cleaned

simba/SimBA.py

@@ -85,14 +85,14 @@
 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.mutual_exclusivity_pop_up import MutualExclusivityPupUp
+# 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
 from simba.ui.pop_ups.pose_bp_drop_pop_up import DropTrackingDataPopUp
 from simba.ui.pop_ups.pose_reorganizer_pop_up import PoseReorganizerPopUp
 from simba.ui.pop_ups.pup_retrieval_pop_up import PupRetrievalPopUp
 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.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
@@ -114,10 +114,9 @@
     ClipVideoPopUp, ConcatenatingVideosPopUp, ConcatenatorPopUp,
     ConvertVideoPopUp, CreateGIFPopUP, CropVideoPopUp, DownsampleVideoPopUp,
     ExtractAllFramesPopUp, ExtractAnnotationFramesPopUp, ExtractSEQFramesPopUp,
-    ExtractSpecificFramesPopUp,
-    ImportFrameDirectoryPopUp, MergeFrames2VideoPopUp, MultiCropPopUp,
-    MultiShortenPopUp, VideoRotatorPopUp,
-    VideoTemporalJoinPopUp)
+    ExtractSpecificFramesPopUp, ImportFrameDirectoryPopUp,
+    MergeFrames2VideoPopUp, MultiCropPopUp, MultiShortenPopUp,
+    VideoRotatorPopUp, VideoTemporalJoinPopUp)
 from simba.ui.pop_ups.visualize_pose_in_dir_pop_up import \
     VisualizePoseInFolderPopUp
 from simba.ui.tkinter_functions import DropDownMenu, Entry_Box, FileSelect
@@ -138,7 +137,7 @@
 
 # from simba.unsupervised.unsupervised_ui import UnsupervisedGUI
 
-sys.setrecursionlimit(10 ** 6)
+sys.setrecursionlimit(10**6)
 currentPlatform = platform.system()
 
 
@@ -155,7 +154,9 @@ def __init__(self):
             icon_link=Links.LOAD_PROJECT.value,
         )
         self.selected_file = FileSelect(
-            self.load_project_frm, "Select file: ", title="Select project_config.ini file"
+            self.load_project_frm,
+            "Select file: ",
+            title="Select project_config.ini file",
         )
         self.load_project_btn = Button(
             self.load_project_frm,
@@ -1128,7 +1129,7 @@ def activate(box, *args):
         roi_feature_frm.grid(row=1, column=0, sticky=NW)
         append_roi_features_by_animal.grid(row=0, column=0, sticky=NW)
         append_roi_features_by_body_part.grid(row=1, column=0, sticky=NW)
-        #remove_roi_features_from_feature_set.grid(row=2, column=0, sticky=NW)
+        # remove_roi_features_from_feature_set.grid(row=2, column=0, sticky=NW)
 
         feature_tools_frm.grid(row=2, column=0, sticky=NW)
         compute_feature_subset_btn.grid(row=0, column=0, sticky=NW)
@@ -1162,7 +1163,7 @@ def activate(box, *args):
         lbl_tools_frm.grid(row=9, column=0, sticky=NW)
         visualize_annotation_img_btn.grid(row=0, column=0, sticky=NW)
         third_party_annotations_btn.grid(row=1, column=0, sticky=NW)
-        #remove_roi_features_from_annotation_set.grid(row=2, column=0, sticky=NW)
+        # remove_roi_features_from_annotation_set.grid(row=2, column=0, sticky=NW)
 
         label_trainmachinemodel.grid(row=6, sticky=W)
         button_trainmachinesettings.grid(row=0, column=0, sticky=NW, padx=5)
@@ -1183,7 +1184,7 @@ def activate(box, *args):
         button_runmachinemodel.grid(row=1, sticky=NW)
         kleinberg_button.grid(row=2, sticky=NW)
         fsttc_button.grid(row=3, sticky=NW)
-        #mutual_exclusivity.grid(row=4, sticky=NW)
+        # mutual_exclusivity.grid(row=4, sticky=NW)
 
