simba-uw-tf-dev 4.5.8__py3-none-any.whl → 4.7.1__py3-none-any.whl

simba/utils/yolo.py

@@ -47,6 +47,9 @@ def fit_yolo(weights_path: Union[str, os.PathLike],
        `Download initial weights <https://huggingface.co/Ultralytics>`__.
        `Example model_yaml <https://github.com/sgoldenlab/simba/blob/master/misc/ex_yolo_model.yaml>`__.
 
+    .. seealso::
+       For the recommended wrapper class with parameter validation, see :class:`simba.model.yolo_fit.FitYolo`.
+
     :param initial_weights: Path to the pre-trained YOLO model weights (usually a `.pt` file). Example weights can be found [here](https://huggingface.co/Ultralytics).
     :param model_yaml: YAML file containing paths to the training, validation, and testing datasets and the object class mappings. Example YAML file can be found [here](https://github.com/sgoldenlab/simba/blob/master/misc/ex_yolo_model.yaml).
     :param save_path: Directory path where the trained model, logs, and results will be saved.
@@ -55,7 +58,7 @@ def fit_yolo(weights_path: Union[str, os.PathLike],
     :return: None. The trained model and associated training logs are saved in the specified `project_path`.
 
     :example:
-    >>> fit_yolo(initial_weights=r"C:\troubleshooting\coco_data\weights\yolov8n-obb.pt", data=r"C:\troubleshooting\coco_data\model.yaml", save_path=r"C:\troubleshooting\coco_data\mdl", batch=16)
+    >>> fit_yolo(initial_weights=r"C:/troubleshooting/coco_data/weights/yolov8n-obb.pt", data=r"C:/troubleshooting/coco_data/model.yaml", save_path=r"C:/troubleshooting/coco_data/mdl", batch=16)
     """
 
     if not _is_cuda_available()[0]:
@@ -83,6 +86,9 @@ def load_yolo_model(weights_path: Union[str, os.PathLike],
     """
     Load a YOLO model.
 
+    .. seealso::
+       For recommended wrapper classes that use this function, see :class:`simba.model.yolo_fit.FitYolo`, :class:`simba.model.yolo_inference.YoloInference`, :class:`simba.model.yolo_pose_inference.YOLOPoseInference`, :class:`simba.model.yolo_seg_inference.YOLOSegmentationInference`, and :class:`simba.model.yolo_pose_track_inference.YOLOPoseTrackInference`.
+
     :param Union[str, os.PathLike] weights_path: Path to model weights (.pt, .engine, etc).
     :param bool verbose: Whether to print loading info.
     :param Optional[str] format: Export format, one of VALID_FORMATS or None to skip export.
@@ -169,6 +175,9 @@ def yolo_predict(model: YOLO,
     """
     Produce YOLO predictions.
 
+    .. seealso::
+       For recommended wrapper classes that use this function, see :class:`simba.model.yolo_inference.YoloInference`, :class:`simba.model.yolo_pose_inference.YOLOPoseInference`, and :class:`simba.model.yolo_seg_inference.YOLOSegmentationInference`.
+
     :param Union[str, os.PathLike] model: Loaded ultralytics.YOLO model. Returned by :func:`~simba.bounding_box_tools.yolo.model.load_yolo_model`.
     :param Union[str, os.PathLike, np.ndarray] source: Path to video, video stream, directory, image, or image as loaded array.
     :param bool half: Whether to use half precision (FP16) for inference to speed up processing.

simba/video_processors/blob_tracking_executor.py

@@ -87,9 +87,9 @@ class BlobTrackingExecutor():
     :param bool center: If True, compute center coordinates. Default: True.
 
