Merge remote-tracking branch 'origin/master'

# Conflicts:
#	simba/data_processors/cuda/angle_3pt.py
#	simba/data_processors/cuda/convex_hull.py
#	simba/data_processors/cuda/count_values_in_range.py
#	simba/data_processors/cuda/create_average_cupy.py
#	simba/data_processors/cuda/create_average_frame_cuda.py
#	simba/data_processors/cuda/direction_two_bps.py
#	simba/data_processors/cuda/euclidan_distance.py
#	simba/data_processors/cuda/is_inside_circle.py
#	simba/data_processors/cuda/sliding_circular_mean.py
#	simba/data_processors/cuda/sliding_resultant_vector_length.py
#	simba/data_processors/cuda/sliding_spearmans_rank.py
#	simba/plotting/blob_plotter.py

simba/SimBA.py

@@ -158,7 +158,7 @@
 from simba.utils.lookups import (get_bp_config_code_class_pairs, get_emojis,
                                  get_icons_paths, load_simba_fonts)
 from simba.utils.printing import stdout_success, stdout_warning
-from simba.utils.read_write import get_video_meta_data, find_core_cnt
+from simba.utils.read_write import find_core_cnt, get_video_meta_data
 from simba.utils.warnings import FFMpegNotFoundWarning, PythonVersionWarning
 from simba.video_processors.video_processing import \
     extract_frames_from_all_videos_in_directory

simba/data_processors/blob_location_computer.py

@@ -2,24 +2,33 @@
 __email__ = "[email protected]"
 
 import os
-from typing import Union, Optional
-import numpy as np
 from copy import deepcopy
+from typing import Optional, 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
-from simba.video_processors.video_processing import video_bg_subtraction, video_bg_substraction_mp
-from simba.mixins.image_mixin import ImageMixin
-from simba.utils.checks import check_if_dir_exists, check_valid_boolean, check_int, check_nvidea_gpu_available, check_str
-from simba.utils.enums import Formats, Options, Methods
-from simba.utils.printing import stdout_success, SimbaTimer
-from simba.utils.read_write import write_df
-from simba.utils.errors import InvalidInputError, FFMPEGCodecGPUError
-from simba.utils.data import savgol_smoother, df_smoother
+
 import pandas as pd
 
+from simba.mixins.image_mixin import ImageMixin
+from simba.utils.checks import (check_if_dir_exists, check_int,
+                                check_nvidea_gpu_available, check_str,
+                                check_valid_boolean)
+from simba.utils.data import df_smoother, savgol_smoother
+from simba.utils.enums import Formats, Methods, Options
+from simba.utils.errors import FFMPEGCodecGPUError, InvalidInputError
+from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.read_write import (find_all_videos_in_directory, get_fn_ext,
+                                    get_video_meta_data, remove_files,
+                                    write_df)
+from simba.video_processors.video_processing import (video_bg_substraction_mp,
+                                                     video_bg_subtraction)
+
+
 class BlobLocationComputer(object):
 
     """

simba/data_processors/cuda/__init__.py

@@ -7,11 +7,10 @@
 from .is_inside_polygon import is_inside_polygon
 from .is_inside_rectangle import is_inside_rectangle
 from .sliding_mean import sliding_mean
-from .sliding_std import sliding_std
 from .sliding_min import sliding_min
+from .sliding_std import sliding_std
 from .sliding_sum import sliding_sum
 
-
 __all__ = ['get_3pt_angle',
            'get_convex_hull',
            'count_values_in_ranges',

simba/data_processors/cuda/create_shap_log.py

@@ -2,19 +2,23 @@
 __email__ = "[email protected]"
 
