScanner method) (PYME.Acquire.zScanner.zScanner method) OnAqTypeChanged() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnAstigQualityControl() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnAverageFramesByStep() (PYME.DSView.modules.filtering.Filterer method) OnBAnalyse() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnBeginEdit() (PYME.ui.MetadataTree.MetadataPanel method) OnBeginLabelEdit() (PYME.DSView.modules.annotation.myListCtrl method) OnBEndHereButton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBLive() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBMid_numRadiobutton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBOptimise() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnBSetAqProtocolButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.ProtocolAcquisitionPane method) OnBSetSpoolDirButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnBSingle() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBSt_endRadiobutton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBStartHereButton() (PYME.Acquire.ui.seqdialog.seqPanel method) OnBStartSpoolButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnBStartStackButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) OnBStopSpoolingButton() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnCalcCRB() (PYME.DSView.modules.psfTools.PSFTools method) OnCalcCRB3DvsBG() (PYME.DSView.modules.psfTools.PSFTools method) OnCalcDecays() (PYME.LMVis.Extras.photophysics.DecayAnalyser method) OnCalcHarmonicRepresentation() (PYME.LMVis.Extras.spherical_harmonics.SphericalHarmonicShellManager method) OnCalcMSDs() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnCalcShift() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCalcShiftmap() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnCalculate() (PYME.DSView.modules.blobMeasure.Measurements method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnCalcWidths() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnCalibrateAstigmatism() (PYME.DSView.modules.psfTools.PSFTools method) OnCalibrateMultiview() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCalibrateShifts() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnCameraFrame() (PYME.Acquire.zScanner.zScanner method) OnCancel() (PYME.Deconv.deconvDialogs.DeconvProgressDialog method) (PYME.Deconv.deconvDialogs.DeconvProgressPanel method) OnCbOn() (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserToggles method) OnCCamera() (PYME.Acquire.ui.selectCameraPanel.CameraChooserPanel method) OnChanDown() (PYME.DSView.modules.composite.CompositeDialog method) OnChange() (PYME.DSView.displayOptions.DisplayOpts method) OnChange3D() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnChangeBackground() (PYME.DSView.modules.psfTools.CRBViewPanel method) OnChangeLineWidth() (PYME.DSView.modules.annotation.LabelPanel method) OnChangeMethod() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnChangePointColour() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnChangeScaleBar() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnChangeStructure() (PYME.DSView.modules.annotation.LabelPanel method) OnChannelFold() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnChanUp() (PYME.DSView.modules.composite.CompositeDialog method) OnChar() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) OnCheckAstigmatismCalibration() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnCheckItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) OnCheckSpacing() (PYME.Acquire.Utils.sarcSpacing.SarcomereChecker method) OnChooseVS() (PYME.Acquire.ui.voxelSizeDialog.VoxelSizeDialog method) OnChPiezoChoice() (PYME.Acquire.ui.seqdialog.seqPanel method) OnClear() (PYME.Acquire.positionTracker.TrackerPanel method) (PYME.Acquire.ui.intensity_trace.TraceROISelectPanel method) OnClearTags() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnCLimChange() (PYME.LMVis.displayPane.DisplayPane method) OnCLimChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnCLimHistChange() (PYME.LMVis.displayPane.DisplayPane method) OnClose() (PYME.LMVis.Extras.showShortcuts.ShowShortcuts method) OnCloseWindow() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.DSView.dsviewer.DSViewFrame method) OnClumpDBSCAN() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnClustersInTime() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnCMapChange() (PYME.LMVis.displayPane.DisplayPane method) OnCMapChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnCoalesce() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnColNameChange() (PYME.LMVis.importTextDialog.ColumnMappingDialog method) OnColoc() (PYME.DSView.modules.coloc.Colocaliser method) (PYME.DSView.modules.fourierRingCorrelation.RingCorrelator method) OnColocBasic() (PYME.DSView.modules.coloc.Colocaliser method) OnColourChanged() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnColourFilterChange() (PYME.LMVis.colourFilterGUI.ColourFilterPane method) onCombobox() (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) OnComplexChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnConfigure() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnCorrelate() (PYME.DSView.modules.composite.ShiftPanel method) OnCrop() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.cropping.Cropper method) OnDarkT() (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnDeconEnd() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconTimer() (PYME.DSView.modules.deconvolution.Deconvolver method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnDeconvBead() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvICTM() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvMovie() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDeconvWiener() (PYME.DSView.modules.deconvolution.Deconvolver method) OnDiagSplit() (PYME.DSView.modules.cropping.Cropper method) OnDoChange() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnDone() (PYME.DSView.modules.segmentation.SegmentationPanel method) OnDoubleClick() (PYME.LMVis.view_clipping_pane.ClippingPanel method) OnDwellKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnEndEdit() (PYME.ui.MetadataTree.MetadataPanel method) ones() (in module PYME.util.shmarray.shmarray) OnExport() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.visgui.visGuiExtras method) OnExportXls() (PYME.DSView.modules.blobMeasure.Measurements method) onExpReady() (PYME.Acquire.frameWrangler.FrameWrangler method) OnExtract() (PYME.DSView.modules.prebleachExtraction.PrebleachExtractor method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractMultiviewPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnExtractPupil() (PYME.DSView.modules.psfTools.PSFTools method) OnExtractSplitPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnFileExit() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnFileOpenStack() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnFilterAdd() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFilterChange() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnFilterClipToSelection() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPane method) OnFilterDelete() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFilterEdit() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFilterItemDeselected() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFilterItemSelected() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFilterListRightClick() (PYME.DSView.modules.measure.filterPan.FilterPane method) (PYME.ui.filterPane.FilterPanel method) OnFindClumps() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnFindMixedClusters() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnFindObjects() (PYME.DSView.modules.blobFinding.BlobFinder method) OnFinish() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) OnFitModel() (PYME.DSView.modules.psfTools.PSFTools method) OnFitModuleChanged() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettingsPanel method) OnFitObjects() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) OnFitQuadraticPatches() (PYME.LMVis.Extras.surface_fitting.SurfaceFitter method) OnFitROI() (PYME.LMVis.visCore.VisGUICore method) OnFlavourChange() (PYME.LMVis.importTextDialog.ImportTextDialog method) OnFold() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) (PYME.ui.autoFoldPanel.collapsingPane method) (PYME.ui.manualFoldPanel.collapsingPane method) OnFrame() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) (PYME.Acquire.protocol.ZStackTaskListProtocol method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) OnFrameGroup() (PYME.Acquire.autofocus.AutoFocus method) (PYME.Acquire.Utils.vibrationAnalysis.VibrAnal method) OnFRC() (PYME.DSView.modules.coloc.Colocaliser method) OnGaussianFilter() (PYME.DSView.modules.filtering.Filterer method) (PYME.DSView.modules.sparkprepare.filterer method) OnGaussianFit() (PYME.DSView.modules.profileFitting.Fitter method) OnGenEvents() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnGenPoints() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnGenShiftmap() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGenShiftmapQuad() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGenShiftmapQuadz() (PYME.LMVis.Extras.shiftmapGenerator.ShiftmapGenerator method) OnGetIDs() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnGetItemText() (PYME.Acquire.sampleInformation.VirtList method) (PYME.DSView.modules.composite.ImageList method) OnGo() (PYME.Acquire.ui.tile_panel.CircularTilePanel method) (PYME.Acquire.ui.tile_panel.MultiwellTilePanel method) (PYME.Acquire.ui.tile_panel.TilePanel method) OnGoto() (PYME.DSView.modules.playback.PlayPanel method) OnHideObject() (PYME.DSView.modules.blobMeasure.Measurements method) OnHome() (PYME.LMVis.visCore.VisGUICore method) OnIdle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) (PYME.LMVis.visCore.VisGUICore method) OnIDTransient() (PYME.LMVis.Extras.flagZMotionArtifacts.motionFlagger method) OnIsodataThresh() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnItemSelected() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) OnJoystickEnable() (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionSliders method) OnKeyPress() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.ui.histLimits.HistLimitPanel method)

OnLabel() (PYME.DSView.modules.filtering.Filterer method) OnLabelActivate() (PYME.DSView.modules.annotation.myListCtrl method) OnLabelSizeThreshold() (PYME.DSView.modules.filtering.Filterer method) OnLabelWatershed() (PYME.DSView.modules.filtering.Filterer method) OnLCSMDoPopup() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) OnLCSMRightDown() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) OnLeftDown() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.MetadataTree.TextEditMixin method) OnLeftUp() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnLineThickness() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnLoadClassifier() (PYME.DSView.modules.annotation.Annotater method) OnLoadExtraDatasource() (PYME.LMVis.visCore.VisGUICore method) OnLoadHarmonicRepresentation() (PYME.LMVis.Extras.spherical_harmonics.SphericalHarmonicShellManager method) OnLUTDrawCB() (PYME.LMVis.displayPane.DisplayPane method) (PYME.LMVis.displayPane.DisplayPaneHorizontal method) (PYME.LMVis.displayPane.DisplayPaneLight method) OnMakeComposites() (PYME.DSView.modules.composite.Compositor method) OnMapAstigmaticZ() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnMappingChange() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnMAquireOnePic() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMAquireStack() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMaxProject() (PYME.DSView.modules.filtering.Filterer method) OnMCA() (PYME.LMVis.Extras.multiColourAnalysis.MultiColAnalyzer method) OnMCamBin() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMCamRoi() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMCamSetPixelSize() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMDChanged() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisDetailsPanel method) OnMDisplayClearSel() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) OnMeanProject() (PYME.DSView.modules.filtering.Filterer method) OnMeasure() (PYME.LMVis.Extras.objectMeasurements.ObjectMeasurer method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) OnMeasureClusters() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnMergeClumps() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnMethodChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) OnMiddleDown() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMiddleUp() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMotion() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnMouseEnterPane() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseLeave() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseLeavePane() (PYME.ui.autoFoldPanel.foldPanel method) OnMouseMove() (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnMouseScrollEvent() (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnNearestNeighbor() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnNeuroglancer() (PYME.DSView.modules.neuroglancer.Neuroglancer method) OnObjApplyThreshold() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnObjMeasure() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnOpen() (PYME.DSView.dsviewer.DSViewFrame method) OnOpenFile() (PYME.LMVis.visCore.VisGUICore method) OnOpenSequence() (PYME.DSView.dsviewer.DSViewFrame method) OnOptimise() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnPaint() (PYME.Acquire.ui.splashScreen.SplashPanel method) (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.scrolledImagePanel.ImagePanel method) (PYME.DSView.splashScreen.SplashPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) OnPairwiseDistanceHistogram() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnPercentileCLim() (PYME.LMVis.displayPane.DisplayPane method) OnPerFrame() (PYME.LMVis.Extras.perFrameVariable.PerFrameVar method) OnPlay() (PYME.DSView.modules.playback.PlayPanel method) OnPlayPosChanged() (PYME.DSView.modules.playback.PlayPanel method) OnPlaySpeedChanged() (PYME.DSView.modules.playback.PlayPanel method) OnPlotAxialProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPlotProfile() (PYME.DSView.modules.multithreshold.MultiThreshold method) (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPlotTemperature() (PYME.LMVis.Extras.temperaturePlot.TempPlotter method) OnPlotWavyProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPointAlphaChange() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnPointSizeChange() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) OnPointwiseColoc() (PYME.LMVis.Extras.pointwiseColoc.PointwiseColocaliser method) OnProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnPSFFileChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) (PYME.DSView.modules.deconvolution.WienerDeconvolver method) OnPSFFromPupil() (PYME.DSView.modules.pupilTools.PupilTools method) OnPSFFromZernikeModes() (PYME.DSView.modules.pupilTools.PupilTools method) OnPSFNotebookPageChanged() (PYME.Deconv.deconvDialogs.DeconvSettingsDialog method) OnPSFROI() (PYME.DSView.modules.object_tagging.ObjectTagger method) (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnQTLeafChange() (PYME.LMVis.quadTreeSettings.QuadTreeSettingsPanel method) OnQueue() (PYME.Acquire.ui.tile_panel.MultiwellProtocolQueuePanel method) OnQuit() (PYME.ui.AUIFrame.AUIFrame method) OnRawDecay() (PYME.DSView.modules.profileFitting.Fitter method) OnRawDecaySimp() (PYME.DSView.modules.profileFitting.Fitter method) OnRecenter() (PYME.LMVis.visCore.VisGUICore method) OnRemoveChan() (PYME.DSView.modules.composite.CompositeDialog method) OnResampleZStack() (PYME.DSView.modules.filtering.Filterer method) OnResetRotation() (PYME.LMVis.visCore.VisGUICore method) OnResize() (PYME.ui.manualFoldPanel.foldPanel method) OnRetrieveIntensitySteps() (PYME.LMVis.Extras.photophysics.DecayAnalyser method) OnRightDown() (PYME.ui.MetadataTree.MetadataPanel method) OnRightUp() (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.MetadataTree.MetadataPanel method) OnRingTest() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnRipleys() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnRipleysMasked() (PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser method) OnRuleChainChanged() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnSave() (PYME.DSView.dsviewer.DSViewFrame method) (PYME.LMVis.visCore.VisGUICore method) (PYME.ui.recArrayView.ArrayPanel method) OnSaveClassifier() (PYME.DSView.modules.annotation.Annotater method) OnSaveObjects() (PYME.DSView.modules.blobMeasure.Measurements method) OnSavePoints() (PYME.LMVis.Extras.pointSetGeneration.Generator method) OnSaveSession() (PYME.LMVis.visCore.VisGUICore method) OnSaveToCluster() (PYME.DSView.dsviewer.DSViewFrame method) OnScaleChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) OnScrollX() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) OnScrollY() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) OnSeekStart() (PYME.DSView.modules.playback.PlayPanel method) OnSegmentAnneal() (PYME.DSView.modules.segmentation.Segmenter method) OnSelectCell() (PYME.DSView.modules.psfTools.PSFQualityPanel method) OnSelectCrosshairs() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectLine() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectObject() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectRectangle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSelectSlide() (PYME.Acquire.sampleInformation.SampleInfoDialog method) OnSelectSquiggle() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSetBlobColour() (PYME.LMVis.triBlobs.BlobSettingsPanel method) OnSetLabels() (PYME.DSView.modules.filtering.Filterer method) OnSetShiftField() (PYME.DSView.modules.splitter.Unmixer method) OnSetShiftmap() (PYME.DSView.modules.composite.CompositeDialog method) OnSetSlide() (PYME.Acquire.sampleInformation.slidePanel method) OnSetSubtractionProfile() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnShiftCorrectFolded() (PYME.LMVis.Extras.multiviewMapping.MultiviewMapper method) OnShowChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnShowThreshold() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSignalFracThresh() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OnSingleEnd() (PYME.Acquire.ui.seqdialog.seqPanel method) OnSize() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) (PYME.LMVis.pipelineView.PipelinePanel method) (PYME.LMVis.view_clipping_pane.ClippingPanel method) (PYME.ui.AUIFrame.AUIFrame method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) (PYME.ui.manualFoldPanel.foldingPane method) (PYME.ui.MetadataTree.MetadataPanel method) (PYME.ui.recArrayView.ArrayPanel method) OnSliceChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) onSlide() (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserSliders_ method) (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionSliders method) OnSortOrderChanged() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) OnSourceChange() (PYME.LMVis.visCore.VisGUICore method) OnSplitChannels() (PYME.DSView.modules.composite.Compositor method) OnSpoolingStarted() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnSpoolingStopped() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnSpoolMethodChanged() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnStart() (PYME.Acquire.ui.focus_lock_gui.FocusLogPanel method) OnStartStopButton() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnStop() (PYME.Acquire.ui.focus_lock_gui.FocusLogPanel method) (PYME.Acquire.ui.tile_panel.MultiwellTilePanel method) (PYME.Acquire.ui.tile_panel.TilePanel method) OnSubtractBackground() (PYME.DSView.modules.psfTools.PSFTools method) OnSynchronise() (PYME.DSView.modules.synchronise.Syncer method) OnTagEdge() (PYME.Acquire.positionTracker.TrackerPanel method) OnTagObject() (PYME.DSView.modules.object_tagging.ObjectTagger method) OnTagPoints() (PYME.DSView.modules.psfExtraction.PsfExtractor method) OnTagPSF() (PYME.DSView.modules.psfExtraction.PsfExtractor method) onTarget() (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.pointScanner.Scanner method) OnTcSpoolFileText() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnTEndPosKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnTextCtrlEnter() (PYME.LMVis.view_clipping_pane.ClippingPanel method) OnTick() (PYME.Acquire.Utils.fastTiler.fastTiler method) OnTile() (PYME.DSView.modules.tiling.Tiler method) OnTilePyramid() (PYME.DSView.modules.tiling.Tiler method) OnTimedSpecies() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) OnTNumSlicesKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnToggleAnalysis() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnToggleAnalysisTrigger() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnToggleLock() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnToggleModule() (PYME.DSView.dsviewer.DSViewFrame method) OnToggleScan() (PYME.Acquire.ui.scanner_panel.ScannerPanel method) OnToggleZStepping() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.ProtocolAcquisitionPane method) OnTrackMolecules() (PYME.LMVis.Extras.particleTracking.ParticleTracker method) OnTStepSizeKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnTStPosKillFocus() (PYME.Acquire.ui.seqdialog.seqPanel method) OnUnmix() (PYME.DSView.modules.splitter.Unmixer method) (PYME.DSView.modules.unmixing.Unmixer method) OnUnmixMax() (PYME.DSView.modules.splitter.Unmixer method) OnUpdateHome() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnUpdateSetpoint() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) OnView() (PYME.DSView.modules.blobMeasure.Measurements method) OnViewBackground() (PYME.DSView.modules.visgui.visGuiExtras method) OnViewBlobs() (PYME.LMVis.visCore.VisGUICore method) OnViewButton() (PYME.Acquire.ui.spool_panel.SpoolingPane method) OnViewFront() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewInterpTriangles() (PYME.LMVis.visCore.VisGUICore method) OnViewPoints() (PYME.LMVis.visCore.VisGUICore method) OnViewPointsprites() (PYME.LMVis.visCore.VisGUICore method) OnViewQuads() (PYME.LMVis.visCore.VisGUICore method) OnViewRight() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewShadedPoints() (PYME.LMVis.visCore.VisGUICore method) OnViewTop() (PYME.LMVis.displayPane.DisplayPaneHorizontal method) OnViewTracks() (PYME.LMVis.visCore.VisGUICore method) OnViewTriangles() (PYME.LMVis.visCore.VisGUICore method) OnViewTriangles3D() (PYME.LMVis.visCore.VisGUICore method) OnViewVoronoi() (PYME.LMVis.visCore.VisGUICore method) OnWheel() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) OnZBinChange() (PYME.LMVis.genImageDialog.GenImageDialog method) OnZero() (PYME.DSView.modules.composite.ShiftPanel method) OnZPlotProfile() (PYME.DSView.modules.profilePlotting.ProfilePlotter method) OnZProjChanged() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) OpaquePointsEngine (class in PYME.LMVis.layers.pointcloud) OpaquePointShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) open_analysis() (PYME.Acquire.SpoolController.SpoolController method) open_surface() (in module PYME.LMVis.Extras.extra_layers) open_view() (PYME.Acquire.SpoolController.SpoolController method) OpenChannel() (PYME.LMVis.visCore.VisGUICore method) openDB() (in module PYME.IO.FileUtils.thumbnailDatabase) OpenEditor() (PYME.contrib.listctrlMixins.TextEditMixin method) (PYME.ui.MetadataTree.TextEditMixin method) openFile() (in module PYME.IO.unifiedIO) OpenFile() (PYME.LMVis.visCore.VisGUICore method) openH5() (in module PYME.IO.h5File) openH5R() (in module PYME.IO.h5rFile) Optimise() (PYME.DSView.displayOptions.DisplayOpts method) OptionsPanel (class in PYME.DSView.DisplayOptionsPanel) orientationChoices (PYME.DSView.DisplayOptionsPanel.OptionsPanel attribute) origin (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.image.ImageStack property) origin_nm() (in module PYME.IO.MetaDataHandler) ortho() (in module PYME.LMVis.mv_math) OSXActivateKludge() (in module PYME.DSView.dsviewer) otsu() (in module PYME.Analysis.thresholding) Output (class in PYME.recipes.traits) output_files (PYME.cluster.rules.Rule property) overlap() (in module PYME.Analysis.Colocalisation.correlationCoeffs) Overlay (class in PYME.DSView.overlays) OverlayLayer (class in PYME.LMVis.layers.OverlayLayer) OverlayPanel (class in PYME.DSView.OverlaysPanel)