     :example:
-    >>> tracker = BlobTrackingExecutor(data=r"C:\troubleshooting\mitra\test\.temp\blob_definitions.pickle")
+    >>> tracker = BlobTrackingExecutor(data=r"C:/troubleshooting/mitra/test/.temp/blob_definitions.pickle")
     >>> tracker.run()
-    >>> tracker = BlobTrackingExecutor(data=r"C:\troubleshooting\mitra\test\.temp\blob_definitions.pickle", batch_size=5000)
+    >>> tracker = BlobTrackingExecutor(data=r"C:/troubleshooting/mitra/test/.temp/blob_definitions.pickle", batch_size=5000)
     >>> tracker.run()
     """
 

simba/video_processors/clahe_ui.py

@@ -1,4 +1,6 @@
 import os
+import threading
+import time
 from typing import Tuple, Union
 
 import cv2
@@ -27,34 +29,71 @@ def interactive_clahe_ui(data: Union[str, os.PathLike]) -> Tuple[float, int]:
     :return Tuple[float, int]: Tuple containing the chosen clip limit and tile size.
 
     :example:
-    >>> video = cv2.imread(r"D:\EPM\sample_2\video_1.mp4")
+    >>> video = cv2.imread(r"D:/EPM/sample_2/video_1.mp4")
     >>> interactive_clahe_ui(data=video)
     """
     global original_img, font_size, x_spacer, y_spacer, txt
 
+    callback_lock = threading.Lock()
+    last_update_time = [0]
+    update_delay = 0.05
+
     def _get_trackbar_values(v):
         global original_img, font_size, x_spacer, y_spacer, txt
-        clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
-        tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
-        if tile_size % 2 == 0: tile_size += 1
-        clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
-        img_clahe = clahe.apply(original_img)
-        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)
-        cv2.imshow(WIN_NAME, img_clahe)
-        cv2.waitKey(100)
+        nonlocal callback_lock, last_update_time, update_delay
+        current_time = time.time()
+        if current_time - last_update_time[0] < update_delay:
+            return
+        
+        if not callback_lock.acquire(blocking=False):
+            return
+        
+        try:
+            if cv2.getWindowProperty(WIN_NAME, cv2.WND_PROP_VISIBLE) < 1:
+                return
+            try:
+                clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
+                tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
+                if tile_size % 2 == 0: tile_size += 1
+                clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
+                img_clahe = clahe.apply(original_img)
+                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)
+                cv2.imshow(WIN_NAME, img_clahe)
+                cv2.waitKey(1)
+                last_update_time[0] = current_time
+            except cv2.error:
+                pass
+        finally:
+            callback_lock.release()
 
     def _change_img(v):
         global original_img, font_size, x_spacer, y_spacer, txt
-        new_frm_id = cv2.getTrackbarPos(SELECT_VIDEO_FRAME, WIN_NAME)
-        original_img = read_frm_of_video(video_path=data, frame_index=new_frm_id, greyscale=True)
-        clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
-        tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
-        if tile_size % 2 == 0: tile_size += 1
-        clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
-        img_clahe = clahe.apply(original_img)
-        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)
-        cv2.imshow(WIN_NAME, img_clahe)
-        cv2.waitKey(100)
+        current_time = time.time()
+        if current_time - last_update_time[0] < update_delay:
+            return
+        
+        if not callback_lock.acquire(blocking=False):
+            return
+        
+        try:
+            if cv2.getWindowProperty(WIN_NAME, cv2.WND_PROP_VISIBLE) < 1:
+                return
+            try:
+                new_frm_id = cv2.getTrackbarPos(SELECT_VIDEO_FRAME, WIN_NAME)
+                original_img = read_frm_of_video(video_path=data, frame_index=new_frm_id, greyscale=True)
+                clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
+                tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
+                if tile_size % 2 == 0: tile_size += 1
+                clahe = cv2.createCLAHE(clipLimit=clip_limit, tileGridSize=(tile_size, tile_size))
+                img_clahe = clahe.apply(original_img)
+                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)
+                cv2.imshow(WIN_NAME, img_clahe)
+                cv2.waitKey(1)
+                last_update_time[0] = current_time
+            except cv2.error:
+                pass
+        finally:
+            callback_lock.release()
 
