Merge remote-tracking branch 'origin/master'

simba/sandbox/CLAHE.py

@@ -1,16 +1,21 @@
 import os
-from datetime import datetime
 import threading
+from datetime import datetime
 from tkinter import *
 from tkinter import Button
-from simba.utils.enums import Keys, Links, Options
+
 from simba.mixins.pop_up_mixin import PopUpMixin
-from simba.ui.tkinter_functions import CreateLabelFrameWithIcon, FileSelect, FolderSelect
-from simba.utils.checks import check_file_exist_and_readable, check_if_dir_exists
+from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, FileSelect,
+                                        FolderSelect)
+from simba.utils.checks import (check_file_exist_and_readable,
+                                check_if_dir_exists)
+from simba.utils.enums import Keys, Links, Options
+from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.read_write import (find_files_of_filetypes_in_directory,
+                                    get_fn_ext)
 from simba.video_processors.clahe_ui import interactive_clahe_ui
 from simba.video_processors.video_processing import clahe_enhance_video
-from simba.utils.read_write import find_files_of_filetypes_in_directory, get_fn_ext
-from simba.utils.printing import stdout_success, SimbaTimer
+
 
 class CLAHEPopUp(PopUpMixin):
     def __init__(self):

simba/sandbox/Geometry_7.py

@@ -1,11 +1,12 @@
 import os
+
 import numpy as np
 
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.geometry_mixin import GeometryMixin
 from simba.mixins.image_mixin import ImageMixin
-from simba.utils.read_write import read_df
 from simba.plotting.geometry_plotter import GeometryPlotter
+from simba.utils.read_write import read_df
 
 CONFIG_PATH = '/Users/simon/Desktop/envs/simba/troubleshooting/RAT_NOR/project_folder/project_config.ini'
 VIDEO_NAME = '2022-06-20_NOB_DOT_4'

simba/sandbox/MitraFeatureExtractor.py

@@ -1,21 +1,25 @@
+import argparse
 import os
+from itertools import product
+from typing import Union
+
 import numpy as np
 import pandas as pd
 from numba.typed import List
-from itertools import product
-import argparse
-from typing import Union
 
+from simba.feature_extractors.perimeter_jit import jitted_hull
 from simba.mixins.abstract_classes import AbstractFeatureExtraction
+from simba.mixins.circular_statistics import CircularStatisticsMixin
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
-from simba.mixins.timeseries_features_mixin import TimeseriesFeatureMixin
 from simba.mixins.statistics_mixin import Statistics
-from simba.mixins.circular_statistics import CircularStatisticsMixin
-from simba.feature_extractors.perimeter_jit import jitted_hull
-from simba.utils.checks import check_if_filepath_list_is_empty, check_all_file_names_are_represented_in_video_log
-from simba.utils.read_write import read_df, get_fn_ext, read_frm_of_video
-from simba.utils.read_write import SimbaTimer, stdout_success, write_df
+from simba.mixins.timeseries_features_mixin import TimeseriesFeatureMixin
+from simba.utils.checks import (
+    check_all_file_names_are_represented_in_video_log,
+    check_if_filepath_list_is_empty)
+from simba.utils.read_write import (SimbaTimer, get_fn_ext, read_df,
+                                    read_frm_of_video, stdout_success,
+                                    write_df)
 
 NOSE = 'nose'
 LEFT_SIDE = 'left_side'

simba/sandbox/ROI_analyzer.py

@@ -1,20 +1,26 @@
 __author__ = "Simon Nilsson"
 
 import os
-from typing import Optional, Union, List
+from typing import List, Optional, Union
+
 import numpy as np
 import pandas as pd
 
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
-from simba.mixins.feature_extraction_supplement_mixin import FeatureExtractionSupplemental
-from simba.utils.checks import check_file_exist_and_readable, check_float, check_valid_lst, check_all_file_names_are_represented_in_video_log, check_that_column_exist
+from simba.mixins.feature_extraction_supplement_mixin import \
+    FeatureExtractionSupplemental
+from simba.utils.checks import (
+    check_all_file_names_are_represented_in_video_log,
+    check_file_exist_and_readable, check_float, check_that_column_exist,
+    check_valid_lst)
+from simba.utils.data import detect_bouts, slice_roi_dict_for_video
 from simba.utils.enums import Keys
-from simba.utils.errors import (MissingColumnsError, CountError, ROICoordinatesNotFoundError)
+from simba.utils.errors import (CountError, MissingColumnsError,
+                                ROICoordinatesNotFoundError)
 from simba.utils.printing import stdout_success
-from simba.utils.read_write import get_fn_ext, read_df, read_data_paths
+from simba.utils.read_write import get_fn_ext, read_data_paths, read_df
 from simba.utils.warnings import NoDataFoundWarning
-from simba.utils.data import slice_roi_dict_for_video, detect_bouts
 
