simba-uw-tf-dev 4.6.4__py3-none-any.whl → 4.6.6__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- simba/data_processors/cuda/geometry.py +45 -27
- simba/data_processors/cuda/image.py +1620 -1600
- simba/data_processors/cuda/statistics.py +17 -9
- simba/data_processors/egocentric_aligner.py +24 -6
- simba/data_processors/kleinberg_calculator.py +6 -2
- simba/feature_extractors/feature_subsets.py +12 -5
- simba/feature_extractors/straub_tail_analyzer.py +0 -2
- simba/mixins/statistics_mixin.py +9 -2
- simba/sandbox/analyze_runtimes.py +30 -0
- simba/sandbox/cuda/egocentric_rotator.py +374 -374
- simba/sandbox/proboscis_to_tip.py +28 -0
- simba/sandbox/test_directionality.py +47 -0
- simba/sandbox/test_nonstatic_directionality.py +27 -0
- simba/sandbox/test_pycharm_cuda.py +51 -0
- simba/sandbox/test_simba_install.py +41 -0
- simba/sandbox/test_static_directionality.py +26 -0
- simba/sandbox/test_static_directionality_2d.py +26 -0
- simba/sandbox/verify_env.py +42 -0
- simba/ui/pop_ups/fsttc_pop_up.py +27 -25
- simba/ui/pop_ups/kleinberg_pop_up.py +3 -2
- simba/utils/data.py +0 -1
- simba/utils/errors.py +441 -440
- simba/utils/lookups.py +1203 -1203
- simba/utils/read_write.py +38 -13
- simba/video_processors/egocentric_video_rotator.py +41 -36
- simba/video_processors/video_processing.py +5247 -5233
- simba/video_processors/videos_to_frames.py +41 -31
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/METADATA +2 -2
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/RECORD +33 -24
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/LICENSE +0 -0
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/WHEEL +0 -0
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/entry_points.txt +0 -0
- {simba_uw_tf_dev-4.6.4.dist-info → simba_uw_tf_dev-4.6.6.dist-info}/top_level.txt +0 -0
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@@ -6,17 +6,17 @@ except:
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from typing_extensions import Literal
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import functools
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import multiprocessing
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import os
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from datetime import datetime
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import cv2
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from simba.utils.checks import (check_if_dir_exists, check_int, check_str,
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check_valid_boolean)
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from simba.utils.data import terminate_cpu_pool
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from simba.utils.data import get_cpu_pool, terminate_cpu_pool
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from simba.utils.printing import SimbaTimer, stdout_success
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from simba.utils.read_write import (find_core_cnt,
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read_frm_of_video)
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from simba.utils.read_write import (find_core_cnt, get_fn_ext,
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get_video_meta_data, read_frm_of_video)
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JPEG, PNG, WEBP = 'jpeg', 'png', 'webp'
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@@ -40,7 +40,7 @@ def _video_to_frms_helper(img_batch: Tuple[int, List[int]],
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else:
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save_path = os.path.join(save_dir, f'{frm_idx}.{img_format}')
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if verbose:
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print(f"Saving image {save_path} ...")
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print(f"Saving image {save_path} ({frm_idx}/{video_meta_data['frame_count']})...")
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img = read_frm_of_video(video_path=cap, frame_index=frm_idx, greyscale=greyscale, clahe=clahe, black_and_white=black_and_white)
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if img_format == WEBP:
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cv2.imwrite(save_path, img, [cv2.IMWRITE_WEBP_QUALITY, quality])
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@@ -51,7 +51,7 @@ def _video_to_frms_helper(img_batch: Tuple[int, List[int]],
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return batch_cnt
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def video_to_frames(video_path: Union[str, os.PathLike],
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save_dir: Union[str, os.PathLike],
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save_dir: Optional[Union[str, os.PathLike]] = None,
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quality: Optional[int] = 95,
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img_format: Literal['png', 'webp'] = 'png',
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verbose: bool = True,
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@@ -61,10 +61,16 @@ def video_to_frames(video_path: Union[str, os.PathLike],
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black_and_white: bool = False,
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include_video_name_in_filename: bool = True):
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"""
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Extract all frames from a video file and save them as individual image files.
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.. csv-table::
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:header: EXPECTED RUNTIMES
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:file: ../../docs/tables/video_to_frames.csv
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:widths: 10, 45, 45
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:align: center
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:header-rows: 1
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.. note::
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Uses multiprocessing for faster frame extraction. Frames are saved with sequential numbering (0, 1, 2, ...).
