HDF5_recorder: Created the ArrayRecorder, HDF5EnumeratedArrayRecorder, this uses an enumeration system to allow storing separate results with the same sort of name. Also, added code to HDF5EnumeratedArrayRecorder to set an attribute for each group key to specify whether it is a logger or data. Allows persistence across different Python sessions or different logger instances.
HDF5_recorder: Created the decorator static_subgrouping_array_recorders. It must be supplied arguments, which are either names for the recorders that will default to EmptyArrayRecorder instances or names with an explicit assignment of the type of recorder.
HDF5_recorder: Added the convenience decorator, static_array_debug_recorder, which adds one recorder with the name array_debug_recorder that is an instance of EmptyArrayRecorder.
HDF5_recorder: Created the function class_static_subgrouping_array_recorders, which has the same idea as the function static_subgrouping_array_recorders; except, it is designed for classes. It ensures that before an instance of a class is constructed a group will be created for that class and all function calls will be stored within it.
HDF5_recorder: Added the convenience decorator, class_static_array_debug_recorder, which adds one recorder with the name array_debug_recorder that is an instance of EmptyArrayRecorder using the decorator class_static_subgrouping_array_recorders.
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.
advanced_image_processing: Was missing conversion to str in Exception.
tiff_file_format: Updated docstring for convert_tiffs to mention z_index.
.gitignore: Added *.pyo and *.pyd files.
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.