 import os
-import shap
+from typing import List, Optional, Tuple, Union
+
 import numpy as np
-from simba.utils.read_write import read_df, write_df
-from simba.mixins.train_model_mixin import TrainModelMixin
-from simba.utils.checks import check_instance, check_valid_lst, check_str, check_int, check_valid_array, \
-    check_valid_dataframe, check_if_dir_exists, check_nvidea_gpu_available
-from typing import Union, Optional, List, Tuple
-from sklearn.ensemble import RandomForestClassifier
 import pandas as pd
+import shap
+from sklearn.ensemble import RandomForestClassifier
+
+from simba.mixins.train_model_mixin import TrainModelMixin
+from simba.utils.checks import (check_if_dir_exists, check_instance, check_int,
+                                check_nvidea_gpu_available, check_str,
+                                check_valid_array, check_valid_dataframe,
+                                check_valid_lst)
 from simba.utils.enums import Formats
-from simba.utils.warnings import NotEnoughDataWarning
-from simba.utils.printing import SimbaTimer, stdout_success
 from simba.utils.errors import FFMPEGCodecGPUError
+from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.read_write import read_df, write_df
+from simba.utils.warnings import NotEnoughDataWarning
 
 
 def create_shap_log(rf_clf: Union[str, os.PathLike, RandomForestClassifier],

simba/data_processors/cuda/imgs_to_grayscale_cupy.py

@@ -2,11 +2,13 @@
 __email__ = "[email protected]"
 
 from typing import Optional
+
 import cupy as cp
 import numpy as np
 
-from simba.utils.read_write import read_img_batch_from_video_gpu
 from simba.utils.checks import check_if_valid_img, check_instance
+from simba.utils.read_write import read_img_batch_from_video_gpu
+
 
 def img_stack_to_grayscale_cupy(imgs: np.ndarray,
                                 batch_size: Optional[int] = 250) -> np.ndarray:

simba/data_processors/cuda/imgs_to_greyscale_cuda.py

@@ -3,8 +3,10 @@
 
 import numpy as np
 from numba import cuda
-from simba.utils.read_write import read_img_batch_from_video_gpu
+
 from simba.utils.checks import check_if_valid_img, check_instance
+from simba.utils.read_write import read_img_batch_from_video_gpu
+
 
 @cuda.jit()
 def _img_stack_to_grayscale(data, results):

simba/data_processors/cuda/sliding_circular_hotspots.py

@@ -2,13 +2,16 @@
 __email__ = "[email protected]"
 
 from typing import Optional
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 import cupy as cp
 import numpy as np
 
+
 def sliding_circular_hotspots(x: np.ndarray,
                               time_window: float,
                               sample_rate: float,

simba/data_processors/cuda/sliding_circular_range.py

@@ -2,13 +2,16 @@
 __email__ = "[email protected]"
 
 from typing import Optional
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 import cupy as cp
 import numpy as np
 
+
 def sliding_circular_hotspots(x: np.ndarray,
                               time_window: float,
                               sample_rate: float,

simba/data_processors/cuda/sliding_circular_std.py

@@ -2,13 +2,16 @@
 __email__ = "[email protected]"
 
 from typing import Optional
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 import cupy as cp
 import numpy as np
 
+
 def sliding_circular_std(x: np.ndarray,
                          time_window: float,
                          sample_rate: float,

simba/data_processors/cuda/sliding_rayleigh_z.py

@@ -2,15 +2,16 @@
 __email__ = "[email protected]"
 
 from typing import Optional, Tuple
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 import cupy as cp
 import numpy as np
 
 
-
 def sliding_rayleigh_z(x: np.ndarray,
                        time_window: float,
                        sample_rate: float,

simba/labelling/labelling_interface.py

@@ -22,13 +22,13 @@
                                 check_int, check_that_column_exist)
 from simba.utils.enums import Options, TagNames
 from simba.utils.errors import FrameRangeError, NoDataError
-from simba.utils.warnings import FrameRangeWarning
 from simba.utils.lookups import (get_labelling_img_kbd_bindings,
                                  get_labelling_video_kbd_bindings)
 from simba.utils.printing import log_event, stdout_success
 from simba.utils.read_write import (get_all_clf_names, get_fn_ext,
                                     get_video_meta_data, read_config_entry,
                                     read_df, write_df)
+from simba.utils.warnings import FrameRangeWarning
 