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timer = SimbaTimer(start=True)
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video_meta_data = get_video_meta_data(video_path=video_path)
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if save_dir is not None:
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check_if_dir_exists(in_dir=save_dir, source=video_to_frames.__name__, raise_error=True)
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else:
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save_dir = os.path.join(get_fn_ext(filepath=video_path)[0], f'{video_meta_data["video_name"]}_frames_{datetime.now().strftime("%Y%m%d%H%M%S")}')
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os.makedirs(save_dir)
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check_valid_boolean(value=verbose, source=f'{video_to_frames.__name__} verbose')
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check_valid_boolean(value=clahe, source=f'{video_to_frames.__name__} clahe')
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check_valid_boolean(value=greyscale, source=f'{video_to_frames.__name__} greyscale')
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@@ -99,35 +109,35 @@ def video_to_frames(video_path: Union[str, os.PathLike],
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check_valid_boolean(value=include_video_name_in_filename, source=f'{video_to_frames.__name__} include_video_name_in_filename')
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check_int(name=f'{video_to_frames.__name__} core_cnt', value=core_cnt, min_value=-1, unaccepted_vals=[0], raise_error=True)
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check_int(name=f'{video_to_frames.__name__} quality', value=quality, min_value=1, max_value=100, raise_error=True)
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core_cnt = find_core_cnt()[0] if core_cnt -1 or core_cnt > find_core_cnt()[0] else core_cnt
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core_cnt = find_core_cnt()[0] if core_cnt == -1 or core_cnt > find_core_cnt()[0] else core_cnt
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check_str(name=f'{video_to_frames.__name__} img_format', value=img_format, options=('jpeg', 'png', 'webp'))
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frm_ids = list(range(0, video_meta_data['frame_count']))
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frm_ids = [frm_ids[i * len(frm_ids) // core_cnt: (i + 1) * len(frm_ids) // core_cnt] for i in range(core_cnt)]
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frm_ids = [(i, j) for i, j in enumerate(frm_ids)]
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terminate_cpu_pool(pool=pool, force=True)
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pool = get_cpu_pool(core_cnt=core_cnt, source=video_to_frames.__name__)
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constants = functools.partial(_video_to_frms_helper,
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verbose=verbose,
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img_format=img_format,
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quality=quality,
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greyscale=greyscale,
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black_and_white=black_and_white,
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include_video_name_in_filename=include_video_name_in_filename,
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video_path=video_path,
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clahe=clahe,
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save_dir=save_dir)
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for cnt, batch_id in enumerate(pool.imap(constants, frm_ids, chunksize=1)):
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if verbose:
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print(f'Video frame batch {batch_id} (of {core_cnt}) complete...')
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terminate_cpu_pool(pool=pool, force=True, source=video_to_frames.__name__)
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timer.stop_timer()
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if verbose:
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stdout_success(msg=f'All frames for video {video_path} saved in {save_dir}', elapsed_time=timer.elapsed_time_str)
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if verbose: stdout_success(msg=f'All frames ({video_meta_data["frame_count"]}) for video {video_path} saved in {save_dir}', elapsed_time=timer.elapsed_time_str)
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# if __name__ == "__main__":
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# video_to_frames(video_path=r"
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# save_dir=
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# video_to_frames(video_path=r"D:\troubleshooting\mitra\project_folder\videos\average_cpu_test\15min.mp4",
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# save_dir=None,
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# black_and_white=False,
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# verbose=True,
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# img_format='
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# clahe=
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# img_format='png',
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# clahe=False,
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# core_cnt=18)
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Metadata-Version: 2.1
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Name: simba-uw-tf-dev
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Version: 4.6.
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Version: 4.6.6
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Summary: Toolkit for computer classification and analysis of behaviors in experimental animals
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Home-page: https://github.com/sgoldenlab/simba
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Author: Simon Nilsson, Jia Jie Choong, Sophia Hwang
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Requires-Dist: kaleido ; python_version >= "3.9"
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Requires-Dist: psutil ; python_version >= "3.9"
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Requires-Dist: h5py (==3.11.0) ; python_version >= "3.9"
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Requires-Dist: numba (==0.
