Reformatted code.
HDF5_serializers: Simplified serializer. Now, also handles NumPy scalar values, as well.
HDF5_logger: Made sure that there is a flush after every log operation. This way, if there is a crash, the most recent debug information can be seen.
advanced_image_processing: Added debug information about individual neurons being fused in fuse_neurons.
advanced_image_processing: Changed "overlayed" to "overlaid".
advanced_image_processing: Removed unused imports.
neuron_matplotlib_viewer: Renamed from neuron_viewer so as to clearly distinguish from the volumina based viewer in progress.
neuron_viewer: Renamed to neuron_matplotlib_viewer.
__init__: Also, changed the name of neuron_viewer to neuron_matplotlib_viewer.
neuron_volumina_viewer: Added the equivalent of the matplotlib based NeuronViewer using Volumina.
advanced_image_processing: Minor changes. Some reformatting. Corrected docstrings.
advanced_iterators: Add the function reformat_slice, which will properly fill all the parameters of a slice. If the parameters are None, then they will be filled with default values. Even the stop value will be specified, if it it is supplied.
advanced_iterators: Added the function len_slice, which determines the length of a slice without having to apply it. If the slice does not have a value for its stop point and a length is not specified, it will raise an exception as the length cannot be determined from that information.
advanced_iterators: Add the function index_axis_at_pos, which will index a NumPy array on a given axis using the position provided and returns a view of the original array.
advanced_numpy: One of the doctests used an older name for dot_product_L2_normalized. This has since been corrected. All doctests passed.
advanced_numpy: Ensured that dot_product_L2_normalized, dot_product_normalized, dot_product_partially_normalized, and dot_product only work on floating point types.
advanced_image_processing: Cleaned up some docstrings. Removed duplicate content from neuron sets. Added default argument for array debug loggers. Removed some now unnecessary checks.
advanced_numpy: Added more doctests for different types of arrays with various dot products and normalization.
advanced_iterators: Added the function reformat_slices, which calls reformat_slice on multiple slices. Also, added the function len_slices, which calls len_slice on multiple slices.
neuron_volumina_viewer: Changed so that time will appear time/basis will appear as a channel. Added a standardized way to transpose axis order from that stored in the HDF5 files. Fixed a bug that caused images not to be properly broadcast for viewer. Add a method to add a grayscale source. Cleaned up code for dealing with fused sources from HDF5. Replaced print statements with logging statements and removed unnecessary logging. Also, cleaned up unused and outdated code pieces.
neuron_volumina_viewer: Implemented simple ColorTableLayer for label images or masks. This fixes #17.
advanced_image_processing: Added exports of wavelet transforms of all scales up to the maximum in the parameters. This fixes #23.