     check_instance(source=interactive_clahe_ui.__name__, instance=data, accepted_types=(np.ndarray, str))
     if isinstance(data, str):
@@ -80,14 +119,18 @@ def interactive_clahe_ui(data: Union[str, os.PathLike]) -> Tuple[float, int]:
             break
         k = cv2.waitKey(1) & 0xFF
         if k == 27:
-            clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
-            tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
-            if tile_size % 2 == 0: tile_size += 1
+            try:
+                clip_limit = cv2.getTrackbarPos(CLIP_LIMIT, WIN_NAME) / 10.0
+                tile_size = cv2.getTrackbarPos(TILE_SIZE, WIN_NAME)
+                if tile_size % 2 == 0: tile_size += 1
+            except cv2.error:
+                clip_limit = 1.0
+                tile_size = 8
             cv2.destroyAllWindows()
             return clip_limit, tile_size
 
 
-#interactive_clahe_ui(data=r"D:\EPM\sample_2\video_1.mp4")
+#interactive_clahe_ui(data=r"C:\troubleshooting\cue_light\t1\project_folder\videos\2025-05-21 16-10-06_cropped.mp4")
 
 # # Function to update CLAHE
 # def update_clahe(x):

simba/video_processors/egocentric_video_rotator.py

@@ -9,10 +9,12 @@ import numpy as np
 from simba.utils.checks import (check_file_exist_and_readable,
                                 check_if_dir_exists, check_if_valid_rgb_tuple,
                                 check_int, check_valid_array,
-                                check_valid_boolean, check_valid_tuple)
+                                check_valid_boolean, check_valid_cpu_pool,
+                                check_valid_tuple)
 from simba.utils.data import (align_target_warpaffine_vectors,
                               center_rotation_warpaffine_vectors,
-                              egocentrically_align_pose)
+                              egocentrically_align_pose, get_cpu_pool,
+                              terminate_cpu_pool)
 from simba.utils.enums import Defaults, Formats
 from simba.utils.printing import SimbaTimer, stdout_success
 from simba.utils.read_write import (concatenate_videos_in_folder,
@@ -35,7 +37,6 @@ def egocentric_video_aligner(frm_range: np.ndarray,
                              gpu: bool = True):
 
     video_meta = get_video_meta_data(video_path=video_path)
-
     batch, frm_range = frm_range[0], frm_range[1]
     save_path = os.path.join(temp_dir, f'{batch}.mp4')
     fourcc = cv2.VideoWriter_fourcc(*f'{Formats.MP4_CODEC.value}')
@@ -57,7 +58,7 @@ def egocentric_video_aligner(frm_range: np.ndarray,
                 final_frame = cv2.warpAffine(rotated_frame, m_translations[img_counter],(video_meta['width'], video_meta['height']), borderValue=fill_clr)
                 writer.write(final_frame)
                 if verbose:
-                    print(f'Creating frame {frame_id} ({video_name}, CPU core: {batch + 1}).')
+                    print(f'Creating frame {frame_id}/{video_meta["frame_count"]} ({video_name}, CPU core: {batch + 1}).')
                 img_counter+=1
     else:
         cap = cv2.VideoCapture(video_path)
@@ -67,7 +68,7 @@ def egocentric_video_aligner(frm_range: np.ndarray,
             final_frame = cv2.warpAffine(rotated_frame, m_translations[frm_idx], (video_meta['width'], video_meta['height']), borderValue=fill_clr)
             writer.write(final_frame)
             if verbose:
-                print(f'Creating frame {frm_id} ({video_name}, CPU core: {batch + 1}).')
+                print(f'Creating frame {frm_id}/{video_meta["frame_count"]} ({video_name}, CPU core: {batch + 1}).')
     writer.release()
     return batch + 1
 
@@ -93,9 +94,9 @@ class EgocentricVideoRotator():
     :param Optional[Union[str, os.PathLike]] save_path: The location where to store the rotated video. If None, saves the video as the same dir as the input video with the `_rotated` suffix.
 
