Merge remote-tracking branch 'origin/master'

# Conflicts: # simba/data_processors/interpolation_smoothing.py
sgoldenlab · Jul 2, 2024 · 930983d · 930983d
2 parents f80a4fa + 1a15961
commit 930983d
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diff --git a/simba/SimBA.py b/simba/SimBA.py
@@ -20,57 +20,81 @@
 
 from simba.bounding_box_tools.boundary_menus import BoundaryMenus
 from simba.cue_light_tools.cue_light_menues import CueLightAnalyzerMenu
-from simba.labelling.labelling_advanced_interface import select_labelling_video_advanced
+from simba.labelling.labelling_advanced_interface import \
+    select_labelling_video_advanced
 from simba.labelling.labelling_interface import select_labelling_video
-from simba.labelling.targeted_annotations_clips import select_labelling_video_targeted_clips
+from simba.labelling.targeted_annotations_clips import \
+    select_labelling_video_targeted_clips
 from simba.model.grid_search_rf import GridSearchRandomForestClassifier
 from simba.model.inference_batch import InferenceBatch
 from simba.model.inference_validation import InferenceValidation
 from simba.model.train_rf import TrainRandomForestClassifier
-from simba.outlier_tools.outlier_corrector_location import OutlierCorrecterLocation
-from simba.outlier_tools.outlier_corrector_movement import OutlierCorrecterMovement
-from simba.outlier_tools.skip_outlier_correction import OutlierCorrectionSkipper
-from simba.plotting.interactive_probability_grapher import InteractiveProbabilityGrapher
+from simba.outlier_tools.outlier_corrector_location import \
+    OutlierCorrecterLocation
+from simba.outlier_tools.outlier_corrector_movement import \
+    OutlierCorrecterMovement
+from simba.outlier_tools.skip_outlier_correction import \
+    OutlierCorrectionSkipper
+from simba.plotting.interactive_probability_grapher import \
+    InteractiveProbabilityGrapher
 from simba.roi_tools.ROI_define import *
 from simba.roi_tools.ROI_menus import *
 from simba.roi_tools.ROI_reset import *
 from simba.third_party_label_appenders.BENTO_appender import BentoAppender
 from simba.third_party_label_appenders.BORIS_appender import BorisAppender
-from simba.third_party_label_appenders.deepethogram_importer import DeepEthogramImporter
-from simba.third_party_label_appenders.ethovision_import import ImportEthovision
-from simba.third_party_label_appenders.observer_importer import NoldusObserverImporter
+from simba.third_party_label_appenders.deepethogram_importer import \
+    DeepEthogramImporter
+from simba.third_party_label_appenders.ethovision_import import \
+    ImportEthovision
+from simba.third_party_label_appenders.observer_importer import \
+    NoldusObserverImporter
 from simba.third_party_label_appenders.solomon_importer import SolomonImporter
 from simba.ui.create_project_ui import ProjectCreatorPopUp
+from simba.ui.import_pose_frame import ImportPoseFrame
+from simba.ui.import_videos_frame import ImportVideosFrame
 from simba.ui.machine_model_settings_ui import MachineModelSettingsPopUp
 from simba.ui.pop_ups.about_simba_pop_up import AboutSimBAPopUp
-from simba.ui.pop_ups.animal_directing_other_animals_pop_up import AnimalDirectingAnimalPopUp
-from simba.ui.pop_ups.append_roi_features_animals_pop_up import AppendROIFeaturesByAnimalPopUp
-from simba.ui.pop_ups.append_roi_features_bodypart_pop_up import AppendROIFeaturesByBodyPartPopUp
+from simba.ui.pop_ups.animal_directing_other_animals_pop_up import \
+    AnimalDirectingAnimalPopUp