P

p_poisson() (in module PYME.Analysis.cramerRao) pa (PYME.Acquire.microscope.Microscope property) pack() (PYME.contrib.lzw.BitPacker method) pack_results() (in module PYME.localization.FitFactories.fitCommon) PagingDecoder (class in PYME.contrib.lzw) PagingEncoder (class in PYME.contrib.lzw) pair_molecules() (in module PYME.Analysis.points.multiview) PanCamera() (PYME.Acquire.microscope.Microscope method) PanSpool (class in PYME.Acquire.ui.HDFSpoolFrame) ParamGroup (class in PYME.localization.MetaDataEdit) parse() (PYME.DSView.logparser.logparser method) parse_csv_header() (in module PYME.IO.csv_flavours) parseLines() (PYME.misc.zemax.Surface method) Parser (class in PYME.util.mProfile.colorize_db_t) parseURL() (in module PYME.IO.clusterIO) partial_pyramid_depth (PYME.Analysis.distributed_pyramid.DistributedImagePyramid property) PartialPyramid (class in PYME.Analysis.distributed_pyramid) ParticleTracker (class in PYME.LMVis.Extras.particleTracking) patch_log_verbosity() (in module PYME.util.log_verbosity) path_elem() (PYME.cluster.webdav.DAVRequestHandler method) path_elem_prev() (PYME.cluster.webdav.DAVRequestHandler method) pd() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) pearson() (in module PYME.Analysis.Colocalisation.correlationCoeffs) performClassification() (in module PYME.Analysis.svmSegment) PerFrameVar (class in PYME.LMVis.Extras.perFrameVariable) persistLength (PYME.simulation.pointsets.WiglyFibreSource attribute) (PYME.simulation.pointsets.WormlikeSource attribute) PHASE (PYME.Acquire.stackSettings.StackSettings attribute) PhaseRampPupil (class in PYME.DSView.modules.psfGeneration) Phi (PYME.DSView.modules.blobMeasure.DataBlock property) PhongShaderProgram (class in PYME.LMVis.shader_programs.GouraudShaderProgram) pick_color() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) pickleSlice() (in module PYME.localization.FitFactories.fitCommon) pickResultsServer() (in module PYME.IO.clusterResults) piecewiseLinear() (in module PYME.Analysis.piecewise) piecewiseMap (class in PYME.Analysis.piecewiseMapping) piezoGoHome() (PYME.Acquire.stackSettings.StackSettings method) Pin() (PYME.ui.manualFoldPanel.foldingPane method) pin_bits (in module PYME.ui.autoFoldPanel) (in module PYME.ui.manualFoldPanel) PinOpen() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) PipelinePanel (class in PYME.LMVis.pipelineView) pixel_index_of_points_in_image() (in module PYME.Analysis.points.coordinate_tools) pixel_to_screen_coordinates() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) pixel_to_screen_coordinates3D() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) pixelSize (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.IO.image.ImageStack property) pkmod_onestate() (in module PYME.Analysis.BleachProfile.intensProf) play() (PYME.LMVis.Extras.animation.VideoPanel method) playback_running (PYME.DSView.modules.playback.PlayPanel property) (PYME.DSView.modules.playback.PlayZTPanel property) player (class in PYME.DSView.modules.playback) PlayEvents() (in module PYME.misc.eventSpy) PlayPanel (class in PYME.DSView.modules.playback) PlayZTPanel (class in PYME.DSView.modules.playback) plot() (in module PYME.Analysis.graphing_filters) (PYME.Acquire.stage_leveling.StageLeveler method) plot_and_fit() (in module PYME.Analysis.points.qpaint) plot_fit_history() (PYME.localization.autopsf.autopsf.ZernikePSFModel method) plot_image_dist_coloc_figure() (in module PYME.Analysis.Colocalisation.edtColoc) plot_results() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) plot_scan() (PYME.Acquire.stage_leveling.StageLeveler static method) plotCRB() (in module PYME.Analysis.PSFGen.genCRBcurves) plotFolded() (in module PYME.LMVis.Extras.multiviewMapping) PlotPanel (class in PYME.contrib.wxPlotPanel) plotProfile() (in module PYME.util.mProfile.tProfile) plotRes() (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) plotResSimp() (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method) plotSample() (in module PYME.localization.autopsf.autopsf) PlotShiftField() (in module PYME.Analysis.points.twoColourPlot) PlotShiftField2() (in module PYME.Analysis.points.twoColourPlot) PlotShiftResiduals() (in module PYME.Analysis.points.twoColourPlot) PlotShiftResidualsS() (in module PYME.Analysis.points.twoColourPlot) Plug() (in module PYME.Acquire.ui.AnalysisSettingsUI) (in module PYME.DSView.modules.annotation) (in module PYME.DSView.modules.arrayView) (in module PYME.DSView.modules.blobFinding) (in module PYME.DSView.modules.blobMeasure) (in module PYME.DSView.modules.camera_maps) (in module PYME.DSView.modules.coloc) (in module PYME.DSView.modules.composite) (in module PYME.DSView.modules.convnet) (in module PYME.DSView.modules.cropping) (in module PYME.DSView.modules.dark_and_flatfield) (in module PYME.DSView.modules.deconvolution) (in module PYME.DSView.modules.eventView) (in module PYME.DSView.modules.fastGraphPanel) (in module PYME.DSView.modules.filtering) (in module PYME.DSView.modules.flowView) (in module PYME.DSView.modules.fourierRingCorrelation) (in module PYME.DSView.modules.gl_image_view) (in module PYME.DSView.modules.metadataView) (in module PYME.DSView.modules.multithreshold) (in module PYME.DSView.modules.neuroglancer) (in module PYME.DSView.modules.object_tagging) (in module PYME.DSView.modules.playback) (in module PYME.DSView.modules.prebleachExtraction) (in module PYME.DSView.modules.profileFitting) (in module PYME.DSView.modules.profilePlotting) (in module PYME.DSView.modules.projections) (in module PYME.DSView.modules.psfExtraction) (in module PYME.DSView.modules.psfGeneration) (in module PYME.DSView.modules.psfTools) (in module PYME.DSView.modules.pupilTools) (in module PYME.DSView.modules.redimension) (in module PYME.DSView.modules.segmentation) (in module PYME.DSView.modules.sheetView) (in module PYME.DSView.modules.shell) (in module PYME.DSView.modules.shiftfield_estimation) (in module PYME.DSView.modules.sparkprepare) (in module PYME.DSView.modules.splitter) (in module PYME.DSView.modules.synchronise) (in module PYME.DSView.modules.tiling) (in module PYME.DSView.modules.unmixing) (in module PYME.DSView.modules.vis3D) (in module PYME.DSView.modules.visgui) (in module PYME.DSView.modules.webview) (in module PYME.LMVis.Extras.animation) (in module PYME.LMVis.Extras.annotation) (in module PYME.LMVis.Extras.clusterAnalysis) (in module PYME.LMVis.Extras.dockedPanel) (in module PYME.LMVis.Extras.extra_layers) (in module PYME.LMVis.Extras.flagZMotionArtifacts) (in module PYME.LMVis.Extras.fusionUtils) (in module PYME.LMVis.Extras.multiColourAnalysis) (in module PYME.LMVis.Extras.multiviewMapping) (in module PYME.LMVis.Extras.objectMeasurements) (in module PYME.LMVis.Extras.particleTracking) (in module PYME.LMVis.Extras.perFrameVariable) (in module PYME.LMVis.Extras.photophysics) (in module PYME.LMVis.Extras.pointSetGeneration) (in module PYME.LMVis.Extras.pointwiseColoc) (in module PYME.LMVis.Extras.QPobjectSegment) (in module PYME.LMVis.Extras.saved_views) (in module PYME.LMVis.Extras.scaleBox) (in module PYME.LMVis.Extras.sequentialSpecies) (in module PYME.LMVis.Extras.setBGImage) (in module PYME.LMVis.Extras.shiftmapGenerator) (in module PYME.LMVis.Extras.showShortcuts) (in module PYME.LMVis.Extras.spherical_harmonics) (in module PYME.LMVis.Extras.subsets) (in module PYME.LMVis.Extras.surface_fitting) (in module PYME.LMVis.Extras.temperaturePlot) (in module PYME.LMVis.Extras.vibration) Point (class in PYME.ui.selection) point_size (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) point_size_px() (PYME.LMVis.layers.pointcloud.Points3DEngine method) point_spacing (PYME.simulation.pointsets.SHNucleusSource attribute) PointCloudRenderLayer (class in PYME.LMVis.layers.pointcloud) pointColour() (PYME.LMVis.visCore.VisGUICore method) pointDensityAtDistance() (in module PYME.Analysis.Colocalisation.edtColoc) PointDisplayOverlay (class in PYME.DSView.overlays) PointDisplaySettings (class in PYME.LMVis.pointSettingsPanel) (class in PYME.LMVis.view_clipping_pane) pointlHood() (PYME.Analysis.points.segmentLL.segmenter method) points() (PYME.simulation.pointsets.PointSource method) Points3DEngine (class in PYME.LMVis.layers.pointcloud) points_from_mask() (in module PYME.Analysis.points.ripleys) points_from_sdf() (in module PYME.simulation.locify) points_hit_test() (PYME.DSView.overlays.PointDisplayOverlay method) points_per_pixel (PYME.simulation.pointsets.ImageSource attribute) PointScanner (class in PYME.Acquire.Utils.MultiPointScanner) (class in PYME.Acquire.Utils.pointScanner) PointScanner3D (class in PYME.Acquire.Utils.pointScanner) PointSettingsPanel (class in PYME.LMVis.pointSettingsPanel) pointSize (PYME.LMVis.pointSettingsPanel.PointDisplaySettings attribute) (PYME.LMVis.view_clipping_pane.PointDisplaySettings attribute) PointSource (class in PYME.simulation.pointsets) PointSpritesEngine (class in PYME.LMVis.layers.pointcloud) PointSpriteShaderProgram (class in PYME.LMVis.shader_programs.PointSpriteShaderProgram) PointwiseColocaliser (class in PYME.LMVis.Extras.pointwiseColoc) poll_timeouts() (PYME.cluster.ruleserver.IntegerIDRule method) PopContext() (PYME.Analysis.processLogger.ContextManager method) populate() (PYME.ui.filterPane.FilterPanel method) populate_filters() (in module PYME.reports.filters) PopulateMetadata() (PYME.Acquire.sampleInformation.SampleInfoDialog method) port (PYME.misc.sqlite_ns.NSInfo attribute) PositionPanel (class in PYME.Acquire.ui.positionUI) PositionPanelV2 (class in PYME.Acquire.ui.positionUI) PositionSliders (class in PYME.Acquire.ui.positionUI) PositionTracker (class in PYME.Acquire.positionTracker) positivity() (in module PYME.Analysis.PSFEst.psfQuality) post_rule() (PYME.cluster.HTTPRulePusher.HTTPRulePusher method) powerMod2D() (in module PYME.Analysis.Tracking.trackUtils) powerMod3D() (in module PYME.Analysis.Tracking.trackUtils) PrebleachExtractor (class in PYME.DSView.modules.prebleachExtraction) prefillSampleData() (in module PYME.Acquire.sampleInformation) PreflightCheck() (PYME.Acquire.protocol.Protocol method) (PYME.Acquire.protocol.TaskListProtocol method) PreflightCheckItem (class in PYME.Acquire.protocol) prep() (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.DeconvMappingBase method) Prepare() (PYME.Acquire.frameWrangler.FrameWrangler method) prepare() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.cluster.rules.LocalisationRule method) (PYME.cluster.rules.RecipeRule method) (PYME.cluster.rules.Rule method) (PYME.Deconv.dec.dec_4pi_c method) preparePSF() (in module PYME.localization.ofind_pri) (in module PYME.localization.ofind_xcorr) (in module PYME.localization.ofind_xcorr_fw) principalAxis (PYME.DSView.modules.blobMeasure.DataBlock property) print_catalog_list() (in module PYME.misc.read_agf) print_cycles() (in module PYME.misc.findCycles) print_glass_list() (in module PYME.misc.read_agf) print_glass_report() (in module PYME.misc.read_agf) prob_predict() (in module PYME.Analysis.svmSegment) probabilities() (PYME.Analysis.svmSegment.svmClassifier method) probePoint() (PYME.Analysis.points.segmentLL.segmenter method) processIntensityTrace() (in module PYME.Analysis.BleachProfile.rawIntensity) processTag() (PYME.cluster.webdav.XMLDict_Parser method) procSkelFile() (in module PYME.Analysis.angleFilter) prof_callback() (PYME.util.fProfile.fProfile.ThreadProfiler method) (PYME.util.fProfile.fProfile.ThreadProfilerRegex method) profile_off() (in module PYME.util.mProfile.tProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) profile_on() (in module PYME.util.mProfile.tProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) (PYME.util.fProfile.fProfile.ThreadProfilerRegex method) profileOff() (in module PYME.util.mProfile.mProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) profileOn() (in module PYME.util.mProfile.mProfile) (PYME.util.fProfile.fProfile.ThreadProfiler method) ProfilePlotter (class in PYME.DSView.modules.profilePlotting) profiler() (in module PYME.util.mProfile.tProfile) profOff() (in module PYME.util.mProfile.p) profOn() (in module PYME.util.mProfile.p) progPanel (class in PYME.LMVis.progGraph) ProgressSelection() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) project() (in module PYME.DSView.modules.projections) Project() (PYME.DSView.modules.filtering.Filterer method) projectZ() (in module PYME.misc.zernike) projectZ_rays() (in module PYME.misc.zernike) propagate() (PYME.Analysis.PSFGen.fourier.FourierPropagator method) (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorClipHNA method) (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorClipHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA method) propagate_r() (PYME.Analysis.PSFGen.fourierHNA.FourierPropagatorHNA method) (PYME.Analysis.PSFGen.fourierHNA2.FourierPropagatorHNA method) Property (in module PYME.misc.mock_traits) Protocol (class in PYME.Acquire.protocol) protocol_settings (PYME.Acquire.ui.spool_panel.ProtocolAcquisitionPane property) protocol_version (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) (PYME.util.webframework.JSONAPIRequestHandler attribute) ProtocolAcquisition (class in PYME.Acquire.protocol_acquisition) ProtocolAcquisitionPane (class in PYME.Acquire.ui.spool_panel) ProtocolAcquisitionSettings (class in PYME.Acquire.SpoolController) ProvideStackMetadata() (PYME.Acquire.stackSettings.StackSettings method) PseudoPointList (class in PYME.localization.ofind) (class in PYME.localization.ofind3d) (class in PYME.localization.ofind_nofilt) (class in PYME.localization.ofind_pri) (class in PYME.localization.ofind_split) (class in PYME.localization.ofind_xcorr) (class in PYME.localization.ofind_xcorr_fw) psf() (PYME.Analysis.PSFGen.fourierHNA.FourierPSF method) psf_calc() (PYME.Analysis.PSFEst.dec.dec_psf method) (PYME.Deconv.dec.ClassicMappingFFTW method) (PYME.Deconv.dec.ClassicMappingNP method) (PYME.Deconv.dec.dec_4pi method) (PYME.Deconv.dec.DeconvMappingBase method) (PYME.Deconv.dec.SpatialConvolutionMapping method) (PYME.Deconv.wiener.dec_wiener method) PSF_from_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) PSFExporter (class in PYME.IO.dataExporter) PsfExtractor (class in PYME.DSView.modules.psfExtraction) PSFFitFactory (class in PYME.localization.FitFactories.InterpFitR) (class in PYME.localization.FitFactories.LatPSFFitR) (class in PYME.localization.FitFactories.PRInterpFitQR) (class in PYME.localization.FitFactories.PRInterpFitR) PSFFitResult (class in PYME.localization.FitFactories.LatPSFFitR) PSFFitResultR() (in module PYME.localization.FitFactories.InterpFitR) (in module PYME.localization.FitFactories.LatPSFFitR) (in module PYME.localization.FitFactories.MultiviewFitInterpNR) (in module PYME.localization.FitFactories.PRInterpFitQR) (in module PYME.localization.FitFactories.PRInterpFitR) (in module PYME.localization.FitFactories.SplitterFitInterpBNR) (in module PYME.localization.FitFactories.SplitterFitInterpNR) PSFFitSettingsDialog (class in PYME.DSView.modules.psfTools) PsfFromPupil() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) PsfFromPupilVect() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) PSFQualityPanel (class in PYME.DSView.modules.psfTools) PSFTools (class in PYME.DSView.modules.psfTools) pty_read() (PYME.Acquire.webui.ipy.IPYTermManager method) ptyproc (PYME.Acquire.webui.ipy.IPYWithClients property) Pupil (class in PYME.DSView.modules.psfGeneration) pupil (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) PupilGenerator (class in PYME.DSView.modules.psfGeneration) pupils (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) pupilSize (PYME.DSView.modules.psfTools.PSFTools attribute) pupilSizeX (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) PupilTools (class in PYME.DSView.modules.pupilTools) purge() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Analysis.tile_pyramid.TileCache method) push() (PYME.cluster.rules.Rule method) put() (PYME.IO.cluster_streaming.Stream method) (PYME.IO.cluster_streaming.Streamer method) put_file() (in module PYME.IO.clusterIO) (PYME.IO.h5File.H5File method) put_files() (in module PYME.IO.clusterIO) put_stream() (PYME.IO.cluster_streaming.Streamer method) PYME module PYME.Acquire module PYME.Acquire.acquire_client module PYME.Acquire.acquire_server module PYME.Acquire.acquirebase module PYME.Acquire.acquiremainframe module PYME.Acquire.acquirewx module PYME.Acquire.acquisition_base module PYME.Acquire.ActionManager module PYME.Acquire.actions module PYME.Acquire.autofocus module PYME.Acquire.event_loop module PYME.Acquire.eventLog module PYME.Acquire.ExecTools module PYME.Acquire.frameWrangler module PYME.Acquire.htsms module PYME.Acquire.htsms.tweeter module PYME.Acquire.microscope module PYME.Acquire.misc module PYME.Acquire.misc.tempLogger module PYME.Acquire.misc.tempLoggerDB module PYME.Acquire.misc.tempMonitor module PYME.Acquire.positionTracker module PYME.Acquire.protocol module PYME.Acquire.protocol_acquisition module PYME.Acquire.PYMEAcquire module PYME.Acquire.sampleInformation module PYME.Acquire.setup module PYME.Acquire.SpoolController module PYME.Acquire.stackSettings module PYME.Acquire.stage_leveling module PYME.Acquire.ui module PYME.Acquire.ui.AnalysisSettingsUI module PYME.Acquire.ui.focus_lock_gui module PYME.Acquire.ui.HDFSpoolFrame module PYME.Acquire.ui.intensity_trace module PYME.Acquire.ui.intsliders module PYME.Acquire.ui.lasersliders module PYME.Acquire.ui.mpd_picosecond_delay_panel module PYME.Acquire.ui.multiview_select module PYME.Acquire.ui.positionUI module PYME.Acquire.ui.preflight module PYME.Acquire.ui.scanner_panel module PYME.Acquire.ui.selectCameraPanel module PYME.Acquire.ui.seqdialog module PYME.Acquire.ui.splashScreen module PYME.Acquire.ui.spool_panel module PYME.Acquire.ui.tile_panel module PYME.Acquire.ui.tilesettingsui module PYME.Acquire.ui.voxelSizeDialog module PYME.Acquire.Utils module PYME.Acquire.Utils.failsafe module PYME.Acquire.Utils.fastTiler module PYME.Acquire.Utils.MultiPointScanner module PYME.Acquire.Utils.pointScanner module PYME.Acquire.Utils.sarcSpacing module PYME.Acquire.Utils.strip_tiler module PYME.Acquire.Utils.tiler module PYME.Acquire.Utils.vibrationAnalysis module PYME.Acquire.webui module PYME.Acquire.webui.ipy module PYME.Acquire.xyztc module PYME.Acquire.zScanner module PYME.Analysis module PYME.Analysis.angleFilter module PYME.Analysis.annealThresh module PYME.Analysis.autoencoder_classifier module PYME.Analysis.binAvg module PYME.Analysis.BleachProfile module PYME.Analysis.BleachProfile.deMod module PYME.Analysis.BleachProfile.fitRecover module PYME.Analysis.BleachProfile.intensProf module PYME.Analysis.BleachProfile.kinModels module PYME.Analysis.BleachProfile.rawIntensity module PYME.Analysis.BleachProfile.rollins module PYME.Analysis.Colocalisation module PYME.Analysis.Colocalisation.colocScaleDep module PYME.Analysis.Colocalisation.correlationCoeffs module PYME.Analysis.Colocalisation.distColoc module PYME.Analysis.Colocalisation.edtColoc module PYME.Analysis.composite module PYME.Analysis.cramerRao module PYME.Analysis.density_filter module PYME.Analysis.deTile module PYME.Analysis.distributed_pyramid module PYME.Analysis.fiducial_matching module PYME.Analysis.gen_sCMOS_maps module PYME.Analysis.graphing_filters module PYME.Analysis.implicitFilter module PYME.Analysis.keep_pairs module PYME.Analysis.MetaData module PYME.Analysis.optic_flow module PYME.Analysis.piecewise module PYME.Analysis.piecewiseMapping module PYME.Analysis.piezo_movement_correction module PYME.Analysis.points module PYME.Analysis.points.arcfit module PYME.Analysis.points.arcfit.arcmf module PYME.Analysis.points.arcfit.setup module PYME.Analysis.points.astigmatism module PYME.Analysis.points.astigmatism.astiglookup module PYME.Analysis.points.astigmatism.astigTools module PYME.Analysis.points.astigmatism.setup module PYME.Analysis.points.cluster_morphology module PYME.Analysis.points.coordinate_tools module PYME.Analysis.points.DeClump module PYME.Analysis.points.DeClump.deClump module PYME.Analysis.points.DeClump.deClumpGUI module PYME.Analysis.points.DeClump.pyDeClump module PYME.Analysis.points.DeClump.setup module PYME.Analysis.points.DeClump.testClump module PYME.Analysis.points.DistHist module PYME.Analysis.points.DistHist.distHist module PYME.Analysis.points.DistHist.distHistThreaded module PYME.Analysis.points.DistHist.setup module PYME.Analysis.points.EdgeDB module PYME.Analysis.points.EdgeDB.edgeDB module PYME.Analysis.points.EdgeDB.edges module PYME.Analysis.points.EdgeDB.edgeTest module PYME.Analysis.points.EdgeDB.segment module PYME.Analysis.points.EdgeDB.setup module PYME.Analysis.points.features module PYME.Analysis.points.features.metal module PYME.Analysis.points.fiducials module PYME.Analysis.points.gen3DTriangs module PYME.Analysis.points.moments module PYME.Analysis.points.multiview module PYME.Analysis.points.objectMeasure module PYME.Analysis.points.qpaint module PYME.Analysis.points.QuadTree module PYME.Analysis.points.QuadTree.pointQT module PYME.Analysis.points.QuadTree.pointQTF module PYME.Analysis.points.QuadTree.QTrend module PYME.Analysis.points.QuadTree.rendQT module PYME.Analysis.points.rings module PYME.Analysis.points.ripleys module PYME.Analysis.points.segmentLL module PYME.Analysis.points.setup module PYME.Analysis.points.SoftRend module PYME.Analysis.points.SoftRend.setup module PYME.Analysis.points.SoftRend.testTetrahedra module PYME.Analysis.points.SoftRend.triRend module PYME.Analysis.points.spherical_harmonics module PYME.Analysis.points.surfit module PYME.Analysis.points.tCluster module PYME.Analysis.points.traveling_salesperson module PYME.Analysis.points.traveling_salesperson.queue_opt module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt module PYME.Analysis.points.traveling_salesperson.setup module PYME.Analysis.points.traveling_salesperson.sort module PYME.Analysis.points.traveling_salesperson.two_opt module PYME.Analysis.points.traveling_salesperson.two_opt_utils module PYME.Analysis.points.twoColour module PYME.Analysis.points.twoColourPlot module PYME.Analysis.processLogger module PYME.Analysis.profile_extraction module PYME.Analysis.PSFEst module PYME.Analysis.PSFEst.dec module PYME.Analysis.PSFEst.extractImages module PYME.Analysis.PSFEst.fit_psf_zernikes module PYME.Analysis.PSFEst.psfQuality module PYME.Analysis.PSFGen module PYME.Analysis.PSFGen.fourier module PYME.Analysis.PSFGen.fourierHNA module PYME.Analysis.PSFGen.fourierHNA2 module PYME.Analysis.PSFGen.genCRBcurves module PYME.Analysis.PSFGen.nijboer_zernike module PYME.Analysis.PSFGen.ps_app module PYME.Analysis.PSFGen.setup module PYME.Analysis.PSFGen.test_ps_app module PYME.Analysis.setup module PYME.Analysis.splitting module PYME.Analysis.svmSegment module PYME.Analysis.thresholding module PYME.Analysis.tile_pyramid module PYME.Analysis.Tracking module PYME.Analysis.Tracking.msd module PYME.Analysis.Tracking.tracking module PYME.Analysis.Tracking.trackUtils module PYME.Analysis.widefieldify module PYME.cluster module PYME.cluster.cluster_of_one module PYME.cluster.dataserver_wsgi module PYME.cluster.distribution module PYME.cluster.HTTPDataServer module PYME.cluster.HTTPRulePusher module PYME.cluster.HTTPTaskPusher module PYME.cluster.PYMERuleNodeServer module PYME.cluster.PYMERuleServer module PYME.cluster.rulenodeserver module PYME.cluster.rules module PYME.cluster.ruleserver module PYME.cluster.status module PYME.cluster.taskWorkerHTTP module PYME.cluster.webdav module PYME.config module PYME.contrib module PYME.contrib.aniso module PYME.contrib.aniso.aniso module PYME.contrib.auiFloatBook module PYME.contrib.congrid module PYME.contrib.dispatch module PYME.contrib.dispatch.dispatcher module PYME.contrib.gohlke module PYME.contrib.gohlke.czifile module PYME.contrib.gohlke.fcsfiles module PYME.contrib.gohlke.setup module PYME.contrib.gohlke.tifffile module PYME.contrib.listctrlMixins module PYME.contrib.lzw module PYME.contrib.pad module PYME.contrib.pad.info_pad module PYME.contrib.pad.pad module PYME.contrib.setup module PYME.contrib.TextCtrlAutoComplete module PYME.contrib.wxPlotPanel module PYME.Deconv module PYME.Deconv.beadGen module PYME.Deconv.dec module PYME.Deconv.dec_test module PYME.Deconv.deconvDialogs module PYME.Deconv.decTask module PYME.Deconv.decThread module PYME.Deconv.fftwWisdom module PYME.Deconv.richardsonLucy module PYME.Deconv.richardsonLucyMV module PYME.Deconv.richardsonLucyMVM module PYME.Deconv.test_block_dec module PYME.Deconv.wiener module PYME.DSView module PYME.DSView.arrayViewPanel module PYME.DSView.displayOptions module PYME.DSView.DisplayOptionsPanel module PYME.DSView.displaySettingsPanel module PYME.DSView.dsviewer module PYME.DSView.eventLogViewer module PYME.DSView.fitInfo module PYME.DSView.htmlServe module PYME.DSView.logparser module PYME.DSView.LUT module PYME.DSView.LUT.lut module PYME.DSView.LUT.setup module PYME.DSView.modules module PYME.DSView.modules.annotation module PYME.DSView.modules.arrayView module PYME.DSView.modules.blobFinding module PYME.DSView.modules.blobMeasure module PYME.DSView.modules.camera_maps module PYME.DSView.modules.coloc module