 PLAY_VIDEO_SCRIPT_PATH = os.path.join(os.path.dirname(simba.__file__), "labelling/play_annotation_video.py")
 PADDING = 5

simba/mixins/image_mixin.py

@@ -22,16 +22,21 @@
 from simba.utils.checks import (check_file_exist_and_readable, check_float,
                                 check_if_dir_exists, check_if_valid_img,
                                 check_if_valid_rgb_tuple, check_instance,
-                                check_int, check_str, check_valid_array,
-                                check_valid_lst, check_valid_tuple, check_valid_boolean,
-                                check_nvidea_gpu_available)
+                                check_int, check_nvidea_gpu_available,
+                                check_str, check_valid_array,
+                                check_valid_boolean, check_valid_lst,
+                                check_valid_tuple)
 from simba.utils.enums import Defaults, Formats, GeometryEnum, Options
-from simba.utils.errors import ArrayError, FrameRangeError, InvalidInputError, FFMPEGCodecGPUError, NotDirectoryError
+from simba.utils.errors import (ArrayError, FFMPEGCodecGPUError,
+                                FrameRangeError, InvalidInputError,
+                                NotDirectoryError)
 from simba.utils.printing import SimbaTimer, stdout_success
 from simba.utils.read_write import (find_core_cnt,
                                     find_files_of_filetypes_in_directory,
-                                    get_fn_ext, get_video_meta_data, write_df,
-                                    read_frm_of_video, read_img_batch_from_video_gpu, find_largest_blob_location)
+                                    find_largest_blob_location, get_fn_ext,
+                                    get_video_meta_data, read_frm_of_video,
+                                    read_img_batch_from_video_gpu, write_df)
+
 
 class ImageMixin(object):
     """

simba/mixins/plotting_mixin.py

@@ -36,7 +36,7 @@
 from simba.utils.lookups import (get_categorical_palettes, get_color_dict,
                                  get_named_colors)
 from simba.utils.printing import SimbaTimer, stdout_success
-from simba.utils.read_write import read_frm_of_video, get_video_meta_data
+from simba.utils.read_write import get_video_meta_data, read_frm_of_video
 
 
 class PlottingMixin(object):

simba/mixins/train_model_mixin.py

@@ -57,10 +57,14 @@
 from simba.plotting.shap_agg_stats_visualizer import \
     ShapAggregateStatisticsVisualizer
 from simba.ui.tkinter_functions import TwoOptionQuestionPopUp
-from simba.utils.checks import (check_float, check_if_dir_exists, check_if_valid_input, check_instance, check_int, check_str, check_that_column_exist, check_file_exist_and_readable)
-from simba.utils.data import (detect_bouts, detect_bouts_multiclass, get_library_version)
-from simba.utils.enums import (ConfigKey, Defaults, Dtypes, Methods,
-                               MLParamKeys, Options, OS)
+from simba.utils.checks import (check_file_exist_and_readable, check_float,
+                                check_if_dir_exists, check_if_valid_input,
+                                check_instance, check_int, check_str,
+                                check_that_column_exist)
+from simba.utils.data import (detect_bouts, detect_bouts_multiclass,
+                              get_library_version)
+from simba.utils.enums import (OS, ConfigKey, Defaults, Dtypes, Methods,
+                               MLParamKeys, Options)
 from simba.utils.errors import (ClassifierInferenceError, ColumnNotFoundError,
                                 CorruptedFileError, DataHeaderError,
                                 FaultyTrainingSetError,

simba/model/inference_batch.py

@@ -3,11 +3,14 @@
 import os
 from copy import deepcopy
 from typing import Union
+
 import numpy as np
 
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.train_model_mixin import TrainModelMixin
-from simba.utils.checks import check_all_file_names_are_represented_in_video_log, check_if_keys_exist_in_dict
+from simba.utils.checks import (
+    check_all_file_names_are_represented_in_video_log,
+    check_if_keys_exist_in_dict)
 from simba.utils.data import plug_holes_shortest_bout
 from simba.utils.enums import TagNames
 from simba.utils.errors import NoFilesFoundError

simba/ui/pop_ups/third_party_annotator_appender_pop_up.py

@@ -7,12 +7,14 @@
 
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.pop_up_mixin import PopUpMixin
-from simba.third_party_label_appenders.third_party_appender import ThirdPartyLabelAppender
-from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, DropDownMenu, FolderSelect)
-from simba.utils.read_write import find_core_cnt
+from simba.third_party_label_appenders.third_party_appender import \
+    ThirdPartyLabelAppender
+from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, DropDownMenu,
+                                        FolderSelect)
 from simba.utils.checks import check_if_dir_exists
-from simba.utils.enums import Formats, Keys, Links, Options, Defaults
+from simba.utils.enums import Defaults, Formats, Keys, Links, Options
 from simba.utils.lookups import get_third_party_appender_file_formats
+from simba.utils.read_write import find_core_cnt
 
