advanced_io: Added the function expand_pathname_list, which takes pathnames and uses regex to expand them into an explicit list of pathnames that match.
tiff_file_format: Created the tiff file format module for converting tiffs to HDF5. Added several functions. The function get_multipage_tiff_shape_dtype gets information about the shape (including the number of pages as time. The shape returned is the same used by VIGRA (unless the page number is one, in which case VIGRA drops this dimension). Also, gets the dtype used. The function get_multipage_tiff_shape_dtype_transformed also gets the shape and dtype, but will transform the shape according to the number of pages per channel and any reshaping that will occur. The function get_standard_tiff_array will read a TIFF file that is multipaged or not and return a standard NumPy 5D array with an axis ordering that is specified. Also, it allows some number of pages to be converted into channels if needed (if not then it only uses the number of channels supplied by the file and the number of pages remain temporal). The function convert_tiffs takes a list or single str (allows for regex in both cases), an axis to concatenate along, the z index to use (hopefully to be removed in the future), and how to convert pages to channels (if needed). Uses advanced_io module for completing regex lists of tiff filenames.
HDF5_importer: Created the HDF5 importer. This is designed to handle external file formats and convert them to an HDF5 file. Added main function to call the selected importer (only TIFF at present) as well as a simple command line interface. This fixes #4.
batch_learner: Refactored old TIFF code. Conversions are now performed through a separate utility, HDF5_importer.
advanced_image_processing: Variable names now matched to expanded parameter packs.
HDF5_serializers: Removed comment old code.
advanced_image_processing: Removed commented old code and completed todos. Added some minor clarification to comments.
neuron_volumina_viewer: Removed commented old code.
batch_learner: For the function generate_save_neurons, added output_group to specify the location in new_file.
batch_learner: Added extension to the resume feature. Now, when the stage is specified it repeats that stage and stops. This way if the results are undesirable they can be fixed. This fixes #36.
advanced_image_processing: Now includes more debug information for the function removing_lines.
wavelet_transform: Fixed argument to append in binomial_1D_array_kernel.
HDF5_importer: Made into a python executable.