PYME.DSView.modules.composite module PYME.DSView.modules.convnet module PYME.DSView.modules.cropping module PYME.DSView.modules.dark_and_flatfield module PYME.DSView.modules.deconvolution module PYME.DSView.modules.eventView module PYME.DSView.modules.extractBlobs module PYME.DSView.modules.fastGraphPanel module PYME.DSView.modules.filtering module PYME.DSView.modules.flowView module PYME.DSView.modules.fourierRingCorrelation module PYME.DSView.modules.gl_image_view module PYME.DSView.modules.measure module PYME.DSView.modules.measure.filterPan module PYME.DSView.modules.metadataView module PYME.DSView.modules.multithreshold module PYME.DSView.modules.neuroglancer module PYME.DSView.modules.object_tagging module PYME.DSView.modules.playback module PYME.DSView.modules.prebleachExtraction module PYME.DSView.modules.profileFitting module PYME.DSView.modules.profilePlotting module PYME.DSView.modules.projections module PYME.DSView.modules.psfExtraction module PYME.DSView.modules.psfGeneration module PYME.DSView.modules.psfTools module PYME.DSView.modules.pupilTools module PYME.DSView.modules.redimension module PYME.DSView.modules.segmentation module PYME.DSView.modules.sheetView module PYME.DSView.modules.shell module PYME.DSView.modules.shiftfield_estimation module PYME.DSView.modules.sparkprepare module PYME.DSView.modules.splitter module PYME.DSView.modules.synchronise module PYME.DSView.modules.tiling module PYME.DSView.modules.unmixing module PYME.DSView.modules.vis3D module PYME.DSView.modules.visgui module PYME.DSView.modules.webview module PYME.DSView.overlays module PYME.DSView.OverlaysPanel module PYME.DSView.scrolledImagePanel module PYME.DSView.setup module PYME.DSView.splashScreen module PYME.DSView.voxSizeDialog module PYME.IO module PYME.IO.acquisition_backends module PYME.IO.buffers module PYME.IO.cluster_directory module PYME.IO.cluster_streaming module PYME.IO.clusterDuplication module PYME.IO.clusterExport module PYME.IO.clusterGlob module PYME.IO.clusterIO module PYME.IO.clusterListing module PYME.IO.clusterResults module PYME.IO.clusterUpload module PYME.IO.compatibility module PYME.IO.countdir module PYME.IO.countdir.countdir module PYME.IO.countdir.setup module PYME.IO.csv_flavours module PYME.IO.dataExporter module PYME.IO.DataSources module PYME.IO.DataSources.AlignDataSource module PYME.IO.DataSources.ArrayDataSource module PYME.IO.DataSources.BaseDataSource module PYME.IO.DataSources.BGSDataSource module PYME.IO.DataSources.BioformatsDataSource module PYME.IO.DataSources.BufferedDataSource module PYME.IO.DataSources.ClusterPZFDataSource module PYME.IO.DataSources.ConcatenatedDataSource module PYME.IO.DataSources.CropDataSource module PYME.IO.DataSources.DcimgDataSource module PYME.IO.DataSources.ElectronsPerSecondDataSource module PYME.IO.DataSources.FlatFieldDataSource module PYME.IO.DataSources.HDFDataSource module PYME.IO.DataSources.HTTPDataSource module PYME.IO.DataSources.ImageSeriesDataSource module PYME.IO.DataSources.MultiviewDataSource module PYME.IO.DataSources.OBFDataSource module PYME.IO.DataSources.RandomDataSource module PYME.IO.DataSources.SupertileDatasource module PYME.IO.DataSources.TiffDataSource module PYME.IO.DataSources.TileDataSource module PYME.IO.DataSources.TQDataSource module PYME.IO.DataSources.UnsplitDataSource module PYME.IO.dataWrap module PYME.IO.dcimg module PYME.IO.events module PYME.IO.FileUtils module PYME.IO.FileUtils.compHdf module PYME.IO.FileUtils.fileID module PYME.IO.FileUtils.fnlGen module PYME.IO.FileUtils.freeSpace module PYME.IO.FileUtils.h5ExFrames module PYME.IO.FileUtils.h5rFormatDef module PYME.IO.FileUtils.h5rToTxt module PYME.IO.FileUtils.h5ToTiffSeries module PYME.IO.FileUtils.IJLut module PYME.IO.FileUtils.nameUtils module PYME.IO.FileUtils.obf_support module PYME.IO.FileUtils.ply module PYME.IO.FileUtils.RawToHdf5 module PYME.IO.FileUtils.readSpeckle module PYME.IO.FileUtils.readTiff module PYME.IO.FileUtils.saveTiffStack module PYME.IO.FileUtils.setup module PYME.IO.FileUtils.SPAD module PYME.IO.FileUtils.stl module PYME.IO.FileUtils.thumbnailDatabase module PYME.IO.FileUtils.TiffSeqToHdf5 module PYME.IO.h5File module PYME.IO.h5rFile module PYME.IO.HTTPSpooler_v2 module PYME.IO.image module PYME.IO.load_psf module PYME.IO.MetaDataHandler module PYME.IO.pyme_h5ls module PYME.IO.PZFFormat module PYME.IO.ragged module PYME.IO.rgb_image module PYME.IO.setup module PYME.IO.Spooler module PYME.IO.tabular module PYME.IO.testClusterSpooling module PYME.IO.unifiedIO module PYME.LMVis module PYME.LMVis.colourFilterGUI module PYME.LMVis.displayPane module PYME.LMVis.dyeRatios module PYME.LMVis.Extras module PYME.LMVis.Extras.animation module PYME.LMVis.Extras.annotation module PYME.LMVis.Extras.clusterAnalysis module PYME.LMVis.Extras.dockedPanel module PYME.LMVis.Extras.extra_layers module PYME.LMVis.Extras.flagZMotionArtifacts module PYME.LMVis.Extras.fusionUtils module PYME.LMVis.Extras.multiColourAnalysis module PYME.LMVis.Extras.multiviewMapping module PYME.LMVis.Extras.objectMeasurements module PYME.LMVis.Extras.particleTracking module PYME.LMVis.Extras.perFrameVariable module PYME.LMVis.Extras.photophysics module PYME.LMVis.Extras.pointSetGeneration module PYME.LMVis.Extras.pointwiseColoc module PYME.LMVis.Extras.QPobjectSegment module PYME.LMVis.Extras.saved_views module PYME.LMVis.Extras.scaleBox module PYME.LMVis.Extras.sequentialSpecies module PYME.LMVis.Extras.setBGImage module PYME.LMVis.Extras.shiftmapGenerator module PYME.LMVis.Extras.showShortcuts module PYME.LMVis.Extras.spherical_harmonics module PYME.LMVis.Extras.subsets module PYME.LMVis.Extras.surface_fitting module PYME.LMVis.Extras.temperaturePlot module PYME.LMVis.Extras.vibration module PYME.LMVis.genImageDialog module PYME.LMVis.gl_offScreenHandler module PYME.LMVis.gl_render3D_shaders module PYME.LMVis.glcanvas_core module PYME.LMVis.imageView module PYME.LMVis.imageView2 module PYME.LMVis.importTextDialog module PYME.LMVis.layer_panel module PYME.LMVis.layers module PYME.LMVis.layers.AxesOverlayLayer module PYME.LMVis.layers.base module PYME.LMVis.layers.image_layer module PYME.LMVis.layers.labels module PYME.LMVis.layers.layer_defaults module PYME.LMVis.layers.LUTOverlayLayer module PYME.LMVis.layers.mesh module PYME.LMVis.layers.octree module PYME.LMVis.layers.OverlayLayer module PYME.LMVis.layers.pointcloud module PYME.LMVis.layers.quiver module PYME.LMVis.layers.ScaleBarOverlayLayer module PYME.LMVis.layers.ScaleBoxOverlayLayer module PYME.LMVis.layers.SelectionOverlayLayer module PYME.LMVis.layers.text module PYME.LMVis.layers.tracks module PYME.LMVis.mv_math module PYME.LMVis.objectDarkMeasure module PYME.LMVis.pipelineView module PYME.LMVis.pointSettingsPanel module PYME.LMVis.progGraph module PYME.LMVis.quadTreeSettings module PYME.LMVis.renderers module PYME.LMVis.rendGauss module PYME.LMVis.setup module PYME.LMVis.setup_exe module PYME.LMVis.shader_programs module PYME.LMVis.shader_programs.DefaultShaderProgram module PYME.LMVis.shader_programs.GLProgram module PYME.LMVis.shader_programs.GouraudShaderProgram module PYME.LMVis.shader_programs.oit_compositor module PYME.LMVis.shader_programs.PointSpriteShaderProgram module PYME.LMVis.shader_programs.shader_loader module PYME.LMVis.shader_programs.shader_program module PYME.LMVis.shader_programs.ShaderProgramFactory module PYME.LMVis.shader_programs.TesselShaderProgram module PYME.LMVis.shader_programs.WireFrameShaderProgram module PYME.LMVis.statusLog module PYME.LMVis.tests module PYME.LMVis.triBlobs module PYME.LMVis.view_clipping_pane module PYME.LMVis.views module PYME.LMVis.visCore module PYME.LMVis.visHelpers module PYME.LMVis.visHelpersMin module PYME.localization module PYME.localization.autopsf module PYME.localization.autopsf.autopsf module PYME.localization.autopsf.roifit module PYME.localization.cInterp module PYME.localization.cInterp.cInterp module PYME.localization.cInterp.setup module PYME.localization.cModels module PYME.localization.cModels.gauss_app module PYME.localization.cModels.setup module PYME.localization.FitFactories module PYME.localization.FitFactories.AstigGaussFitFR module PYME.localization.FitFactories.AstigGaussGPUFitFR module PYME.localization.FitFactories.BeadConvolvedAstigGaussFit module PYME.localization.FitFactories.ChecksumFR module PYME.localization.FitFactories.ChecksumGPUFR module PYME.localization.FitFactories.ChecksumMultifitSR module PYME.localization.FitFactories.ConfocCOIR module PYME.localization.FitFactories.Dumbell3DFitR module PYME.localization.FitFactories.DumbellFitR module PYME.localization.FitFactories.FFBase module PYME.localization.FitFactories.fitCommon module PYME.localization.FitFactories.Gauss3DFitR module PYME.localization.FitFactories.GaussFitConstrR module PYME.localization.FitFactories.GaussMultifitLinesR module PYME.localization.FitFactories.GaussMultifitR module PYME.localization.FitFactories.GaussMultifitSR module PYME.localization.FitFactories.InterpFitR module PYME.localization.FitFactories.InterpFitWFR module PYME.localization.FitFactories.Interpolators module PYME.localization.FitFactories.Interpolators.baseInterpolator module PYME.localization.FitFactories.Interpolators.CSInterpolator module PYME.localization.FitFactories.Interpolators.CubeSInterpolatorP module PYME.localization.FitFactories.Interpolators.CubicSplineInterpolator module PYME.localization.FitFactories.Interpolators.LinearInterpolator module PYME.localization.FitFactories.Interpolators.LinearPInterpolatorP module PYME.localization.FitFactories.LatFitCOIR module PYME.localization.FitFactories.LatGaussFitFR module PYME.localization.FitFactories.LatObjFindFR module PYME.localization.FitFactories.LatPSFFitR module PYME.localization.FitFactories.MultiviewFitInterpNR module PYME.localization.FitFactories.PRInterpFitQR module PYME.localization.FitFactories.PRInterpFitR module PYME.localization.FitFactories.ROIExtractNR module PYME.localization.FitFactories.SpecGaussFitFR module PYME.localization.FitFactories.SplitterFitCOIR module PYME.localization.FitFactories.SplitterFitFNR module PYME.localization.FitFactories.SplitterFitFusionR module PYME.localization.FitFactories.SplitterFitInterpBNR module PYME.localization.FitFactories.SplitterFitInterpNR module PYME.localization.FitFactories.SplitterFitScavNR module PYME.localization.FitFactories.SplitterMultifitSR module PYME.localization.FitFactories.SplitterObjFindR module PYME.localization.FitFactories.SplitterROIExtractNR module PYME.localization.FitFactories.SplitterShiftEstFR module PYME.localization.FitFactories.zEstimators module PYME.localization.FitFactories.zEstimators.astigEstimator module PYME.localization.FitFactories.zEstimators.biplaneEstimator module PYME.localization.FitFactories.zEstimators.genericDualEstimator module PYME.localization.FitFactories.zEstimators.genericEstimator module PYME.localization.FitFactories.zEstimators.priEstimator module PYME.localization.MetaDataEdit module PYME.localization.ofind module PYME.localization.ofind3d module PYME.localization.ofind_nofilt module PYME.localization.ofind_pri module PYME.localization.ofind_split module PYME.localization.ofind_xcorr module PYME.localization.ofind_xcorr_fw module PYME.localization.remFitBuf module PYME.localization.setup module PYME.localization.splitting module PYME.localization.Test module PYME.localization.Test.fitTestJig module PYME.localization.Test.fitTestJigSCMOS module PYME.localization.Test.fitTestJigWC module PYME.localization.twist module PYME.misc module PYME.misc.aligned_array module PYME.misc.aniso module PYME.misc.big_sur_fix module PYME.misc.check_for_updates module PYME.misc.colormaps module PYME.misc.colorsys module PYME.misc.computerName module PYME.misc.coverslipGeometries module PYME.misc.cython_numpy_monkey module PYME.misc.depGraph module PYME.misc.dirSize module PYME.misc.diskCleanup module PYME.misc.django_widgets module PYME.misc.djangoRecarray module PYME.misc.editgrid module PYME.misc.eventSpy module PYME.misc.exceptions module PYME.misc.facsPlot module PYME.misc.fbpIcons module PYME.misc.fftw_compat module PYME.misc.findCycles module PYME.misc.fortran_interrupt_defeat module PYME.misc.glassModel module PYME.misc.hash32 module PYME.misc.hillcurve module PYME.misc.hybrid_ns module PYME.misc.kdFit module PYME.misc.locate module PYME.misc.memmap module PYME.misc.memUsage module PYME.misc.mock_ctypes module PYME.misc.mock_traits module PYME.misc.mock_traitsui module PYME.misc.pyme_zeroconf module PYME.misc.pyro_tracebacks module PYME.misc.read_agf module PYME.misc.sffake module PYME.misc.snells module PYME.misc.sqlite_ns module PYME.misc.sqlitendarray module PYME.misc.taskDef module PYME.misc.tempDB module PYME.misc.TiffImagePlugin module PYME.misc.TiSettings module PYME.misc.VolProj module PYME.misc.wxThread module PYME.misc.zemax module PYME.misc.zernike module PYME.pyme_warnings module PYME.recipes.traits module PYME.reports module PYME.reports.filters module PYME.resources module PYME.resources.setup module PYME.setup module PYME.setup_exe module PYME.simulation module PYME.simulation.locify module PYME.simulation.pointsets module PYME.simulation.wormlike module PYME.simulation.wormlike2 module PYME.simulation.wormlike3 module PYME.simulation.wormlike_curled module PYME.tileviewer module PYME.tileviewer.tileviewer module PYME.ui module PYME.ui.about_dlg module PYME.ui.AUIFrame module PYME.ui.autoFoldPanel module PYME.ui.cascading_layout module PYME.ui.crop_dialog module PYME.ui.editFilterDialog module PYME.ui.fastGraph module PYME.ui.filterPane module PYME.ui.histLimits module PYME.ui.layerFoldPanel module PYME.ui.manualFoldPanel module PYME.ui.MetadataTree module PYME.ui.mytimer module PYME.ui.patch_traitsui module PYME.ui.progress module PYME.ui.recArrayView module PYME.ui.selection module PYME.ui.shell module PYME.ui.wx_compat module PYME.update_version module PYME.util module PYME.util.authenticate module PYME.util.execfile module PYME.util.fProfile module PYME.util.fProfile.convertProfile module PYME.util.fProfile.fProfile module PYME.util.fProfile.viewProfile module PYME.util.install_dependencies module PYME.util.log_verbosity module PYME.util.mProfile module PYME.util.mProfile.colorize_db_t module PYME.util.mProfile.mProfile module PYME.util.mProfile.p module PYME.util.mProfile.tProfile module PYME.util.pymelauncher module PYME.util.shmarray module PYME.util.shmarray.shmarray module PYME.util.shmarray.shmTest module PYME.util.webframework module PYME.version module PYMEAcquireBase (class in PYME.Acquire.acquirebase) PYMEAcquireServerMixin (class in PYME.Acquire.acquire_server) PYMEDeprecationWarning PYMEHTTPRequestHandler (class in PYME.cluster.HTTPDataServer) pymeimage_cmd (PYME.Acquire.SpoolController.SpoolController property) PYMEMainFrame (class in PYME.Acquire.acquiremainframe) pymevis_cmd (PYME.Acquire.SpoolController.SpoolController property) PyramidLayer (class in PYME.Analysis.tile_pyramid) pzf_index (PYME.IO.DataSources.HDFDataSource.DataSource property) (PYME.IO.h5File.H5File property) PZFCompression (PYME.IO.h5File.H5File attribute) PZFTileCache (class in PYME.Analysis.tile_pyramid) PZFTileIO (class in PYME.Analysis.tile_pyramid)

