some fixes

simba/SimBA.py

@@ -3,6 +3,8 @@
 import os.path
 import warnings
 
+from simba.ui.pop_ups.append_bodypart_directionality_features_pop_up import AppendBodyPartDirectionalityFeaturesPopUp
+
 warnings.filterwarnings("ignore", category=FutureWarning)
 warnings.filterwarnings("ignore", category=DeprecationWarning)
 from simba.ui.pop_ups.direction_animal_to_bodypart_settings_pop_up import DirectionAnimalToBodyPartSettingsPopUp
@@ -140,7 +142,7 @@
 
 # from simba.unsupervised.unsupervised_ui import UnsupervisedGUI
 
-sys.setrecursionlimit(10**6)
+sys.setrecursionlimit(10 ** 6)
 currentPlatform = platform.system()
 
 
@@ -597,6 +599,14 @@ def activate(box, *args):
                 config_path=self.config_path
             ),
         )
+        append_body_part_directionality_features = Button(
+            roi_feature_frm,
+            text="APPEND BODY PART DIRECTIONALITY DATA TO FEATURES (CAUTION)",
+            fg="green",
+            command=lambda: AppendBodyPartDirectionalityFeaturesPopUp(
+                config_path=self.config_path
+            ),
+        )
         # remove_roi_features_from_feature_set = Button(
         #     roi_feature_frm,
         #     text="REMOVE ROI FEATURES FROM FEATURE SET",
@@ -1145,6 +1155,7 @@ 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)
+        append_body_part_directionality_features.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)
@@ -1255,7 +1266,6 @@ def directing_other_animals_analysis(self):
     def directing_animal_to_bp_analysis(self):
         _ = DirectionAnimalToBodyPartSettingsPopUp(config_path=self.config_path)
 
-
     def directing_other_animals_visualizer(self):
         _ = DirectingOtherAnimalsVisualizerPopUp(config_path=self.config_path)
 

simba/data_processors/directing_animal_to_bodypart.py

@@ -146,7 +146,7 @@ def create_directionality_dfs(self):
             for animal_permutation, permutation_data in video_data.items():
                 for bp_name, bp_data in permutation_data.items():
                     directing_df = (
-                        bp_data#[bp_data["Directing_BOOL"] == 1]
+                        bp_data  # [bp_data["Directing_BOOL"] == 1]
                         .reset_index()
                         .rename(
                             columns={
@@ -194,14 +194,15 @@ def save_directionality_dfs(self):
         -------
         None
         """
-        if not os.path.exists(self.body_part_directionality_df_dir):
-            os.makedirs(self.body_part_directionality_df_dir)
+        output_dir = os.path.join(self.body_part_directionality_df_dir, self.bodypart_direction)
+        if not os.path.exists(output_dir):
+            os.makedirs(output_dir)
         for video_name, video_data in self.directionality_df_dict.items():
-            save_name = os.path.join(self.body_part_directionality_df_dir, video_name + ".csv")
+            save_name = os.path.join(output_dir, video_name + ".csv")
             video_data.to_csv(save_name)
             print(f"Detailed directional data saved for video {video_name}...")
         stdout_success(
-            msg=f"All detailed directional data saved in the {self.body_part_directionality_df_dir} directory"
+            msg=f"All detailed directional data saved in the {output_dir} directory"
 
         )
 
@@ -238,7 +239,7 @@ def summary_statistics(self):
             .set_index("Video")
         )
         self.save_path = os.path.join(
-            self.logs_path, "Body_part_directions_data_{}.csv".format(str(self.datetime))
+            self.logs_path, "Body_part_directions_data_{}_{}.csv".format(str(self.bodypart_direction, self.datetime))
         )
         self.summary_df.to_csv(self.save_path)
         self.timer.stop_timer()

simba/mixins/pop_up_mixin.py

@@ -43,10 +43,10 @@ class PopUpMixin(object):
     """
 
     def __init__(
-        self,
-        title: str,
-        config_path: Optional[str] = None,
-        size: Tuple[int, int] = (960,720),
+            self,
+            title: str,
+            config_path: Optional[str] = None,
+            size: Tuple[int, int] = (960, 720),
     ):
         self.root = Toplevel()
         self.root.minsize(size[0], size[1])
@@ -92,7 +92,7 @@ def create_clf_checkboxes(self, main_frm: Frame, clfs: List[str]):
         self.choose_clf_frm.grid(row=self.children_cnt_main(), column=0, sticky=NW)
 
