simba-uw-tf-dev 4.5.8__py3-none-any.whl → 4.6.2__py3-none-any.whl

simba/SimBA.py

@@ -966,8 +966,8 @@ class App(object):
         video_process_menu.add_cascade(label="Drop body-parts from tracking data", compound="left", image=self.menu_icons["trash"]["img"], command=DropTrackingDataPopUp, font=Formats.FONT_REGULAR.value)
         extract_frames_menu = Menu(video_process_menu, font=Formats.FONT_REGULAR.value)
         extract_frames_menu.add_command(label="Extract defined frames", command=ExtractSpecificFramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["frames"]["img"], compound="left")
-        extract_frames_menu.add_command(label="Extract frames from single video", command=SingleVideo2FramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["video"]["img"], compound="left")
-        extract_frames_menu.add_command(label="Extract frames from multiple video", command=MultipleVideos2FramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["stack"]["img"], compound="left")
+        extract_frames_menu.add_command(label="Extract frames from single video", command=SingleVideo2FramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["frames_2"]["img"], compound="left")
+        extract_frames_menu.add_command(label="Extract frames from multiple videos", command=MultipleVideos2FramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["stack"]["img"], compound="left")
         extract_frames_menu.add_command(label="Extract frames from seq files", command=ExtractSEQFramesPopUp, font=Formats.FONT_REGULAR.value, image=self.menu_icons["fire"]["img"], compound="left")
         video_process_menu.add_cascade(label="Extract frames...", compound="left", image=self.menu_icons["frames"]["img"], menu=extract_frames_menu, font=Formats.FONT_REGULAR.value)
 

simba/assets/lookups/tooptips.json

@@ -29,5 +29,14 @@
   "LOCATION_FRAME_COUNT": "The location in the video where the \n frame count is positioned.",
   "ROTATE_FILL_COLOR": "When video is rotated, there may be empty space not \n covered by the video. What color should this space have?",
   "VIDEO_DIR": "Directory containing videos.",
-  "SAVE_DIR": "Directory where to save results."
+  "SAVE_DIR": "Directory where to save results.",
+  "CONCAT_HEIGHT": "If join involves aligning videos horizontally, this values \nwill be used to ensure videos have the same height. ",
+  "CONCAT_WIDTH": "If join involves aligning videos vertically, this values \nwill be used to ensure videos have the same width. ",
+  "CONCAT_RES_HEADER": "When stacking videos horizontally and/or vertically, \n the videos need to be same height and/or width. Here, \n select what resolution to use.",
+  "EGOCENTRIC_DATA_DIR": "Folder containing pose-estimation CSV data.\n Can be sub-directory in 'project_folder/csv' folder.\n Should contain same file names as the VIDEO files",
+  "EGOCENTRIC_VIDEO_DIR": "Folder containing videos.\n Should contain same file names as the DATA files.",
+  "EGOCENTRIC_ANCHOR": "This body-part will be placed in the center of the video",
+  "EGOCENTRIC_DIRECTION_ANCHOR": "This body-part will be placed at N degrees relative to the anchor",
+  "EGOCENTRIC_DIRECTION": "The anchor body-part will always be placed at these degrees relative to the center anchor",
+  "CORE_COUNT": "Higher core counts speeds up processing but may require more RAM memory"
 }