Q

qpaint1mod() (in module PYME.Analysis.points.qpaint) qpaint2mod() (in module PYME.Analysis.points.qpaint) QPObjectSegmenter (class in PYME.LMVis.Extras.QPobjectSegment) qsToRecarray() (in module PYME.misc.djangoRecarray) qtBranchNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtLeafNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtNode (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) qtRec (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF) QTRendererNode (class in PYME.Analysis.points.QuadTree.QTrend) qtRoot (class in PYME.Analysis.points.QuadTree.pointQT) (class in PYME.Analysis.points.QuadTree.pointQTF)

quad_rot_surf_misfit() (in module PYME.Analysis.points.surfit) quad_surf_mf() (in module PYME.Analysis.points.arcfit.arcmf) quad_surf_mf_fpos() (in module PYME.Analysis.points.arcfit.arcmf) QuadTreeRenderer (class in PYME.LMVis.renderers) QuadTreeSettings (class in PYME.LMVis.quadTreeSettings) QuadTreeSettingsPanel (class in PYME.LMVis.quadTreeSettings) queue_action() (PYME.Acquire.ActionManager.ActionManagerWebWrapper method) queue_actions() (PYME.Acquire.ActionManager.ActionManager method) (PYME.Acquire.ActionManager.ActionManagerWebWrapper method) queue_base_tile_update() (PYME.Analysis.distributed_pyramid.PartialPyramid method) queue_two_opt() (PYME.Analysis.points.traveling_salesperson.queue_opt.TSPQueue method) QueueAction() (PYME.Acquire.ActionManager.ActionManager method) QueueMDHandler (class in PYME.IO.MetaDataHandler) QuiverEngine (class in PYME.LMVis.layers.quiver) QuiverRenderLayer (class in PYME.LMVis.layers.quiver)

R

R (PYME.DSView.modules.blobMeasure.DataBlock property) r (PYME.DSView.modules.blobMeasure.DataBlock property) r_sph_harm() (in module PYME.Analysis.points.spherical_harmonics) radial_analysis_tabular() (in module PYME.Analysis.points.rings) radial_distance_to_shell() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) RadialDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) radialDistN() (PYME.DSView.modules.blobMeasure.BlobObject method) RaggedBase (class in PYME.IO.ragged) RaggedCache (class in PYME.IO.ragged) RaggedJSON (class in PYME.IO.ragged) RaggedVLArray (class in PYME.IO.ragged) RandomSelectionFilter (class in PYME.IO.tabular) randomSelectionFilter() (in module PYME.IO.tabular) RandomSource (class in PYME.IO.tabular) (class in PYME.simulation.pointsets) randomSource() (in module PYME.IO.tabular) RangeParam (class in PYME.localization.MetaDataEdit) rasterize() (PYME.DSView.modules.annotation.AnnotationList method) Rater (class in PYME.cluster.rulenodeserver) read() (in module PYME.IO.unifiedIO) (PYME.Acquire.webui.ipy.TTYDummy method) (PYME.misc.TiSettings.TiSettings method) read3DTiff() (in module PYME.IO.FileUtils.readTiff) read_bead_data() (in module PYME.Analysis.points.twoColour) read_cached_zar() (in module PYME.misc.zemax) read_cat_from_lines() (in module PYME.misc.read_agf) read_cat_from_string() (in module PYME.misc.read_agf) read_file() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) read_file_with_path() (PYME.LMVis.shader_programs.shader_loader.ShaderLoader method) read_glasscat() (in module PYME.misc.read_agf) read_h5f_cols() (in module PYME.Analysis.points.twoColour) read_shader() (in module PYME.LMVis.shader_programs.shader_program) readbytes() (in module PYME.contrib.lzw) readline() (PYME.Acquire.webui.ipy.TTYDummy method) readSpeckles() (in module PYME.IO.FileUtils.readSpeckle) readZar() (in module PYME.misc.zemax) rebin() (in module PYME.Analysis.Colocalisation.distColoc) rebuild() (PYME.ui.MetadataTree.MetadataPanel method) recArrayInput() (in module PYME.IO.tabular) RecArraySource (class in PYME.IO.tabular) receiver() (in module PYME.contrib.dispatch.dispatcher) RecipePusher (class in PYME.cluster.HTTPRulePusher) (class in PYME.cluster.HTTPTaskPusher) RecipeRule (class in PYME.cluster.rules) RecipeRuleFactory (class in PYME.cluster.rules) RecipeTaskError (class in PYME.cluster.taskWorkerHTTP) recolor() (in module PYME.Analysis.BleachProfile.intensProf) recommendedVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) reconstruct_quad_surf() (in module PYME.Analysis.points.surfit) reconstruct_quad_surf_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_P() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_P_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_Pr() (in module PYME.Analysis.points.surfit) reconstruct_quad_surfaces_Pr_region_cropped() (in module PYME.Analysis.points.surfit) reconstruct_shell() (in module PYME.Analysis.points.spherical_harmonics) reconstruct_tiles_deterministic() (PYME.DSView.modules.tiling.Tiler method) reconstruct_tiles_events() (PYME.DSView.modules.tiling.Tiler method) record_pyme_version() (PYME.IO.MetaDataHandler.MDHandlerBase method) recreate() (PYME.IO.MetaDataHandler.CachingMDHandler class method) (PYME.misc.eventSpy.eventInfo method) recvMember() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.TempDirCollection method) Red() (in module PYME.misc.colormaps) redimension() (in module PYME.DSView.modules.redimension) RedimensionDialog (class in PYME.DSView.modules.redimension) Redraw() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) reduce_catalog() (in module PYME.misc.read_agf) refill() (PYME.LMVis.Extras.animation.VideoPanel method) refine_zernike() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) refine_zernikes() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) refr() (PYME.ui.fastGraph.SpecGraphPanel method) refract (PYME.misc.zemax.DefaultGlass attribute) RefrData() (PYME.DSView.displaySettingsPanel.dispSettingsPanel method) (PYME.DSView.displaySettingsPanel.dispSettingsPanel2 method) refresh() (PYME.Acquire.ui.focus_lock_gui.FocusLockPanel method) refresh_canvas() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) refresh_choices() (PYME.simulation.pointsets.ImageSource method) (PYME.simulation.pointsets.PointSource method) refresh_settings() (PYME.IO.buffers.backgroundBufferM method) refresh_warpdrive() (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory method) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory method) RefreshHists() (PYME.DSView.DisplayOptionsPanel.OptionsPanel method) RefreshRows() (PYME.contrib.listctrlMixins.ListRowHighlighter method) RefreshScrollbars() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) RefreshView() (PYME.LMVis.visCore.VisGUICore method) reg_of() (in module PYME.Analysis.optic_flow) RegenFilter() (PYME.LMVis.visCore.VisGUICore method) RegenSizer() (PYME.ui.autoFoldPanel.foldPanel method) (PYME.ui.manualFoldPanel.foldPanel method) register() (PYME.cluster.rules.RuleGroupWatcher method) (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) register_acquisition_type() (PYME.Acquire.SpoolController.SpoolController method) register_acquisition_ui() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) register_camera() (PYME.Acquire.microscope.Microscope method) register_cmap() (PYME.misc.colormaps.CMapDict method) register_endpoint() (in module PYME.util.webframework) register_event_handler() (in module PYME.Acquire.eventLog) register_file() (PYME.IO.cluster_directory.DirectoryInfoManager method) register_piezo() (PYME.Acquire.microscope.Microscope method) register_service() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) registerChangeListener() (PYME.Acquire.microscope.StateManager method) registerHandler() (PYME.Acquire.microscope.StateManager method) rel_path_as_posix() (in module PYME.IO.FileUtils.nameUtils) release() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.FlatFieldDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) release_rule_tasks() (PYME.cluster.ruleserver.RuleServer method) release_VM() (in module PYME.IO.DataSources.BioformatsDataSource) reloadData() (PYME.IO.DataSources.AlignDataSource.DataSource method) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) (PYME.IO.DataSources.BioformatsDataSource.DataSource method) (PYME.IO.DataSources.BufferedDataSource.DataSource method) (PYME.IO.DataSources.ConcatenatedDataSource.DataSource method) (PYME.IO.DataSources.CropDataSource.DataSource method) (PYME.IO.DataSources.DcimgDataSource.DataSource method) (PYME.IO.DataSources.HDFDataSource.DataSource method) (PYME.IO.DataSources.ImageSeriesDataSource.DataSource method) (PYME.IO.DataSources.MultiviewDataSource.DataSource method) (PYME.IO.DataSources.OBFDataSource.DataSource method) (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource method) (PYME.IO.DataSources.TiffDataSource.DataSource method) (PYME.IO.DataSources.TileDataSource.TileDataSource method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) remap_data_2d() (in module PYME.Analysis.composite) remap_splitter_coords() (in module PYME.localization.splitting) remap_splitter_coords_() (in module PYME.localization.splitting) RemoteSpoolSeries (class in PYME.Acquire.actions) remove() (PYME.Acquire.ActionManager.MutablePriorityQueue method) (PYME.Analysis.tile_pyramid.TileCache method) remove_actions() (PYME.Acquire.ActionManager.ActionManager method) remove_event_handler() (in module PYME.Acquire.eventLog) remove_inactive_services() (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) remove_newlines() (in module PYME.DSView.modules.psfTools) remove_service() (PYME.misc.pyme_zeroconf.ZCListener method) removeFrame() (PYME.IO.buffers.bgFrameBuffer method) (PYME.IO.buffers.bgFrameBufferC method) (PYME.IO.DataSources.BGSDataSource.bgFrameBuffer method) removeInternalFaces() (in module PYME.Analysis.points.gen3DTriangs) rend() (in module PYME.Analysis.points.surfit) rend_density_estimate() (in module PYME.LMVis.visHelpers) render() (PYME.DSView.modules.annotation.AnnotateBase method) (PYME.LMVis.Extras.annotation.AnnotationOverlayLayer method) (PYME.LMVis.layers.AxesOverlayLayer.AxesOverlayLayer method) (PYME.LMVis.layers.base.BaseEngine method) (PYME.LMVis.layers.base.BaseLayer method) (PYME.LMVis.layers.base.EngineLayer method) (PYME.LMVis.layers.image_layer.ImageEngine method) (PYME.LMVis.layers.labels.LabelLayer method) (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer method) (PYME.LMVis.layers.mesh.FlatFaceEngine method) (PYME.LMVis.layers.mesh.OITShadedFaceEngine method) (PYME.LMVis.layers.mesh.ShadedFaceEngine method) (PYME.LMVis.layers.mesh.TesselEngine method) (PYME.LMVis.layers.mesh.WireframeEngine method) (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) (PYME.LMVis.layers.pointcloud.Points3DEngine method) (PYME.LMVis.layers.quiver.QuiverEngine method) (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) (PYME.LMVis.layers.SelectionOverlayLayer.SelectionOverlayLayer method) (PYME.LMVis.layers.text.Text method) (PYME.LMVis.layers.tracks.Track3DEngine method)

