simba-uw-tf-dev 4.6.6__py3-none-any.whl → 4.6.8__py3-none-any.whl

simba/plotting/gantt_creator.py

@@ -2,6 +2,7 @@ __author__ = "Simon Nilsson; sronilsson@gmail.com"
 
 import os
 import shutil
+from copy import deepcopy
 from typing import List, Optional, Union
 
 import cv2
@@ -16,7 +17,7 @@ from simba.utils.checks import (
 from simba.utils.data import create_color_palette, detect_bouts
 from simba.utils.enums import Formats, Options
 from simba.utils.errors import NoSpecifiedOutputError
-from simba.utils.lookups import get_named_colors
+from simba.utils.lookups import get_fonts, get_named_colors
 from simba.utils.printing import stdout_success
 from simba.utils.read_write import get_fn_ext, read_df
 
@@ -60,16 +61,18 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
 
     def __init__(self,
                  config_path: Union[str, os.PathLike],
-                 data_paths: List[Union[str, os.PathLike]],
+                 data_paths: Optional[Union[Union[str, os.PathLike], List[Union[str, os.PathLike]]]] = None,
                  width: int = 640,
                  height: int = 480,
                  font_size: int = 8,
                  font_rotation: int = 45,
+                 font: Optional[str] = None,
                  palette: str = 'Set1',
-                 frame_setting: Optional[bool] = False,
-                 video_setting: Optional[bool] = False,
-                 last_frm_setting: Optional[bool] = True,
-                 hhmmss: Optional[bool] = True):
+                 frame_setting: bool = False,
+                 video_setting: bool = False,
+                 last_frm_setting: bool = True,
+                 hhmmss: bool = True,
+                 clf_names: Optional[List[str]] = None):
 
         if ((frame_setting != True) and (video_setting != True) and (last_frm_setting != True)):
             raise NoSpecifiedOutputError(msg="SIMBA ERROR: Please select gantt videos, frames, and/or last frame.")
@@ -78,7 +81,13 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
         check_int(value=height, min_value=1, name=f'{self.__class__.__name__} height')
         check_int(value=font_size, min_value=1, name=f'{self.__class__.__name__} font_size')
         check_int(value=font_rotation, min_value=0, max_value=180, name=f'{self.__class__.__name__} font_rotation')
-        check_valid_lst(data=data_paths, source=f'{self.__class__.__name__} data_paths', valid_dtypes=(str,), min_len=1)
+        if isinstance(data_paths, list):
+            check_valid_lst(data=data_paths, source=f'{self.__class__.__name__} data_paths', valid_dtypes=(str,), min_len=1)
+        elif isinstance(data_paths, str):
+            check_file_exist_and_readable(file_path=data_paths)
+            data_paths = [data_paths]
+        else:
+            data_paths = deepcopy(self.machine_results_paths)
         check_valid_boolean(value=hhmmss, source=f'{self.__class__.__name__} hhmmss', raise_error=False)
         palettes = Options.PALETTE_OPTIONS_CATEGORICAL.value + Options.PALETTE_OPTIONS.value
         check_str(name=f'{self.__class__.__name__} palette', value=palette, options=palettes)
@@ -90,7 +99,12 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
         if not os.path.exists(self.gantt_plot_dir): os.makedirs(self.gantt_plot_dir)
         self.frame_setting, self.video_setting, self.last_frm_setting = frame_setting, video_setting, last_frm_setting
         self.width, self.height, self.font_size, self.font_rotation = width, height, font_size, font_rotation
-        self.data_paths, self.hhmmss = data_paths, hhmmss
+        if font is not None:
+            check_str(name=f'{self.__class__.__name__} font', value=font, options=list(get_fonts().keys()), raise_error=True)
+        if clf_names is not None:
+            check_valid_lst(data=clf_names, source=f'{self.__class__.__name__} clf_names', valid_dtypes=(str,), valid_values=self.clf_names, min_len=1, raise_error=True)
+            self.clf_names = clf_names
+        self.data_paths, self.hhmmss, self.font = data_paths, hhmmss, font
         self.colours = get_named_colors()
         self.colour_tuple_x = list(np.arange(3.5, 203.5, 5))
 
@@ -121,6 +135,7 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
                                      font_size=self.font_size,
                                      font_rotation=self.font_rotation,
                                      video_name=self.video_name,
+                                     font=self.font,
                                      save_path=os.path.join(self.gantt_plot_dir, f"{self.video_name }_final_image.png"),
                                      palette=self.clr_lst,
                                      hhmmss=self.hhmmss)
@@ -135,6 +150,7 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
                                                 width=self.width,
                                                 height=self.height,
                                                 font_size=self.font_size,
+                                                font=self.font,
                                                 font_rotation=self.font_rotation,
                                                 video_name=self.video_name,
                                                 palette=self.clr_lst,
@@ -156,13 +172,16 @@ class GanttCreatorSingleProcess(ConfigReader, PlottingMixin):
 # test = GanttCreatorSingleProcess(config_path=r"C:\troubleshooting\mitra\project_folder\project_config.ini",
 #                                 frame_setting=False,
 #                                 video_setting=False,
-#                                 data_paths=[r"C:\troubleshooting\mitra\project_folder\csv\machine_results\592_MA147_Gq_CNO_0515.csv"],
+#                                 data_paths=[r"C:\troubleshooting\mitra\project_folder\csv\machine_results\501_MA142_Gi_CNO_0516.csv"],
 #                                 last_frm_setting=True,
 #                                 width=640,
 #                                 height= 480,
 #                                 font_size=10,
+#                                  font=None,
 #                                 font_rotation=45,
-#                                 palette='Set1')
+#                                 hhmmss=False,
+#                                 palette='Set1',
+#                                 clf_names=['straub_tail'])
 # test.run()
 
