simba-uw-tf-dev 4.6.2__py3-none-any.whl → 4.7.1__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

@@ -1,16 +1,41 @@
 __author__ = "Simon Nilsson; sronilsson@gmail.com"
 
-import time
 import warnings
 
 warnings.simplefilter(action="ignore", category=FutureWarning)
 import functools
+import gc
 import multiprocessing
 import os
 import platform
+import sys
+from copy import deepcopy
 from typing import List, Optional, Union
 
 import cv2
+
+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
 
@@ -20,13 +45,15 @@ from simba.utils.checks import (
     check_all_file_names_are_represented_in_video_log,
     check_file_exist_and_readable, check_int, check_str,
     check_that_column_exist, check_valid_boolean, check_valid_lst)
-from simba.utils.data import create_color_palette, detect_bouts
+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,
-                                    get_fn_ext, read_df)
+                                    get_current_time, get_fn_ext, read_df)
 
 HEIGHT = "height"
 WIDTH = "width"
@@ -46,6 +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):
@@ -67,6 +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,
@@ -78,11 +107,17 @@ def gantt_creator_mp(data: np.array,
             cv2.imwrite(frame_save_path, plot)
         if video_setting:
             video_writer.write(plot)
-        print(f"Gantt frame created: {current_frm + 1}, Video: {video_name}, Processing core: {batch_id + 1}")
+        # Clear memory after each frame
+        del plot
+        if current_frm % 100 == 0:  # Periodic garbage collection to prevent memory buildup
+            gc.collect()
+        print(f"[{get_current_time()}] Gantt frame created: {current_frm + 1}, Video: {video_name}, Processing core: {batch_id + 1}")
 
     if video_setting:
         video_writer.release()
+        del video_writer
 
+    gc.collect()
     return batch_id
 
 
@@ -120,7 +155,7 @@ class GanttCreatorMultiprocess(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,
                  frame_setting: Optional[bool] = False,
                  video_setting: Optional[bool] = False,
                  last_frm_setting: Optional[bool] = True,
@@ -128,15 +163,16 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
                  height: int = 480,
                  font_size: int = 8,
                  font_rotation: int = 45,
+                 font: Optional[str] = None,
                  palette: str = 'Set1',
-                 core_cnt: Optional[int] = -1,
-                 hhmmss: bool = False):
+                 core_cnt: int = -1,
+                 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):
             raise NoSpecifiedOutputError(msg="SIMBA ERROR: Please select gantt videos, frames, and/or last frame.", source=self.__class__.__name__)
         check_file_exist_and_readable(file_path=config_path)
-        check_valid_lst(data=data_paths, source=f'{self.__class__.__name__} data_paths', valid_dtypes=(str,), min_len=1)
         check_int(value=width, min_value=1, name=f'{self.__class__.__name__} width')
         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')
@@ -144,14 +180,26 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
         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)
-        for file_path in data_paths: check_file_exist_and_readable(file_path=file_path)
         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)
+        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)
+        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)
@@ -159,6 +207,10 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
 
     def run(self):
         check_all_file_names_are_represented_in_video_log(video_info_df=self.video_info_df, data_paths=self.data_paths)
+        if self.video_setting or self.frame_setting:
+            self.pool = get_cpu_pool(core_cnt=self.core_cnt, maxtasksperchild=self.maxtasksperchild, verbose=True, source=self.__class__.__name__)
+        else:
+            self.pool = None
         for file_cnt, file_path in enumerate(self.data_paths):
             video_timer = SimbaTimer(start=True)
             _, self.video_name, _ = get_fn_ext(file_path)
@@ -185,6 +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)
@@ -192,33 +245,32 @@ class GanttCreatorMultiprocess(ConfigReader, PlottingMixin):
             if self.video_setting or self.frame_setting:
                 frame_data = np.array_split(list(range(0, len(self.data_df))), self.core_cnt)
                 frame_data = [(i, x) for i, x in enumerate(frame_data)]
-                print(f"Creating gantt, multiprocessing (chunksize: {(self.multiprocess_chunksize)}, cores: {self.core_cnt})...")
-                with multiprocessing.Pool(self.core_cnt, maxtasksperchild=self.maxtasksperchild) as pool:
-                    constants = functools.partial(gantt_creator_mp,
-                                                  video_setting=self.video_setting,
-                                                  frame_setting=self.frame_setting,
-                                                  video_save_dir=self.temp_folder,
-                                                  frame_folder_dir=self.save_frame_folder_dir,
-                                                  bouts_df=self.bouts_df,
-                                                  clf_names=self.clf_names,
-                                                  fps=self.fps,
-                                                  width=self.width,
-                                                  height=self.height,
-                                                  font_size=self.font_size,
-                                                  font_rotation=self.font_rotation,
-                                                  video_name=self.video_name,
-                                                  palette=self.clr_lst,
-                                                  hhmmss=self.hhmmss)
-                    for cnt, result in enumerate(pool.imap(constants, frame_data, chunksize=self.multiprocess_chunksize)):
-                        print(f'Batch {result+1/self.core_cnt} complete...')
-                pool.terminate()
-                pool.join()
+                print(f"[{get_current_time()}] Creating gantt, multiprocessing (chunksize: {(self.multiprocess_chunksize)}, cores: {self.core_cnt})...")
+                constants = functools.partial(gantt_creator_mp,
+                                              video_setting=self.video_setting,
+                                              frame_setting=self.frame_setting,
+                                              video_save_dir=self.temp_folder,
+                                              frame_folder_dir=self.save_frame_folder_dir,
+                                              bouts_df=self.bouts_df,
+                                              clf_names=self.clf_names,
+                                              fps=self.fps,
+                                              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,
+                                              hhmmss=self.hhmmss)
+                for cnt, result in enumerate(self.pool.imap(constants, frame_data, chunksize=self.multiprocess_chunksize)):
+                    print(f'[{get_current_time()}] Batch {result+1}/{self.core_cnt} complete...')
                 if self.video_setting:
-                    print(f"Joining {self.video_name} multiprocessed video...")
+                    print(f"[{get_current_time()}] Joining {self.video_name} multiprocessed video...")
                     concatenate_videos_in_folder(in_folder=self.temp_folder, save_path=self.save_video_path)
                 video_timer.stop_timer()
                 print(f"Gantt video {self.video_name} complete (elapsed time: {video_timer.elapsed_time_str}s) ...")
 
+        terminate_cpu_pool(pool=self.pool, force=False, source=self.__class__.__name__)
         self.timer.stop_timer()
         stdout_success(msg=f"Gantt visualizations for {len(self.data_paths)} videos created in {self.gantt_plot_dir} directory", elapsed_time=self.timer.elapsed_time_str)
 
@@ -235,7 +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()
 
 
 # test = GanttCreatorMultiprocess(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/RAT_NOR/project_folder/project_config.ini',