renderFit() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) renderTetrahedra() (in module PYME.Analysis.points.gen3DTriangs) RenderTetrahedra() (in module PYME.Analysis.points.SoftRend.triRend) rendGauss() (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) rendGauss3D() (in module PYME.LMVis.visHelpers) rendGaussNested() (in module PYME.LMVis.rendGauss) rendGaussNestedPS() (in module PYME.LMVis.rendGauss) rendGaussNestedXYCorr() (in module PYME.LMVis.rendGauss) rendGaussP() (in module PYME.LMVis.rendGauss) rendGaussProd() (in module PYME.LMVis.visHelpers) rendHist() (in module PYME.LMVis.rendGauss) (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendHist3D() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendHistF() (in module PYME.LMVis.rendGauss) rendJitTet() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTri() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTri2() (in module PYME.LMVis.visHelpers) rendJitTriang() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendJitTriang2() (in module PYME.LMVis.visHelpers) rendJTet() (in module PYME.LMVis.visHelpers) rendP() (in module PYME.Analysis.Colocalisation.colocScaleDep) rendQT() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTa() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTan() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendQTe() (in module PYME.Analysis.points.QuadTree.QTrend) (in module PYME.Analysis.points.QuadTree.rendQT) rendS() (in module PYME.Analysis.Colocalisation.colocScaleDep) rendSurfs() (in module PYME.Analysis.points.surfit) rendSurfsT() (in module PYME.Analysis.points.surfit) rendTri() (in module PYME.LMVis.visHelpers) (in module PYME.LMVis.visHelpersMin) rendTri2() (in module PYME.LMVis.visHelpers) rendVoronoi() (in module PYME.LMVis.visHelpers) replace_names() (in module PYME.IO.csv_flavours) replNoneWith1() (in module PYME.localization.FitFactories.fitCommon) (in module PYME.localization.FitFactories.Gauss3DFitR) (in module PYME.localization.FitFactories.SpecGaussFitFR) (in module PYME.localization.FitFactories.SplitterMultifitSR) (in module PYME.localization.FitFactories.SplitterObjFindR) (in module PYME.localization.FitFactories.SplitterShiftEstFR) report() (in module PYME.util.mProfile.mProfile) (in module PYME.util.mProfile.p) requeue_missed() (PYME.Acquire.ui.tile_panel.MultiwellProtocolQueuePanel method) requiredVariables (PYME.LMVis.importTextDialog.ColumnMappingDialog attribute) reset() (PYME.misc.TiffImagePlugin.ImageFileDirectory method) ResetDataStack() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) ResetSelection() (PYME.DSView.displayOptions.DisplayOpts method) resident() (in module PYME.misc.memUsage) resize_to_smallest() (PYME.Acquire.webui.ipy.IPYWithClients method) resizeColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) resizeLastColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) resizePSF() (in module PYME.Deconv.wiener) resolve() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) ResponseNotAllowed() (in module PYME.cluster.dataserver_wsgi) ResponseNotFound() (in module PYME.cluster.dataserver_wsgi) ResponseOK() (in module PYME.cluster.dataserver_wsgi) result_params (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) results (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) ResultsFilter (class in PYME.IO.tabular) resultsFilter() (in module PYME.IO.tabular) ResultsView (class in PYME.DSView.modules.sheetView) RetrieveObjects() (PYME.DSView.modules.blobMeasure.Measurements method) retrieveValue() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.ShiftFieldParam method) (PYME.localization.MetaDataEdit.StringParam method) return_home() (PYME.Acquire.Utils.pointScanner.Scanner method) returnLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) reversal_swap() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) reversal_two_opt() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) rgb_to_hls() (in module PYME.misc.colorsys) rgb_to_hsv() (in module PYME.misc.colorsys) rgb_to_yiq() (in module PYME.misc.colorsys) RichardsonLucyDeconvolution (class in PYME.Deconv.richardsonLucy) right() (PYME.LMVis.views.View method) ring() (in module PYME.Analysis.points.rings) ring_corr() (in module PYME.Analysis.points.rings) ring_corr_goal() (in module PYME.Analysis.points.rings) ring_paint() (in module PYME.Analysis.points.rings) ring_theory() (in module PYME.Analysis.points.rings) ring_theory_cdf() (in module PYME.Analysis.points.rings) RingCorrelator (class in PYME.DSView.modules.fourierRingCorrelation) ripleys_dh() (in module PYME.Analysis.points.ripleys) ripleys_dl() (in module PYME.Analysis.points.ripleys) ripleys_h() (in module PYME.Analysis.points.ripleys) ripleys_k() (in module PYME.Analysis.points.ripleys) ripleys_k_from_mask_points() (in module PYME.Analysis.points.ripleys) ripleys_l() (in module PYME.Analysis.points.ripleys) rlbead (class in PYME.Deconv.richardsonLucy) (class in PYME.Deconv.richardsonLucyMV) (class in PYME.Deconv.richardsonLucyMVM) robustLin2Lhood() (in module PYME.Analysis.points.twoColour) robustLin3Lhood() (in module PYME.Analysis.points.twoColour) robustLin3zLhood() (in module PYME.Analysis.points.twoColour) robustLinLhood() (in module PYME.Analysis.points.twoColour) roi_at() (in module PYME.Analysis.angleFilter) roi_crop_image() (in module PYME.IO.DataSources.CropDataSource) roi_list (PYME.tileviewer.tileviewer.TileServer attribute) rootdir() (PYME.cluster.webdav.DirCollection method) ROT90 (PYME.DSView.displayOptions.DisplayOpts attribute) round_sf() (in module PYME.reports.filters) Rp() (in module PYME.misc.snells) Rs() (in module PYME.misc.snells) Rule (class in PYME.cluster.rules) (class in PYME.cluster.ruleserver) rule_type (PYME.cluster.rules.RuleFactory property) RuleFactory (class in PYME.cluster.rules) RuleGroupWatcher (class in PYME.cluster.rules) RuleServer (class in PYME.cluster.ruleserver) RuleWatcher (class in PYME.cluster.rules) run() (PYME.Acquire.acquire_server.AcquireHTTPServerMixin method) (PYME.Acquire.acquiremainframe.PYMEMainFrame method) (PYME.Acquire.acquirewx.AcquireWxHTTPServer method) (PYME.Acquire.ExecTools.GUIInitTask method) (PYME.cluster.cluster_of_one.ClusterOfOne method) (PYME.cluster.HTTPDataServer.statusPoller method) (PYME.cluster.rulenodeserver.ServerThread method) (PYME.cluster.ruleserver.ServerThread method) (PYME.Deconv.decThread.decThread method) (PYME.IO.testClusterSpooling.TestSpooler method) (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.wxThread.wxThread method) (PYME.util.mProfile.tProfile.T method) run_recipe_for_locations (PYME.tileviewer.tileviewer.TileServer attribute) run_t() (in module PYME.Analysis.points.SoftRend.testTetrahedra) runTests() (in module PYME.Analysis.PSFEst.psfQuality) (in module PYME.util.mProfile.tProfile) (PYME.localization.Test.fitTestJig.fitTestJig method) (PYME.localization.Test.fitTestJigSCMOS.fitTestJig method) (PYME.localization.Test.fitTestJigWC.fitTestJig method)

