advanced_numpy: Renamed to expanded_numpy.
expanded_numpy: Renamed from advanced_numpy.
__init__: Renamed advanced_numpy to expanded_numpy.
advanced_image_processing: Renamed advanced_numpy to expanded_numpy.
neuron_volumina_viewer: Renamed advanced_numpy to expanded_numpy.
tiff_file_format: Renamed advanced_numpy to expanded_numpy.

This is related to issue #40.
advanced_io: Renamed to additional_io.
additional_io: Renamed from advanced_io.
tiff_file_format: Renamed advanced_io to additional_io.

This is related to issue #40.
advanced_iterators: Renamed to additional_generators.
additional_generators: Renamed from advanced_iterators.
__init__: Renamed advanced_iterators to additional_generators.
advanced_image_processing: Renamed advanced_iterators to additional_generators.
expanded_numpy: Renamed advanced_iterators to additional_generators.
neuron_volumina_viewer: Renamed advanced_iterators to additional_generators.
tiff_file_format: Renamed advanced_iterators to additional_generators.
random_dictionary_learning_data: Renamed advanced_iterators to additional_generators.

This is related to issue #40.
advanced_debugging: Renamed to debugging_tools.
debugging_tools: Renamed from advanced_debugging.
__init__: Renamed advanced_debugging to debugging_tools.
additional_generators: Renamed advanced_debugging to debugging_tools.
additional_io: Renamed advanced_debugging to debugging_tools.
advanced_image_processing: Renamed advanced_debugging to debugging_tools.
batch_learner: Renamed advanced_debugging to debugging_tools.
denoising: Renamed advanced_debugging to debugging_tools.
expanded_numpy: Renamed advanced_debugging to debugging_tools.
HDF5_importer: Renamed advanced_debugging to debugging_tools.
HDF5_logger: Renamed advanced_debugging to debugging_tools.
HDF5_serializers: Renamed advanced_debugging to debugging_tools.
neuron_matplotlib_viewer: Renamed advanced_debugging to debugging_tools.
neuron_volumina_viewer: Renamed advanced_debugging to debugging_tools.
read_config: Renamed advanced_debugging to debugging_tools.
simple_image_processing: Renamed advanced_debugging to debugging_tools.
tiff_file_format: Renamed advanced_debugging to debugging_tools.
wavelet_transform: Renamed advanced_debugging to debugging_tools.

This finally fixes issue #40.
HDF5_logger: Added the ability for HDF5ArrayLogger instances to overwrite values in the HDF5 file if specified so in the constructor.
batch_learner: Changed so that explicit deletion of intermediate data is not required.
batch_learner: Changed reading the original images to use the resume_logger.
batch_learner: Found a search that was not occurring in the right location in the HDF5 file.
batch_learner: Removed directory deletion. Now, run_stage = "all" will rerun all stages; whereas, run_stage = "" will resume at the last non-run stage.
batch_learner: Refactored neuron generation (as well as intermediate results) into a new function called generate_neurons. This fixes issue #42.
advanced_image_processing: In the function preprocess_data, the internal variables for optional preprocessing steps were renamed to make it clear the preprocessing step may not have occurred. Also, renamed the internal variable name new_data_i_zero_mask_i_outline_interpolation to new_data_i_zero_mask_interpolation in removing_lines. This fixes issue #49.
advanced_image_processing: Renamed the function removing_lines to remove_zeroed_lines. Also, renamed related paramter keys. This fixes issue #48.
advanced_image_processing: Dropped an unused parameter for extended_region_local_maxima_properties.
HDF5_logger: Renamed to HDF5_recorder.
HDF5_recorder: Renamed from HDF5_logger. Renamed everything from logger to recorder.
__init__: Refactored to include changes in HDF5_recorder.
advanced_image_processing: Refactored to include changes in HDF5_recorder.
batch_learner: Refactored to include changes in HDF5_recorder.
wavelet_transform: Refactored to include changes in HDF5_recorder.

This fixes issue #45.
advanced_image_processing: Added assertion check to the function extract_quantile inside of extract_f0 in the module advanced_image_processing. Checks to make sure only one quantile is requested.
advanced_image_processing: Moved extract_quantile into extract_f0 directly. This fixes issue #51.
simple_image_processing: The function zeroed_mean_images was taking unnecessary arguments.
advanced_image_processing: Inside ExtendedRegionProps, ensured intensity and label image are copied in so as to ensure purity.
advanced_image_processing: Cleaned up ExtendedRegionProps and extended_region_local_maxima_properties and all code using it to clearly state that local maxima are used not centroids.
advanced_image_processing: Adjustment to allow for having optional upper or lower bounds.