PYME.Analysis.tile_pyramid module¶

class PYME.Analysis.tile_pyramid.CacheEntry(data, saved)¶

Bases: tuple

Create new instance of CacheEntry(data, saved)

data¶: Alias for field number 0

saved¶: Alias for field number 1

class PYME.Analysis.tile_pyramid.ClusterPZFTileCache(max_size=1000)¶: Bases: TileCache

class PYME.Analysis.tile_pyramid.ClusterPZFTileIO(base_dir, suff='img')¶: Bases: PZFTileIO

class PYME.Analysis.tile_pyramid.ImagePyramid(storage_directory, pyramid_tile_size=256, mdh=None, n_tiles_x=0, n_tiles_y=0, depth=0, x0=0, y0=0, pixel_size=1, backend=<class 'PYME.Analysis.tile_pyramid.PZFTileIO'>)¶

Bases: object

finish_base_tiles()¶

classmethod frame_weights(frame_shape)¶

get_layer_tile_coords(level)¶

get_oversize_tile(layer, x, y, span=2)¶

Get an over-sized tile - allows processing on overlapping tiles

Parameters

span: size of tile as a multiple of the underlying tile size

get_tile(layer, x, y)¶

property layers¶

classmethod load_existing(storage_directory)¶

loads an ImagePyramid from a given directory.

Parameters

storage_directorystr: root directory of an ImagePyramid instance.

Returns

ImagePyramid: based on storage_directory contents.

property mdh¶

ndim = 2¶

update_base_tile(tile_x, tile_y, data, weights, tile_offset=(0, 0), frame_offset=(0, 0), frame_shape=None)¶

update_base_tiles_from_frame(x, y, frame, weights='auto')¶

add tile to the pyramid

Parameters

xint: x origin of the tile (frame), relative to minimum x position of all tiles, in units of pixels
yint: y origin of the tile (frame), relative to minimum y position of all tiles, in units of pixels
framendarray: the tile frame to add
weightsndarray: weights for averaging with overlapping base tiles

update_pyramid()¶

class PYME.Analysis.tile_pyramid.NumpyTileIO(base_dir, suff='img')¶

Bases: TileIO

delete_tile(layer, x, y)¶

flush()¶

get_layer_tile_coords(layer=0)¶

get_tile(layer, x, y)¶

save_tile(layer, x, y, data)¶

tile_exists(layer, x, y)¶

class PYME.Analysis.tile_pyramid.PZFTileCache(max_size=1000)¶: Bases: TileCache

class PYME.Analysis.tile_pyramid.PZFTileIO(base_dir, suff='img', tile_cache=<class 'PYME.Analysis.tile_pyramid.PZFTileCache'>)¶: Bases: NumpyTileIO

class PYME.Analysis.tile_pyramid.PyramidLayer(pyramid, layer)¶

Bases: object

A layer of and ImagePyramid, implements an array-like interface to the tiles within the layer

dtype¶: alias of float32

ndim = 5¶

property shape¶

class PYME.Analysis.tile_pyramid.SqliteTileIO(base_dir, suff='img')¶

Bases: TileIO

delete_tile(layer, x, y)¶

flush()¶

get_layer_tile_coords(layer=0)¶

get_tile(layer, x, y)¶

save_tile(layer, x, y, data)¶

tile_exists(layer, x, y)¶

class PYME.Analysis.tile_pyramid.TileCache(max_size=1000)¶

Bases: object

exists(filename)¶

flush()¶

load(filename)¶

purge()¶

remove(filename)¶

save(filename, data)¶

class PYME.Analysis.tile_pyramid.TileIO¶

Bases: object

delete_tile(layer, x, y)¶

flush()¶

get_layer_tile_coords(layer)¶

get_tile(layer, x, y)¶

save_tile(layer, x, y, data)¶

tile_exists(layer, x, y)¶

PYME.Analysis.tile_pyramid.atleast_nd(a, n)¶

PYME.Analysis.tile_pyramid.blob(data)¶

PYME.Analysis.tile_pyramid.create_pyramid_from_dataset(filename, outdir, tile_size=128, **kwargs)¶

PYME.Analysis.tile_pyramid.get_position_from_events(events, mdh)¶: Use acquisition events to create a mapping between frame number and stage position

PYME.Analysis.tile_pyramid.infer_tileio_backend(base_directory)¶

find TileIO backend for a given ImagePyramid

Parameters

base_directorystr: root directory of an ImagePyramid instance

Returns

class: which TileIO derived class the ImagePyramid can be built with.

Raises

IOError: If no file with an extension in TILEIO_EXT is found.

PYME.Analysis.tile_pyramid.tile_pyramid(out_folder, ds, xm, ym, mdh, split=False, skipMoveFrames=False, shiftfield=None, mixmatrix=[[1.0, 0.0], [0.0, 1.0]], correlate=False, dark=None, flat=None, pyramid_tile_size=256)¶

Create a tile pyramid from which an ImagePyramid can be created

Parameters

out_folderstr: directory to save pyramid tiles(/directories)
dsPYME.IO.DataSources.BaseDataSource, np.ndarray: array-like image
xmnp.ndarray or PYME.Analysis.piecewiseMapping.piecewiseMap: x positions of frames in ds. Raw stage positions in [um]. ImagePyramid origin will be at at minimum x, and offset to camera chip origin will be handled in SupertileDatasource tile_coords_um method. to the camera chip origin.
ymnp.ndarray or PYME.Analysis.piecewiseMapping.piecewiseMap: y positions of frames in ds. Raw stage positions in [um]. ImagePyramid origin will be at at minimum y, and offset to camera chip origin will be handled in SupertileDatasource tile_coords_um method.
mdhPYME.IO.MetaDataHandler.MDataHandlerBase: metadata for ds
splitbool, optional: whether this is a splitter datasource and should be treated like one, by default False
skipMoveFramesbool, optional: flag to drop frames which are the first frame acquired at a given position, by default False
shiftfield[type], optional: required for splitter data, see PYME.Acquire.Hardware.splitter, by default None
mixmatrixlist, optional: for splitter data, see PYME.Acquire.Hardware.splitter, by default [[1., 0.], [0., 1.]]
correlatebool, optional: whether to add a 300 pixel padding to the edges, by default False
darkndarray, float, optional: (appropriately-cropped or scalar) dark frame (analog-digital offset) calibration to subtract when adding frames to the pyramid, by default None, in which case Camera.ADOffset from metadata will be used, if available
flatndarray, optional: (appropriately-cropped or scalar) flatfield calibration to apply to frames when adding them to the pyramid, by default None
pyramid_tile_sizeint, optional: base tile size, by default 256 pixels

Returns

ImagePyramid: coalesced/averaged/etc multilevel ImagePyramid instance

Notes

Code is currently somewhat alpha in that the splitter functionality is more or less untested, and we only get tile orientations right for primary cameras (i.e. when the stage is registered with multipliers to match the camera, rather than camera registered with orientation metadata to match it to the stage)