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Danielsf/dev/downsampled/video#415

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danielsf merged 42 commits intomainAllenInstitute/ophys_etl_pipelines:mainfrom danielsf/dev/downsampled/videoAllenInstitute/ophys_etl_pipelines:danielsf/dev/downsampled/videoCopy head branch name to clipboardJan 25, 2022

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Commits on Jan 24, 2022

• rough implementation of code to get mp4

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• actually use quantiles

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• finer, fainter reticles

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• output movie at 31hz regardless

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• alpha=0.5 for reticles

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• output fps is 8*output_hz

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• use different codec for avi

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• make kernel_size optional (None means no spatial smoothing at all)

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• add CLI for video downsampling

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• factor out step to write array to video

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• further factor out code to create array from HDF5 file

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• add utility for creating side-by-side videos

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• factor out normalization of video

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• rename downsample_video/__main__ -> downsample_video/single_video

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• move common elements of DownsampleVideoSchema to base schema

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• add CLI for generating side-by-side video

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• allow users to set speed_up_factor

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• no smoothing if kernel_size == 0

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• typo in error message

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• pep8 changes

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• add docstrings to downsample_video/utils.py

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• add unit test for _video_worker

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• make output_path in test pathlib.Path

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• _video_worker raises an exception if asked to start on a bad frame

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• explicitly test on input_slice[0]%n_frames == 0

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• test create_downsampled_video_h5; make sure it fails if a process fails

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• add smoke test for _write_array_to_video

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• add tests for _min_max_from_h5

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• test video_array_from_h5

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• if border would exclude all pixels, disregard border

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• add test for create_downsampled_video

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Commits on Jan 25, 2022

• add smoke test for side-by-side video creation

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• update docstring in test

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• add descriptions to DownsampleBaseSchema parameters

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• add test for single_video module

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• add smoketest for side_by_side_video module

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• rename module -> video instead of downsample_video

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• rename schemas and runners to remove mention of downsampling

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• fix documentation of speed_up_factor

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• use np.clip to clip data

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• move video creation methods to top of utils file

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• replace print statements with logger calls

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