GitHub PushEvent at 2014-08-09 00:27:15
Repository: nanshe
Actor: jakirkham
Payload: {"shas":[["de5d92d69d9bfa40e78d8351e1de1c121966dcbc","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_numpy: Renamed to expanded_numpy.\nexpanded_numpy: Renamed from advanced_numpy.\n__init__: Renamed advanced_numpy to expanded_numpy.\nadvanced_image_processing: Renamed advanced_numpy to expanded_numpy.\nneuron_volumina_viewer: Renamed advanced_numpy to expanded_numpy.\ntiff_file_format: Renamed advanced_numpy to expanded_numpy.\n\nThis is related to issue #40.","John Kirkham",false],["3a0db6ec32b641b64f163c18bafbf0ea7173ec7e","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_io: Renamed to additional_io.\nadditional_io: Renamed from advanced_io.\ntiff_file_format: Renamed advanced_io to additional_io.\n\nThis is related to issue #40.","John Kirkham",false],["1b7dfee9ac9f9ff949239d0c0e51d57453f49d9a","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_iterators: Renamed to additional_generators.\nadditional_generators: Renamed from advanced_iterators.\n__init__: Renamed advanced_iterators to additional_generators.\nadvanced_image_processing: Renamed advanced_iterators to additional_generators.\nexpanded_numpy: Renamed advanced_iterators to additional_generators.\nneuron_volumina_viewer: Renamed advanced_iterators to additional_generators.\ntiff_file_format: Renamed advanced_iterators to additional_generators.\nrandom_dictionary_learning_data: Renamed advanced_iterators to additional_generators.\n\nThis is related to issue #40.","John Kirkham",false],["81d548bfabd60da8c23034938b4f3f60903dc14d","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_debugging: Renamed to debugging_tools.\ndebugging_tools: Renamed from advanced_debugging.\n__init__: Renamed advanced_debugging to debugging_tools.\nadditional_generators: Renamed advanced_debugging to debugging_tools.\nadditional_io: Renamed advanced_debugging to debugging_tools.\nadvanced_image_processing: Renamed advanced_debugging to debugging_tools.\nbatch_learner: Renamed advanced_debugging to debugging_tools.\ndenoising: Renamed advanced_debugging to debugging_tools.\nexpanded_numpy: Renamed advanced_debugging to debugging_tools.\nHDF5_importer: Renamed advanced_debugging to debugging_tools.\nHDF5_logger: Renamed advanced_debugging to debugging_tools.\nHDF5_serializers: Renamed advanced_debugging to debugging_tools.\nneuron_matplotlib_viewer: Renamed advanced_debugging to debugging_tools.\nneuron_volumina_viewer: Renamed advanced_debugging to debugging_tools.\nread_config: Renamed advanced_debugging to debugging_tools.\nsimple_image_processing: Renamed advanced_debugging to debugging_tools.\ntiff_file_format: Renamed advanced_debugging to debugging_tools.\nwavelet_transform: Renamed advanced_debugging to debugging_tools.\n\nThis finally fixes issue #40.","John Kirkham",false],["0727793a3c2771059a329eec6fd2a6766fa3a1cd","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","HDF5_logger: Added the ability for HDF5ArrayLogger instances to overwrite values in the HDF5 file if specified so in the constructor.","John Kirkham",false],["7ab01cd950c29e01434ff7c9c9664519310685c2","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","batch_learner: Changed so that explicit deletion of intermediate data is not required.","John Kirkham",false],["129f776b9040af97834efbcb20f9934b95995631","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","batch_learner: Changed reading the original images to use the resume_logger.","John Kirkham",false],["2f16b8e78b404a5a091abdfdb28888546ef5f8c2","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","batch_learner: Found a search that was not occurring in the right location in the HDF5 file.","John Kirkham",false],["c939d822556a0a934444fe081c01a6267c73f165","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","batch_learner: Removed directory deletion. Now, run_stage = \"all\" will rerun all stages; whereas, run_stage = \"\" will resume at the last non-run stage.","John Kirkham",false],["6cc5d14ca18d9c720b3f94ce5e28ca3ff8ca39da","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","batch_learner: Refactored neuron generation (as well as intermediate results) into a new function called generate_neurons. This fixes issue #42.","John Kirkham",false],["233faaf6f10b7953035e0709a22f6a11e38571cb","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","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.","John Kirkham",false],["facde1b83af09909440b3c32ea9a273df9cf5382","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_image_processing: Renamed the function removing_lines to remove_zeroed_lines. Also, renamed related paramter keys. This fixes issue #48.","John Kirkham",false],["237a65f3fb81994e4f1de5b2130b60b9b34668c6","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_image_processing: Dropped an unused parameter for extended_region_local_maxima_properties.","John Kirkham",false],["f0b827dd58473f7a3e1b5b3fb1928800ef3bf9c8","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","HDF5_logger: Renamed to HDF5_recorder.\nHDF5_recorder: Renamed from HDF5_logger. Renamed everything from logger to recorder.\n__init__: Refactored to include changes in HDF5_recorder.\nadvanced_image_processing: Refactored to include changes in HDF5_recorder.\nbatch_learner: Refactored to include changes in HDF5_recorder.\nwavelet_transform: Refactored to include changes in HDF5_recorder.\n\nThis fixes issue #45.","John Kirkham",false],["0a630f61a5885aa5b1dcda2a9e463ccab73add04","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","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.","John Kirkham",false],["7f4e9dd232a18aff1b8737c64bb823ff480cfb47","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_image_processing: Moved extract_quantile into extract_f0 directly. This fixes issue #51.","John Kirkham",false],["3412f7c9bc40fc8f3c6821c0cbed7f149bb475bf","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","simple_image_processing: The function zeroed_mean_images was taking unnecessary arguments.","John Kirkham",false],["3893bd083055fcbf48288f7c4d2dc72958de293e","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_image_processing: Inside ExtendedRegionProps, ensured intensity and label image are copied in so as to ensure purity.","John Kirkham",false],["8e4a1027bfac02b61b0154c7960e5a6c14109c1f","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","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.","John Kirkham",false],["6549a0e2ed92f4b0f8cd92a87b9e409d4d649c34","f62e5e898bee75be9eee0691c7e4e7a84b990c01@janelia.hhmi.org","advanced_image_processing: Adjustment to allow for having optional upper or lower bounds.","John Kirkham",false]],"size":194,"ref":"refs/heads/future_master","head":"470cc2ce33d4d963de31abadf202d78d72dbebbf"}