 

simba/plotting/gantt_creator_mp.py

@@ -8,16 +8,37 @@ import gc
 import multiprocessing
 import os
 import platform
+import sys
 from copy import deepcopy
 from typing import List, Optional, Union
 
 import cv2
-import matplotlib
+
+is_pycharm_ipython = True
+try:
+    module_names = list(sys.modules.keys())
+    if any('pydev' in str(mod).lower() for mod in module_names):
+        is_pycharm_ipython = True
+    elif 'IPython' in sys.modules or 'ipython' in sys.modules:
+        is_pycharm_ipython = True
+    else:
+        is_pycharm_ipython = False
+except Exception:
+    is_pycharm_ipython = True
+
+if not is_pycharm_ipython:
+    if 'MPLBACKEND' not in os.environ:  os.environ['MPLBACKEND'] = 'Agg'
+    try:
+        import matplotlib
+        matplotlib.use('Agg', force=False)
+    except (RecursionError, RuntimeError, ValueError, SystemError):
+        import matplotlib
+else:
+    import matplotlib
+
 import numpy as np
 import pandas as pd
 
-matplotlib.use('Agg')
-
 from simba.mixins.config_reader import ConfigReader
 from simba.mixins.plotting_mixin import PlottingMixin
 from simba.utils.checks import (
@@ -28,6 +49,7 @@ from simba.utils.data import (create_color_palette, detect_bouts, get_cpu_pool,
                               terminate_cpu_pool)
 from simba.utils.enums import Formats, Options
 from simba.utils.errors import NoSpecifiedOutputError
+from simba.utils.lookups import get_fonts
 from simba.utils.printing import SimbaTimer, stdout_success
 from simba.utils.read_write import (concatenate_videos_in_folder,
                                     create_directory, find_core_cnt,
@@ -51,6 +73,7 @@ def gantt_creator_mp(data: np.array,
                      width: int,
                      height: int,
                      font_size: int,
+                     font: str,
                      font_rotation: int,
                      palette: np.ndarray,
                      hhmmss: bool):
@@ -72,6 +95,7 @@ def gantt_creator_mp(data: np.array,
                                                width=width,
                                                height=height,
                                                font_size=font_size,
+                                               font=font,
                                                font_rotation=font_rotation,
                                                video_name=video_name,
                                                save_path=None,
@@ -139,9 +163,11 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
                  height: int = 480,
                  font_size: int = 8,
                  font_rotation: int = 45,
+                 font: Optional[str] = None,
                  palette: str = 'Set1',
                  core_cnt: int = -1,
-                 hhmmss: bool = False):
+                 hhmmss: bool = False,
+                 clf_names: Optional[List[str]] = None):
 
         check_file_exist_and_readable(file_path=config_path)
         if (not frame_setting) and (not video_setting) and (not last_frm_setting):
@@ -157,6 +183,8 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
         check_int(name=f"{self.__class__.__name__} core_cnt",value=core_cnt, min_value=-1, unaccepted_vals=[0], max_value=find_core_cnt()[0])
         self.core_cnt = find_core_cnt()[0] if core_cnt == -1 or core_cnt > find_core_cnt()[0] else core_cnt
         self.width, self.height, self.font_size, self.font_rotation, self.hhmmss = width, height, font_size, font_rotation, hhmmss
+        if font is not None:
+            check_str(name=f'{self.__class__.__name__} font', value=font, options=list(get_fonts().keys()), raise_error=True)
         ConfigReader.__init__(self, config_path=config_path, create_logger=False)
         if isinstance(data_paths, list):
             check_valid_lst(data=data_paths, source=f'{self.__class__.__name__} data_paths', valid_dtypes=(str,), min_len=1)
@@ -166,9 +194,12 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
         else:
             data_paths = deepcopy(self.machine_results_paths)
         for file_path in data_paths: check_file_exist_and_readable(file_path=file_path)
+        if clf_names is not None:
+            check_valid_lst(data=clf_names, source=f'{self.__class__.__name__} clf_names', valid_dtypes=(str,), valid_values=self.clf_names, min_len=1, raise_error=True)
+            self.clf_names = clf_names
         PlottingMixin.__init__(self)
         self.clr_lst = create_color_palette(pallete_name=palette, increments=len(self.body_parts_lst) + 1, as_int=True, as_rgb_ratio=True)
-        self.frame_setting, self.video_setting, self.data_paths, self.last_frm_setting = frame_setting, video_setting,data_paths, last_frm_setting
+        self.frame_setting, self.video_setting, self.data_paths, self.last_frm_setting, self.font = frame_setting, video_setting,data_paths, last_frm_setting, font
         if not os.path.exists(self.gantt_plot_dir): os.makedirs(self.gantt_plot_dir)
         if platform.system() == "Darwin":
             multiprocessing.set_start_method("spawn", force=True)
@@ -206,6 +237,7 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
                                      font_size=self.font_size,
                                      font_rotation=self.font_rotation,
                                      video_name=self.video_name,
+                                     font=self.font,
                                      save_path=os.path.join(self.gantt_plot_dir, f"{self.video_name}_final_image.png"),
                                      palette=self.clr_lst,
                                      hhmmss=self.hhmmss)
@@ -225,6 +257,7 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
                                               width=self.width,
                                               height=self.height,
                                               font_size=self.font_size,
+                                              font=self.font,
                                               font_rotation=self.font_rotation,
                                               video_name=self.video_name,
                                               palette=self.clr_lst,
@@ -254,18 +287,18 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
 #                                     font_rotation= 45)
 #     test.run()
 