     def create_cb_frame(
-        self, main_frm: Frame, cb_titles: List[str], frm_title: str
+            self, main_frm: Frame, cb_titles: List[str], frm_title: str
     ) -> Dict[str, BooleanVar]:
         cb_frm = LabelFrame(
             main_frm, text=frm_title, font=Formats.LABELFRAME_HEADER_FORMAT.value
@@ -106,11 +106,11 @@ def create_cb_frame(
         return cb_dict
 
     def create_dropdown_frame(
-        self,
-        main_frm: Frame,
-        drop_down_titles: List[str],
-        drop_down_options: List[str],
-        frm_title: str,
+            self,
+            main_frm: Frame,
+            drop_down_titles: List[str],
+            drop_down_options: List[str],
+            frm_title: str,
     ):
         dropdown_frm = LabelFrame(
             main_frm, text=frm_title, font=Formats.LABELFRAME_HEADER_FORMAT.value
@@ -209,8 +209,33 @@ def create_run_frm(self, run_function: object, title: str = "RUN"):
         self.run_frm.grid(row=self.children_cnt_main() + 1, column=0, sticky=NW)
         self.run_btn.grid(row=0, column=0, sticky=NW)
 
+    def create_choose_number_of_body_parts_directionality_frm(
+            self, path_to_directionality_dir: str, run_function: object
+    ):
+        self.bp_cnt_frm = LabelFrame(
+            self.main_frm,
+            text="SELECT DIR",
+            font=Formats.LABELFRAME_HEADER_FORMAT.value,
+        )
+        root, types_of_directionality, files = list(os.walk(path_to_directionality_dir))[0]
+        self.bp_cnt_dropdown = DropDownMenu(
+            self.bp_cnt_frm,
+            "# of body-parts directionality",
+            list(types_of_directionality),
+            "20",
+        )
+        self.bp_cnt_dropdown.setChoices(types_of_directionality[0])
+        self.bp_cnt_confirm_btn = Button(
+            self.bp_cnt_frm,
+            text="Confirm",
+            command=lambda: run_function,
+        )
+        self.bp_cnt_frm.grid(row=0, sticky=NW)
+        self.bp_cnt_dropdown.grid(row=0, column=0, sticky=NW)
+        self.bp_cnt_confirm_btn.grid(row=0, column=1, sticky=NW)
+
     def create_choose_number_of_body_parts_frm(
-        self, project_body_parts: List[str], run_function: object
+            self, project_body_parts: List[str], run_function: object
     ):
         self.bp_cnt_frm = LabelFrame(
             self.main_frm,
@@ -244,7 +269,7 @@ def add_value_to_listbox(self, list_box: Listbox, value: float):
         list_box.insert(0, value)
 
     def add_values_to_several_listboxes(
-        self, list_boxes: List[Listbox], values: List[float]
+            self, list_boxes: List[Listbox], values: List[float]
     ):
         if len(list_boxes) != len(values):
             raise CountError(msg="Value count and listboxes count are not equal")
@@ -270,7 +295,7 @@ def create_choose_bp_frm(self, project_body_parts, run_function):
         for bp_cnt in range(int(self.bp_cnt_dropdown.getChoices())):
             self.body_parts_dropdowns[bp_cnt] = DropDownMenu(
                 self.body_part_frm,
-                f"Body-part {str(bp_cnt+1)}:",
+                f"Body-part {str(bp_cnt + 1)}:",
                 project_body_parts,
                 "25",
             )
@@ -326,7 +351,7 @@ def choose_bp_threshold_frm(self, parent: LabelFrame):
         self.probability_entry.grid(row=0, column=0, sticky=NW)
 
     def enable_dropdown_from_checkbox(
-        self, check_box_var: BooleanVar, dropdown_menus: List[DropDownMenu]
+            self, check_box_var: BooleanVar, dropdown_menus: List[DropDownMenu]
     ):
         if check_box_var.get():
             for menu in dropdown_menus:
@@ -336,13 +361,13 @@ def enable_dropdown_from_checkbox(
                 menu.disable()
 
     def create_entry_boxes_from_entrybox(
-        self, count: int, parent: Frame, current_entries: list
+            self, count: int, parent: Frame, current_entries: list
     ):
         check_int(name="CLASSIFIER COUNT", value=count, min_value=1)
         for entry in current_entries:
             entry.destroy()
         for clf_cnt in range(int(count)):
-            entry = Entry_Box(parent, f"Classifier {str(clf_cnt+1)}:", labelwidth=15)
+            entry = Entry_Box(parent, f"Classifier {str(clf_cnt + 1)}:", labelwidth=15)
             current_entries.append(entry)
             entry.grid(row=clf_cnt + 2, column=0, sticky=NW)
 