 
 class ROIAnalyzer(ConfigReader, FeatureExtractionMixin):

simba/sandbox/ROI_plotter.py

@@ -3,20 +3,23 @@
 import itertools
 import os
 from copy import deepcopy
-from typing import Tuple, Optional, Union, Dict
+from typing import Dict, Optional, Tuple, Union
 
 import cv2
 import numpy as np
 
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.plotting_mixin import PlottingMixin
 from simba.roi_tools.ROI_analyzer import ROIAnalyzer
-from simba.utils.data import create_color_palettes, slice_roi_dict_for_video, detect_bouts
-from simba.utils.checks import check_float, check_if_keys_exist_in_dict, check_file_exist_and_readable, check_video_and_data_frm_count_align
+from simba.utils.checks import (check_file_exist_and_readable, check_float,
+                                check_if_keys_exist_in_dict,
+                                check_video_and_data_frm_count_align)
+from simba.utils.data import (create_color_palettes, detect_bouts,
+                              slice_roi_dict_for_video)
 from simba.utils.enums import Formats, Paths, TagNames, TextOptions
 from simba.utils.errors import DuplicationError, NoFilesFoundError
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (get_fn_ext, get_video_meta_data)
+from simba.utils.read_write import get_fn_ext, get_video_meta_data
 from simba.utils.warnings import DuplicateNamesWarning
 
 SHOW_BODY_PARTS = 'show_body_part'

simba/sandbox/ROI_plotter_mp.py

@@ -5,7 +5,7 @@
 import os
 import platform
 import shutil
-from typing import Optional, Union, Dict, Tuple
+from typing import Dict, Optional, Tuple, Union
 
 import cv2
 import numpy as np
@@ -14,17 +14,19 @@
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.plotting_mixin import PlottingMixin
 from simba.roi_tools.ROI_analyzer import ROIAnalyzer
-from simba.utils.data import create_color_palettes, detect_bouts, slice_roi_dict_for_video
-from simba.utils.enums import Paths, TagNames, TextOptions, Formats
+from simba.utils.checks import (check_file_exist_and_readable, check_float,
+                                check_if_keys_exist_in_dict, check_int,
+                                check_video_and_data_frm_count_align)
+from simba.utils.data import (create_color_palettes, detect_bouts,
+                              slice_roi_dict_for_video)
+from simba.utils.enums import Formats, Paths, TagNames, TextOptions
 from simba.utils.errors import NoFilesFoundError
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (concatenate_videos_in_folder, get_fn_ext, get_video_meta_data, find_core_cnt)
+from simba.utils.read_write import (concatenate_videos_in_folder,
+                                    find_core_cnt, get_fn_ext,
+                                    get_video_meta_data)
 from simba.utils.warnings import DuplicateNamesWarning
-from simba.utils.checks import (check_float,
-                                check_int,
-                                check_if_keys_exist_in_dict,
-                                check_file_exist_and_readable,
-                                check_video_and_data_frm_count_align)
+
 pd.options.mode.chained_assignment = None
 
 SHOW_BODY_PARTS = 'show_body_part'

simba/sandbox/abod.py

@@ -1,14 +1,16 @@
-from typing import Union, Optional
+from typing import Optional, Union
+
 import numpy as np
 import pandas as pd
-from sklearn.covariance import EllipticEnvelope
 from pyod.models.abod import ABOD
-
-from simba.utils.checks import check_valid_array, check_float, check_int
-from sklearn.neighbors import LocalOutlierFactor
+from sklearn.covariance import EllipticEnvelope
 from sklearn.datasets import make_blobs
-from simba.mixins.plotting_mixin import PlottingMixin
+from sklearn.neighbors import LocalOutlierFactor
+
 from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
+from simba.mixins.plotting_mixin import PlottingMixin
+from simba.utils.checks import check_float, check_int, check_valid_array
+
 
 def angle_based_od(data: np.ndarray,
                    k: Union[int, float] = 5,

simba/sandbox/add_body_part.py

@@ -1,11 +1,13 @@
 import os.path
+
 import numpy as np
 import pandas as pd
 
-from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
 from simba.mixins.config_reader import ConfigReader
-from simba.utils.read_write import read_df, write_df, get_fn_ext, read_frm_of_video
+from simba.mixins.feature_extraction_mixin import FeatureExtractionMixin
 from simba.utils.checks import check_if_dir_exists
+from simba.utils.read_write import (get_fn_ext, read_df, read_frm_of_video,
+                                    write_df)
 