+from simba.ui.pop_ups.append_roi_features_animals_pop_up import \
+    AppendROIFeaturesByAnimalPopUp
+from simba.ui.pop_ups.append_roi_features_bodypart_pop_up import \
+    AppendROIFeaturesByBodyPartPopUp
 from simba.ui.pop_ups.archive_files_pop_up import ArchiveProcessedFilesPopUp
 from simba.ui.pop_ups.batch_preprocess_pop_up import BatchPreProcessPopUp
-from simba.ui.pop_ups.boolean_conditional_slicer_pup_up import BooleanConditionalSlicerPopUp
-from simba.ui.pop_ups.clf_add_remove_print_pop_up import (AddClfPopUp, PrintModelInfoPopUp, RemoveAClassifierPopUp)
+from simba.ui.pop_ups.boolean_conditional_slicer_pup_up import \
+    BooleanConditionalSlicerPopUp
+from simba.ui.pop_ups.clf_add_remove_print_pop_up import (
+    AddClfPopUp, PrintModelInfoPopUp, RemoveAClassifierPopUp)
 from simba.ui.pop_ups.clf_by_roi_pop_up import ClfByROIPopUp
 from simba.ui.pop_ups.clf_by_timebins_pop_up import TimeBinsClfPopUp
-from simba.ui.pop_ups.clf_descriptive_statistics_pop_up import ClfDescriptiveStatsPopUp
+from simba.ui.pop_ups.clf_descriptive_statistics_pop_up import \
+    ClfDescriptiveStatsPopUp
 from simba.ui.pop_ups.clf_plot_pop_up import SklearnVisualizationPopUp
-from simba.ui.pop_ups.clf_probability_plot_pop_up import VisualizeClassificationProbabilityPopUp
-from simba.ui.pop_ups.clf_validation_plot_pop_up import ClassifierValidationPopUp
+from simba.ui.pop_ups.clf_probability_plot_pop_up import \
+    VisualizeClassificationProbabilityPopUp
+from simba.ui.pop_ups.clf_validation_plot_pop_up import \
+    ClassifierValidationPopUp
 from simba.ui.pop_ups.csv_2_parquet_pop_up import (Csv2ParquetPopUp,
                                                    Parquet2CsvPopUp)
 from simba.ui.pop_ups.data_plot_pop_up import DataPlotterPopUp
-from simba.ui.pop_ups.directing_animal_to_bodypart_plot_pop_up import DirectingAnimalToBodyPartVisualizerPopUp
-from simba.ui.pop_ups.directing_other_animals_plot_pop_up import DirectingOtherAnimalsVisualizerPopUp
-from simba.ui.pop_ups.direction_animal_to_bodypart_settings_pop_up import DirectionAnimalToBodyPartSettingsPopUp
+from simba.ui.pop_ups.directing_animal_to_bodypart_plot_pop_up import \
+    DirectingAnimalToBodyPartVisualizerPopUp
+from simba.ui.pop_ups.directing_other_animals_plot_pop_up import \
+    DirectingOtherAnimalsVisualizerPopUp
+from simba.ui.pop_ups.direction_animal_to_bodypart_settings_pop_up import \
+    DirectionAnimalToBodyPartSettingsPopUp
 from simba.ui.pop_ups.distance_plot_pop_up import DistancePlotterPopUp
 from simba.ui.pop_ups.fsttc_pop_up import FSTTCPopUp
 from simba.ui.pop_ups.gantt_pop_up import GanttPlotPopUp
 from simba.ui.pop_ups.heatmap_clf_pop_up import HeatmapClfPopUp
 from simba.ui.pop_ups.heatmap_location_pop_up import HeatmapLocationPopup
+from simba.ui.pop_ups.interpolate_pop_up import InterpolatePopUp
 from simba.ui.pop_ups.kleinberg_pop_up import KleinbergPopUp
 from simba.ui.pop_ups.make_path_plot_pop_up import MakePathPlotPopUp
 from simba.ui.pop_ups.movement_analysis_pop_up import MovementAnalysisPopUp
-from simba.ui.pop_ups.movement_analysis_time_bins_pop_up import MovementAnalysisTimeBinsPopUp
+from simba.ui.pop_ups.movement_analysis_time_bins_pop_up import \
+    MovementAnalysisTimeBinsPopUp
 from simba.ui.pop_ups.mutual_exclusivity_pop_up import MutualExclusivityPupUp
 from simba.ui.pop_ups.outlier_settings_pop_up import OutlierSettingsPopUp
 from simba.ui.pop_ups.path_plot_pop_up import PathPlotPopUp