@@ -353,12 +378,12 @@ def create_animal_names_entry_boxes(self, animal_cnt: str):
         if not hasattr(self, "multi_animal_id_list"):
             self.multi_animal_id_list = []
             for i in range(int(animal_cnt)):
-                self.multi_animal_id_list.append(f"Animal {i+1}")
+                self.multi_animal_id_list.append(f"Animal {i + 1}")
         self.animal_names_frm = Frame(self.animal_settings_frm, pady=5, padx=5)
         self.animal_name_entry_boxes = {}
         for i in range(int(animal_cnt)):
             self.animal_name_entry_boxes[i + 1] = Entry_Box(
-                self.animal_names_frm, f"Animal {str(i+1)} name: ", "25"
+                self.animal_names_frm, f"Animal {str(i + 1)} name: ", "25"
             )
             if i <= len(self.multi_animal_id_list) - 1:
                 self.animal_name_entry_boxes[i + 1].entry_set(
@@ -369,10 +394,10 @@ def create_animal_names_entry_boxes(self, animal_cnt: str):
         self.animal_names_frm.grid(row=1, column=0, sticky=NW)
 
     def enable_entrybox_from_checkbox(
-        self,
-        check_box_var: BooleanVar,
-        entry_boxes: List[Entry_Box],
-        reverse: bool = False,
+            self,
+            check_box_var: BooleanVar,
+            entry_boxes: List[Entry_Box],
+            reverse: bool = False,
     ):
         if reverse:
             if check_box_var.get():
@@ -390,16 +415,16 @@ def enable_entrybox_from_checkbox(
                     box.set_state("disable")
 
     def create_import_pose_menu(
-        self, parent_frm: Frame, idx_row: int = 0, idx_column: int = 0
+            self, parent_frm: Frame, idx_row: int = 0, idx_column: int = 0
     ):
         def run_call(
-            data_type: str,
-            interpolation: str,
-            smoothing: str,
-            smoothing_window: str,
-            animal_names: dict,
-            data_path: str,
-            tracking_data_type: str or None = None,
+                data_type: str,
+                interpolation: str,
+                smoothing: str,
+                smoothing_window: str,
+                animal_names: dict,
+                data_path: str,
+                tracking_data_type: str or None = None,
         ):
             smooth_settings = {}
             smooth_settings["Method"] = smoothing
@@ -880,7 +905,7 @@ def import_menu(data_type_choice: str):
             self.data_type_dropdown.grid(row=0, column=0, sticky=NW)
 
     def create_import_videos_menu(
-        self, parent_frm: Frame, idx_row: int = 0, idx_column: int = 0
+            self, parent_frm: Frame, idx_row: int = 0, idx_column: int = 0
     ):
         def run_import(multiple_videos: bool):
             if multiple_videos:
@@ -991,7 +1016,6 @@ def run_import(multiple_videos: bool):
     #     #self.main_frm.config(width=e.x_root, height=e.y_root)
     #     #self.main_frm.update()
 
-
 # test = PopUpMixin(config_path='/Users/simon/Desktop/envs/troubleshooting/two_animals_16bp_032023/project_folder/project_config.ini',
 #                   title='ss')
 # test.create_import_pose_menu(parent_frm=test.main_frm)

simba/pose_configurations/bp_names/bp_names.csv

@@ -10,3 +10,5 @@ Ear_left_1,Ear_right_1,Nose_1,Tail_base_1,Ear_left_2,Right_ear_2,Nose_2,Tail_bas
 Ear_left_1,Ear_right_1,Nose_1,Center_1,Lat_left_1,Lat_right_1,Tail_base_1,Ear_left_2,Ear_right_2,Nose_2,Center_2,Lat_left_2,Lat_right_2,Tail_base_2,,
 Ear_left_1,Ear_right_1,Nose_1,Center_1,Lat_left_1,Lat_right_1,Tail_base_1,Tail_end_1,Ear_left_2,Ear_right_2,Nose_2,Center_2,Lat_left_2,Lat_right_2,Tail_base_2,Tail_end_2
 3D,,,,,,,,,,,,,,,
+nose,left_ear,right_ear,tail_base,bug_center
+nose,right_hand,left_hand,right_leg,left_leg,tail_base