-if __name__ == "__main__":
-    test = GanttCreatorMultiprocess(config_path=r"D:\troubleshooting\maplight_ri\project_folder\project_config.ini",
-                                    frame_setting=False,
-                                    video_setting=True,
-                                    data_paths=r"D:\troubleshooting\maplight_ri\project_folder\csv\machine_results\Trial_1_C24_D1_1.csv",
-                                    last_frm_setting=False,
-                                    width=640,
-                                    height= 480,
-                                    font_size=10,
-                                    font_rotation= 45,
-                                    core_cnt=16)
-    test.run()
+# if __name__ == "__main__":
+#     test = GanttCreatorMultiprocess(config_path=r"D:\troubleshooting\maplight_ri\project_folder\project_config.ini",
+#                                     frame_setting=False,
+#                                     video_setting=True,
+#                                     data_paths=r"D:\troubleshooting\maplight_ri\project_folder\csv\machine_results\Trial_1_C24_D1_1.csv",
+#                                     last_frm_setting=False,
+#                                     width=640,
+#                                     height= 480,
+#                                     font_size=10,
+#                                     font_rotation= 45,
+#                                     core_cnt=16)
+#     test.run()
 
 
 # test = GanttCreatorMultiprocess(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/RAT_NOR/project_folder/project_config.ini',

simba/plotting/heat_mapper_clf_mp.py

@@ -98,14 +98,14 @@ class HeatMapperClfMultiprocess(ConfigReader, PlottingMixin):
 
 
     :example II:
-    >>> test = HeatMapperClfMultiprocess(config_path=r"C:\troubleshooting\RAT_NOR\project_folder\project_config.ini",
+    >>> test = HeatMapperClfMultiprocess(config_path=r"C:/troubleshooting/RAT_NOR/project_folder/project_config.ini",
     >>>                          style_attr = {'palette': 'jet', 'shading': 'gouraud', 'bin_size': 50, 'max_scale': 'auto'},
     >>>                          final_img_setting=True,
     >>>                          video_setting=True,
     >>>                          frame_setting=True,
     >>>                          bodypart='Ear_left',
     >>>                          clf_name='straub_tail',
-    >>>                          data_paths=[r"C:\troubleshooting\RAT_NOR\project_folder\csv\test\2022-06-20_NOB_DOT_4.csv"])
+    >>>                          data_paths=[r"C:/troubleshooting/RAT_NOR/project_folder/csv/test/2022-06-20_NOB_DOT_4.csv"])
     >>> test.run()
     """
 

simba/pose_importers/simba_blob_importer.py

@@ -44,10 +44,10 @@ class SimBABlobImporter(ConfigReader):
     :param Optional[bool] verbose: If True, prints progress messages. Default: True.
 
     :example:
-    >>> r = SimBABlobImporter(config_path=r"C:\troubleshooting\simba_blob_project\project_folder\project_config.ini", data_path=r'C:\troubleshooting\simba_blob_project\data')
+    >>> r = SimBABlobImporter(config_path=r"C:/troubleshooting/simba_blob_project/project_folder/project_config.ini", data_path=r'C:/troubleshooting/simba_blob_project/data')
     >>> r.run()
-    >>> r = SimBABlobImporter(config_path=r"C:\troubleshooting\simba_blob_project\project_folder\project_config.ini", 
-    ...                       data_path=r'C:\troubleshooting\simba_blob_project\data',
+    >>> r = SimBABlobImporter(config_path=r"C:/troubleshooting/simba_blob_project/project_folder/project_config.ini", 
+    ...                       data_path=r'C:/troubleshooting/simba_blob_project/data',
     ...                       smoothing_settings={'method': 'savitzky-golay', 'time_window': 100},
     ...                       interpolation_settings={'method': 'nearest', 'type': 'body-parts'})
     >>> r.run()

simba/roi_tools/roi_aggregate_stats_mp.py

@@ -168,7 +168,7 @@ class ROIAggregateStatisticsAnalyzerMultiprocess(ConfigReader, FeatureExtraction
     :param save_path (str | os.PathLike, optional): Path to save summary statistics.
 