@@ -80,17 +104,22 @@
 from simba.ui.pop_ups.quick_path_plot_pop_up import QuickLineplotPopup
 from simba.ui.pop_ups.remove_roi_features_pop_up import RemoveROIFeaturesPopUp
 from simba.ui.pop_ups.roi_analysis_pop_up import ROIAnalysisPopUp
-from simba.ui.pop_ups.roi_analysis_time_bins_pop_up import ROIAnalysisTimeBinsPopUp
+from simba.ui.pop_ups.roi_analysis_time_bins_pop_up import \
+    ROIAnalysisTimeBinsPopUp
 from simba.ui.pop_ups.roi_features_plot_pop_up import VisualizeROIFeaturesPopUp
-from simba.ui.pop_ups.roi_size_standardizer_popup import ROISizeStandardizerPopUp
+from simba.ui.pop_ups.roi_size_standardizer_popup import \
+    ROISizeStandardizerPopUp
 from simba.ui.pop_ups.roi_tracking_plot_pop_up import VisualizeROITrackingPopUp
-from simba.ui.pop_ups.set_machine_model_parameters_pop_up import SetMachineModelParameters
+from simba.ui.pop_ups.set_machine_model_parameters_pop_up import \
+    SetMachineModelParameters
 from simba.ui.pop_ups.severity_analysis_pop_up import AnalyzeSeverityPopUp
 from simba.ui.pop_ups.smoothing_popup import SmoothingPopUp
-from simba.ui.pop_ups.interpolate_pop_up import InterpolatePopUp
-from simba.ui.pop_ups.spontaneous_alternation_pop_up import SpontaneousAlternationPopUp
-from simba.ui.pop_ups.subset_feature_extractor_pop_up import FeatureSubsetExtractorPopUp
-from simba.ui.pop_ups.third_party_annotator_appender_pop_up import ThirdPartyAnnotatorAppenderPopUp
+from simba.ui.pop_ups.spontaneous_alternation_pop_up import \
+    SpontaneousAlternationPopUp
+from simba.ui.pop_ups.subset_feature_extractor_pop_up import \
+    FeatureSubsetExtractorPopUp
+from simba.ui.pop_ups.third_party_annotator_appender_pop_up import \
+    ThirdPartyAnnotatorAppenderPopUp
 from simba.ui.pop_ups.validation_plot_pop_up import ValidationVideoPopUp
 from simba.ui.pop_ups.video_processing_pop_up import (
     BackgroundRemoverPopUp, BoxBlurPopUp, BrightnessContrastPopUp,
@@ -114,20 +143,22 @@
     SuperimposeTextPopUp, SuperimposeTimerPopUp, SuperimposeVideoNamesPopUp,
     SuperimposeVideoPopUp, SuperimposeWatermarkPopUp, UpsampleVideosPopUp,
     VideoRotatorPopUp, VideoTemporalJoinPopUp)
-from simba.ui.pop_ups.visualize_pose_in_dir_pop_up import VisualizePoseInFolderPopUp
+from simba.ui.pop_ups.visualize_pose_in_dir_pop_up import \
+    VisualizePoseInFolderPopUp
 from simba.ui.tkinter_functions import DropDownMenu, Entry_Box, FileSelect
 from simba.ui.video_info_ui import VideoInfoTable
-from simba.ui.import_pose_frame import ImportPoseFrame
-from simba.ui.import_videos_frame import ImportVideosFrame
-from simba.utils.checks import (check_ffmpeg_available, check_file_exist_and_readable, check_int)
+from simba.utils.checks import (check_ffmpeg_available,
+                                check_file_exist_and_readable, check_int)
 from simba.utils.custom_feature_extractor import CustomFeatureExtractor
 from simba.utils.enums import OS, Defaults, Formats, Paths, TagNames
 from simba.utils.errors import InvalidInputError
-from simba.utils.lookups import (get_bp_config_code_class_pairs, get_emojis, get_icons_paths)
+from simba.utils.lookups import (get_bp_config_code_class_pairs, get_emojis,
+                                 get_icons_paths)
 from simba.utils.printing import stdout_success, stdout_warning
 from simba.utils.read_write import 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
+from simba.video_processors.video_processing import \
+    extract_frames_from_all_videos_in_directory
 