     :example:
-    >>> DATA_PATH = "C:\501_MA142_Gi_Saline_0513.csv"
-    >>> VIDEO_PATH = "C:\501_MA142_Gi_Saline_0513.mp4"
-    >>> SAVE_PATH = "C:\501_MA142_Gi_Saline_0513_rotated.mp4"
+    >>> DATA_PATH = "C:/501_MA142_Gi_Saline_0513.csv"
+    >>> VIDEO_PATH = "C:/501_MA142_Gi_Saline_0513.mp4"
+    >>> SAVE_PATH = "C:/501_MA142_Gi_Saline_0513_rotated.mp4"
     >>> ANCHOR_LOC = np.array([250, 250])
 
     >>> df = read_df(file_path=DATA_PATH, file_type='csv')
@@ -115,7 +116,8 @@ class EgocentricVideoRotator():
                  fill_clr: Tuple[int, int, int] = (0, 0, 0),
                  core_cnt: int = -1,
                  save_path: Optional[Union[str, os.PathLike]] = None,
-                 gpu: Optional[bool] = True):
+                 gpu: Optional[bool] = True,
+                 pool: bool = None):
 
         check_file_exist_and_readable(file_path=video_path)
         self.video_meta_data = get_video_meta_data(video_path=video_path)
@@ -126,10 +128,14 @@ class EgocentricVideoRotator():
         check_valid_boolean(value=[verbose], source=f'{self.__class__.__name__} verbose')
         check_if_valid_rgb_tuple(data=fill_clr)
         check_int(name=f'{self.__class__.__name__} core_cnt', value=core_cnt, min_value=-1, unaccepted_vals=[0])
-        if core_cnt > find_core_cnt()[0] or core_cnt == -1:
-            self.core_cnt = find_core_cnt()[0]
+        if core_cnt > find_core_cnt()[0] or core_cnt == -1: self.core_cnt = find_core_cnt()[0]
+        else: self.core_cnt = core_cnt
+        if pool is not None:
+            check_valid_cpu_pool(value=pool, source=self.__class__.__name__, max_cores=find_core_cnt()[0], min_cores=2, raise_error=True)
+            self.pool_termination_flag = True
         else:
-            self.core_cnt = core_cnt
+            self.pool_termination_flag = False
+        self.pool = get_cpu_pool(core_cnt=self.core_cnt, source=self.__class__.__name__) if pool is None else pool
         video_dir, self.video_name, _ = get_fn_ext(filepath=video_path)
         if save_path is not None:
             self.save_dir = os.path.dirname(save_path)
@@ -152,39 +158,35 @@ class EgocentricVideoRotator():
         frm_list = np.arange(0, self.video_meta_data['frame_count'])
         frm_list = np.array_split(frm_list, self.core_cnt)
         frm_list = [(cnt, x) for cnt, x in enumerate(frm_list)]
-        if self.verbose:
-            print(f"Creating rotated video {self.video_name}, multiprocessing (chunksize: {1}, cores: {self.core_cnt})...")
-        with multiprocessing.Pool(self.core_cnt, maxtasksperchild=Defaults.LARGE_MAX_TASK_PER_CHILD.value) as pool:
-            constants = functools.partial(egocentric_video_aligner,
-                                          temp_dir=temp_dir,
-                                          video_name=self.video_name,
-                                          video_path=self.video_path,
-                                          centers=self.centers,
-                                          rotation_vectors=self.rotation_vectors,
-                                          target=self.anchor_loc,
-                                          verbose=self.verbose,
-                                          fill_clr=self.fill_clr,
-                                          gpu=self.gpu)
-            for cnt, result in enumerate(pool.imap(constants, frm_list, chunksize=1)):
-                if self.verbose:
-                    print(f"Rotate batch {result}/{self.core_cnt} complete...")
-            pool.terminate()
-            pool.join()
-
+        if self.verbose: print(f"Creating rotated video {self.video_name}, multiprocessing (chunksize: {1}, cores: {self.core_cnt})...")
+
+        constants = functools.partial(egocentric_video_aligner,
+                                      temp_dir=temp_dir,
+                                      video_name=self.video_name,
+                                      video_path=self.video_path,
+                                      centers=self.centers,
+                                      rotation_vectors=self.rotation_vectors,
+                                      target=self.anchor_loc,
+                                      verbose=self.verbose,
+                                      fill_clr=self.fill_clr,
+                                      gpu=self.gpu)
+        for cnt, result in enumerate(self.pool.imap(constants, frm_list, chunksize=1)):
+            if self.verbose: print(f"Rotate batch {result}/{self.core_cnt} complete...")
+        if self.pool_termination_flag: terminate_cpu_pool(pool=self.pool, force=False)
         concatenate_videos_in_folder(in_folder=temp_dir, save_path=self.save_path, remove_splits=True, gpu=self.gpu, verbose=self.verbose)
         video_timer.stop_timer()
         stdout_success(msg=f"Egocentric rotation video {self.save_path} complete", elapsed_time=video_timer.elapsed_time_str, source=self.__class__.__name__)
 