 #CHANGE THIS TO THE PATH OF YOUR SIMBA PROJECT CONFIG
 CONFIG_PATH = '/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini'

simba/sandbox/adjusted_rand.py

@@ -1,5 +1,6 @@
 import numpy as np
-from sklearn.metrics import (adjusted_mutual_info_score, adjusted_rand_score, fowlkes_mallows_score)
+from sklearn.metrics import (adjusted_mutual_info_score, adjusted_rand_score,
+                             fowlkes_mallows_score)
 
 
 def cluster_comparison(x: np.ndarray, y: np.ndarray, method: str = 'adjusted_rand_score'):

simba/sandbox/adjusted_rand_score.py

@@ -1,6 +1,9 @@
 import numpy as np
+from sklearn.metrics import (adjusted_mutual_info_score, adjusted_rand_score,
+                             fowlkes_mallows_score)
+
 from simba.utils.checks import check_valid_array
-from sklearn.metrics import adjusted_rand_score, fowlkes_mallows_score, adjusted_mutual_info_score
+
 
 def adjusted_rand(x: np.ndarray, y: np.ndarray) -> float:
     """

simba/sandbox/advanced_interpolator.py

@@ -5,6 +5,7 @@
 
 import numpy as np
 import pandas as pd
+
 pd.options.mode.chained_assignment = None
 
 
@@ -14,11 +15,14 @@
     from typing_extensions import Literal
 
 from simba.mixins.config_reader import ConfigReader
-from simba.utils.checks import (check_valid_boolean, check_instance, check_that_column_exist, check_str, check_file_exist_and_readable)
+from simba.utils.checks import (check_file_exist_and_readable, check_instance,
+                                check_str, check_that_column_exist,
+                                check_valid_boolean)
 from simba.utils.errors import DataHeaderError, InvalidInputError
 from simba.utils.printing import SimbaTimer, stdout_success
-from simba.utils.read_write import (find_files_of_filetypes_in_directory, get_fn_ext, read_df, write_df, copy_files_to_directory)
-
+from simba.utils.read_write import (copy_files_to_directory,
+                                    find_files_of_filetypes_in_directory,
+                                    get_fn_ext, read_df, write_df)
 
 BODY_PART_TYPE = 'body-part'
 ANIMAL_TYPE = 'animal'

simba/sandbox/advanced_smoothing.py

@@ -3,6 +3,7 @@
 import os
 from copy import deepcopy
 from typing import Any, Dict, Optional, Union
+
 import pandas as pd
 
 try:
@@ -11,14 +12,18 @@
     from typing_extensions import Literal
 
 from simba.mixins.config_reader import ConfigReader
-from simba.utils.checks import (check_valid_boolean, check_instance, check_str, check_int, check_that_column_exist, check_file_exist_and_readable)
+from simba.utils.checks import (check_file_exist_and_readable, check_instance,
+                                check_int, check_str, check_that_column_exist,
+                                check_valid_boolean)
+from simba.utils.data import df_smoother, savgol_smoother
 from simba.utils.enums import Methods, TagNames
-from simba.utils.errors import DataHeaderError, NoFilesFoundError, InvalidInputError
+from simba.utils.errors import (DataHeaderError, InvalidInputError,
+                                NoFilesFoundError)
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (find_files_of_filetypes_in_directory,
+from simba.utils.read_write import (copy_files_to_directory,
+                                    find_files_of_filetypes_in_directory,
                                     find_video_of_file, get_fn_ext,
-                                    get_video_meta_data, read_df, write_df, copy_files_to_directory)
-from simba.utils.data import savgol_smoother, df_smoother
+                                    get_video_meta_data, read_df, write_df)
 
 BODY_PART_TYPE = 'body-part'
 ANIMAL_TYPE = 'animal'

simba/sandbox/annotations_mitra.py

@@ -1,9 +1,11 @@
-import pandas as pd
 import glob
 import os
-from simba.utils.read_write import get_fn_ext
 import shutil
 
+import pandas as pd
+
+from simba.utils.read_write import get_fn_ext
+
 # ANNOTATED_VIDEOS_PATH = '/Users/simon/Desktop/envs/simba/troubleshooting/mitra/annotated_videos.csv'
 # DATA_PATH = '/Users/simon/Desktop/envs/simba/troubleshooting/mitra/project_folder/csv/input_csv/originals'
 # OUT_DIR = '/Users/simon/Desktop/envs/simba/troubleshooting/mitra/project_folder/csv/input_csv/'