Merge remote-tracking branch 'origin/master'

# Conflicts:
#	simba/data_processors/cuda/convex_hull.py

simba/data_processors/cuda/angle_3pt.py

@@ -1,10 +1,12 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-from numba import cuda
+import math
+
 import numpy as np
+from numba import cuda
+
 from simba.utils.read_write import read_df
-import math
 
 THREADS_PER_BLOCK = 256
 @cuda.jit

simba/data_processors/cuda/count_values_in_range.py

@@ -2,8 +2,8 @@
 __email__ = "[email protected]"
 
 
-from numba import cuda
 import numpy as np
+from numba import cuda
 
 THREADS_PER_BLOCK = 256
 

simba/data_processors/cuda/create_average_cupy.py

@@ -2,17 +2,24 @@
 __email__ = "[email protected]"
 
 
-from typing import Union, Optional
 import os
+from typing import Optional, Union
+
+import cupy as cp
 import cv2
 import numpy as np
-import cupy as cp
 
-from simba.utils.errors import InvalidInputError, FFMPEGCodecGPUError
-from simba.utils.checks import check_file_exist_and_readable, check_int, check_if_string_value_is_valid_video_timestamp, check_that_hhmmss_start_is_before_end,check_if_dir_exists, check_nvidea_gpu_available
-from simba.utils.read_write import get_video_meta_data, check_if_hhmmss_timestamp_is_valid_part_of_video, get_fn_ext, read_img_batch_from_video_gpu
+from simba.utils.checks import (check_file_exist_and_readable,
+                                check_if_dir_exists,
+                                check_if_string_value_is_valid_video_timestamp,
+                                check_int, check_nvidea_gpu_available,
+                                check_that_hhmmss_start_is_before_end)
 from simba.utils.data import find_frame_numbers_from_time_stamp
+from simba.utils.errors import FFMPEGCodecGPUError, InvalidInputError
 from simba.utils.printing import stdout_success
+from simba.utils.read_write import (
+    check_if_hhmmss_timestamp_is_valid_part_of_video, get_fn_ext,
+    get_video_meta_data, read_img_batch_from_video_gpu)
 
 
 def create_average_frm(video_path: Union[str, os.PathLike],

simba/data_processors/cuda/create_average_frame_cuda.py

@@ -1,20 +1,27 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-from typing import Union, Optional
 import os
+from typing import Optional, Union
+
+import cupy as cp
 import cv2
 import numpy as np
-import cupy as cp
+from numba import cuda
 
-from simba.utils.errors import InvalidInputError, FFMPEGCodecGPUError
-from simba.utils.checks import check_file_exist_and_readable, check_int, check_if_string_value_is_valid_video_timestamp, \
-    check_that_hhmmss_start_is_before_end, check_if_dir_exists, check_nvidea_gpu_available, check_instance, check_if_valid_img
-from simba.utils.read_write import get_video_meta_data, check_if_hhmmss_timestamp_is_valid_part_of_video, get_fn_ext, \
-    read_img_batch_from_video_gpu
+from simba.utils.checks import (check_file_exist_and_readable,
+                                check_if_dir_exists,
+                                check_if_string_value_is_valid_video_timestamp,
+                                check_if_valid_img, check_instance, check_int,
+                                check_nvidea_gpu_available,
+                                check_that_hhmmss_start_is_before_end)
 from simba.utils.data import find_frame_numbers_from_time_stamp
+from simba.utils.errors import FFMPEGCodecGPUError, InvalidInputError
 from simba.utils.printing import stdout_success
-from numba import cuda
+from simba.utils.read_write import (
+    check_if_hhmmss_timestamp_is_valid_part_of_video, get_fn_ext,
+    get_video_meta_data, read_img_batch_from_video_gpu)
+
 
 def average_3d_stack_cupy(image_stack: np.ndarray) -> np.ndarray:
     num_frames, height, width, _ = image_stack.shape

simba/data_processors/cuda/direction_two_bps.py

@@ -1,9 +1,10 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
+import math
+
 import numpy as np
 from numba import cuda
-import math
 
 THREADS_PER_BLOCK = 1024
 

simba/data_processors/cuda/euclidan_distance.py

@@ -1,11 +1,13 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-from numba import cuda
+import math
+
 import numpy as np
-from simba.utils.read_write import read_df
+from numba import cuda
+
 from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
-import math
+from simba.utils.read_write import read_df
 
 THREADS_PER_BLOCK = 128
 

simba/data_processors/cuda/is_inside_circle.py

@@ -1,9 +1,10 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
+import math
+
 import numpy as np
 from numba import cuda
-import math
 
 THREADS_PER_BLOCK = 1024
 @cuda.jit

simba/data_processors/cuda/sliding_circular_mean.py

@@ -1,10 +1,12 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-import numpy as np
-import cupy
 from typing import Optional
 
+import cupy
+import numpy as np
+
+
 def sliding_circular_mean(x: np.ndarray,
                           time_window: float,
                           sample_rate: int,

simba/data_processors/cuda/sliding_resultant_vector_length.py

@@ -1,10 +1,12 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-import numpy as np
-import cupy
 from typing import Optional
 
+import cupy
+import numpy as np
+
+
 def sliding_resultant_vector_length(x: np.ndarray,
                                     time_window: float,
                                     sample_rate: int,

simba/data_processors/cuda/sliding_spearmans_rank.py

@@ -1,10 +1,11 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-import numpy as np
-import cupy as cp
 from typing import Optional
 
+import cupy as cp
+import numpy as np
+
 
 def sliding_spearmans_rank(x: np.ndarray,
                            y: np.ndarray,

simba/plotting/blob_plotter.py

@@ -1,25 +1,34 @@
 __author__ = "Simon Nilsson"
 __email__ = "[email protected]"
 
-from typing import List, Tuple
 import os
-from typing import Union, Optional
+from typing import List, Optional, Tuple, Union
+
 import numpy as np
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
-from simba.utils.read_write import find_all_videos_in_directory, get_fn_ext, remove_files, get_video_meta_data, find_core_cnt, concatenate_videos_in_folder
-from simba.utils.checks import check_if_dir_exists, check_valid_boolean, check_int, check_nvidea_gpu_available, check_str, check_if_valid_rgb_tuple
-from simba.utils.enums import Options, TextOptions, Defaults
-from simba.utils.printing import stdout_success, SimbaTimer
-from simba.utils.errors import InvalidInputError, FFMPEGCodecGPUError
-from simba.data_processors.blob_location_computer import BlobLocationComputer
-from simba.mixins.plotting_mixin import PlottingMixin
-import multiprocessing
+
 import functools
+import multiprocessing
+
 from numba import jit
 
+from simba.data_processors.blob_location_computer import BlobLocationComputer
+from simba.mixins.plotting_mixin import PlottingMixin
+from simba.utils.checks import (check_if_dir_exists, check_if_valid_rgb_tuple,
+                                check_int, check_nvidea_gpu_available,
+                                check_str, check_valid_boolean)
+from simba.utils.enums import Defaults, Options, TextOptions
+from simba.utils.errors import FFMPEGCodecGPUError, InvalidInputError
+from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.read_write import (concatenate_videos_in_folder,
+                                    find_all_videos_in_directory,
+                                    find_core_cnt, get_fn_ext,
+                                    get_video_meta_data, remove_files)
+
 
 class BlobPlotter(PlottingMixin):
     """