 sys.setrecursionlimit(10**6)
 currentPlatform = platform.system()

diff --git a/simba/data_processors/interpolate.py b/simba/data_processors/interpolate.py
@@ -1,8 +1,10 @@
 import pandas as pd
+
 pd.options.mode.chained_assignment = None
 import os
-from typing import Optional, Union, List
 from copy import deepcopy
+from typing import List, Optional, Union
+
 import numpy as np
 
 try:
@@ -11,12 +13,15 @@
     from typing_extensions import Literal
 
 from simba.mixins.config_reader import ConfigReader
-from simba.utils.checks import (check_str, check_valid_lst, check_file_exist_and_readable)
+from simba.utils.checks import (check_file_exist_and_readable, check_str,
+                                check_valid_lst)
+from simba.utils.data import animal_interpolator, body_part_interpolator
 from simba.utils.enums import TagNames
 from simba.utils.errors import DataHeaderError, InvalidInputError
 from simba.utils.printing import SimbaTimer, log_event, 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.data import animal_interpolator, body_part_interpolator
+from simba.utils.read_write import (copy_files_to_directory,
+                                    find_files_of_filetypes_in_directory,
+                                    get_fn_ext, read_df, write_df)
 
 
 class Interpolate(ConfigReader):

diff --git a/simba/data_processors/interpolation_smoothing.py b/simba/data_processors/interpolation_smoothing.py
@@ -20,7 +20,8 @@
 from simba.utils.enums import Methods, TagNames
 from simba.utils.errors import DataHeaderError, NoFilesFoundError
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (find_files_of_filetypes_in_directory, find_video_of_file, get_fn_ext, get_video_meta_data, read_df, write_df)
+from simba.utils.read_write import (find_files_of_filetypes_in_directory, find_video_of_file, get_fn_ext,
+                                    get_video_meta_data, read_df, write_df)
 
 
 class Interpolate(ConfigReader):
@@ -815,4 +816,3 @@ def run(self):
 #                  input_dir: str,
 #                  time_window: int,
 #                  smoothing_method: str):
-
diff --git a/simba/data_processors/smoothing.py b/simba/data_processors/smoothing.py
@@ -1,8 +1,8 @@
 __author__ = "Simon Nilsson"
 
 import os
-from typing import Union, List, Optional
 from copy import deepcopy
+from typing import List, Optional, Union
 
 import pandas as pd
 
@@ -12,12 +12,17 @@
     from typing_extensions import Literal
 
 from simba.mixins.config_reader import ConfigReader
-from simba.utils.checks import (check_str, check_int, check_valid_lst, check_file_exist_and_readable)
+from simba.utils.checks import (check_file_exist_and_readable, check_int,
+                                check_str, check_valid_lst)
+from simba.utils.data import df_smoother, savgol_smoother
 from simba.utils.enums import TagNames
 from simba.utils.errors import InvalidInputError, NoFilesFoundError
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (find_files_of_filetypes_in_directory, find_video_of_file, get_fn_ext, read_video_info, get_video_meta_data, read_df, write_df, copy_files_to_directory)
-from simba.utils.data import savgol_smoother, df_smoother
+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,
+                                    read_video_info, write_df)
 
 
 class Smoothing(ConfigReader):

diff --git a/simba/mixins/pop_up_mixin.py b/simba/mixins/pop_up_mixin.py
@@ -3,17 +3,20 @@
 import os
 from tkinter import *
 from tkinter import ttk
-from typing import Callable, Dict, List, Optional, Tuple, Union, Any
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import PIL.Image
 from PIL import ImageTk
 
 from simba.mixins.config_reader import ConfigReader
-from simba.ui.tkinter_functions import (DropDownMenu, Entry_Box, FileSelect, hxtScrollbar)
-from simba.utils.checks import (check_float, check_int, check_valid_lst, check_instance)
+from simba.ui.tkinter_functions import (DropDownMenu, Entry_Box, FileSelect,
+                                        hxtScrollbar)
+from simba.utils.checks import (check_float, check_instance, check_int,
+                                check_valid_lst)
 from simba.utils.enums import Formats, Options
 from simba.utils.errors import CountError, NoFilesFoundError
-from simba.utils.lookups import (get_color_dict, get_icons_paths, get_named_colors)
+from simba.utils.lookups import (get_color_dict, get_icons_paths,
+                                 get_named_colors)
 from simba.utils.read_write import find_core_cnt
 
 

diff --git a/simba/pose_importers/dlc_importer_csv.py b/simba/pose_importers/dlc_importer_csv.py
@@ -2,16 +2,21 @@
 
 import os
 import shutil
-from typing import List, Union, Dict, Optional, Any
+from typing import Any, Dict, List, Optional, Union
+
 import pandas as pd
 
