simba-uw-tf-dev 4.6.1__py3-none-any.whl → 4.6.3__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/SimBA.py +2 -2
- simba/assets/icons/frames_2.png +0 -0
- simba/data_processors/agg_clf_counter_mp.py +52 -53
- simba/data_processors/cuda/image.py +3 -1
- simba/data_processors/cue_light_analyzer.py +5 -9
- simba/mixins/geometry_mixin.py +14 -28
- simba/mixins/image_mixin.py +10 -14
- simba/mixins/train_model_mixin.py +2 -2
- simba/plotting/ROI_feature_visualizer_mp.py +3 -5
- simba/plotting/clf_validator_mp.py +4 -5
- simba/plotting/cue_light_visualizer.py +6 -7
- simba/plotting/directing_animals_visualizer_mp.py +2 -3
- simba/plotting/distance_plotter_mp.py +378 -378
- simba/plotting/frame_mergerer_ffmpeg.py +137 -137
- simba/plotting/gantt_creator_mp.py +59 -31
- simba/plotting/geometry_plotter.py +270 -272
- simba/plotting/heat_mapper_clf_mp.py +2 -4
- simba/plotting/heat_mapper_location_mp.py +2 -2
- simba/plotting/light_dark_box_plotter.py +2 -2
- simba/plotting/path_plotter_mp.py +26 -29
- simba/plotting/plot_clf_results_mp.py +455 -454
- simba/plotting/pose_plotter_mp.py +27 -32
- simba/plotting/probability_plot_creator_mp.py +288 -288
- simba/plotting/roi_plotter_mp.py +29 -30
- simba/plotting/single_run_model_validation_video_mp.py +427 -427
- simba/plotting/spontaneous_alternation_plotter.py +2 -3
- simba/plotting/yolo_pose_track_visualizer.py +31 -27
- simba/plotting/yolo_pose_visualizer.py +32 -34
- simba/plotting/yolo_seg_visualizer.py +2 -3
- simba/roi_tools/roi_aggregate_stats_mp.py +4 -3
- simba/roi_tools/roi_clf_calculator_mp.py +3 -3
- simba/sandbox/cuda/egocentric_rotator.py +374 -0
- simba/sandbox/get_cpu_pool.py +5 -0
- simba/ui/pop_ups/clf_add_remove_print_pop_up.py +3 -1
- simba/ui/pop_ups/egocentric_alignment_pop_up.py +6 -3
- simba/ui/pop_ups/multiple_videos_to_frames_popup.py +10 -11
- simba/ui/pop_ups/single_video_to_frames_popup.py +10 -10
- simba/ui/pop_ups/video_processing_pop_up.py +63 -63
- simba/ui/tkinter_functions.py +7 -1
- simba/utils/data.py +89 -12
- simba/utils/enums.py +1 -0
- simba/utils/printing.py +9 -8
- simba/utils/read_write.py +3726 -3721
- simba/video_processors/clahe_ui.py +65 -22
- simba/video_processors/egocentric_video_rotator.py +6 -9
- simba/video_processors/video_processing.py +21 -10
- simba/video_processors/videos_to_frames.py +3 -2
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/METADATA +1 -1
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/RECORD +53 -50
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/LICENSE +0 -0
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/WHEEL +0 -0
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/entry_points.txt +0 -0
- {simba_uw_tf_dev-4.6.1.dist-info → simba_uw_tf_dev-4.6.3.dist-info}/top_level.txt +0 -0
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import os
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import threading
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import time
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from typing import Tuple, Union
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import cv2
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@@ -32,29 +34,66 @@ def interactive_clahe_ui(data: Union[str, os.PathLike]) -> Tuple[float, int]:
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"""
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global original_img, font_size, x_spacer, y_spacer, txt
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callback_lock = threading.Lock()
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last_update_time = [0]
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update_delay = 0.05
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def _get_trackbar_values(v):
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global original_img, font_size, x_spacer, y_spacer, txt
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nonlocal callback_lock, last_update_time, update_delay
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current_time = time.time()
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if current_time - last_update_time[0] < update_delay:
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return
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if not callback_lock.acquire(blocking=False):
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return
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try:
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if cv2.getWindowProperty(WIN_NAME, cv2.WND_PROP_VISIBLE) < 1:
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return
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try:
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clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
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tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
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if tile_size % 2 == 0: tile_size += 1
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clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
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img_clahe = clahe.apply(original_img)
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cv2.putText(img_clahe, txt,(TextOptions.BORDER_BUFFER_X.value, TextOptions.BORDER_BUFFER_Y.value + y_spacer), TextOptions.FONT.value, font_size, (255, 255, 255), 3)
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cv2.imshow(WIN_NAME, img_clahe)
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cv2.waitKey(1)
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last_update_time[0] = current_time
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except cv2.error:
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pass
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finally:
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callback_lock.release()
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def _change_img(v):
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global original_img, font_size, x_spacer, y_spacer, txt
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current_time = time.time()
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if current_time - last_update_time[0] < update_delay:
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return
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if not callback_lock.acquire(blocking=False):
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return
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try:
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if cv2.getWindowProperty(WIN_NAME, cv2.WND_PROP_VISIBLE) < 1:
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return
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try:
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new_frm_id = cv2.getTrackbarPos(SELECT_VIDEO_FRAME, WIN_NAME)
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original_img = read_frm_of_video(video_path=data, frame_index=new_frm_id, greyscale=True)
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clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