 
 class ThirdPartyAnnotatorAppenderPopUp(PopUpMixin, ConfigReader):

simba/ui/pop_ups/video_processing_pop_up.py

@@ -59,18 +59,17 @@
     convert_to_mov, convert_to_mp4, convert_to_png, convert_to_tiff,
     convert_to_webm, convert_to_webp,
     convert_video_powerpoint_compatible_format, copy_img_folder,
-    create_average_frm, crop_multiple_videos,
-    crop_multiple_videos_polygons, crop_single_video, crop_single_video_circle,
-    crop_single_video_polygon, crossfade_two_videos, downsample_video,
-    extract_frame_range, extract_frames_single_video, flip_videos,
-    frames_to_movie, gif_creator, multi_split_video, remove_beginning_of_video,
-    resize_videos_by_height, resize_videos_by_width, reverse_videos,
-    roi_blurbox, rotate_video, superimpose_elapsed_time,
-    superimpose_frame_count, superimpose_freetext, superimpose_overlay_video,
-    superimpose_video_names, superimpose_video_progressbar,
-    temporal_concatenation, upsample_fps, video_bg_substraction_mp,
-    video_bg_subtraction, video_concatenator, video_to_bw, video_to_greyscale,
-    watermark_video)
+    create_average_frm, crop_multiple_videos, crop_multiple_videos_polygons,
+    crop_single_video, crop_single_video_circle, crop_single_video_polygon,
+    crossfade_two_videos, downsample_video, extract_frame_range,
+    extract_frames_single_video, flip_videos, frames_to_movie, gif_creator,
+    multi_split_video, remove_beginning_of_video, resize_videos_by_height,
+    resize_videos_by_width, reverse_videos, roi_blurbox, rotate_video,
+    superimpose_elapsed_time, superimpose_frame_count, superimpose_freetext,
+    superimpose_overlay_video, superimpose_video_names,
+    superimpose_video_progressbar, temporal_concatenation, upsample_fps,
+    video_bg_substraction_mp, video_bg_subtraction, video_concatenator,
+    video_to_bw, video_to_greyscale, watermark_video)
 
 sys.setrecursionlimit(10**7)
 

simba/utils/checks.py

@@ -22,7 +22,8 @@
                                 NoDataError, NoFilesFoundError, NoROIDataError,
                                 NotDirectoryError, ParametersFileError,
                                 StringError)
-from simba.utils.warnings import (CorruptedFileWarning, FrameRangeWarning, NoDataFoundWarning, InvalidValueWarning)
+from simba.utils.warnings import (CorruptedFileWarning, FrameRangeWarning,
+                                  InvalidValueWarning, NoDataFoundWarning)
 
 
 def check_file_exist_and_readable(file_path: Union[str, os.PathLike]) -> None:

simba/utils/data.py

@@ -10,20 +10,22 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
+import cv2
 import h5py
 import numpy as np
 import pandas as pd
 from numba import jit, prange, typed
 from pylab import *
 from scipy import stats
 from scipy.signal import savgol_filter
-import cv2
 
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 from joblib import Parallel, delayed
+
 from simba.utils.checks import (check_file_exist_and_readable, check_float,
                                 check_if_df_field_is_boolean,
                                 check_if_dir_exists,

simba/utils/read_write.py

@@ -15,18 +15,20 @@
 from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional, Tuple, Union
+
 try:
     from typing import Literal
 except:
     from typing_extensions import Literal
+
 from urllib.parse import urlparse
-from numba import prange, njit
 
 import cv2
 import numpy as np
 import pandas as pd
 import pkg_resources
 import pyarrow as pa
+from numba import njit, prange
 from pyarrow import csv
 from shapely.geometry import (LineString, MultiLineString, MultiPolygon, Point,
                               Polygon)