         label_machineresults.grid(row=9, sticky=W, pady=5)
         button_process_datalog.grid(row=2, column=0, sticky=W, padx=3)
@@ -1831,13 +1832,13 @@ def __init__(self):
         if OS.PYTHON_VER.value != "3.6":
             PythonVersionWarning(
                 msg=f"SimBA is not extensively tested beyond python 3.6. You are using python {OS.PYTHON_VER.value}. If you encounter errors in python>3.6, please report them on GitHub or Gitter and we will fix! (links in the help toolbar)",
-                source="python different than 3.6"
+                source="python different than 3.6",
             )
 
         if not check_ffmpeg_available():
             FFMpegNotFoundWarning(
                 msg='SimBA could not find a FFMPEG installation on computer (as evaluated by "ffmpeg" returning None). SimBA works best with FFMPEG and it is recommended to install it on your computer',
-                source="ffmpeg checker"
+                source="ffmpeg checker",
             )
 
     def restart(self):

simba/data_processors/agg_clf_calculator.py

@@ -157,7 +157,7 @@ def save(self) -> None:
         self.results_df = (
             self.results_df[
                 self.results_df["Measure"].isin(
-                    self.chosen_measures# + self.video_meta_data
+                    self.chosen_measures  # + self.video_meta_data
                 )
             ]
             .sort_values(by=["Video", "Classifier", "Measure"])

simba/mixins/train_model_mixin.py

@@ -1290,7 +1290,8 @@ def clf_predict_proba(
             else:
                 raise FeatureNumberMismatchError(
                     f"The model expects {clf_n_features} features. The data contains {len(x_df.columns)} features.",
-                    source=self.__class__.__name__)
+                    source=self.__class__.__name__,
+                )
         p_vals = clf.predict_proba(x_df)
         if p_vals.shape[1] != 2:
             raise ClassifierInferenceError(

simba/roi_tools/ROI_define.py

@@ -41,7 +41,7 @@ class ROI_definitions(ConfigReader):
 
     """
 
-    def __init__(self, config_path: str, video_path: str,image_data : ROI_image_class):
+    def __init__(self, config_path: str, video_path: str, image_data: ROI_image_class):
         ConfigReader.__init__(self, config_path=config_path)
         self.video_path = video_path
         _, self.file_name, self.file_ext = get_fn_ext(self.video_path)
@@ -110,7 +110,6 @@ def on_close(self):
         self.master.destroy()
         self.root.destroy()
 
-
     def show_video_info(self):
         self.video_info_frame = LabelFrame(
             self.master,
@@ -313,7 +312,7 @@ def apply_from_other_videos_menu(self):
         )
         self.apply_from_other_video.grid(row=7, sticky=W)
         self.video_dropdown.config(direction=RIGHT)
-        self.video_dropdown.grid(row=1, column=1,sticky="ew", pady=20)
+        self.video_dropdown.grid(row=1, column=1, sticky="ew", pady=20)
         self.apply_button.grid(row=1, column=3, sticky=W, pady=10)
 
     def select_shape(self):
@@ -545,10 +544,10 @@ def draw_menu(self):
 
     def show_shape_information(self):
         if (
-                len(self.image_data.out_rectangles)
-                + len(self.image_data.out_circles)
-                + len(self.image_data.out_polygon)
-                == 0
+            len(self.image_data.out_rectangles)
+            + len(self.image_data.out_circles)
+            + len(self.image_data.out_polygon)
+            == 0
         ):
             print("No shapes to print info for.")
 
