pyfibre.core.base_file_parser module

class pyfibre.core.base_file_parser.BaseFileParser

Bases: traits.has_traits.ABCHasStrictTraits

abstract get_file_sets(filenames)

From a given list of file names, returns a dictionary where each entry represents the files required to create an instance of a multi image. Each key will be passed on as the name of the multi image, used during further PyFibre operations. Each value could be passed in as the filenames argument to the class create_image_stack method.

Returns

file_sets – List containing FileSet objects that hold a collection of files to be loaded in as a single image

Return type

list of FileSet

Examples

For a given list of files and multi image reader:

>>> file_list = ['/path/to/an/image',
...              '/path/to/another/image',
...              '/path/to/nothing']
>>> file_parser = MyFileParser()

If each “image” file path could be loaded in as a separate MultiImage, the return value of collate_files would be:

>>> file_sets = file_parser.get_supported_file_sets(file_list)
>>> print(file_sets)
... {"a file name": ['/path/to/an/image'],
...  "another file name": ['/path/to/another/image']}

Alternatively, if both “image” file paths were required to load a single MultiImage, then a return value could be:

>>> file_sets = file_parser.get_supported_file_sets(file_list)
>>> print(file_sets)
... {"a file name": ['/path/to/an/image',
...                  '/path/to/another/image']}

class pyfibre.core.base_file_parser.FileSet

Bases: traits.has_traits.HasStrictTraits

Small container class that represents a collection of related image files that can be loaded as a MultiImage