S

SA (PYME.DSView.modules.blobMeasure.DataBlock property) safe_read() (in module PYME.IO.unifiedIO) SampleInfoDialog (class in PYME.Acquire.sampleInformation) SarcomereChecker (class in PYME.Acquire.Utils.sarcSpacing) satCheck() (PYME.Acquire.microscope.Microscope method) save() (PYME.Analysis.svmSegment.svmClassifier method) (PYME.Analysis.tile_pyramid.TileCache method) (PYME.Analysis.Tracking.trackUtils.Clump method) Save() (PYME.IO.image.ImageStack method) save() (PYME.IO.image.ImageStack method) (PYME.LMVis.Extras.animation.VideoPanel method) (PYME.misc.TiffImagePlugin.ImageFileDirectory method) save_as_png() (in module PYME.DSView.modules.arrayView) save_as_series_of_png() (in module PYME.DSView.modules.arrayView) save_attachments() (PYME.contrib.gohlke.czifile.CziFile method) save_ply() (in module PYME.IO.FileUtils.ply) save_session() (PYME.LMVis.visCore.VisGUICore method) save_stl() (PYME.DSView.modules.vis3D.Visualiser method) save_stl_binary() (in module PYME.IO.FileUtils.stl) save_surface() (in module PYME.LMVis.Extras.extra_layers) (PYME.DSView.modules.vis3D.MeshViewFrame method) save_tile() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) save_u3d() (PYME.DSView.modules.vis3D.Visualiser method) save_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) save_wisdom() (in module PYME.Deconv.fftwWisdom) save_x3d() (PYME.DSView.modules.vis3D.Visualiser method) saveBlobs() (in module PYME.DSView.modules.extractBlobs) saved (PYME.Analysis.tile_pyramid.CacheEntry attribute) saveDeconvolution() (PYME.DSView.modules.deconvolution.Deconvolver method) saveFilter() (in module PYME.IO.FileUtils.h5rToTxt) saveFits() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) SaveMetadata() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) (PYME.LMVis.visCore.VisGUICore method) SavePerspective() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) savePositions() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) saveResultsToFile() (PYME.localization.autopsf.autopsf.ZernikePSFModel method) saveShiftmaps() (PYME.DSView.modules.blobFinding.BlobFinder method) (PYME.DSView.modules.shiftfield_estimation.BlobFinder method) saveTiffMultipage() (in module PYME.IO.FileUtils.saveTiffStack) sc (PYME.Analysis.points.twoColour.lin3Model attribute) (PYME.Analysis.points.twoColour.lin3zModel attribute) scalar_column_source() (in module PYME.IO.tabular) scalar_dict_source() (in module PYME.IO.tabular) scale (PYME.DSView.arrayViewPanel.ArrayViewPanel property) scale() (in module PYME.LMVis.mv_math) scale_m() (in module PYME.LMVis.mv_math) ScaleBarOverlay (class in PYME.DSView.overlays) ScaleBarOverlayLayer (class in PYME.LMVis.layers.ScaleBarOverlayLayer) ScaleBoxOverlayLayer (class in PYME.LMVis.layers.ScaleBoxOverlayLayer) ScaleBoxPanel (class in PYME.LMVis.Extras.scaleBox) scaled_projection() (in module PYME.Analysis.points.coordinate_tools) scaled_shell_from_hdf() (in module PYME.Analysis.points.spherical_harmonics) ScaledShell (class in PYME.Analysis.points.spherical_harmonics) scaleFactor (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) scaling (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) scaling_factors (PYME.Analysis.points.spherical_harmonics.SHShell property) SCAN_MODES (PYME.Acquire.stackSettings.StackSettings attribute) Scanner (class in PYME.Acquire.Utils.pointScanner) ScannerPanel (class in PYME.Acquire.ui.scanner_panel) scatterdens() (in module PYME.LMVis.Extras.multiColourAnalysis) schemes() (PYME.DSView.modules.blobMeasure.Measurements method) schemes3D() (PYME.DSView.modules.blobMeasure.Measurements method) scope_state_longpoll() (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) scope_tweet() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) Scroll() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) ScrolledImagePanel (class in PYME.DSView.scrolledImagePanel) se_diff_l2_mean() (in module PYME.Analysis.BleachProfile.rollins) secondaryAxis (PYME.DSView.modules.blobMeasure.DataBlock property) sefm() (in module PYME.Analysis.BleachProfile.rollins) segment() (in module PYME.Analysis.points.EdgeDB.edgeDB) (in module PYME.Analysis.points.EdgeDB.segment) (in module PYME.Analysis.points.gen3DTriangs) (PYME.Analysis.points.EdgeDB.edges.EdgeDB method) SegmentationPanel (class in PYME.DSView.modules.segmentation) segmenter (class in PYME.Analysis.points.segmentLL) Segmenter (class in PYME.DSView.modules.segmentation) segmentNR() (in module PYME.Analysis.points.gen3DTriangs) segments() (PYME.contrib.gohlke.czifile.CziFile method) select_annotation() (PYME.DSView.modules.annotation.AnnotateBase method) selectBeforePopup() (in module PYME.contrib.listctrlMixins) Selection (class in PYME.ui.selection) SelectionFilter (class in PYME.IO.tabular) SelectionOverlayLayer (class in PYME.LMVis.layers.SelectionOverlayLayer) SelectionSettings (class in PYME.LMVis.gl_render3D_shaders) (class in PYME.LMVis.glcanvas_core) SelfAvoidingWormlikeChain (class in PYME.simulation.wormlike2) Sellmeier() (in module PYME.misc.glassModel) send() (PYME.contrib.dispatch.dispatcher.Signal method) send_error() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) send_head() (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) send_robust() (PYME.contrib.dispatch.dispatcher.Signal method) sendData() (PYME.cluster.webdav.DirCollection method) (PYME.cluster.webdav.FileMember method) seqPanel (class in PYME.Acquire.ui.seqdialog) SeqProgressPanel (class in PYME.Acquire.ui.seqdialog) sequence_id (PYME.IO.acquisition_backends.Backend property) serialise() (PYME.Acquire.actions.Action method) (PYME.LMVis.layers.base.BaseLayer method) series (PYME.contrib.gohlke.tifffile.TIFFfile attribute) seriesName (PYME.Acquire.SpoolController.SpoolController property) server_for_chunk() (in module PYME.Analysis.distributed_pyramid) server_version (PYME.cluster.webdav.DAVRequestHandler attribute) servers (PYME.Analysis.distributed_pyramid.DistributedImagePyramid property) ServerThread (class in PYME.cluster.rulenodeserver) (class in PYME.cluster.ruleserver) set_box_dimensions() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_c() (PYME.Acquire.xyztc.XYZTCAcquisition method) set_clipping() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_clipping_uniforms() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_color() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_dim_order_and_size() (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource method) set_fitting_points() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) set_lock_mode() (PYME.DSView.modules.annotation.AnnotateBase method) set_lut() (PYME.LMVis.layers.image_layer.ImageEngine method) (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer method) set_modelviewmatrix() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_modelviewprojectionmatrix() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_normalmatrix() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_offset() (PYME.LMVis.layers.OverlayLayer.OverlayLayer method) set_point_size() (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_protocol() (PYME.Acquire.SpoolController.ProtocolAcquisitionSettings method) set_readonly() (PYME.IO.MetaDataHandler.DictMDHandler method) set_roi_locations (PYME.tileviewer.tileviewer.TileServer attribute) set_scale_bar_depth() (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) set_scale_bar_length() (PYME.LMVis.layers.ScaleBarOverlayLayer.ScaleBarOverlayLayer method) set_server() (in module PYME.Acquire.webui) set_shader_program() (PYME.LMVis.layers.base.ShaderMixin method) (PYME.LMVis.shader_programs.GLProgram.GLProgram method) set_shiftfield() (PYME.Analysis.splitting.ShiftCorrector method) set_starts() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_t() (PYME.Acquire.xyztc.TiledXYZTCMixin method) (PYME.Acquire.xyztc.XYZTCAcquisition method) set_texture() (PYME.LMVis.layers.image_layer.ImageEngine method) (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer method) (PYME.LMVis.layers.text.Text method) set_tick_distance() (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) set_tile_source (PYME.tileviewer.tileviewer.TileServer attribute) set_values() (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) set_variables() (PYME.IO.tabular.MappingFilter method) set_view() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_x() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_y() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_view_z() (PYME.LMVis.Extras.saved_views.ViewPanel method) set_well_positions() (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) set_z() (PYME.Acquire.xyztc.XYZTCAcquisition method) SetAspect() (PYME.DSView.displayOptions.DisplayOpts method) SetBackend() (PYME.Analysis.processLogger.ContextManager method) setBackgroundBufferPCT() (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource method) (PYME.IO.DataSources.BGSDataSource.XYZTCBgsSource method) SetCameraShutter() (in module PYME.Acquire.protocol) SetCaption() (PYME.ui.manualFoldPanel.foldingPane method) SetCentredRoi() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) SetCharts() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) SetCMap() (PYME.DSView.displayOptions.DisplayOpts method) SetColor() (PYME.contrib.wxPlotPanel.PlotPanel method) setColour() (PYME.IO.tabular.ColourFilter method) SetColumnCount() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) SetContinuousMode() (in module PYME.Acquire.protocol) setCreatorChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetData() (PYME.IO.image.ImageStack method) (PYME.ui.fastGraph.FastGraphPanel method) (PYME.ui.histLimits.HistLimitPanel method) SetDataStack() (PYME.DSView.arrayViewPanel.ArrayViewPanel method) (PYME.DSView.displayOptions.DisplayOpts method) setDefaultNamespace() (in module PYME.Acquire.ExecTools) SetDirection() (PYME.Acquire.stackSettings.StackSettings method) setDyeChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetEMGain() (in module PYME.Acquire.protocol) SetEndPos() (PYME.Acquire.stackSettings.StackSettings method) setEntry() (PYME.IO.MetaDataHandler.CachingMDHandler method) (PYME.IO.MetaDataHandler.CopyOnWriteMDHandler method) (PYME.IO.MetaDataHandler.DictMDHandler method) (PYME.IO.MetaDataHandler.HDFMDHandler method) (PYME.IO.MetaDataHandler.MDHandlerBase method) (PYME.IO.MetaDataHandler.NestedClassMDHandler method) (PYME.IO.MetaDataHandler.QueueMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) setEventNumbers() (PYME.ui.filterPane.FilterPane method) SetEventSource() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) SetFilter() (PYME.Acquire.sampleInformation.VirtList method) SetFit() (PYME.LMVis.visCore.VisGUICore method) SetFitResults() (PYME.DSView.fitInfo.fitDispPanel method) SetGain() (PYME.DSView.displayOptions.DisplayOpts method) SetHighlightColor() (PYME.contrib.listctrlMixins.ListRowHighlighter method) SetHighlightMode() (PYME.contrib.listctrlMixins.ListRowHighlighter method) SetIntegTime() (in module PYME.Acquire.protocol) setItem() (PYME.Acquire.microscope.StateManager method) setItems() (PYME.Acquire.microscope.StateManager method) setMapping() (PYME.IO.tabular.MappingFilter method) (PYME.LMVis.Extras.QPobjectSegment.QPObjectSegmenter method) SetMaster() (PYME.DSView.modules.composite.CompositeDialog method) SetMessage() (PYME.Acquire.ui.splashScreen.SplashScreen method) (PYME.DSView.splashScreen.SplashScreen method) SetMinMax() (PYME.ui.histLimits.HistLimitPanel method) SetOffset() (PYME.DSView.displayOptions.DisplayOpts method) SetOrientation() (PYME.DSView.displayOptions.DisplayOpts method) SetPattern() (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) SetPercentile() (PYME.ui.histLimits.HistLimitPanel method) setPopupMenu() (PYME.contrib.listctrlMixins.ListCtrlSelectionManagerMix method) SetPos() (PYME.Acquire.microscope.Microscope method) SetPrevPos() (PYME.Acquire.stackSettings.StackSettings method) SetPropagate() (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettings method) SetRange() (PYME.DSView.eventLogViewer.eventLogPanel method) (PYME.DSView.eventLogViewer.eventLogTPanel method) setResizeColumn() (PYME.contrib.listctrlMixins.ListCtrlAutoWidthMixin method) SetResults() (PYME.DSView.fitInfo.FitInfoPanel method) setResults() (PYME.IO.tabular.FitResultsSource method) SetScale() (PYME.DSView.displayOptions.DisplayOpts method) SetScanChannel() (PYME.Acquire.stackSettings.StackSettings method) SetSelection() (PYME.DSView.displayOptions.DisplayOpts method) SetSeqLength() (PYME.Acquire.stackSettings.StackSettings method) SetShiftField() (PYME.Analysis.splitting.Unmixer method) (PYME.IO.DataSources.UnsplitDataSource.DataSource method) SetShiftmap() (PYME.DSView.modules.composite.ImageList method) SetShifts() (PYME.IO.DataSources.AlignDataSource.DataSource method) SetSlice() (PYME.DSView.displayOptions.DisplayOpts method) setSlideChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetSpoolDir() (PYME.Acquire.SpoolController.SpoolController method) SetSpoolMethod() (PYME.Acquire.SpoolController.SpoolController method) SetStartMode() (PYME.Acquire.stackSettings.StackSettings method) SetStartPos() (PYME.Acquire.stackSettings.StackSettings method) setStatus() (PYME.LMVis.statusLog.StatusLogger method) SetStatus() (PYME.LMVis.visCore.VisGUICore method) SetStatusDispFcn() (in module PYME.LMVis.statusLog) SetStepSize() (PYME.Acquire.stackSettings.StackSettings method) setStructureChoices() (PYME.Acquire.sampleInformation.SampleInfoDialog method) SetThresholdMode() (PYME.ui.histLimits.HistLimitPanel method) SetTimedSpecies() (PYME.LMVis.Extras.sequentialSpecies.TimedSpecies method) settings() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) (PYME.Acquire.stackSettings.StackSettings method) settings_dict() (PYME.LMVis.layers.base.BaseLayer method) (PYME.LMVis.layers.base.EngineLayer method) settings_longpoll() (PYME.Acquire.stackSettings.StackSettings method) settingsDB (PYME.Acquire.microscope.Microscope property) setup_logging() (in module PYME.Acquire.PYMEAcquire) setup_off_screen() (PYME.LMVis.gl_offScreenHandler.OffScreenHandler method) setValue() (PYME.Acquire.microscope.StateHandler method) SetValue() (PYME.ui.histLimits.HistLimitPanel method) SetValueAndFire() (PYME.ui.histLimits.HistLimitPanel method) SetVirtualSize() (PYME.DSView.scrolledImagePanel.ScrolledImagePanel method) SetVoxelSize() (PYME.Acquire.microscope.Microscope method) sffake (class in PYME.Analysis.points.twoColour) (class in PYME.misc.sffake) ShadedFaceEngine (class in PYME.LMVis.layers.mesh)

ShadedPointsEngine (class in PYME.LMVis.layers.pointcloud) shader_program (PYME.LMVis.layers.base.ShaderMixin property) ShaderLoader (class in PYME.LMVis.shader_programs.shader_loader) ShaderMixin (class in PYME.LMVis.layers.base) ShaderProgram (class in PYME.LMVis.shader_programs.shader_program) ShaderProgramFactory (class in PYME.LMVis.shader_programs.ShaderProgramFactory) shape (PYME.Acquire.xyztc.XYZTCAcquisition property) (PYME.Analysis.tile_pyramid.PyramidLayer property) (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.DataSources.ArrayDataSource.ArrayDataSource property) (PYME.IO.DataSources.ArrayDataSource.XYZTCArrayDataSource property) (PYME.IO.DataSources.BaseDataSource.BaseDataSource property) (PYME.IO.DataSources.BaseDataSource.XYTCDataSource property) (PYME.IO.DataSources.BaseDataSource.XYZSubvolume property) (PYME.IO.DataSources.BaseDataSource.XYZTCDataSource property) (PYME.IO.dataWrap.ListWrapper property) shell_coordinates() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) shift_and_rot_model() (in module PYME.Analysis.points.twoColour) shift_and_rot_model_eval() (in module PYME.Analysis.points.twoColour) shift_x (PYME.localization.FitFactories.FFBase.FFBase property) shift_y (PYME.localization.FitFactories.FFBase.FFBase property) ShiftCorrector (class in PYME.Analysis.splitting) ShiftFieldParam (class in PYME.localization.MetaDataEdit) ShiftItem() (PYME.DSView.modules.composite.ImageList method) ShiftmapGenerator (class in PYME.LMVis.Extras.shiftmapGenerator) ShiftmapSelectionDialog (class in PYME.DSView.modules.composite) ShiftModel (class in PYME.Analysis.points.twoColour) ShiftPanel (class in PYME.DSView.modules.composite) shininess (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) shmarray (class in PYME.util.shmarray.shmarray) SHNucleusSource (class in PYME.simulation.pointsets) shortAxisDist() (PYME.DSView.modules.blobMeasure.BlobObject method) show (PYME.ui.manualFoldPanel.CaptionButton property) Show() (PYME.DSView.displayOptions.DisplayOpts method) show() (PYME.LMVis.Extras.dockedPanel.DockedPanel static method) (PYME.LMVis.layers.ScaleBoxOverlayLayer.ScaleBoxOverlayLayer method) show_about_dlg() (in module PYME.ui.about_dlg) show_bounds (PYME.LMVis.layers.LUTOverlayLayer.LUTOverlayLayer attribute) show_box() (PYME.LMVis.Extras.scaleBox.ScaleBoxPanel method) show_lut (PYME.LMVis.layers.base.EngineLayer attribute) show_shortcuts() (in module PYME.LMVis.Extras.showShortcuts) show_traceback_dialog() (in module PYME.ui.progress) ShowDataGrid() (in module PYME.misc.editgrid) showFlow (PYME.DSView.modules.flowView.FlowView attribute) showGLFrame() (in module PYME.LMVis.gl_render3D_shaders) (in module PYME.LMVis.glcanvas_core) ShowHistLimitFrame() (in module PYME.ui.histLimits) ShowIso() (PYME.misc.VolProj.Isosurf method) ShowPreflightResults() (in module PYME.Acquire.ui.preflight) ShowProj() (PYME.misc.VolProj.Isosurf method) ShowShortcuts (class in PYME.LMVis.Extras.showShortcuts) ShowTextCtrl() (PYME.LMVis.view_clipping_pane.ClippingPanel method) SHShell (class in PYME.Analysis.points.spherical_harmonics) shutdown (PYME.Acquire.webui.ipy.IPYTermManager attribute) shutdown() (PYME.cluster.cluster_of_one.ClusterOfOne method) (PYME.cluster.rulenodeserver.ServerThread method) (PYME.cluster.ruleserver.ServerThread method) Signal (class in PYME.contrib.dispatch.dispatcher) signalFraction() (in module PYME.Analysis.thresholding) sim_params (PYME.localization.Test.fitTestJigSCMOS.fitTestJig property) sim_pic() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) SimpleLayer (class in PYME.LMVis.layers.base) SimpleMDHandler (class in PYME.IO.MetaDataHandler) SimpleSampleInfoPanel (class in PYME.Acquire.sampleInformation) simplify_catalog() (in module PYME.misc.read_agf) SimultaeneousSpoolSeries (class in PYME.Acquire.actions) Single() (PYME.Acquire.zScanner.zScanner method) SingleTargetTimer() (PYME.Acquire.event_loop.EventLoop method) Singleton (class in PYME.Analysis.points.features.metal) SIUnit (class in PYME.IO.FileUtils.obf_support) size (PYME.IO.clusterListing.FileInfo attribute) (PYME.ui.layerFoldPanel.LUTBitmap property) (PYME.ui.manualFoldPanel.CaptionButton property) size_x() (in module PYME.Analysis.PSFEst.psfQuality) sizeC (PYME.IO.DataSources.BaseDataSource.XYTCDataSource attribute) (PYME.IO.DataSources.BGSDataSource.XTZCBackgroundSource property) sizeX (PYME.DSView.modules.pupilTools.PupilTools attribute) sizeZ (PYME.DSView.modules.pupilTools.PupilTools attribute) SLICE_XY (PYME.DSView.displayOptions.DisplayOpts attribute) SLICE_XZ (PYME.DSView.displayOptions.DisplayOpts attribute) SLICE_YZ (PYME.DSView.displayOptions.DisplayOpts attribute) SliceBuffer (class in PYME.IO.buffers) sliceChoices (PYME.DSView.DisplayOptionsPanel.OptionsPanel attribute) sliceSize (PYME.IO.image.ImageStack property) slidePanel (class in PYME.Acquire.sampleInformation) SlowComputation (class in PYME.ui.progress) snake_refine_trace() (PYME.DSView.modules.annotation.AnnotateBase method) sorted_selection (PYME.DSView.displayOptions.DisplayOpts property) SortListItems() (PYME.contrib.listctrlMixins.ColumnSorterMixin method) source (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) sources (PYME.LMVis.Extras.pointSetGeneration.Generator attribute) SpatialConvolutionMapping (class in PYME.Deconv.dec) SpecGraphPanel (class in PYME.ui.fastGraph) SpeciesDialog (class in PYME.LMVis.Extras.sequentialSpecies) sphere_expansion() (in module PYME.Analysis.points.spherical_harmonics) sphere_expansion_clean() (in module PYME.Analysis.points.spherical_harmonics) SpheresEngine (class in PYME.LMVis.layers.pointcloud) spherical_to_cartesian() (in module PYME.Analysis.points.coordinate_tools) SphericalHarmonicShellManager (class in PYME.LMVis.Extras.spherical_harmonics) SplashPanel (class in PYME.Acquire.ui.splashScreen) (class in PYME.DSView.splashScreen) SplashScreen (class in PYME.Acquire.ui.splashScreen) (class in PYME.DSView.splashScreen) split_cluster_url() (in module PYME.IO.unifiedIO) split_image() (in module PYME.localization.splitting) split_path() (PYME.cluster.webdav.DAVRequestHandler method) split_points_by_grid() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) split_points_kmeans() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) splitattrs() (in module PYME.cluster.webdav) splitGaussWeightedMisfit() (in module PYME.localization.cModels.gauss_app) SplittingInfo (class in PYME.Analysis.splitting) splWrap() (in module PYME.localization.FitFactories.SplitterFitFNR) (in module PYME.localization.FitFactories.SplitterFitFusionR) (in module PYME.localization.FitFactories.SplitterFitScavNR) spoof_focus_events_from_ontarget() (in module PYME.Analysis.piezo_movement_correction) SpoolController (class in PYME.Acquire.SpoolController) SpoolControllerWrapper (class in PYME.Acquire.SpoolController) spoolData() (PYME.IO.clusterExport.ImageFrameSource method) Spooler (class in PYME.IO.HTTPSpooler_v2) (class in PYME.IO.Spooler) spoolImageFromFile() (PYME.IO.clusterExport.ImageFrameSource method) spooling_finished() (PYME.Acquire.acquire_client.AcquireClient method) spooling_info() (PYME.Acquire.acquire_client.AcquireClient method) spooling_paused() (PYME.Acquire.frameWrangler.FrameWrangler method) spooling_stopped() (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.IO.testClusterSpooling.DummyFramewrangler method) SpoolingPane (class in PYME.Acquire.ui.spool_panel) SpoolLocalLocalizationRule (class in PYME.cluster.rules) SpoolLocalLocalizationRuleFactory (class in PYME.cluster.rules) SpoolSeries (class in PYME.Acquire.actions) SpoolStopped() (PYME.Acquire.SpoolController.SpoolController method) SQLiteNS (class in PYME.misc.sqlite_ns) SqliteTileIO (class in PYME.Analysis.tile_pyramid) Stack (class in PYME.IO.FileUtils.obf_support) stack_footer_v1_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v1a_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v2_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v3_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v4_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v5_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v5a_unpack() (in module PYME.IO.FileUtils.obf_support) stack_footer_v6_unpack() (in module PYME.IO.FileUtils.obf_support) stack_header_unpack() (in module PYME.IO.FileUtils.obf_support) StackSettings (class in PYME.Acquire.stackSettings) stacksize() (in module PYME.misc.memUsage) StageLeveler (class in PYME.Acquire.stage_leveling) start (PYME.contrib.gohlke.czifile.CziFile attribute) (PYME.ui.selection.Selection property) start() (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.strip_tiler.StripTiler method) (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) (PYME.Acquire.Utils.tiler.TileAcquisition method) (PYME.Acquire.xyztc.XYZTCAcquisition method) Start() (PYME.Acquire.zScanner.zScanner method) START_AND_END (PYME.Acquire.stackSettings.StackSettings attribute) start_ind (PYME.Analysis.points.traveling_salesperson.queue_opt.TSPQueue property) start_ipython() (PYME.Acquire.webui.ipy.IPY method) start_next() (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) start_poll() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) start_reading() (PYME.Acquire.webui.ipy.IPYTermManager method) start_spooling() (PYME.Acquire.acquire_client.AcquireClient method) (PYME.Acquire.SpoolController.SpoolController method) (PYME.Acquire.SpoolController.SpoolControllerWrapper method) startDuplicator() (in module PYME.IO.clusterDuplication) startEstROI() (in module PYME.localization.autopsf.roifit) startFrameWrangler() (PYME.Acquire.microscope.Microscope method) startGuess() (PYME.Deconv.dec.ICTMDeconvolution method) (PYME.Deconv.richardsonLucy.RichardsonLucyDeconvolution method) StartSelection() (PYME.LMVis.imageView.ImageViewPanel method) (PYME.LMVis.imageView2.ImageViewPanel method) StartServing() (in module PYME.DSView.htmlServe) (PYME.DSView.modules.blobMeasure.Measurements method) StartSpool() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.IO.HTTPSpooler_v2.Spooler method) (PYME.IO.Spooler.Spooler method) stat() (in module PYME.IO.clusterIO) state (PYME.Acquire.acquire_client.AcquireClient property) StateAction (class in PYME.Acquire.actions) StateHandler (class in PYME.Acquire.microscope) StateManager (class in PYME.Acquire.microscope) StaticFileHandler (class in PYME.util.webframework) status() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Acquire.xyztc.XYZTCAcquisition method) (PYME.cluster.rules.Rule method) (PYME.cluster.ruleserver.RuleServer method) (PYME.IO.Spooler.Spooler method) StatusBarUpdate() (PYME.Acquire.acquiremainframe.PYMEMainFrame method) StatusInfo (class in PYME.cluster.status) StatusLogger (class in PYME.LMVis.statusLog) statusPoller (class in PYME.cluster.HTTPDataServer) steplength (PYME.simulation.pointsets.WormlikeSource attribute) stokesEinstein() (in module PYME.Analysis.Tracking.msd) stop() (PYME.Acquire.acquisition_base.AcquisitionBase method) (PYME.Acquire.event_loop.EventLoop method) (PYME.Acquire.frameWrangler.FrameWrangler method) (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) (PYME.Acquire.Utils.pointScanner.Scanner method) (PYME.Acquire.Utils.tiler.MultiwellCircularTiler method) (PYME.Acquire.Utils.tiler.TileAcquisition method) (PYME.Acquire.xyztc.XYZTCAcquisition method) Stop() (PYME.Acquire.zScanner.zScanner method) stop() (PYME.cluster.HTTPDataServer.statusPoller method) (PYME.cluster.rulenodeserver.NodeServer method) (PYME.cluster.ruleserver.RuleServer method) stop_spooling() (PYME.Acquire.SpoolController.SpoolControllerWrapper method) stopDuplicator() (in module PYME.IO.clusterDuplication) StopSpool() (PYME.Acquire.protocol_acquisition.ProtocolAcquisition method) (PYME.IO.Spooler.Spooler method) StopSpooling() (PYME.Acquire.SpoolController.SpoolController method) storage (PYME.Acquire.acquisition_base.AcquisitionBase property) store_frame() (PYME.IO.acquisition_backends.Backend method) (PYME.IO.acquisition_backends.ClusterBackend method) (PYME.IO.acquisition_backends.HDFBackend method) (PYME.IO.acquisition_backends.MemoryBackend method) (PYME.IO.acquisition_backends.TiffFolderBackend method) store_scan() (PYME.Acquire.stage_leveling.StageLeveler method) Str (in module PYME.misc.mock_traits) str_presenter() (in module PYME.cluster.taskWorkerHTTP) Stream (class in PYME.IO.cluster_streaming) Streamer (class in PYME.IO.cluster_streaming) strength (PYME.DSView.modules.psfGeneration.PhaseRampPupil attribute) strict_options() (in module PYME.IO.csv_flavours) StringParam (class in PYME.localization.MetaDataEdit) StripTiler (class in PYME.Acquire.Utils.strip_tiler) stylesheet (PYME.util.mProfile.colorize_db_t.Parser attribute) subblock_directory (PYME.contrib.gohlke.czifile.CziFile attribute) subblocks() (PYME.contrib.gohlke.czifile.CziFile method) subsampidx() (in module PYME.LMVis.Extras.multiColourAnalysis) subsearch() (PYME.Analysis.PSFEst.dec.dec method) (PYME.Deconv.dec.ICTMDeconvolution method) suggest_cluster_filename() (in module PYME.IO.clusterExport) sum (PYME.DSView.modules.blobMeasure.DataBlock property) SupertileDataSource (class in PYME.IO.DataSources.SupertileDatasource) Surface (class in PYME.misc.zemax) SurfaceFitter (class in PYME.LMVis.Extras.surface_fitting) svm_segment() (PYME.DSView.modules.annotation.Annotater method) svmClassifier (class in PYME.Analysis.svmSegment) sync_to_display_opts() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) Syncer (class in PYME.DSView.modules.synchronise) Synchronise() (PYME.DSView.displayOptions.DisplayOpts method)