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Requires-Dist: numba (==0.63.1) ; python_version >= "3.9"
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Requires-Dist: numexpr (==2.10.0) ; python_version >= "3.9"
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Requires-Dist: statsmodels (==0.14.2) ; python_version >= "3.9"
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Requires-Dist: shap (==0.42.0) ; python_version >= "3.9"
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@@ -524,7 +524,7 @@ simba/data_processors/cue_light_clf_statistics.py,sha256=Msv1xe3tq4yn3j5sFswso-v
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simba/data_processors/cue_light_movement_statistics.py,sha256=xQKJNdA2i1MOhMwct-MdTbJPPP75O-aOnHT292Zl1c4,9058
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simba/data_processors/directing_animal_to_bodypart.py,sha256=xsB5jiAUg4sIYBhEyINvxofJo6xL2zP554t_ysi7MCQ,11079
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simba/data_processors/directing_other_animals_calculator.py,sha256=Ikif_lPh0RfOj7q5ijMcPGh5kEBLse1P91gaz30UXcs,18234
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simba/data_processors/egocentric_aligner.py,sha256=
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simba/data_processors/egocentric_aligner.py,sha256=bry1SuiBSYRZX-bjLGpSY2xYJ2l5OYInst_kVxWREHU,13265
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simba/data_processors/find_animal_blob_location.py,sha256=whSxaCSLtRQGZchMBffYSlTI7LIFE7YphNaztmMzMv0,27698
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simba/data_processors/freezing_detector.py,sha256=p9H44jfyzkuEFCHyAKee-xcvFNrw_a5vSSZm9FMLaZk,10199
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simba/data_processors/fsttc_calculator.py,sha256=fW09KZ62GiBNgwEPV1n5SsIImRzPpbiP0yiNeTiexL0,20639
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simba/data_processors/interpolate.py,sha256=GaLvrqS-iVB9TA0eEsCO3dnUCxVD_0KwWqWYZsRlyOM,8006
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simba/data_processors/interpolate_pose.py,sha256=RME5CxN-oJTiRab4iMQLMRmc7rmdsvXz490wyguDT3Q,7139
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simba/data_processors/interpolation_smoothing.py,sha256=aeN4klghvxXUDV8yu_tiXVUAV4Bxu_y0jmNGnpJe6vw,39132
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simba/data_processors/kleinberg_calculator.py,sha256=
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simba/data_processors/kleinberg_calculator.py,sha256=fPIgwuhFgVJvszahOsMe2MGhF5qBhQ-EXEb7e_35OtI,14738
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simba/data_processors/light_dark_box_analyzer.py,sha256=FaXBkuAzI2YZToBvswCTjv1epYK6SiysQTepIQ_-qPc,9514
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simba/data_processors/movement_calculator.py,sha256=tqDzgMIH23iz_U6ABqva2VpG2Yu8GV1__DK6I6-rd7Y,12393
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simba/data_processors/mutual_exclusivity_corrector.py,sha256=XuLk8gd2oXAunpP3yJTIcfeoWofpO1iv2EFY6QcEEU8,8729
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simba/data_processors/cuda/circular_statistics.py,sha256=EYhnkL0Fe_Ec9PU2kciv7RyDQdBELPH3HcH9BCnMfdo,34286
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simba/data_processors/cuda/create_shap_log.py,sha256=yQlWb1RKjagwCKtahifSw8Esr4VOVsTuCAx7fLSfSvU,9603
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simba/data_processors/cuda/data.py,sha256=tZLunARZVlk1plh7atR3PY5QADMPZXfbYE92uvYkx1g,11831
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simba/data_processors/cuda/statistics.py,sha256=
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simba/data_processors/cuda/geometry.py,sha256=jkocYwWcweQ1U6DxVDxP3vifuZdxpyZHQ5_J_GeNgGU,25522
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simba/data_processors/cuda/image.py,sha256=s0XwQkY1_D23PCBMk-zrSDOW4FlSsDq3QeIFYvuSsdE,84379
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simba/data_processors/cuda/statistics.py,sha256=YnexlgHdi-GSezUfU8il0vgaW8mwVffIOR3be_t6r2A,46383