-from simba.mixins.config_reader import ConfigReader
 from simba.data_processors.interpolate import Interpolate
 from simba.data_processors.smoothing import Smoothing
-from simba.utils.checks import (check_file_exist_and_readable, check_int, check_str, check_if_keys_exist_in_dict, check_instance)
+from simba.mixins.config_reader import ConfigReader
+from simba.utils.checks import (check_file_exist_and_readable,
+                                check_if_keys_exist_in_dict, check_instance,
+                                check_int, check_str)
 from simba.utils.errors import FileExistError, InvalidInputError
 from simba.utils.printing import SimbaTimer, stdout_success
-from simba.utils.read_write import (get_fn_ext, get_number_of_header_columns_in_df, find_files_of_filetypes_in_directory)
+from simba.utils.read_write import (find_files_of_filetypes_in_directory,
+                                    get_fn_ext,
+                                    get_number_of_header_columns_in_df)
 
 DLC_ = 'DLC_'
 DeepCut = 'DeepCut'

diff --git a/simba/pose_importers/madlc_importer.py b/simba/pose_importers/madlc_importer.py
@@ -19,11 +19,12 @@
 from simba.utils.checks import (check_file_exist_and_readable,
                                 check_if_dir_exists,
                                 check_if_keys_exist_in_dict, check_instance,
-                                check_str, check_valid_lst, check_int)
+                                check_int, check_str, check_valid_lst)
 from simba.utils.enums import Formats, Methods, Options
 from simba.utils.errors import BodypartColumnNotFoundError
 from simba.utils.printing import SimbaTimer, stdout_success
-from simba.utils.read_write import (find_all_videos_in_project, get_video_meta_data, write_df)
+from simba.utils.read_write import (find_all_videos_in_project,
+                                    get_video_meta_data, write_df)
 
 
 class MADLCImporterH5(ConfigReader, PoseImporterMixin):

diff --git a/simba/pose_importers/sleap_csv_importer.py b/simba/pose_importers/sleap_csv_importer.py
@@ -2,7 +2,7 @@
 
 import os
 from copy import deepcopy
-from typing import Union, Dict, List, Any, Optional
+from typing import Any, Dict, List, Optional, Union
 
 import numpy as np
 import pandas as pd
@@ -11,11 +11,16 @@
 from simba.data_processors.smoothing import Smoothing
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.pose_importer_mixin import PoseImporterMixin
-from simba.utils.checks import check_that_column_exist, check_str, check_int, check_if_keys_exist_in_dict, check_if_dir_exists, check_valid_lst
+from simba.utils.checks import (check_if_dir_exists,
+                                check_if_keys_exist_in_dict, check_int,
+                                check_str, check_that_column_exist,
+                                check_valid_lst)
 from simba.utils.enums import Methods, TagNames
 from simba.utils.errors import CountError
 from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import (clean_sleap_file_name, find_all_videos_in_project, get_fn_ext, get_video_meta_data, write_df)
+from simba.utils.read_write import (clean_sleap_file_name,
+                                    find_all_videos_in_project, get_fn_ext,
+                                    get_video_meta_data, write_df)
 
 TRACK = "track"
 INSTANCE_SCORE = "instance.score"

diff --git a/simba/pose_importers/sleap_h5_importer.py b/simba/pose_importers/sleap_h5_importer.py
@@ -10,12 +10,17 @@
 from simba.data_processors.smoothing import Smoothing
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.pose_importer_mixin import PoseImporterMixin
-from simba.utils.checks import check_file_exist_and_readable
-from simba.utils.checks import check_str, check_int, check_if_keys_exist_in_dict, check_if_dir_exists, check_valid_lst
+from simba.utils.checks import (check_file_exist_and_readable,
+                                check_if_dir_exists,
+                                check_if_keys_exist_in_dict, check_int,
+                                check_str, check_valid_lst)
 from simba.utils.enums import Methods, TagNames
 from simba.utils.errors import BodypartColumnNotFoundError
-from simba.utils.printing import (SimbaTimer, log_event, stdout_success, stdout_warning)
-from simba.utils.read_write import (clean_sleap_file_name, find_all_videos_in_project, get_fn_ext, get_video_meta_data, write_df)
+from simba.utils.printing import (SimbaTimer, log_event, stdout_success,
+                                  stdout_warning)
+from simba.utils.read_write import (clean_sleap_file_name,
+                                    find_all_videos_in_project, get_fn_ext,
+                                    get_video_meta_data, write_df)
 
 
 class SLEAPImporterH5(ConfigReader, PoseImporterMixin):