T

T (class in PYME.util.mProfile.tProfile) (in module PYME.Acquire.protocol) t1() (in module PYME.util.mProfile.tProfile) t_pos (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) table_representation (PYME.Analysis.points.spherical_harmonics.ScaledShell property) TablesBackend (class in PYME.Analysis.processLogger) TabularBase (class in PYME.IO.tabular) Tag (class in PYME.cluster.webdav) Tag() (PYME.Acquire.positionTracker.PositionTracker method) Task (class in PYME.misc.taskDef) task_advertisements() (PYME.cluster.ruleserver.RuleServer method) TASK_DONE (PYME.Acquire.ExecTools.BGInitTask attribute) TASK_FAILED (PYME.Acquire.ExecTools.BGInitTask attribute) TASK_INFO_DTYPE (PYME.cluster.ruleserver.IntegerIDRule attribute) TASK_RUNNING (PYME.Acquire.ExecTools.BGInitTask attribute) TaskError (class in PYME.cluster.taskWorkerHTTP) TaskListProtocol (class in PYME.Acquire.protocol) TaskListTask (class in PYME.Acquire.protocol) TaskResult (class in PYME.misc.taskDef) tasksLoop() (PYME.cluster.taskWorkerHTTP.taskWorker method) taskWorker (class in PYME.cluster.taskWorkerHTTP) te() (in module PYME.util.mProfile.mProfile) (in module PYME.util.mProfile.p) TempDirCollection (class in PYME.cluster.webdav) template (PYME.cluster.taskWorkerHTTP.RecipeTaskError attribute) (PYME.cluster.taskWorkerHTTP.TaskError attribute) template_fill() (in module PYME.cluster.rulenodeserver) TempPlotter (class in PYME.LMVis.Extras.temperaturePlot) terminate() (PYME.Acquire.webui.ipy.IPYWithClients method) tertiaryAxis (PYME.DSView.modules.blobMeasure.DataBlock property) TesselEngine (class in PYME.LMVis.layers.mesh) TesselShaderProgram (class in PYME.LMVis.shader_programs.TesselShaderProgram) test() (in module PYME.Analysis.points.EdgeDB.edgeTest) (in module PYME.contrib.pad) (in module PYME.util.shmarray.shmTest) test_function() (in module PYME.util.mProfile.tProfile) test_method() (PYME.util.mProfile.tProfile.T method) test_ps_app() (in module PYME.Analysis.PSFGen.test_ps_app) test_value (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) testObj() (in module PYME.Analysis.points.gen3DTriangs) testPattern() (in module PYME.simulation.locify) TestSpooler (class in PYME.IO.testClusterSpooling) Text (class in PYME.LMVis.layers.text) text (PYME.LMVis.layers.text.Text property) textColour (PYME.LMVis.layers.labels.LabelLayer attribute) TextEditMixin (class in PYME.contrib.listctrlMixins) (class in PYME.ui.MetadataTree) TextfileSource (class in PYME.IO.tabular) textfileSource() (in module PYME.IO.tabular) TextShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) tfoef() (in module PYME.Analysis.BleachProfile.rollins) tformat() (PYME.IO.MetaDataHandler.MDHandlerBase static method) th() (in module PYME.Analysis.angleFilter) th2() (in module PYME.Analysis.angleFilter) then() (PYME.Acquire.actions.StateAction method) Theta (PYME.DSView.modules.blobMeasure.DataBlock property) theta_t() (in module PYME.misc.snells) thiolInt() (in module PYME.Analysis.BleachProfile.deMod) thread_profiler (in module PYME.util.fProfile.fProfile) ThreadedHTTPServer (class in PYME.cluster.HTTPDataServer) ThreadProfiler (class in PYME.util.fProfile.fProfile) ThreadProfilerRegex (class in PYME.util.fProfile.fProfile) thresholdedManders() (in module PYME.Analysis.Colocalisation.correlationCoeffs) thresholds (PYME.DSView.displayOptions.DisplayOpts property) Tick() (PYME.Acquire.ActionManager.ActionManager method) (PYME.Acquire.positionTracker.PositionTracker method) (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.seqdialog.SeqProgressPanel method) (PYME.Acquire.ui.splashScreen.SplashScreen method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) tick() (PYME.Acquire.Utils.MultiPointScanner.PointScanner method) (PYME.Acquire.Utils.pointScanner.PointScanner3D method) Tick() (PYME.Deconv.deconvDialogs.DeconvProgressDialog method) (PYME.Deconv.deconvDialogs.DeconvProgressPanel method) (PYME.DSView.modules.segmentation.SegmentationPanel method) (PYME.DSView.splashScreen.SplashScreen method) TIFFfile (class in PYME.contrib.gohlke.tifffile) TiffFolderBackend (class in PYME.IO.acquisition_backends) TiffMP (class in PYME.IO.FileUtils.saveTiffStack) TiffSeriesExporter (class in PYME.IO.dataExporter) TiffStackExporter (class in PYME.IO.dataExporter) tile_coords (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource property) tile_coords_um (PYME.IO.DataSources.SupertileDatasource.SupertileDataSource property) tile_exists() (PYME.Analysis.tile_pyramid.NumpyTileIO method) (PYME.Analysis.tile_pyramid.SqliteTileIO method) (PYME.Analysis.tile_pyramid.TileIO method) tile_pyramid() (in module PYME.Analysis.tile_pyramid) TileAcquisition (class in PYME.Acquire.Utils.tiler) TileCache (class in PYME.Analysis.tile_pyramid) TileDataSource (class in PYME.IO.DataSources.TileDataSource) TiledXYZTCMixin (class in PYME.Acquire.xyztc) TiledZStackAcquisition (class in PYME.Acquire.xyztc) TileIO (class in PYME.Analysis.tile_pyramid)

TilePanel (class in PYME.Acquire.ui.tile_panel) Tiler (class in PYME.DSView.modules.tiling) Tiler() (in module PYME.Acquire.Utils.tiler) TileServer (class in PYME.tileviewer.tileviewer) TileSettingsUI (class in PYME.Acquire.ui.tilesettingsui) time_block_subset() (in module PYME.LMVis.Extras.subsets) TimedSpecies (class in PYME.LMVis.Extras.sequentialSpecies) timeout (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) timeout_two_opt() (in module PYME.Analysis.points.traveling_salesperson.two_opt) timeoutTesting (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler attribute) times_to_frames() (in module PYME.Analysis.piecewiseMapping) TimeSettings() (in module PYME.Acquire.xyztc) TiSettings (class in PYME.misc.TiSettings) to_bytes() (in module PYME.IO.clusterIO) to_csv() (PYME.IO.tabular.TabularBase method) to_hdf() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) (PYME.IO.ragged.RaggedBase method) (PYME.IO.tabular.TabularBase method) to_JSON() (PYME.Analysis.points.twoColour.ShiftModel method) (PYME.IO.events.MemoryEventLogger method) (PYME.IO.MetaDataHandler.MDHandlerBase method) to_json() (PYME.IO.ragged.RaggedBase method) to_JSON() (PYME.IO.tabular.TabularBase method) to_json() (PYME.LMVis.views.VideoView method) (PYME.LMVis.views.View method) to_pandas() (PYME.IO.tabular.TabularBase method) to_pyoptic() (PYME.misc.zemax.ZMX method) to_recarray() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) (PYME.IO.events.MemoryEventLogger method) (PYME.IO.tabular.TabularBase method) to_string() (PYME.cluster.taskWorkerHTTP.TaskError method) toDataFrame() (PYME.IO.tabular.TabularBase method) toggle_roi (PYME.tileviewer.tileviewer.TileServer attribute) ToggleFold() (PYME.ui.manualFoldPanel.foldingPane method) ToggleItem() (PYME.contrib.listctrlMixins.CheckListCtrlMixin method) TogglePin() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) top() (PYME.LMVis.views.View method) toPyOptic() (PYME.misc.zemax.ZMX method) total_frames (PYME.cluster.rules.LocalisationRule property) (PYME.cluster.rules.SpoolLocalLocalizationRule property) total_nglasses() (in module PYME.misc.read_agf) toXls() (PYME.DSView.modules.blobMeasure.Measurements method) ToZarr() (PYME.DSView.modules.neuroglancer.Neuroglancer method) tp (PYME.DSView.displayOptions.DisplayOpts property) Tp() (in module PYME.misc.snells) tqPopFcn() (in module PYME.localization.remFitBuf) TracebackDialog (class in PYME.ui.progress) traceModel() (in module PYME.Analysis.BleachProfile.intensProf) traceModelDE() (in module PYME.Analysis.BleachProfile.intensProf) traceModelDE1() (in module PYME.Analysis.BleachProfile.intensProf) TraceROISelectPanel (class in PYME.Acquire.ui.intensity_trace) Track (class in PYME.Analysis.Tracking.trackUtils) Track3DEngine (class in PYME.LMVis.layers.tracks) Tracker (class in PYME.Analysis.Tracking.tracking) TrackerPanel (class in PYME.Acquire.positionTracker) TrackerPlotPanel (class in PYME.Acquire.positionTracker) TrackManager (class in PYME.Analysis.Tracking.trackUtils) TrackRenderLayer (class in PYME.LMVis.layers.tracks) train() (PYME.Analysis.svmSegment.svmClassifier method) train_naive_bayes() (PYME.DSView.modules.annotation.Annotater method) train_svm() (PYME.DSView.modules.annotation.Annotater method) trainAndClassify() (PYME.Analysis.svmSegment.svmClassifier method) trainClassifier() (in module PYME.Analysis.svmSegment) trajectory (PYME.Analysis.Tracking.trackUtils.Track property) translate() (in module PYME.LMVis.mv_math) translate_m() (in module PYME.LMVis.mv_math) translate_path() (PYME.cluster.dataserver_wsgi.dataserver method) (PYME.cluster.HTTPDataServer.PYMEHTTPRequestHandler method) translateSeparators() (in module PYME.IO.FileUtils.nameUtils) TransparentPointsEngine (class in PYME.LMVis.layers.pointcloud) TransparentPointShaderProgram (class in PYME.LMVis.shader_programs.DefaultShaderProgram) Triangle3DRenderer (class in PYME.LMVis.renderers) TriangleRenderer (class in PYME.LMVis.renderers) TriangleRendererW (class in PYME.LMVis.renderers) TriangleRenderLayer (class in PYME.LMVis.layers.mesh) trianglesEqual() (in module PYME.Analysis.points.gen3DTriangs) Ts() (in module PYME.misc.snells) tsoef() (in module PYME.Analysis.BleachProfile.rollins) tsp_chunk_two_opt_multiproc() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) tsp_sort() (in module PYME.Analysis.points.traveling_salesperson.sort) TSPQueue (class in PYME.Analysis.points.traveling_salesperson.queue_opt) ttest_ind() (in module PYME.Analysis.points.moments) TTYDummy (class in PYME.Acquire.webui.ipy) turnAllLasersOff() (PYME.Acquire.microscope.Microscope method) twistCal() (in module PYME.localization.twist) two_opt() (in module PYME.Analysis.points.traveling_salesperson.two_opt) two_opt_section() (in module PYME.Analysis.points.traveling_salesperson.sectioned_two_opt) two_opt_swap() (in module PYME.Analysis.points.traveling_salesperson.two_opt) two_opt_test() (in module PYME.Analysis.points.traveling_salesperson.two_opt) (in module PYME.Analysis.points.traveling_salesperson.two_opt_utils) TxtExporter (class in PYME.IO.dataExporter) type (PYME.IO.clusterListing.FileInfo attribute)