     :example:
-    >>> analyzer = ROIAggregateStatisticsAnalyzerMultiprocess(config_path=r"C:\troubleshooting\mitra\project_folder\project_config.ini", body_parts=['Center'], first_entry_time=True, threshold=0.0, calculate_distances=True, transpose=False, detailed_bout_data=True)
+    >>> analyzer = ROIAggregateStatisticsAnalyzerMultiprocess(config_path=r"C:/troubleshooting/mitra/project_folder/project_config.ini", body_parts=['Center'], first_entry_time=True, threshold=0.0, calculate_distances=True, transpose=False, detailed_bout_data=True)
     >>> analyzer.run()
     >>> analyzer.save()
     """

simba/roi_tools/roi_clf_calculator_mp.py

@@ -150,7 +150,7 @@ class ROIClfCalculatorMultiprocess(ConfigReader):
        'GitHub tutorial <https://github.com/sgoldenlab/simba/blob/master/docs/Scenario2.md#part-4--analyze-machine-results`__.
 
     :example:
-    >>> analyzer = ROIClfCalculatorMultiprocess(config_path=r"D:\troubleshooting\maplight_ri\project_folder\project_config.ini", bp_names=['resident_NOSE'], clf_names=['attack'], clf_time=True, started_bout_cnt=True, ended_bout_cnt=False, bout_table=True, transpose=True, core_cnt=20)
+    >>> analyzer = ROIClfCalculatorMultiprocess(config_path=r"D:/troubleshooting/maplight_ri/project_folder/project_config.ini", bp_names=['resident_NOSE'], clf_names=['attack'], clf_time=True, started_bout_cnt=True, ended_bout_cnt=False, bout_table=True, transpose=True, core_cnt=20)
     >>> analyzer.run()
     >>> analyzer.save()
     """

simba/third_party_label_appenders/transform/coco_keypoints_to_yolo.py

@@ -54,15 +54,15 @@ class COCOKeypoints2Yolo:
     :return: None
 
     :example:
-    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:\cvat_annotations\frames\coco_keypoints_1\s1\annotations\s1.json", img_dir=r"D:\cvat_annotations\frames\simon", save_dir=r"D:\cvat_annotations\frames\yolo_keypoints", clahe=True)
+    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:/cvat_annotations/frames/coco_keypoints_1/s1/annotations/s1.json", img_dir=r"D:/cvat_annotations/frames/simon", save_dir=r"D:/cvat_annotations/frames/yolo_keypoints", clahe=True)
     >>> runner.run()
 
     :example II:
-    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:\cvat_annotations\frames\coco_keypoints_1\merged.json", img_dir=r"D:\cvat_annotations\frames", save_dir=r"D:\cvat_annotations\frames\yolo", clahe=False)
+    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:/cvat_annotations/frames/coco_keypoints_1/merged.json", img_dir=r"D:/cvat_annotations/frames", save_dir=r"D:/cvat_annotations/frames/yolo", clahe=False)
     >>> runner.run()
 
     :example III:
-    >>> runner = COCOKeypoints2Yolo(coco_path=r"E:\netholabs_videos\mosaics\subset\to_annotate\2d_mosaic_batch_1.json", img_dir=r"E:\netholabs_videos\mosaics\subset\to_annotate", save_dir=r"E:\netholabs_videos\mosaics\yolo_mdl", clahe=False)
+    >>> runner = COCOKeypoints2Yolo(coco_path=r"E:/netholabs_videos/mosaics/subset/to_annotate/2d_mosaic_batch_1.json", img_dir=r"E:/netholabs_videos/mosaics/subset/to_annotate", save_dir=r"E:/netholabs_videos/mosaics/yolo_mdl", clahe=False)
     >>> runner.run()
 
      :references:

simba/third_party_label_appenders/transform/coco_keypoints_to_yolo_bbox.py

@@ -58,11 +58,11 @@ class COCOKeypoints2YoloBbox:
     :return: None
 
     :example:
-    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:\cvat_annotations\frames\coco_keypoints_1\s1\annotations\s1.json", img_dir=r"D:\cvat_annotations\frames\simon", save_dir=r"D:\cvat_annotations\frames\yolo_keypoints", clahe=True)
+    >>> runner = COCOKeypoints2YoloBbox(coco_path=r"D:/cvat_annotations/frames/coco_keypoints_1/s1/annotations/s1.json", img_dir=r"D:/cvat_annotations/frames/simon", save_dir=r"D:/cvat_annotations/frames/yolo_keypoints", clahe=True)
     >>> runner.run()
 
     :example II:
-    >>> runner = COCOKeypoints2Yolo(coco_path=r"D:\cvat_annotations\frames\coco_keypoints_1\merged.json", img_dir=r"D:\cvat_annotations\frames", save_dir=r"D:\cvat_annotations\frames\yolo", clahe=False)
+    >>> runner = COCOKeypoints2YoloBbox(coco_path=r"D:/cvat_annotations/frames/coco_keypoints_1/merged.json", img_dir=r"D:/cvat_annotations/frames", save_dir=r"D:/cvat_annotations/frames/yolo", clahe=False)
     >>> runner.run()
 
