This is the culmination of work fixes #75.
Also, this goes a long way towards addressing #25.
advanced_image_processing: Updates to use ArrayRecorder dictionary style of storage. Also, removed the array_debug_recorder from parameters and added a decorator instead, which provides access to the array_debug_recorder through a static variable. Configures functions beneath it to use an array_debug_recorder of the same kind in a subgroup.
nanshe_learner: Modified construction of resume_logger and array_debug_recorder to follow new constraints from HDF5_recorder. Updates to use ArrayRecorder dictionary style of storage. Also, removed the array_debug_recorder from parameters and added a decorator instead, which provides access to the array_debug_recorder through a static variable. Configures functions beneath it to use an array_debug_recorder of the same kind in a subgroup.
wavelet_transform: Updates to use ArrayRecorder dictionary style of storage. Also, removed the array_debug_recorder from parameters and added a decorator instead, which provides access to the array_debug_recorder through a static variable. Configures functions beneath it to use an array_debug_recorder of the same kind in a subgroup.
HDF5_importer: Renamed to nanshe_converter.
nanshe_converter: Renamed from HDF5_importer.
nanshe_learner: Refactored name change of HDF5_importer to nanshe_converter.
HDF5_serializers: Added check in create_numpy_structured_array_in_HDF5 to ensure the given data is either of type numpy.ndarray or convertible to it.
debugging_tools: Changed "Exiting " to "Exiting callable: ".
advanced_image_processing: Added the function extract_neurons, which will extract neurons from an image given a stack of masks.
expanded_numpy: Created the function enumerate_masks to simplify the process of converting masks stacks into labeled stacks. The conversion to label image is left up to the developer's discretion.
setup: Added to provide configurations for the package. Setup so that doctests in the project folder and the test folder are run by default when running nosetest.
test_additional_io: Created a test for the additional_io module. Just tests the function expand_pathname_list. This closes #69.
__init__: Added test_additional_io to __all__ and imported it as well.
test_HDF5_searchers: Added a test for HDF5_searchers.get_matching_paths. This fixes #76.
__init__: Added test_HDF5_searchers to __all__ and imported it as well.
test_HDF5_searchers: Added a test for HDF5_searchers.get_matching_paths_groups. This fixes #77.
test_HDF5_searchers: Added test for HDF5_searchers.get_matching_grouped_paths. This fixes #78.
test_HDF5_searchers: Added test for HDF5_searchers.get_matching_grouped_paths_found. This fixes #79.
test_HDF5_serializers: Added test_HDF5_serializers for testing the HDF5_serializers module. This will address issues #81 and #82.
__init__: Added test_HDF5_serializers to __all__ and imported it as well.
test_HDF5_serializers: Added tests for create_numpy_structured_array_in_HDF5 from HDF5_serializers. This fixes #81.
test_HDF5_serializers: Added tests for read_numpy_structured_array_from_HDF5 from HDF5_serializers. This fixes #82.
test_debugging_tools: Added for testing the module debugging_tools. This will address issues #71 and #83.
__init__: Added test_debugging_tools to __all__ and imported it as well.
test_debugging_tools: Added tests for log_call from debugging_tools. This fixes #71.
test_debugging_tools: Added tests for log_class from debugging_tools. This fixes #83.
test_advanced_image_processing: Added for testing the module advanced_image_processing. This will address issues #98, #99, #100, #101, #102, #103, #104, #105, #106, #107, #108, #109, #110, #111, #112, #113, #114, #115, and #116.
__init__: Added test_advanced_image_processing to __all__ and imported it as well.
test_advanced_image_processing: Added tests for remove_zeroed_lines from advanced_image_processing. This fixes #98.