fissa.extraction module#

DataHandler classes to handle and manipulate image and ROI objects.

Authors:

Sander W Keemink <swkeemink@scimail.eu>
Scott C Lowe <scott.code.lowe@gmail.com>

class fissa.extraction.DataHandlerAbstract[source]#

Bases: abc.ABC

Abstract class for a data handler.

See also

DataHandlerTifffile, DataHandlerPillow

Methods

`extracttraces`(masks)	Extract from data the average signal within each mask, across time.
`get_frame_size`()	Determine the shape of each frame within the recording.
`getmean`()	Determine the mean image across all frames.
`image2array`()	Load data (from a path) as an array, or similar internal structure.
`rois2masks`(rois, data)	Convert ROIs into a collection of binary masks.

abstract extracttraces(masks)[source]#

Extract from data the average signal within each mask, across time.

Must return a 2D numpy.ndarray.

Parameters

datadata_type: The same object as returned by image2array().
masksmask_type: The same object as returned by rois2masks().

Returns

tracesnumpy.ndarray: Trace for each mask, shaped (len(masks), n_frames).

abstract get_frame_size()[source]#

Determine the shape of each frame within the recording.

Parameters

datadata_type: The same object as returned by image2array().

Returns

shapetuple of ints: The 2D, y-by-x, shape of each frame in the movie.

abstract getmean()[source]#

Determine the mean image across all frames.

Must return a 2D numpy.ndarray.

Parameters

datadata_type: The same object as returned by image2array().

Returns

meannumpy.ndarray: Mean image as a 2D, y-by-x, array.

abstract image2array()[source]#

Load data (from a path) as an array, or similar internal structure.

Parameters

imageimage_type: Some handle to, or representation of, the raw imagery data.

Returns

datadata_type: Internal representation of the images which will be used by all the other methods in this class.

classmethod rois2masks(rois, data)[source]#

Convert ROIs into a collection of binary masks.

Parameters

roisstr or list of array_like: Either a string containing a path to an ImageJ roi zip file, or a list of arrays encoding polygons, or list of binary arrays representing masks.
datadata_type: The same object as returned by image2array().

Returns

masksmask_type: Masks, in a format accepted by extracttraces().

See also

fissa.roitools.getmasks, fissa.roitools.readrois

class fissa.extraction.DataHandlerPillow[source]#

Bases: fissa.extraction.DataHandlerAbstract

Extract data from TIFF images frame-by-frame using Pillow (PIL.Image).

Slower, but less memory-intensive than DataHandlerTifffile.

Methods

`extracttraces`(data, masks)	Extract the average signal within each mask across the data.
`get_frame_size`(data)	Determine the shape of each frame within the recording.
`getmean`(data)	Determine the mean image across all frames.
`image2array`(image)	Open an image file as a `PIL.Image` instance.
`rois2masks`(rois, data)	Convert ROIs into a collection of binary masks.

static extracttraces(data, masks)[source]#

Extract the average signal within each mask across the data.

Parameters

dataPIL.Image: An open PIL.Image handle to a multi-frame TIFF image.
maskslist of array_like: List of binary arrays.

Returns

tracesnumpy.ndarray: Trace for each mask, shaped (len(masks), n_frames).

static get_frame_size(data)[source]#

Determine the shape of each frame within the recording.

Parameters

dataPIL.Image: An open PIL.Image handle to a multi-frame TIFF image.

Returns

shapetuple of ints: The 2D, y-by-x, shape of each frame in the movie.

static getmean(data)[source]#

Determine the mean image across all frames.

Parameters

dataPIL.Image: An open PIL.Image handle to a multi-frame TIFF image.

Returns

meannumpy.ndarray: y-by-x array for the mean values.

static image2array(image)[source]#

Open an image file as a PIL.Image instance.

Parameters

imagestr or file: A filename (string) of a TIFF image file, a pathlib.Path object, or a file object.

Returns

dataPIL.Image: Handle from which frames can be loaded.

class fissa.extraction.DataHandlerTifffile[source]#

Bases: fissa.extraction.DataHandlerAbstract

Extract data from TIFF images using tifffile.

Methods

`extracttraces`(data, masks)	Extract a temporal trace for each spatial mask.
`get_frame_size`(data)	Determine the shape of each frame within the recording.
`getmean`(data)	Determine the mean image across all frames.
`image2array`(image)	Load a TIFF image from disk.
`rois2masks`(rois, data)	Convert ROIs into a collection of binary masks.

static extracttraces(data, masks)[source]#

Extract a temporal trace for each spatial mask.

Parameters

dataarray_like: Data array as made by image2array(), shaped (frames, y, x).
maskslist of array_like: List of binary arrays.

Returns

tracesnumpy.ndarray: Trace for each mask, shaped (len(masks), n_frames).

static get_frame_size(data)[source]#

Determine the shape of each frame within the recording.

Parameters

datadata_type: The same object as returned by image2array().

Returns

shapetuple of ints: The 2D, y-by-x, shape of each frame in the movie.

static getmean(data)[source]#

Determine the mean image across all frames.

Parameters

dataarray_like: Data array as made by image2array(), shaped (frames, y, x).

Returns

numpy.ndarray: y by x array for the mean values

static image2array(image)[source]#

Load a TIFF image from disk.

Parameters

imagestr or array_like shaped (time, height, width): Either a path to a TIFF file, or array_like data.

Returns

numpy.ndarray: A 3D array containing the data, with dimensions corresponding to (frames, y_coordinate, x_coordinate).

class fissa.extraction.DataHandlerTifffileLazy[source]#

Bases: fissa.extraction.DataHandlerAbstract

Extract data from TIFF images using tifffile, with lazy loading.

Methods

`extracttraces`(data, masks)	Extract a temporal trace for each spatial mask.
`get_frame_size`(data)	Determine the shape of each frame within the recording.
`getmean`(data)	Determine the mean image across all frames.
`image2array`(image)	Load a TIFF image from disk.
`rois2masks`(rois, data)	Convert ROIs into a collection of binary masks.

static extracttraces(data, masks)[source]#

Extract a temporal trace for each spatial mask.

Parameters

datatifffile.TiffFile: Open tifffile.TiffFile object.
maskslist of array_like: List of binary arrays.

Returns

tracesnumpy.ndarray: Trace for each mask, shaped (len(masks), n_frames).

static get_frame_size(data)[source]#

Determine the shape of each frame within the recording.

Parameters

datadata_type: The same object as returned by image2array().

Returns

shapetuple of ints: The 2D, y-by-x, shape of each frame in the movie.

static getmean(data)[source]#

Determine the mean image across all frames.

Parameters

datatifffile.TiffFile: Open tifffile.TiffFile object.

Returns

numpy.ndarray: y by x array for the mean values

static image2array(image)[source]#

Load a TIFF image from disk.

Parameters

imagestr: A path to a TIFF file.

Returns

datatifffile.TiffFile: Open tifffile.TiffFile object.

fissa.deltaf module

fissa.neuropil module