      :references:

simba/ui/pop_ups/clf_plot_pop_up.py

@@ -49,8 +49,8 @@ class SklearnVisualizationPopUp(PopUpMixin, ConfigReader):
         pose_palettes = Options.PALETTE_OPTIONS_CATEGORICAL.value + Options.PALETTE_OPTIONS.value
         PopUpMixin.__init__(self, title="VISUALIZE CLASSIFICATION (SKLEARN) RESULTS", icon='photos')
         bp_threshold_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="BODY-PART VISUALIZATION THRESHOLD", icon_name='threshold', icon_link=Links.SKLEARN_PLOTS.value, padx=5, pady=5, relief='solid')
-        self.bp_threshold_lbl = SimBALabel(parent=bp_threshold_frm, txt="Body-parts detected below the set threshold won't be shown in the output videos.", font=Formats.FONT_REGULAR_ITALICS.value)
-        self.bp_threshold_entry = Entry_Box(parent=bp_threshold_frm, fileDescription='BODY-PART PROBABILITY THRESHOLD: ', labelwidth=40, entry_box_width=15, value=0.00, img='green_dice')
+        self.bp_threshold_lbl = SimBALabel(parent=bp_threshold_frm, txt="Body-parts detected below the set threshold won't be shown in the output videos (use 0.0 to see all body-part predictions)", font=Formats.FONT_REGULAR_ITALICS.value)
+        self.bp_threshold_entry = Entry_Box(parent=bp_threshold_frm, fileDescription='BODY-PART PROBABILITY THRESHOLD: ', labelwidth=40, entry_box_width=15, value=0.00, img='green_dice', justify='center')
         self.get_bp_probability_threshold()
 
         bp_threshold_frm.grid(row=0, column=0, sticky=NW)

simba/ui/pop_ups/gantt_pop_up.py

@@ -13,6 +13,7 @@ from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, SimbaButton,
 from simba.utils.checks import check_if_filepath_list_is_empty
 from simba.utils.enums import Formats, Links, Options
 from simba.utils.errors import NoSpecifiedOutputError
+from simba.utils.lookups import get_fonts
 from simba.utils.read_write import find_files_of_filetypes_in_directory
 
 
@@ -29,7 +30,9 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
         check_if_filepath_list_is_empty(filepaths=self.machine_results_paths,error_msg=f"SIMBA ERROR: Zero files found in the {self.machine_results_dir} directory. Create classification results before visualizing gantt charts",)
         palettes = Options.PALETTE_OPTIONS_CATEGORICAL.value + Options.PALETTE_OPTIONS.value
         self.data_paths = find_files_of_filetypes_in_directory(directory=self.machine_results_dir, extensions=[f'.{self.file_type}'], as_dict=True)
-        max_file_name_len = max(len(k) for k in self.data_paths) + 5
+        max_file_name_len, fonts = max(len(k) for k in self.data_paths) + 5, list(get_fonts(sort_alphabetically=True).keys())
+        fonts.insert(0, 'AUTO')
+        default_font = 'Arial' if 'Arial' in fonts else 'AUTO'
         PopUpMixin.__init__(self, config_path=config_path, title="VISUALIZE GANTT PLOTS", icon='gantt_small')
 
         self.style_settings_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="STYLE SETTINGS", icon_name='settings', icon_link=Links.GANTT_PLOTS.value, relief='solid', padx=5, pady=5)
@@ -39,6 +42,15 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
         self.palette_dropdown = SimBADropDown(parent=self.style_settings_frm, dropdown_options=palettes, label='COLOR PALETTE: ', label_width=30, dropdown_width=30, value='Set1', img='palette_small')
         self.time_format_dropdown = SimBADropDown(parent=self.style_settings_frm, dropdown_options=['SECONDS', 'HH:MM:SS'], label='X-AXIS TIME FORMAT: ', label_width=30, dropdown_width=30, value='SECONDS', img='timer_2')
         self.core_dropdown = SimBADropDown(parent=self.style_settings_frm, dropdown_options=list(range(1, self.cpu_cnt+1)), label='CPU CORES: ', label_width=30, dropdown_width=30, value=int(self.cpu_cnt/2), img='cpu_small')
+        self.font_dropdown = SimBADropDown(parent=self.style_settings_frm, dropdown_options=fonts, label='FONT: ', label_width=30, dropdown_width=30, value=default_font, img='font')
+
+
+        self.clf_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="BEHAVIORS", icon_name='forest', icon_link=Links.GANTT_PLOTS.value, relief='solid', padx=5, pady=5)
+        self.clf_choices = {}
+        for cnt, clf_name in enumerate(self.clf_names):
+            gantt_frames_cb, self.gantt_frames_var = SimbaCheckbox(parent=self.clf_frm, txt=clf_name, val=True)
+            self.clf_choices[clf_name] = self.gantt_frames_var
+            gantt_frames_cb.grid(row=cnt, column=0, sticky=NW)
 
         self.settings_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="VISUALIZATION SETTINGS", icon_name='eye', icon_link=Links.GANTT_PLOTS.value, relief='solid', padx=5, pady=5)
         gantt_frames_cb, self.gantt_frames_var = SimbaCheckbox(parent=self.settings_frm, txt='CREATE FRAMES', txt_img='frames', val=False)
@@ -57,18 +69,20 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
         self.font_rotation_dropdown.grid(row=2, sticky=NW)
         self.palette_dropdown.grid(row=3, sticky=NW)
         self.time_format_dropdown.grid(row=4, sticky=NW)
-        self.core_dropdown.grid(row=5, sticky=NW)
+        self.font_dropdown.grid(row=5, sticky=NW)
+        self.core_dropdown.grid(row=6, sticky=NW)
 