-if __name__ == "__main__":
-    DATA_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\data\501_MA142_Gi_Saline_0513.csv"
-    VIDEO_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513.mp4"
-    SAVE_PATH = r"C:\Users\sroni\OneDrive\Desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513_rotated.mp4"
-    ANCHOR_LOC = np.array([250, 250])
-
-    df = read_df(file_path=DATA_PATH, file_type='csv')
-    bp_cols = [x for x in df.columns if not x.endswith('_p')]
-    data = df[bp_cols].values.reshape(len(df), int(len(bp_cols)/2), 2).astype(np.int32)
-
-    _, centers, rotation_vectors = egocentrically_align_pose(data=data, anchor_1_idx=5, anchor_2_idx=2, anchor_location=ANCHOR_LOC, direction=0)
-    rotater = EgocentricVideoRotator(video_path=VIDEO_PATH, centers=centers, rotation_vectors=rotation_vectors, anchor_location=(400, 100), save_path=SAVE_PATH, verbose=True)
-    rotater.run()
+# if __name__ == "__main__":
+#     DATA_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\data\501_MA142_Gi_Saline_0513.csv"
+#     VIDEO_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513.mp4"
+#     SAVE_PATH = r"C:\Users\sroni\OneDrive\Desktop\desktop\rotate_ex\videos\501_MA142_Gi_Saline_0513_rotated.mp4"
+#     ANCHOR_LOC = np.array([250, 250])
+#
+#     df = read_df(file_path=DATA_PATH, file_type='csv')
+#     bp_cols = [x for x in df.columns if not x.endswith('_p')]
+#     data = df[bp_cols].values.reshape(len(df), int(len(bp_cols)/2), 2).astype(np.int32)
+#
+#     _, centers, rotation_vectors = egocentrically_align_pose(data=data, anchor_1_idx=5, anchor_2_idx=2, anchor_location=ANCHOR_LOC, direction=0)
+#     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)
+#     rotater.run()

simba/video_processors/multi_cropper.py

@@ -49,7 +49,7 @@ class MultiCropper(object):
 
 
     :example:
-    >>> cropper = MultiCropper(file_type='mp4', input_folder=r'C:\troubleshooting\mitra\test', output_folder=r'C:\troubleshooting\mitra\test\cropped', crop_cnt=2, gpu=True)
+    >>> cropper = MultiCropper(file_type='mp4', input_folder=r'C:/troubleshooting/mitra/test', output_folder=r'C:/troubleshooting/mitra/test/cropped', crop_cnt=2, gpu=True)
     >>> cropper.run()
     """