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tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
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if tile_size % 2 == 0: tile_size += 1
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clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
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img_clahe = clahe.apply(original_img)
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cv2.putText(img_clahe, txt,(TextOptions.BORDER_BUFFER_X.value, TextOptions.BORDER_BUFFER_Y.value + y_spacer), TextOptions.FONT.value, font_size, (255, 255, 255), 3)
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cv2.imshow(WIN_NAME, img_clahe)
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cv2.waitKey(1)
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last_update_time[0] = current_time
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except cv2.error:
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pass
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finally:
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callback_lock.release()
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check_instance(source=interactive_clahe_ui.__name__, instance=data, accepted_types=(np.ndarray, str))
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if isinstance(data, str):
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break
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k = cv2.waitKey(1) & 0xFF
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if k == 27:
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try:
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clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
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tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
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if tile_size % 2 == 0: tile_size += 1
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except cv2.error:
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clip_limit = 1.0
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tile_size = 8
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cv2.destroyAllWindows()
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return clip_limit, tile_size
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#interactive_clahe_ui(data=r"
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#interactive_clahe_ui(data=r"C:\troubleshooting\cue_light\t1\project_folder\videos\2025-05-21 16-10-06_cropped.mp4")
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# # Function to update CLAHE
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# def update_clahe(x):
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@@ -12,7 +12,7 @@ from simba.utils.checks import (check_file_exist_and_readable,
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check_valid_boolean, check_valid_tuple)
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from simba.utils.data import (align_target_warpaffine_vectors,
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center_rotation_warpaffine_vectors,
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egocentrically_align_pose)
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egocentrically_align_pose, terminate_cpu_pool)
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from simba.utils.enums import Defaults, Formats
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from simba.utils.printing import SimbaTimer, stdout_success
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from simba.utils.read_write import (concatenate_videos_in_folder,
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video_meta = get_video_meta_data(video_path=video_path)
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batch, frm_range = frm_range[0], frm_range[1]
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save_path = os.path.join(temp_dir, f'{batch}.mp4')
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fourcc = cv2.VideoWriter_fourcc(*f'{Formats.MP4_CODEC.value}')
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for cnt, result in enumerate(pool.imap(constants, frm_list, chunksize=1)):
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if self.verbose:
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print(f"Rotate batch {result}/{self.core_cnt} complete...")
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pool.join()
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terminate_cpu_pool(pool=pool, force=False)
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concatenate_videos_in_folder(in_folder=temp_dir, save_path=self.save_path, remove_splits=True, gpu=self.gpu, verbose=self.verbose)
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video_timer.stop_timer()
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stdout_success(msg=f"Egocentric rotation video {self.save_path} complete", elapsed_time=video_timer.elapsed_time_str, source=self.__class__.__name__)
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if __name__ == "__main__":
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DATA_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\data\501_MA142_Gi_Saline_0513.csv"
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VIDEO_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513.mp4"
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SAVE_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513_rotated.mp4"
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DATA_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\data\501_MA142_Gi_Saline_0513.csv"
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VIDEO_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513.mp4"
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SAVE_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513_rotated.mp4"
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ANCHOR_LOC = np.array([250, 250])
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df = read_df(file_path=DATA_PATH, file_type='csv')
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data = df[bp_cols].values.reshape(len(df), int(len(bp_cols)/2), 2).astype(np.int32)
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_, centers, rotation_vectors = egocentrically_align_pose(data=data, anchor_1_idx=5, anchor_2_idx=2, anchor_location=ANCHOR_LOC, direction=0)
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rotater = EgocentricVideoRotator(video_path=VIDEO_PATH, centers=centers, rotation_vectors=rotation_vectors, anchor_location=(400, 100), save_path=SAVE_PATH, verbose=True)
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rotater = EgocentricVideoRotator(video_path=VIDEO_PATH, centers=centers, rotation_vectors=rotation_vectors, anchor_location=(400, 100), save_path=SAVE_PATH, verbose=True, core_cnt=16)
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if img.mode in ('RGBA', 'LA'): img = img.convert('RGB')
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print(f"Converting file {file_cnt + 1}/{len(file_paths)} ...")
