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.
nanshe_learner: Changed mechanism of determining path to the nanshe_learner executable to queue up subprocess calls in generate_neurons_blocks.
HDF5_serializers: Corrected case of unicode filename. Also, corrected a bug with region refs that were gotten to through an External Link.
nanshe_learner: Turned off using external links to the input file for the blocks case. Presently, copies the input file data into the output file, which appears to work.
nanshe_learner: Added debug output for merging the results from blocks in generate_neurons_blocks.
expanded_numpy: Changed expand_enumerate to use numpy.uint64 by default.
nanshe_learner: Fixes for regionrefs that point to an externally linked file.
HDF5_cacher: WIP. A possible method of granular resume and organized debug output.