-        self.settings_frm.grid(row=1, sticky=NW, padx=10, pady=10)
+        self.clf_frm.grid(row=1, sticky=NW, padx=10, pady=10)
+        self.settings_frm.grid(row=2, sticky=NW, padx=10, pady=10)
         gantt_videos_cb.grid(row=0, sticky=NW)
         gantt_frames_cb.grid(row=1, sticky=W)
         gantt_last_frame_cb.grid(row=2, sticky=NW)
 
-        self.run_single_video_frm.grid(row=2, sticky=NW)
+        self.run_single_video_frm.grid(row=3, sticky=NW)
         self.run_single_video_btn.grid(row=0, sticky=NW)
         self.single_video_dropdown.grid(row=0, column=1, sticky=NW)
 
-        self.run_multiple_videos.grid(row=3, sticky=NW)
+        self.run_multiple_videos.grid(row=4, sticky=NW)
         self.run_multiple_video_btn.grid(row=0, sticky=NW)
 
         self.main_frm.mainloop()
@@ -85,8 +99,14 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
         video_setting = self.gantt_videos_var.get()
         last_frm_setting = self.gantt_last_frame_var.get()
         palette = self.palette_dropdown.get_value()
+        font = self.font_dropdown.get_value()
+        font = None if font == 'AUTO' else font
         hhmmss = True if self.time_format_dropdown.get_value() == 'HH:MM:SS' else False
-
+        clf_names = []
+        for clf_name, clf_val in self.clf_choices.items():
+            if clf_val.get(): clf_names.append(clf_name)
+        if len(clf_names) < 1:
+            raise NoSpecifiedOutputError(msg="Select AT LEAST one behavior name.")
         if not frame_setting and not video_setting and not last_frm_setting:
             raise NoSpecifiedOutputError(msg="SIMBA ERROR: Please select gantt videos, frames, and/or last frame.")
 
@@ -103,6 +123,8 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
                                                      data_paths=data_paths,
                                                      width=width,
                                                      height=height,
+                                                     font=font,
+                                                     clf_names=clf_names,
                                                      font_size=font_size,
                                                      font_rotation=font_rotation,
                                                      core_cnt=core_cnt,
@@ -116,7 +138,9 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
                                                       last_frm_setting=last_frm_setting,
                                                       data_paths=data_paths,
                                                       width=width,
+                                                      font=font,
                                                       height=height,
+                                                      clf_names=clf_names,
                                                       font_size=font_size,
                                                       font_rotation=font_rotation,
                                                       palette=palette)
@@ -124,6 +148,7 @@ class GanttPlotPopUp(PopUpMixin, ConfigReader):
 
 
 #_ = GanttPlotPopUp(config_path=r"D:\troubleshooting\maplight_ri\project_folder\project_config.ini")
+#_ = GanttPlotPopUp(config_path=r"C:\troubleshooting\mitra\project_folder\project_config.ini")
 # _ = GanttPlotPopUp(config_path=r"/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini")
 
  # _ = GanttPlotPopUp(config_path=r"C:\troubleshooting\RAT_NOR\project_folder\project_config.ini")

simba/ui/pop_ups/video_processing_pop_up.py

@@ -1708,7 +1708,7 @@ class ClipMultipleVideosByTimestamps(PopUpMixin):
             check_that_hhmmss_start_is_before_end(start_time=start, end_time=end, name=video_name)
             check_if_hhmmss_timestamp_is_valid_part_of_video(timestamp=start, video_path=self.video_paths[video_name])
             check_if_hhmmss_timestamp_is_valid_part_of_video(timestamp=end, video_path=self.video_paths[video_name])
-            clip_video_in_range(file_path=self.video_paths[video_name], start_time=start, end_time=end, out_dir=self.save_dir, overwrite=True, include_clip_time_in_filename=False, gpu=gpu, quality=quality_pct)
+            clip_video_in_range(file_path=self.video_paths[video_name], start_time=start, end_time=end, out_dir=self.save_dir, overwrite=True, include_clip_time_in_filename=False, gpu=gpu, quality=quality_pct, codec='libx264', verbose=True)
         timer.stop_timer()
         stdout_success(msg=f"{len(self.entry_boxes)} videos clipped by time-stamps and saved in {self.save_dir}", elapsed_time=timer.elapsed_time_str,)
 

simba/utils/custom_feature_extractor.py

@@ -30,7 +30,7 @@ class CustomFeatureExtractor(ConfigReader):
     4. Handle cases of multiple classes and missing configuration arguments.
     5. Invokes the feature extraction process if conditions are met.
 