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print(f"Converting file {file_cnt + 1}/{len(file_paths)} ({file_name}) ...")
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Create an image representing the average frame of a segment in a video or an entire video.
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See :func:`simba.data_processors.cuda.image.create_average_frm_cupy`, :func:`simba.data_processors.cuda.image.create_average_frm_cuda` for GPU acceleration.
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.. csv-table::
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:header: EXPECTED RUNTIMES
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:file: ../../docs/tables/create_average_frame.csv
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.. video:: _static/img/create_average_frm_1.webm
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See :func:`simba.data_processors.cuda.image.create_average_frm_cupy`, :func:`simba.data_processors.cuda.image.create_average_frm_cuda` for GPU acceleration.
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:param Union[str, os.PathLike] video_path: The path to the video to create the average frame from. Default: None.
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:param Optional[int] start_frm: The first frame in the segment to create the average frame from. Default: None.
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:param Optional[int] end_frm: The last frame in the segment to create the average frame from. Default: None.
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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: 4.6.3
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Summary: Toolkit for computer classification and analysis of behaviors in experimental animals
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scripts/upgrade_simba_keep_configs.py,sha256=yk1hnt9of44FjGRINcis4RopUgNV_QIyRABv-sf--58,5274
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simba/SimBA.py,sha256=
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simba/data_processors/agg_clf_calculator.py,sha256=QR94LzQxrJ8eEyMZy4O5pSTgVUwrUUnzj1mK3tHcacQ,17362
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simba/data_processors/agg_clf_counter_mp.py,sha256=
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simba/data_processors/agg_clf_counter_mp.py,sha256=rjjdJUGh6ODjwY3BtPK4AuK8XsoCoZHHxYtbE6q-vGk,19982
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simba/data_processors/boolean_conditional_calculator.py,sha256=_uDuznm3JS7npqcNcmieH53ZOzoJ7mDqX8QwSaAWlIc,9685
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simba/data_processors/circling_detector.py,sha256=LLHulslIy6S1BdoCB40MxWmy8M25qscH7qmmrqv-Qc8,8936
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simba/data_processors/cue_light_analyzer.py,sha256=
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simba/data_processors/cue_light_clf_statistics.py,sha256=Msv1xe3tq4yn3j5sFswso-vS8UegcFC8wR4Ln0RgIoA,8582
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simba/data_processors/cuda/data.py,sha256=tZLunARZVlk1plh7atR3PY5QADMPZXfbYE92uvYkx1g,11831
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simba/data_processors/cuda/image.py,sha256=
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simba/data_processors/cuda/image.py,sha256=bygbKdztyD0mpZuvUZYA7uaVs5CoDVT9urGjKhKRZfU,85178
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simba/data_processors/cuda/statistics.py,sha256=G9jVSWQThf_jMcNsOxeM20o4wMFSteJamZivqYcqyMQ,45951
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simba/data_processors/cuda/utils.py,sha256=0Z51kEItgDl9MfPQ9_jvClzR2_pvIWxFkLcjb3xdDE8,8584
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simba/mixins/geometry_mixin.py,sha256=-dsittLxTLJzP817Uh1wnR2yfPkiJ2m9pL58VqUdUv0,234551
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simba/model/grid_search_multiclass_rf.py,sha256=NEneqrtsaZmybUNqDGJ1E3CwCSy4z34Cv7H8CG6-WGQ,16543
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simba/plotting/plot_clf_results_mp.py,sha256=46qiq9k5dD8wZBRfvCYThkYiPnvmeCEKZy2XEp2N3h4,32340