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simba/data_processors/cuda/timeseries.py,sha256=12UWvjSrnriOsT9UmDJJVyWSito_ueIrH1Gy5m1cCCA,16416
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simba/data_processors/cuda/utils.py,sha256=0Z51kEItgDl9MfPQ9_jvClzR2_pvIWxFkLcjb3xdDE8,8584
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simba/feature_extractors/.DS_Store,sha256=SiyR4U0h7Ehg8KGJf5cXr85BYdcZfvGGcRmp1GMVuzQ,6148
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simba/feature_extractors/feature_extractor_8bps_2_animals.py,sha256=0mlOUPStO3LfdlmU970Wmw5x40o9sVJ6UzrKg248mtI,36308
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simba/feature_extractors/feature_extractor_9bp.py,sha256=dMzigppwKODXpVPKwkqZoboAR3roYik1LYKWBnhZwnQ,37327
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simba/feature_extractors/feature_extractor_user_defined.py,sha256=w8hgtYGk6Ux_X1mIYleEABVmxkLPUf23TfWYe-G75UI,9917
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simba/feature_extractors/feature_subsets.py,sha256=CXoGuhZNfQmEhrgm8kb0rZi755buO-IGKVTAzpF6BV4,27471
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simba/feature_extractors/gerbil_featurizer.py,sha256=EeBlAXiTsM2oHMfs0M1wlm9LWrQVZuLUY2WuOQIDMnw,11994
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simba/feature_extractors/mitra_feature_extractor.py,sha256=pmLp2A5jfkia6wtD7X39TmMDukeCxbmUPmdVFgmCUZ4,30027
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simba/feature_extractors/perimeter_jit.py,sha256=Pe7IlxeGTEQfpkt9iiAq97OG9r0mQ4kE6VderLyNFmg,8621
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simba/feature_extractors/rat_social_featurizer.py,sha256=eOJt6O4QR8kY0fJ2tAmRGLYAQSLkZoc3VoQ5F6MSN90,7345
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simba/feature_extractors/riptortus_featurizer.py,sha256=3XA_GfxmcuZOSkC1HxOebcGh5Y47pZtgaFR8Kb6lexQ,34518
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simba/feature_extractors/misc/add_probability_cnt_features.py,sha256=5mHH7IEA7a_vv9i1q7nUOYfY5FT9o6RF0LwSEaW6CUM,2932
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@@ -624,7 +624,7 @@ simba/mixins/network_mixin.py,sha256=s_OsF6VSlsa2vb5sysDQKErLp4D5EfBF1MVQ_yKWC_Y
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simba/mixins/pop_up_mixin.py,sha256=tAKC3Axp1jgQ8VH2GfvKO5HbLUpZzo_aWou2xS-SYxc,24701
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simba/mixins/pose_importer_mixin.py,sha256=bYl17qQcJAdd93_q-tDof8V1f5-OGeI9id7K8YGmN1E,22358
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simba/mixins/statistics_mixin.py,sha256
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simba/mixins/statistics_mixin.py,sha256=-5_qPcmFmApcBxnqYg6CXL6j8N9BZ2FI9n-bIoaBA_Q,271327
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simba/mixins/timeseries_features_mixin.py,sha256=O3RMAfOHNSTr1cGEGDcaOCE8wpcKrDD_1rRbbqZb5yU,139305
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simba/mixins/unsupervised_mixin.py,sha256=2R1pV4UxFxxwQcM_PzrdQNcx3NMcLDhLu4llGZUTDfY,5370
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simba/sandbox/alyssa_ethan.py,sha256=U8xjTQd8UV94DBskjxUZwh7VwUhQPCmJtencVsqAEqo,27192
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simba/sandbox/amber_featurizer.py,sha256=O5ePbbb0non5JV9Mwoa9N3PxZVEHtXt4R4yjjHVoObw,69423
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simba/sandbox/analyze_runtimes.py,sha256=pkKQXTdxNUWgWzprVe9AdS3mmky-M2b2Zi3bhDk1mwI,1102
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simba/sandbox/angle_3pt.py,sha256=QZ41V_mS1QEzn2j17uKcFD8soagSlK-R7pff0mdz4ZI,2672
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simba/sandbox/append_targets'.py,sha256=f8lB0FFdJy97uZuEyfWsJYOf2Uw05skSGjH3uiLFtrQ,4106
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simba/sandbox/pose_vis_gpu.py,sha256=OGDA2xcrCrYx2ubkZvFqhqvRJA5dtsdvud8LJfFNFG8,1737
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simba/sandbox/proboscis_to_tip.py,sha256=wxjjAaAlDO_GGFa7xp4oM1rMWyXKgYIPD-NYbuznX-8,1445
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simba/sandbox/px_to_mm.py,sha256=2dLMuHteEzlD35vYIGsN6zfZVUPuWw2Vun39XXeBJqU,9394