-    .. notes::
+    .. note::
 
         `Tutorial <https://github.com/sgoldenlab/simba/blob/master/docs/extractFeatures.md>`_.
 

simba/utils/data.py

@@ -1785,8 +1785,8 @@ def fft_lowpass_filter(data: np.ndarray, cut_off: float = 0.1) -> np.ndarray:
 
     :example:
     >>> from simba.utils.read_write import read_df
-    >>> IN_PATH = r"C:\troubleshooting\RAT_NOR\project_folder\csv\outlier_corrected_movement_location\2022-06-20_NOB_DOT_4.csv"
-    >>> OUT_PATH = r"C:\troubleshooting\RAT_NOR\project_folder\csv\outlier_corrected_movement_location\2022-06-20_NOB_DOT_4_filtered.csv"
+    >>> IN_PATH = r"C:/troubleshooting/RAT_NOR/project_folder/csv/outlier_corrected_movement_location/2022-06-20_NOB_DOT_4.csv"
+    >>> OUT_PATH = r"C:/troubleshooting/RAT_NOR/project_folder/csv/outlier_corrected_movement_location/2022-06-20_NOB_DOT_4_filtered.csv"
     >>> df = read_df(file_path=IN_PATH)
     >>> data = df.values
     >>> x = fft_lowpass_filter(data=data, cut_off=0.1)

simba/utils/read_write.py

@@ -97,13 +97,20 @@ def read_df(file_path: Union[str, os.PathLike],
     .. note::
        For improved runtime, defaults to :external:py:meth:`pyarrow.csv.write_cs` if file type is ``csv``.
 
-    :parameter str file_path: Path to data file
-    :parameter str file_type: Type of data. OPTIONS: 'parquet', 'csv', 'pickle'.
-    :parameter Optional[bool]: If the input file has an initial index column. Default: True.
-    :parameter Optional[List[str]] remove_columns: If not None, then remove columns in lits.
-    :parameter Optional[List[str]] usecols: If not None, then keep columns in list.
-    :parameter bool check_multiindex: check file is multi-index headers. Default: False.
-    :parameter int multi_index_headers_to_keep: If reading multi-index file, and we want to keep one of the dropped multi-index levels as the header in the output file, specify the index of the multiindex hader as int.
+    .. csv-table::
+       :header: EXPECTED RUNTIMES
+       :file: ../../docs/tables/read_df.csv
+       :widths: 10, 45, 45
+       :align: center
+       :header-rows: 1
+
+    :param str file_path: Path to data file
+    :param str file_type: Type of data. OPTIONS: 'parquet', 'csv', 'pickle'.
+    :param Optional[bool]: If the input file has an initial index column. Default: True.
+    :param Optional[List[str]] remove_columns: If not None, then remove columns in lits.
+    :param Optional[List[str]] usecols: If not None, then keep columns in list.
+    :param bool check_multiindex: check file is multi-index headers. Default: False.
+    :param int multi_index_headers_to_keep: If reading multi-index file, and we want to keep one of the dropped multi-index levels as the header in the output file, specify the index of the multiindex hader as int.
     :return: Table data in pd.DataFrame format.
     :rtype: pd.DataFrame
 
@@ -207,11 +214,18 @@ def write_df(df: pd.DataFrame,
     .. note::
        For improved runtime, defaults to ``pyarrow.csv`` if file_type == ``csv``.
 
-    :parameter pd.DataFrame df: Pandas dataframe to save to disk.
-    :parameter str file_type: Type of data. OPTIONS: ``parquet``, ``csv``,  ``pickle``.
-    :parameter str save_path: Location where to store the data.
-    :parameter bool check_multiindex: check if input file is multi-index headers. Default: False.
-    :parameter bool verbose: Prints message on completion. Default: False.
+    .. csv-table::
+       :header: EXPECTED RUNTIMES
+       :file: ../../docs/tables/write_df.csv
+       :widths: 10, 45, 45
+       :align: center
+       :header-rows: 1
+
+    :param pd.DataFrame df: Pandas dataframe to save to disk.
+    :param str file_type: Type of data. OPTIONS: ``parquet``, ``csv``,  ``pickle``.
+    :param str save_path: Location where to store the data.
+    :param bool check_multiindex: check if input file is multi-index headers. Default: False.
+    :param bool verbose: Prints message on completion. Default: False.
 
     :example:
     >>> write_df(df=df, file_type='csv', save_path='project_folder/csv/input_csv/Video_1.csv')
@@ -1130,8 +1144,8 @@ def get_file_name_info_in_directory(directory: Union[str, os.PathLike], file_typ
     :return dict: All found files as values and file base names as keys.
 