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simba/plotting/probability_plot_creator.py,sha256=8BHYtCtPXungLxzI0ZkCKUoDhuYBJsGefsChzHwrDLI,11878
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simba/plotting/probability_plot_creator_mp.py,sha256=
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simba/plotting/sam_plotter.py,sha256=XAQuFv-GJkTOno-PeEemUaz0CL83QH1SygJ6Cf1UsgI,6507
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simba/plotting/single_run_model_validation_video.py,sha256=75tP0f6UFK-ZpGDWxqLfaWlLrDybkBlEBoN_eKuRTBg,25973
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simba/plotting/spontaneous_alternation_plotter.py,sha256=HIgUEMhPCLq7qNXowbFp0bgCPLTvvwf8_DwlOiuWqA8,13117
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simba/plotting/yolo_pose_track_visualizer.py,sha256=uNQIHOPY-mEqgWY6ufkloedZGIgRCB9vyueG2bErVBc,17328
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simba/plotting/yolo_pose_visualizer.py,sha256=_iYELRtBNs6xJze-fyORdoqvdTtswtTvWYVZCX5sDMs,25510
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simba/plotting/yolo_seg_visualizer.py,sha256=JoGvmESNgqJI9nxId-GVt1mIGoF12Jx3seclz6lxmnA,9221
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simba/plotting/tools/tkinter_tools.py,sha256=TSLSRvNqTtQz6IYLFLeQ5w72UU1r6X43_ywYOQLAQT4,6895
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simba/roi_tools/interactive_roi_bufferer.py,sha256=IcEVv1R8K2-zmw3ouK4sk3Tk46TZbUg0ElV436tK4ec,11604
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simba/roi_tools/roi_aggregate_statistics_analyzer.py,sha256=qNSKublSxPuMatqpUplEU5chRg1uycM-pYMZMwj9GkI,22303
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simba/roi_tools/roi_clf_calculator.py,sha256=pOvUbKCPSPOEkAoxeJ_LQM4PXHODkp8IU56iwghm4qo,17634
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simba/roi_tools/roi_clf_calculator_mp.py,sha256=nYIKTqTAX68sZwDO-CLkSPp1HyBd3P20jk8dyj-VM-I,20630
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simba/roi_tools/roi_ruler.py,sha256=3sBFBQx7gwKAw9Pk_5c4NxAdFwSEZusYEX62xKNo2JU,10956
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simba/roi_tools/roi_selector_circle_tkinter.py,sha256=aS_1g8bK7cL7SAyvHFeSyGJf9ODYYqmWkoVEtUzKp9Y,4859
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simba/sandbox/get_convex_hull_cuda.py,sha256=cXC8CkJZ8JaqT4imago_e_Tnk7jfWZ19GPzYmNpq6YM,461
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simba/sandbox/get_cpu_pool.py,sha256=iSpLfmpsPtNl5QwwLOHi7luMYe8cf1aF4iS_la7tBWs,119
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simba/sandbox/cuda/egocentric_rotator.py,sha256=m6zZFaSrADF4CoDwTPAYTaZDu98bP_kFp5mWTKxM7dw,21123
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simba/sandbox/cuda/jitted_line_crosses_to_static_targets.py,sha256=zaO7R8nE64QQlzjTZDDFP0LqOkMTjxYPwUAmvejQSXA,4907
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simba/sandbox/maplight/add_videos_to_dlc_config.py,sha256=QUsdlOpc6XcF46vuHOxgbhY66A2lj3L6m84OD7Q9uwY,1176
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simba/ui/pop_ups/clf_add_remove_print_pop_up.py,sha256=7zYWW3X1OHQxuUVOiVt27h0J5L3qVaJNv23AFxTRVUw,7147
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simba/ui/pop_ups/clf_annotation_counts_pop_up.py,sha256=8HeTc4XJt_yHwm7UqoKAQmXSOAdvRd70h2AbR-JzcWM,1959
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simba/ui/pop_ups/clf_by_roi_pop_up.py,sha256=95oTHZXchehmuOrP9cxJkBzyLqDcN8ZJLqUSZ0Yh98k,8709
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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/movement_analysis_time_bins_pop_up.py,sha256=rIRXw1gbHyx37lqctf9pz5vUemzN1c4ywKLfRcywnT4,9310
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simba/ui/pop_ups/mutual_exclusivity_pop_up.py,sha256=Rp_DchWtlVWUVL47q2HaeUc0mUpgonuiHRj4Och1sPQ,11862
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simba/ui/pop_ups/single_video_to_frames_popup.py,sha256=--Ex2j7sYdWbHC5Ea-Lf_FInCEXZShlzS9Idzt1s7f4,5326
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simba/ui/pop_ups/sleap_csv_predictions_to_yolo_popup.py,sha256=_sY7scL_Eb7duGqkYT2qwOfs7mB8ndMaCQvIZDNUKXo,7048