simba/pose_configurations/configuration_names/pose_config_names.csv

@@ -10,3 +10,5 @@ Multi-animals; 4 body-parts
 Multi-animals; 7 body-parts
 Multi-animals; 8 body-parts
 3D tracking
+mouse_and_bug
+from_below

simba/pose_configurations/no_animals/no_animals.csv

@@ -10,3 +10,5 @@
 2
 2
 1
+1
+1

simba/pose_importers/dlc_importer_csv.py

@@ -70,12 +70,13 @@ def import_dlc_csv(config_path: Union[str, os.PathLike], source: str) -> List[st
         new_file_name_wo_ext = new_file_name.split(".")[0]
         video_basename = os.path.basename(file_path)
         print(f"Importing {video_name} to SimBA project...")
-        if new_file_name_wo_ext in imported_file_names:
-            raise FileExistError(
-                "SIMBA IMPORT ERROR: {} already exist in project. Remove file from project or rename imported video file name before importing.".format(
-                    new_file_name
-                )
-            )
+        #if new_file_name_wo_ext in imported_file_names:
+            # raise FileExistError(
+            #     "SIMBA IMPORT ERROR: {} already exist in project. Remove file from project or rename imported video file name before importing.".format(
+            #         new_file_name
+            #     )
+            # )
+
         shutil.copy(file_path, input_csv_dir)
         shutil.copy(file_path, original_file_name_dir)
         os.rename(

simba/ui/pop_ups/append_bodypart_directionality_features_pop_up.py

@@ -0,0 +1,59 @@
+__author__ = "Tzuk Polinsky"
+
+import glob
+import os
+
+import pandas
+
+from simba.mixins.config_reader import ConfigReader
+from simba.mixins.pop_up_mixin import PopUpMixin
+from simba.roi_tools.ROI_feature_analyzer import ROIFeatureCreator
+from simba.utils.errors import NoROIDataError
+
+
+class AppendBodyPartDirectionalityFeaturesPopUp(PopUpMixin, ConfigReader):
+    def __init__(self, config_path: str):
+        PopUpMixin.__init__(self, config_path=config_path, title="APPEND BODY PART DIRECTIONALITY FEATURES")
+        ConfigReader.__init__(self, config_path=config_path)
+        if not os.path.isfile(self.roi_coordinates_path):
+            raise NoROIDataError(
+                msg="SIMBA ERROR: No ROIs have been defined. Please define ROIs before appending ROI-based features"
+            )
+        self.create_choose_number_of_body_parts_directionality_frm(
+            path_to_directionality_dir=self.body_part_directionality_df_dir, run_function=self.run
+        )
+        # self.main_frm.mainloop()
+
+    def run(self):
+        settings = {}
+        settings["body_parts_directionality"] = {}
+        for bp_cnt, bp_dropdown in self.bp_cnt_dropdown.items():
+            settings["body_parts_directionality"] = bp_dropdown.getChoices()
+        directionality_data_path = os.path.join(self.body_part_directionality_df_dir,
+                                                settings["body_parts_directionality"])
+        data_dic = {}
+        for root, dirs, files in os.walk(directionality_data_path):
+            for file in files:
+                data = pandas.read_csv(os.path.join(root, file))["Directing_BOOL"]
+                data_dic[file] = data
+        files_found = glob.glob(
+            self.outlier_corrected_dir + "/*." + self.file_type
+        )
+        concatenate_data = {}
+        for file in files_found:
+            data = pandas.read_csv(os.path.join(root, file))
+            c_data = pandas.concat([data, data_dic[file]])
+            concatenate_data[file] = c_data
+        for file_name, data in concatenate_data.items():
+            save_path = os.path.join(
+                self.features_dir, file_name + "." + self.file_type
+            )
+            data.to_csv(save_path)
+
+        # roi_feature_creator = ROIFeatureCreator(
+        #     config_path=self.config_path, settings=settings
+        # )
+        # roi_feature_creator.run()
+        # roi_feature_creator.save()
+
+# _ = AppendROIFeaturesByBodyPartPopUp(config_path='/Users/simon/Desktop/envs/troubleshooting/two_animals_16bp_032023/project_folder/project_config.ini')