PYME.recipes.measurement module

class PYME.recipes.measurement.AddMetadataToMeasurements(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Adds metadata entries as extra column(s) to the output

This was written to allow key parameters or experimental variables to be tracked prior to aggregating / concatenating measurements from multiple different images. By adding, e.g. the sample labelling, or a particular experimental parameter to an output table as an extra column we can then aggregate and group that data in processing.

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.BinnedHistogram(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates a histogram of a given measurement key, binned by a separate value

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.FitDumbells(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.FitPoints(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Apply one of the fit modules from PYME.localization.FitFactories to each of the points in the provided in inputPositions

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.Histogram(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates a histogram of a given measurement key

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.ImageCumulativeHistogram(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates a histogram of a given measurement key

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.ImageHistogram(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates a histogram of a given measurement key

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.IntensityAtPoints(*args, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Apply one of the fit modules from PYME.localization.FitFactories to each of the points in the provided in inputPositions

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.MeanNeighbourDistances(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates mean distance to nearest neighbour in a triangulation of the supplied points

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.Measure2D(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Module with one image input and one image output

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.MultifitBlobs(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.NearestNeighbourDistances(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates the nearest neighbour distances between supplied points using a kdtree

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.PairwiseDistanceHistogram(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Calculates a histogram of pairwise distances

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)
class PYME.recipes.measurement.Plot(parent=None, **kwargs)

Bases: PYME.recipes.base.ModuleBase

Take just certain columns of a variable

Attributes

default_view
hide_in_overview
inputs
outputs
pipeline_view
pipeline_view_min

Methods

execute(namespace)
trait_items_event(event_trait,name,items_event)
trait_property_changed(...)
traits_init()
traits_inited([True])
execute(namespace)