ActImgCollection#

Warning

This library and its documentation are still under development.

This section documents the ActImgCollection class and its methods.

ActImgCollection class and attributes#

meshure.actimg_collection.ActImgCollection(root_path: str, res_path: str = None, only_subdirs: list[str] = None, specify_subdirs: list = None, focal_planes: pandas.core.frame.DataFrame = None)#

ActImgCollection methods#

meshure.actimg_collection.ActImgCollection.print_summary(self, specify_subdirs=None, interact=False)#

Summary of files.

meshure.actimg_collection.ActImgCollection.get_focal_planes(self, filepath)#

Read in focal planes.

Parameters:

filepath (str) –

Filepath specifies a csv file with four fields (named exactly: ‘File name’, ‘Type’, ‘Basal’, ‘Cytoplasmic’, ‘Notes’). File name = name of tiff file Type = cell type, either ‘Untransduced’ or ‘CAR’ Basal = one or two comma separated integers specifying the focal plane (or focal plane [start, end])

These are converted to a list inside the function

Cytoplasmic = one or two comma separated integers specifying the focal plane (or focal plane [start, end])

These are converted to a list inside the function

Notes = field not used by this function.

Returns:

self.focal_planes – ???

Return type:

pandas DataFrame

Raises:

Warning – If the filenames in the CSV file are not unique, a warning is raised but the program is executed.

meshure.actimg_collection.ActImgCollection.redefine_pipeline(self, new_pipeline)#
meshure.actimg_collection.ActImgCollection.parametrise_pipeline(self, substack=None, theta=None, thetas=None, sigma=2, threshold=None, dest_dir=None)#

Fill in parameters based on function calls in pipeline.

Parameters:

  • substack (list of ints) –

  • theta (float) –

  • thetas (list of floats) –

  • sigma (float) –

  • threshold (float) –

Returns:

dict

Return type:

meshure.actimg_collection.ActImgCollection.run_analysis(self, visualise_as_html: bool = False, return_parameters: bool = False, save_as_single_csv: bool = True)#

Runs analysis on selected subdirs.

ActImgCollection hidden methods#

meshure.actimg_collection.ActImgCollection._initialise_curr_filenames_and_planes(self, subdir)#

Called inside analysis loop. Subsets the current filenames which are being processed based on subdir.

Parameters:

subdir (str) –

Returns:

  • curr_filenames (list)

  • curr_filepath (list)

meshure.actimg_collection.ActImgCollection._initialise_res_dir(self, subdir)#

Initialise results directory.

meshure.actimg_collection.ActImgCollection._pipeline_construct(self, actin_img_instance, func)#
meshure.actimg_collection.ActImgCollection._analysis_pipeline(self, filename, filepath, curr_planes)#

???

meshure.actimg_collection.ActImgCollection._extract_parameters(self, actimgbinary)#
meshure.actimg_collection.ActImgCollection._return_params(self)#
meshure.actimg_collection.ActImgCollection._visualise_html(self, subdir: str, curr_planes: DataFrame, include_steps: list | None = None)#

??? :returns: hidden :rtype: makes file named as …..