@@ -691,10 +690,10 @@ def set_interact_state(self, c_interact):
     def call_delete_all_rois(self):
         self.shape_info_btn.configure(text="Show shape info.")
         if (
-                len(self.image_data.out_rectangles)
-                + len(self.image_data.out_circles)
-                + len(self.image_data.out_polygon)
-                == 0
+            len(self.image_data.out_rectangles)
+            + len(self.image_data.out_circles)
+            + len(self.image_data.out_polygon)
+            == 0
         ):
             NoDataFoundWarning(msg="SimBA finds no ROIs to delete.")
         else:
@@ -714,7 +713,7 @@ def get_duplicate_shape_name(self):
                 c_no += 1
             else:
                 self.new_shape_data["Name"] = (
-                        str(self.shape_type) + ": " + self.new_name
+                    str(self.shape_type) + ": " + self.new_name
                 )
                 break
 
@@ -728,7 +727,7 @@ def get_duplicate_coords(self):
             )
             for shape in self.image_data.out_rectangles:
                 if (shape["topLeftX"] == self.new_shape_x) and (
-                        shape["topLeftY"] == self.new_shape_y
+                    shape["topLeftY"] == self.new_shape_y
                 ):
                     self.new_shape_x += self.duplicate_jump_size
                     self.new_shape_y += self.duplicate_jump_size
@@ -741,7 +740,7 @@ def get_duplicate_coords(self):
             )
             for shape in self.image_data.out_circles:
                 if (shape["centerY"] == self.new_shape_x) and (
-                        shape["centerY"] == self.new_shape_y
+                    shape["centerY"] == self.new_shape_y
                 ):
                     self.new_shape_x += self.duplicate_jump_size
                     self.new_shape_y += self.duplicate_jump_size
@@ -754,7 +753,7 @@ def get_duplicate_coords(self):
             )
             for shape in self.image_data.out_polygon:
                 if (shape["Center_X"] == self.new_shape_x) and (
-                        shape["centerY"] == self.new_shape_y
+                    shape["centerY"] == self.new_shape_y
                 ):
                     self.new_shape_x += self.duplicate_jump_size
                     self.new_shape_y += self.duplicate_jump_size
@@ -764,9 +763,9 @@ def call_duplicate_ROI(self):
         self.shape_info_btn.configure(text="Show shape info.")
         if shape_name[0] != "None":
             all_roi_list = (
-                    self.image_data.out_rectangles
-                    + self.image_data.out_circles
-                    + self.image_data.out_polygon
+                self.image_data.out_rectangles
+                + self.image_data.out_circles
+                + self.image_data.out_polygon
             )
             self.shape_type, shape_name = shape_name[0], shape_name[1]
             self.current_shape_data = [
@@ -849,11 +848,11 @@ def save_data(self):
             polygons_found = pd.read_hdf(self.roi_coordinates_path, key="polygons")
             other_vid_rectangles = rectangles_found[
                 rectangles_found["Video"] != self.file_name
-                ]
+            ]
             other_vid_circles = circles_found[circles_found["Video"] != self.file_name]
             other_vid_polygons = polygons_found[
                 polygons_found["Video"] != self.file_name
-                ]
+            ]
 
             new_rectangles = pd.DataFrame.from_dict(self.image_data.out_rectangles)
             new_circles = pd.DataFrame.from_dict(self.image_data.out_circles)
@@ -916,9 +915,9 @@ def __init__(self, shape_data, image_data):
             shape_name = shape_data.selected_video.get().split(": ")
             if shape_name[0] != "None":
                 self.all_roi_list = (
-                        shape_data.image_data.out_rectangles
-                        + shape_data.image_data.out_circles
-                        + shape_data.image_data.out_polygon
+                    shape_data.image_data.out_rectangles
+                    + shape_data.image_data.out_circles
+                    + shape_data.image_data.out_polygon
                 )
                 self.shape_type, self.shape_name = shape_name[0], shape_name[1]
                 current_shape_data = [
@@ -1119,6 +1118,7 @@ def save_prefs(self, image_data):
         image_data.duplicate_jump_size = self.duplicate_jump_size.get()
         stdout_success(msg="Saved ROI preference settings.")
 
+
 #
 # test = ROI_definitions(config_path='/Users/simon/Desktop/envs/simba_dev/tests/test_data/mouse_open_field/project_folder/project_config.ini',
 #                       video_path='/Users/simon/Desktop/envs/simba_dev/tests/test_data/mouse_open_field/project_folder/videos/Video1.mp4')