     :example:
-    >>> get_file_name_info_in_directory(directory='C:\project_folder\csv\machine_results', file_type='csv')
-    >>> {'Video_1': 'C:\project_folder\csv\machine_results\Video_1'}
+    >>> get_file_name_info_in_directory(directory='C:/project_folder/csv/machine_results', file_type='csv')
+    >>> {'Video_1': 'C:/project_folder/csv/machine_results/Video_1'}
     """
 
     results = {}
@@ -2630,7 +2644,7 @@ def bento_file_reader(file_path: Union[str, os.PathLike],
     :rtype: Dict[str, pd.DataFrame]
 
     :example:
-    >>> bento_file_reader(file_path=r"C:\troubleshooting\bento_test\bento_files\20240812_crumpling3.annot")
+    >>> bento_file_reader(file_path=r"C:/troubleshooting/bento_test/bento_files/20240812_crumpling3.annot")
     """
 
     def _orient_columns_melt(df: pd.DataFrame) -> pd.DataFrame:
@@ -2953,7 +2967,7 @@ def labelme_to_dlc(labelme_dir: Union[str, os.PathLike],
     :return: None
 
     :example:
-    >>> labelme_dir = r'D:\ts_annotations'
+    >>> labelme_dir = r'D:/ts_annotations'
     >>> labelme_to_dlc(labelme_dir=labelme_dir)
     """
 
@@ -3597,8 +3611,8 @@ def osf_download(project_id: str, save_dir: Union[str, os.PathLike], storage: st
     :param bool overwrite: If True, overwrite existing files. If False, skip existing files (default: False).
 
     :example:
-    >>> osf_download(project_id="7fgwn", save_dir=r'E:\rgb_white_vs_black_imgs')
-    >>> osf_download(project_id="kym42", save_dir=r'E:\crim13_imgs', overwrite=True)
+    >>> osf_download(project_id="7fgwn", save_dir=r'E:/rgb_white_vs_black_imgs')
+    >>> osf_download(project_id="kym42", save_dir=r'E:/crim13_imgs', overwrite=True)
     """
 
     _ = get_pkg_version(pkg='osfclient', raise_error=True)

simba/utils/yolo.py

@@ -47,6 +47,9 @@ def fit_yolo(weights_path: Union[str, os.PathLike],
        `Download initial weights <https://huggingface.co/Ultralytics>`__.
        `Example model_yaml <https://github.com/sgoldenlab/simba/blob/master/misc/ex_yolo_model.yaml>`__.
 
+    .. seealso::
+       For the recommended wrapper class with parameter validation, see :class:`simba.model.yolo_fit.FitYolo`.
+
     :param initial_weights: Path to the pre-trained YOLO model weights (usually a `.pt` file). Example weights can be found [here](https://huggingface.co/Ultralytics).
     :param model_yaml: YAML file containing paths to the training, validation, and testing datasets and the object class mappings. Example YAML file can be found [here](https://github.com/sgoldenlab/simba/blob/master/misc/ex_yolo_model.yaml).
     :param save_path: Directory path where the trained model, logs, and results will be saved.
@@ -55,7 +58,7 @@ def fit_yolo(weights_path: Union[str, os.PathLike],
     :return: None. The trained model and associated training logs are saved in the specified `project_path`.
 
     :example:
-    >>> fit_yolo(initial_weights=r"C:\troubleshooting\coco_data\weights\yolov8n-obb.pt", data=r"C:\troubleshooting\coco_data\model.yaml", save_path=r"C:\troubleshooting\coco_data\mdl", batch=16)
+    >>> fit_yolo(initial_weights=r"C:/troubleshooting/coco_data/weights/yolov8n-obb.pt", data=r"C:/troubleshooting/coco_data/model.yaml", save_path=r"C:/troubleshooting/coco_data/mdl", batch=16)
     """
 
     if not _is_cuda_available()[0]:
@@ -83,6 +86,9 @@ def load_yolo_model(weights_path: Union[str, os.PathLike],
     """
     Load a YOLO model.
 
+    .. seealso::
+       For recommended wrapper classes that use this function, see :class:`simba.model.yolo_fit.FitYolo`, :class:`simba.model.yolo_inference.YoloInference`, :class:`simba.model.yolo_pose_inference.YOLOPoseInference`, :class:`simba.model.yolo_seg_inference.YOLOSegmentationInference`, and :class:`simba.model.yolo_pose_track_inference.YOLOPoseTrackInference`.
+
     :param Union[str, os.PathLike] weights_path: Path to model weights (.pt, .engine, etc).
     :param bool verbose: Whether to print loading info.
     :param Optional[str] format: Export format, one of VALID_FORMATS or None to skip export.
@@ -169,6 +175,9 @@ def yolo_predict(model: YOLO,
     """
     Produce YOLO predictions.
 
+    .. seealso::
+       For recommended wrapper classes that use this function, see :class:`simba.model.yolo_inference.YoloInference`, :class:`simba.model.yolo_pose_inference.YOLOPoseInference`, and :class:`simba.model.yolo_seg_inference.YOLOSegmentationInference`.
+
     :param Union[str, os.PathLike] model: Loaded ultralytics.YOLO model. Returned by :func:`~simba.bounding_box_tools.yolo.model.load_yolo_model`.
     :param Union[str, os.PathLike, np.ndarray] source: Path to video, video stream, directory, image, or image as loaded array.
     :param bool half: Whether to use half precision (FP16) for inference to speed up processing.