U

U() (in module PYME.Analysis.PSFGen.nijboer_zernike) Unfold() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) UnifiedLoader (class in PYME.reports) uniform_blob_paint() (in module PYME.Analysis.points.rings) uniform_random_radial_density() (PYME.Analysis.points.spherical_harmonics.ScaledShell method) uniform_theory() (in module PYME.Analysis.points.rings) uniform_theory_cdf() (in module PYME.Analysis.points.rings) unitnames (PYME.IO.FileUtils.obf_support.SIUnit attribute) units (PYME.IO.MetaDataHandler.VoxelSize attribute) unixdate2httpdate() (in module PYME.cluster.webdav) unixdate2iso8601() (in module PYME.cluster.webdav) Unmix() (PYME.Analysis.splitting.Unmixer method) Unmixer (class in PYME.Analysis.splitting) (class in PYME.DSView.modules.splitter) (class in PYME.DSView.modules.unmixing) UnMixSettingsDlg (class in PYME.DSView.modules.unmixing) unnest_dtype() (in module PYME.IO.tabular) unNestDtype() (in module PYME.IO.tabular) unNestNames() (in module PYME.IO.tabular) unpack() (PYME.contrib.lzw.BitUnpacker method) unpackbyte() (in module PYME.contrib.lzw) unpickleSlice() (in module PYME.localization.FitFactories.fitCommon) UnPin() (PYME.ui.autoFoldPanel.foldingPane method) (PYME.ui.manualFoldPanel.foldingPane method) Unplug() (in module PYME.DSView.modules.flowView) unregister() (PYME.misc.hybrid_ns.HybridNS method) (PYME.misc.pyme_zeroconf.ZeroConfNS method) (PYME.misc.sqlite_ns.SQLiteNS method) Update() (in module PYME.DSView.modules.eventView) update() (PYME.Acquire.htsms.tweeter.LazyScopeTweeter method) (PYME.Acquire.microscope.StateManager method) (PYME.Acquire.sampleInformation.slidePanel method) (PYME.Acquire.stackSettings.StackSettings method) (PYME.Acquire.ui.AnalysisSettingsUI.AnalysisSettingsPanel method) (PYME.Acquire.ui.intsliders.IntegrationSliders method) (PYME.Acquire.ui.intsliders.IntegrationSliders_ method) (PYME.Acquire.ui.lasersliders.LaserSliders method) (PYME.Acquire.ui.lasersliders.LaserSliders_ method) (PYME.Acquire.ui.lasersliders.LaserToggles method) (PYME.Acquire.ui.mpd_picosecond_delay_panel.DelayPanel method) (PYME.Acquire.ui.multiview_select.MultiviewSelect method) (PYME.Acquire.ui.positionUI.PositionPanel method) (PYME.Acquire.ui.positionUI.PositionPanelV2 method) (PYME.Acquire.ui.positionUI.PositionSliders method) (PYME.DSView.dsviewer.DSViewFrame method) (PYME.DSView.modules.deconvolution.Deconvolver method) (PYME.DSView.modules.playback.PlayPanel method) (PYME.DSView.modules.playback.PlayZTPanel method) (PYME.LMVis.layer_panel.LayerPane method) (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.labels.LabelLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) (PYME.ui.filterPane.FilterPane method) (PYME.ui.filterPane.FilterPanel method) update_base_tile() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method) update_base_tiles_from_frame() (PYME.Analysis.tile_pyramid.ImagePyramid method) update_cache() (PYME.IO.clusterListing.DirCache method)

update_config() (in module PYME.config) update_data() (PYME.LMVis.layers.labels.LabelLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) update_datasource_panel() (PYME.LMVis.visCore.VisGUICore method) update_display() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) update_from_datasource() (PYME.LMVis.layers.image_layer.ImageRenderLayer method) (PYME.LMVis.layers.labels.LabelLayer method) (PYME.LMVis.layers.mesh.TriangleRenderLayer method) (PYME.LMVis.layers.octree.OctreeRenderLayer method) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer method) (PYME.LMVis.layers.quiver.QuiverRenderLayer method) (PYME.LMVis.layers.tracks.TrackRenderLayer method) update_from_settings() (PYME.Acquire.ui.tilesettingsui.TileSettingsUI method) update_json() (PYME.Acquire.stackSettings.StackSettings method) update_levels() (PYME.ui.histLimits.HistLimitDialog method) update_pyramid() (PYME.Analysis.distributed_pyramid.DistributedImagePyramid method) (PYME.Analysis.distributed_pyramid.PartialPyramid method) (PYME.Analysis.tile_pyramid.ImagePyramid method) update_region_size() (PYME.Acquire.ui.tilesettingsui.TileSettingsUI method) update_scope_state() (PYME.Acquire.acquire_client.AcquireClient method) (PYME.Acquire.acquire_server.PYMEAcquireServerMixin method) update_settings() (PYME.Acquire.SpoolController.SpoolController method) (PYME.Acquire.ui.tilesettingsui.TileSettingsUI method) update_spooler_compression_settings() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) update_status() (PYME.Acquire.htsms.tweeter.FakeAPI method) update_trace() (PYME.Acquire.ui.intensity_trace.IntensityTracePanel method) update_ui() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) update_version() (in module PYME.update_version) update_version_hg() (in module PYME.update_version) update_yaml_keys() (in module PYME.config) updateBuffers() (PYME.localization.remFitBuf.BufferManager method) UpdateColourFilterChoices() (PYME.LMVis.colourFilterGUI.ColourFilterPane method) UpdateDisp() (PYME.Acquire.ui.seqdialog.seqPanel method) (PYME.DSView.fitInfo.FitInfoPanel method) UpdateFreeSpace() (PYME.Acquire.ui.HDFSpoolFrame.PanSpool method) (PYME.Acquire.ui.spool_panel.SpoolingPane method) updateMetadata() (PYME.IO.h5rFile.H5RFile method) UpdatePointColourChoices() (PYME.LMVis.pointSettingsPanel.PointSettingsPanel method) UpdateState (class in PYME.Acquire.actions) updateStatus() (in module PYME.cluster.HTTPDataServer) updateTrack() (PYME.Analysis.Tracking.tracking.Tracker method) updateValue() (PYME.localization.MetaDataEdit.BoolFloatParam method) (PYME.localization.MetaDataEdit.BoolParam method) (PYME.localization.MetaDataEdit.ChoiceParam method) (PYME.localization.MetaDataEdit.FilenameParam method) (PYME.localization.MetaDataEdit.FloatListParam method) (PYME.localization.MetaDataEdit.FloatParam method) (PYME.localization.MetaDataEdit.IntParam method) (PYME.localization.MetaDataEdit.RangeParam method) (PYME.localization.MetaDataEdit.StringParam method) updateView() (PYME.Acquire.Utils.fastTiler.fastTiler method) updateVX() (PYME.Deconv.richardsonLucyMVM.MotionCompensatingRichardsonLucy method) upload_directory() (in module PYME.IO.clusterUpload) upload_glob() (in module PYME.IO.clusterUpload) UPRIGHT (PYME.DSView.displayOptions.DisplayOpts attribute) URI (PYME.misc.sqlite_ns.NSInfo attribute) use() (PYME.LMVis.shader_programs.shader_program.ShaderProgram method) use_oit() (PYME.LMVis.layers.mesh.OITShadedFaceEngine method) UserError UserErrorDialog (class in PYME.ui.progress)

V

V() (in module PYME.Analysis.PSFGen.nijboer_zernike) validate() (PYME.recipes.traits.FileOrURI method) (PYME.recipes.traits.Input method) (PYME.recipes.traits.Output method) validate_token() (in module PYME.util.authenticate) values (PYME.simulation.pointsets.WRDictEnum property) varnames (PYME.Analysis.Tracking.trackUtils.Clump property) vec3_to_vec4() (in module PYME.LMVis.mv_math) vectDistanceHistogram3D() (in module PYME.Analysis.points.DistHist.distHist) vector_features_3d() (PYME.Analysis.points.features.metal.Backend method) vector_property (PYME.LMVis.layers.quiver.QuiverRenderLayer attribute) vectorial (PYME.DSView.modules.pupilTools.PupilTools attribute) verbose_fix_name() (in module PYME.IO.unifiedIO) Verify() (PYME.Acquire.stackSettings.StackSettings method) verify_cluster_results_filename() (in module PYME.cluster.HTTPRulePusher) (in module PYME.cluster.HTTPTaskPusher) (in module PYME.cluster.rules) vertexColour (PYME.LMVis.layers.mesh.TriangleRenderLayer attribute) (PYME.LMVis.layers.pointcloud.PointCloudRenderLayer attribute) (PYME.LMVis.layers.tracks.TrackRenderLayer attribute) VibrAnal (class in PYME.Acquire.Utils.vibrationAnalysis) VibrationAnalyser (class in PYME.LMVis.Extras.vibration) VibrationSpecgram() (PYME.LMVis.Extras.vibration.VibrationAnalyser method) VideoFrame (class in PYME.LMVis.Extras.animation) VideoPanel (class in PYME.LMVis.Extras.animation) VideoView (class in PYME.LMVis.views) View (class in PYME.LMVis.views) view (PYME.Acquire.acquiremainframe.PYMEMainFrame property)

View() (in module PYME.misc.mock_traitsui) View3D() (in module PYME.DSView.dsviewer) view_id (PYME.LMVis.views.View property) view_limits (PYME.LMVis.view_clipping_pane.ClippingPanel property) view_vector (PYME.LMVis.shader_programs.GouraudShaderProgram.GouraudShaderProgram attribute) ViewClippingPanel (class in PYME.LMVis.view_clipping_pane) ViewIm3D() (in module PYME.DSView.dsviewer) ViewPanel (class in PYME.LMVis.Extras.saved_views) VirtList (class in PYME.Acquire.sampleInformation) VisGUICore (class in PYME.LMVis.visCore) visGuiExtras (class in PYME.DSView.modules.visgui) visible (PYME.LMVis.layers.base.BaseLayer attribute) visible_bounds (PYME.DSView.arrayViewPanel.ArrayViewPanel property) Visualiser (class in PYME.DSView.modules.vis3D) vlj() (in module PYME.Analysis.PSFGen.nijboer_zernike) VoronoiRenderer (class in PYME.LMVis.renderers) voxels (PYME.IO.image.ImageStack property) VoxelSize (class in PYME.IO.MetaDataHandler) voxelsize (PYME.DSView.arrayViewPanel.ArrayViewPanel property) (PYME.DSView.modules.composite.CompositeDialog property) (PYME.IO.image.ImageStack property) voxelsize_nm (PYME.IO.image.ImageStack property) (PYME.IO.MetaDataHandler.MDHandlerBase property) voxelsize_x() (in module PYME.Analysis.PSFEst.psfQuality) voxelsize_z_dec() (in module PYME.Analysis.PSFEst.psfQuality) voxelsize_z_loc() (in module PYME.Analysis.PSFEst.psfQuality) VoxelSizeDialog (class in PYME.Acquire.ui.voxelSizeDialog) VoxSizeDialog (class in PYME.DSView.voxSizeDialog) vp (PYME.Acquire.acquiremainframe.PYMEMainFrame property)

W

wait_close() (PYME.IO.h5rFile.H5RFile method) wait_for_init() (PYME.Acquire.microscope.Microscope method) walk() (in module PYME.IO.clusterIO) Warn() (in module PYME.LMVis.Extras.multiColourAnalysis) (in module PYME.LMVis.Extras.QPobjectSegment) warn() (in module PYME.pyme_warnings) warpCorrectRedImage() (in module PYME.Analysis.points.twoColour) watch() (PYME.cluster.rules.Rule method) (PYME.cluster.rules.RuleGroupWatcher method) (PYME.cluster.rules.RuleWatcher method) wavelength (PYME.DSView.modules.psfGeneration.PupilGenerator attribute) (PYME.DSView.modules.psfTools.PSFTools attribute) (PYME.DSView.modules.pupilTools.PupilTools attribute) wavetableZScanner (class in PYME.Acquire.zScanner) WeakRef (in module PYME.misc.mock_traits) WebAuth() (PYME.cluster.webdav.DAVRequestHandler method) weightedAverage() (in module PYME.Analysis.points.DeClump.pyDeClump) weightedAverage_() (in module PYME.Analysis.points.DeClump.pyDeClump) WFNodeServer (class in PYME.cluster.rulenodeserver) WFPSFFitFactory (class in PYME.localization.FitFactories.InterpFitWFR) WFRuleServer (class in PYME.cluster.ruleserver) White() (in module PYME.misc.colormaps) widefield_pupil_and_propagator() (in module PYME.Analysis.PSFGen.fourierHNA) (in module PYME.Analysis.PSFGen.fourierHNA2) widefieldify() (in module PYME.Analysis.widefieldify) WidefieldPupil (class in PYME.DSView.modules.psfGeneration) width() (in module PYME.Analysis.angleFilter) (PYME.IO.image.ImageBounds method) (PYME.LMVis.visHelpersMin.ImageBounds method) width_filter() (in module PYME.Analysis.angleFilter) width_filter_m() (in module PYME.Analysis.angleFilter) width_o() (in module PYME.Analysis.angleFilter) WienerDeconvolver (class in PYME.DSView.modules.deconvolution) wiglyFibre() (in module PYME.simulation.wormlike2) (in module PYME.simulation.wormlike3)

WiglyFibreSource (class in PYME.simulation.pointsets) WinDLL (in module PYME.misc.mock_ctypes) WireframeEngine (class in PYME.LMVis.layers.mesh) WireFrameShaderProgram (class in PYME.LMVis.shader_programs.WireFrameShaderProgram) with_constant() (in module PYME.contrib.pad.pad) with_linear_ramp() (in module PYME.contrib.pad.pad) with_maximum() (in module PYME.contrib.pad.pad) with_mean() (in module PYME.contrib.pad.pad) with_median() (in module PYME.contrib.pad.pad) with_minimum() (in module PYME.contrib.pad.pad) with_reflect() (in module PYME.contrib.pad.pad) with_wrap() (in module PYME.contrib.pad.pad) WormlikeChain (class in PYME.simulation.wormlike) (class in PYME.simulation.wormlike2) (class in PYME.simulation.wormlike3) (class in PYME.simulation.wormlike_curled) WormlikeChain2D (class in PYME.simulation.wormlike3) WormlikeSource (class in PYME.simulation.pointsets) Wrap() (in module PYME.IO.dataWrap) WRDictEnum (class in PYME.simulation.pointsets) write() (in module PYME.IO.unifiedIO) (PYME.Acquire.webui.ipy.TTYDummy method) (PYME.cluster.webdav.BufWriter method) (PYME.DSView.logparser.logwriter method) (PYME.IO.MetaDataHandler.SimpleMDHandler method) write_metadata() (PYME.DSView.modules.psfExtraction.PsfExtractor method) write_response() (PYME.util.webframework.HTTPResponse method) writebytes() (in module PYME.contrib.lzw) WriteSimple() (PYME.IO.MetaDataHandler.MDHandlerBase method) writeTiff() (in module PYME.IO.FileUtils.saveTiffStack) writeXML() (PYME.IO.MetaDataHandler.OMEXMLMDHandler method) (PYME.IO.MetaDataHandler.XMLMDHandler method) wsgiref_server() (in module PYME.cluster.dataserver_wsgi) wxThread (class in PYME.misc.wxThread)

X

x (PYME.IO.MetaDataHandler.VoxelSize attribute) X (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory attribute) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory attribute) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory attribute) x (PYME.tileviewer.tileviewer.Location attribute) (PYME.ui.selection.Point property) x0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) XC (PYME.DSView.modules.blobMeasure.DataBlock property)

XMLDict_Parser (class in PYME.cluster.webdav) XMLMDHandler (class in PYME.IO.MetaDataHandler) xp (PYME.DSView.displayOptions.DisplayOpts property) xRange (PYME.simulation.pointsets.RandomSource attribute) XTZCBackgroundSource (class in PYME.IO.DataSources.BGSDataSource) XYTCDataSource (class in PYME.IO.DataSources.BaseDataSource) XYTCWrapper (class in PYME.IO.DataSources.BaseDataSource) XYZSubvolume (class in PYME.IO.DataSources.BaseDataSource) XYZTCAcquisition (class in PYME.Acquire.xyztc) XYZTCArrayDataSource (class in PYME.IO.DataSources.ArrayDataSource) XYZTCBgsSource (class in PYME.IO.DataSources.BGSDataSource) XYZTCDataSource (class in PYME.IO.DataSources.BaseDataSource) XYZTCWrapper (class in PYME.IO.DataSources.BaseDataSource)

Y

y (PYME.IO.MetaDataHandler.VoxelSize attribute) Y (PYME.localization.FitFactories.AstigGaussGPUFitFR.GaussianFitFactory attribute) (PYME.localization.FitFactories.ChecksumGPUFR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.ChecksumMultifitSR.ChecksumFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitLinesR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitR.GaussianFitFactory attribute) (PYME.localization.FitFactories.GaussMultifitSR.GaussianFitFactory attribute) (PYME.localization.FitFactories.SplitterMultifitSR.GaussianFitFactory attribute)

y (PYME.tileviewer.tileviewer.Location attribute) (PYME.ui.selection.Point property) y0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) YC (PYME.DSView.modules.blobMeasure.DataBlock property) Yellow() (in module PYME.misc.colormaps) yiq_to_rgb() (in module PYME.misc.colorsys) yp (PYME.DSView.displayOptions.DisplayOpts property) yRange (PYME.simulation.pointsets.RandomSource attribute)

Z

z (PYME.IO.MetaDataHandler.VoxelSize attribute) (PYME.ui.selection.Point property) z() (in module PYME.misc.zernike) z0() (PYME.localization.FitFactories.Gauss3DFitR.GaussFitResult method) (PYME.localization.FitFactories.LatPSFFitR.PSFFitResult method) z_nm (PYME.LMVis.layers.image_layer.ImageRenderLayer property) z_pos (PYME.LMVis.layers.image_layer.ImageRenderLayer attribute) ZC (PYME.DSView.modules.blobMeasure.DataBlock property) ZCListener (class in PYME.misc.pyme_zeroconf) ZDEPSHIFT (PYME.Analysis.points.twoColour.lin3zModel attribute) zernike() (in module PYME.misc.zernike) zernike_residuals() (PYME.Analysis.PSFEst.fit_psf_zernikes.ZernikePSFFitter method) zernikeIm() (in module PYME.misc.zernike) ZernikeMode (class in PYME.DSView.modules.psfGeneration)

ZernikePSF (class in PYME.Analysis.PSFGen.fourierHNA) ZernikePSFFitter (class in PYME.Analysis.PSFEst.fit_psf_zernikes) ZernikePSFModel (class in PYME.localization.autopsf.autopsf) ZeroConfNS (class in PYME.misc.pyme_zeroconf) zeros() (in module PYME.util.shmarray.shmarray) ZMX (class in PYME.misc.zemax) zp (PYME.DSView.displayOptions.DisplayOpts property) zRange (PYME.simulation.pointsets.RandomSource attribute) zScale (PYME.simulation.pointsets.WiglyFibreSource attribute) zScanner (class in PYME.Acquire.zScanner) zSpacing (PYME.DSView.modules.pupilTools.PupilTools attribute) ZStackAcquisition (class in PYME.Acquire.xyztc) ZStackTaskListProtocol (class in PYME.Acquire.protocol) ZTileSettingsUI (class in PYME.Acquire.ui.tilesettingsui)