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simba/ui/pop_ups/visualize_pose_in_dir_pop_up.py,sha256=PpFs0zaqF4dnHJ_yH-PqYgsjAyxYPVP427Soj-kYtM0,8838
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simba/utils/printing.py,sha256=L13f5prOnuswDqa4XttEBoQ3y3wNLm0W_ZvyxYQTbYw,5230
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simba/utils/read_write.py,sha256=lKLG-MEgXRtN7NWaLlOa356rUFgdNrWbgtUHrISPa_w,187302
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simba/utils/warnings.py,sha256=K7w1RiDL4Un7rGaabOVCGc9fHcaKxk66iZyNLS_AtOE,8121
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simba/utils/yolo.py,sha256=4RTC1JYnZ7WgaWmf70cZATbUtjRQfJ1HyhJhglpAEcs,18482
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simba/utils/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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simba/video_processors/blob_tracking_executor.py,sha256=W24Men4nzN4nkKaOsq-ERuSavkVRR-BeFzW-0LVNEY4,18395
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simba/video_processors/brightness_contrast_ui.py,sha256=nWmzho1WeJuIp3CuDjJmqMIzge2sTZn6_H0lWyZYaz0,5202
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simba/video_processors/calculate_px_dist.py,sha256=se9M1Kv6VxjVTZqSBmdmx29fg10s-1tL1UqJ6353Iqc,10029
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simba/video_processors/clahe_ui.py,sha256=
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simba/video_processors/egocentric_video_rotator.py,sha256=
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simba/video_processors/clahe_ui.py,sha256=2I6Z0bGapU1Fo6iO-mKLbQiUnE3G6qNu-Of8Z8VvC6s,7150
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simba/video_processors/egocentric_video_rotator.py,sha256=iDA6m5CsSrD_Mn6vnvU_skIacH5fyuH8ejNX15-Iua0,11970
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simba/video_processors/extract_frames.py,sha256=7FgZBg3YfUgDr13xSDFh-XcSjSqbDc3I_Af2zUgcDIQ,3088
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simba/video_processors/extract_seqframes.py,sha256=Yz_Head-9IVB4sJQfh1Oe1EStC0G-Y8Q9a5DDeCbigo,4926
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simba/video_processors/multi_cropper.py,sha256=n_DSGv9abhSgAsDpb-VULmNVFRPADZRpVyBnARvm5No,8697
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simba/video_processors/roi_selector.py,sha256=5N3s0Bi1Ub6c9gjE_-mV7AWr8Fqg7HQKdBKBF6whurg,8522
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simba/video_processors/roi_selector_circle.py,sha256=SD_lv6V3MGiIQd0VtUFSKe83ySW_qvE1t8xsgAlr2hI,6436
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simba/video_processors/roi_selector_polygon.py,sha256=DMtilt__gGwNu6VV73CWbnPqrPBXkan1_akUqGEzfGw,6742
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simba/video_processors/video_processing.py,sha256=
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simba/video_processors/videos_to_frames.py,sha256=
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simba/video_processors/video_processing.py,sha256=ho9bz1rjl1eEomA4yfndIc46xtnvdgFNv5JJSX28n7w,311986
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simba/video_processors/videos_to_frames.py,sha256=WqAjEa5enrrkKqwDkL8HhFlbgt1Sf67k2zeCQhVKryM,7323
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simba_uw_tf_dev-4.6.3.dist-info/LICENSE,sha256=Sjn362upcvYFypam-b-ziOXU1Wl5GGuTt5ICrGimzyA,1720
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simba_uw_tf_dev-4.6.3.dist-info/METADATA,sha256=PHM_iOtDP2yiUr1qmqFxpmnqxbV1oVWM3D3ukGU7LwE,11375
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simba_uw_tf_dev-4.6.3.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
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simba_uw_tf_dev-4.6.3.dist-info/entry_points.txt,sha256=Nfh_EbfDGdKftLjCnGWtQrBHENiDYMdgupwLyLpU5dc,44
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simba_uw_tf_dev-4.6.3.dist-info/top_level.txt,sha256=ogtimvlqDxDTOBAPfT2WaQ2pGAAbKRXG8z8eUTzf6TU,14
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simba_uw_tf_dev-4.6.3.dist-info/RECORD,,
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