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simba/sandbox/pypi_sizes.py,sha256=4w6tR9mb772e7GfwqcTtb_Ms4doqtjq8i8zg9HAk-v8,1037
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simba/sandbox/temporal_align.py,sha256=SIA_GxLakCzREVUKWUwXJtprO6bq5gAvbmYuiCg5QHg,3866
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simba/sandbox/test_camera_movement.py,sha256=dKzjT8l14U1bjiM7-Pt7AkCdpaBK_1vmXs3zBWf-xCQ,2567
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simba/sandbox/test_directionality.py,sha256=40d2u6wLqRoK4TXccs6DRJ-YqZ7gdEmuqGvOONRsqBM,1513
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simba/sandbox/test_nonstatic_directionality.py,sha256=Ol359G3TnAnKyPVUquTD5HaF99QEGmiHn2rvkOfjPkw,975
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simba/sandbox/test_pycharm_cuda.py,sha256=MvU2oOMcPHlCoL1JySaAtetjKpWAXhLQDGwJyWskaTE,1600
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simba/sandbox/test_simba_install.py,sha256=eBpP1YxUy4gHEJ-t3ZXoy7WYsR8Z4u4cPJnXFiwAS5g,1205
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simba/sandbox/test_static_directionality.py,sha256=v8pJX_P7PuIXvT8LMdZ0xOzwQCkSeqxDAJZBbvmSk0E,872
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simba/sandbox/test_static_directionality_2d.py,sha256=huXC3NVdfWziiZqStmlme_Mrq3nV2gmguAde3CxJqqE,957
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simba/sandbox/time_stamp_calculator.py,sha256=iMVc7c6uAuXsrV8ywZU6Xovl_iTFAB4vjlLYsHaZtuc,1613
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simba/sandbox/time_stitching.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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simba/sandbox/update_merge_coco_kp.py,sha256=3fuiGJym9CpBpPPgdp9w1UK1dYhn9wzmec29X6vfCaY,7724
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simba/sandbox/verify_env.py,sha256=E3Tx8a8uDzcZQdwvmYs2bp7x-hac_im5I9uVZv9wAZE,1347
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simba/sandbox/video_meta_data_get.py,sha256=foTzEuuqd0gYCVz54fWF4bITpANfBfCglNdLvRdpXj0,1979
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simba/sandbox/cuda/jitted_line_crosses_to_static_targets.py,sha256=zaO7R8nE64QQlzjTZDDFP0LqOkMTjxYPwUAmvejQSXA,4907
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simba/sandbox/maplight/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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simba/sandbox/maplight/add_videos_to_dlc_config.py,sha256=QUsdlOpc6XcF46vuHOxgbhY66A2lj3L6m84OD7Q9uwY,1176
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simba/ui/pop_ups/egocentric_alignment_pop_up.py,sha256=BJEQXOxo0yuyj4nEiH0YeYuSsq5-3KfaE_DXUEcmU-Y,7085
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simba/ui/pop_ups/extract_annotation_frames_pop_up.py,sha256=IxSed3wZoDftHs7YfykJzHgg8_SiCqU1t_1Us9XGgWg,5975
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simba/ui/pop_ups/fsttc_pop_up.py,sha256=
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simba/ui/pop_ups/gantt_pop_up.py,sha256=gkqg74sxjHsaB-FHLIXW-275wuZMwjC7cPKfrn0jVOA,9234
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simba/ui/pop_ups/heatmap_location_pop_up.py,sha256=LeQPzcjLSCCn8my-dvIIQ9DDTNtblxPSmCp7x4Ob7YY,8645
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simba_uw_tf_dev-4.6.6.dist-info/LICENSE,sha256=Sjn362upcvYFypam-b-ziOXU1Wl5GGuTt5ICrGimzyA,1720
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simba_uw_tf_dev-4.6.6.dist-info/METADATA,sha256=ASJGWQiiTkJXyvs1q2Dhv1-wthrllCogYq9bTITgH8k,11375
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simba_uw_tf_dev-4.6.6.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
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simba_uw_tf_dev-4.6.6.dist-info/entry_points.txt,sha256=Nfh_EbfDGdKftLjCnGWtQrBHENiDYMdgupwLyLpU5dc,44
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simba_uw_tf_dev-4.6.6.dist-info/top_level.txt,sha256=ogtimvlqDxDTOBAPfT2WaQ2pGAAbKRXG8z8eUTzf6TU,14
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