simba/plotting/frame_mergerer_ffmpeg.py

@@ -1,196 +1,137 @@
-__author__ = "Simon Nilsson; sronilsson@gmail.com"
-
-import os
-import shutil
-from datetime import datetime
-from typing import List, Optional, Union
-
-try:
-    from typing import Literal
-except ImportError:
-    from typing_extensions import Literal
-
-from simba.mixins.config_reader import ConfigReader
-from simba.utils.checks import (check_ffmpeg_available,
-                                check_file_exist_and_readable, check_int,
-                                check_nvidea_gpu_available, check_str,
-                                check_valid_lst)
-from simba.utils.enums import Paths, TagNames
-from simba.utils.errors import FFMPEGCodecGPUError
-from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.read_write import copy_files_to_directory, get_fn_ext
-from simba.video_processors.video_processing import (
-    horizontal_video_concatenator, mixed_mosaic_concatenator,
-    mosaic_concatenator, vertical_video_concatenator)
-
-HORIZONTAL = "horizontal"
-VERTICAL = "vertical"
-MOSAIC = "mosaic"
-MIXED_MOSAIC = "mixed_mosaic"
-ACCEPTED_TYPES = [HORIZONTAL, VERTICAL, MOSAIC, MIXED_MOSAIC]
-
-
-class FrameMergererFFmpeg(ConfigReader):
-    """
-    Merge separate visualizations of classifications, descriptive statistics etc., into  single video mosaic.
-
-    .. note::
-       `GitHub tutorial <https://github.com/sgoldenlab/simba/blob/master/docs/tutorial.md#step-12-merge-frames>`_.
-
-        .. image:: _static/img/mosaic_videos.gif
-          :width: 600
-          :align: center
-
-    :parameter str config_path: Optional path to SimBA project config file in Configparser format.
-    :parameter Literal["horizontal", "vertical", "mosaic", "mixed_mosaic"] concat_type: Type of concatenation. OPTIONS: 'horizontal', 'vertical', 'mosaic', 'mixed_mosaic'.
-    :parameter List[Union[str, os.PathLike]] video_paths: List with videos to concatenate.
-    :parameter Optional[int] video_height: Optional height of the canatenated videos. Required if concat concat_type is not mixed_mosaic.
-    :parameter int video_width: Optional wisth of the canatenated videos. Required if concat concat_type is not mixed_mosaic.
-    :parameter Optional[bool] gpu: If True, use NVIDEA FFMpeg GPU codecs. Default False.
-
-    :example:
-    >>> video_paths = ['/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4', '/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4']
-    >>> merger = FrameMergererFFmpeg(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini', video_paths=videos, video_height=600, video_width=600, concat_type='mosaic')
-    >>> merger.run()
-    """
-
-    def __init__(
-        self,
-        concat_type: Literal["horizontal", "vertical", "mosaic", "mixed_mosaic"],
-        video_paths: List[Union[str, os.PathLike]],
-        video_height: Optional[int] = None,
-        video_width: Optional[int] = None,
-        config_path: Optional[str] = None,
-        gpu: Optional[bool] = False,
-    ):
-
-        if gpu and not check_nvidea_gpu_available():
-            raise FFMPEGCodecGPUError(
-                msg="NVIDEA GPU not available (as evaluated by nvidea-smi returning None",
-                source=self.__class__.__name__,
-            )
-        check_ffmpeg_available()
-        check_str(
-            name=f"{FrameMergererFFmpeg.__name__} concat_type",
-            value=concat_type,
-            options=ACCEPTED_TYPES,
-        )
-        check_valid_lst(
-            data=video_paths,
-            source=f"{self.__class__.__name__} video_paths",
-            valid_dtypes=(str,),
-            min_len=2,
-        )
-        for i in video_paths:
-            check_file_exist_and_readable(file_path=i)
-        if concat_type != MIXED_MOSAIC:
-            check_int(
-                name=f"{FrameMergererFFmpeg.__name__} video_height",
-                value=video_height,
-                min_value=0,
-            )
-            check_int(
-                name=f"{FrameMergererFFmpeg.__name__} video_width",
-                value=video_height,
-                min_value=0,
-            )
-        if config_path is not None:
-            ConfigReader.__init__(self, config_path=config_path)
-            log_event(
-                logger_name=str(__class__.__name__),
-                log_type=TagNames.CLASS_INIT.value,
-                msg=self.create_log_msg_from_init_args(locals=locals()),
-            )
-            self.output_dir = os.path.join(
-                self.project_path, Paths.CONCAT_VIDEOS_DIR.value
-            )
-            self.output_path = os.path.join(
-                self.project_path,
-                Paths.CONCAT_VIDEOS_DIR.value,
-                f"merged_video_{self.datetime}.mp4",
-            )
-        else:
-            self.timer = SimbaTimer(start=True)
-            self.datetime = datetime.now().strftime("%Y%m%d%H%M%S")
-            self.output_dir, _, _ = get_fn_ext(filepath=video_paths[0])
-            self.output_path = os.path.join(
-                self.output_dir, f"merged_video_{self.datetime}.mp4"
-            )
-
-        self.video_height, self.video_width, self.gpu = video_height, video_width, gpu
-        self.video_paths, self.concat_type = video_paths, concat_type
-        if not os.path.exists(self.output_dir):
-            os.makedirs(self.output_dir)
-
-    def run(self):
-        if self.concat_type == HORIZONTAL:
-            _ = horizontal_video_concatenator(
-                video_paths=self.video_paths,
-                save_path=self.output_path,
-                height_px=self.video_height,
-                gpu=self.gpu,
-                verbose=True,
-            )
-        elif self.concat_type == VERTICAL:
-            _ = vertical_video_concatenator(
-                video_paths=self.video_paths,
-                save_path=self.output_path,
-                width_px=self.video_width,
-                gpu=self.gpu,
-                verbose=True,
-            )
-        elif self.concat_type == MOSAIC:
-            _ = mosaic_concatenator(
-                video_paths=self.video_paths,
-                save_path=self.output_path,
-                width_px=self.video_width,
-                height_px=self.video_height,
-                gpu=self.gpu,
-                verbose=True,
-            )
-        else:
-            _ = mixed_mosaic_concatenator(
-                video_paths=self.video_paths,
-                save_path=self.output_path,
-                gpu=self.gpu,
-                verbose=True,
-            )
-        self.timer.stop_timer()
-        stdout_success(
-            msg=f"Merged video saved at {self.output_path}",
-            source=self.__class__.__name__,
-            elapsed_time=self.timer.elapsed_time_str,
-        )
-
-
-# videos = ['/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4', '/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4']
-#
-# merger = FrameMergererFFmpeg(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini',
-#                     video_paths=videos,
-#                     video_height=600,
-#                     video_width=600,
-#                     concat_type='vertical') #horizontal, vertical, mosaic, mixed_mosaic
-# merger.run()
-
-
-#
-# FrameMergererFFmpeg(config_path=None,
-#                     frame_types={'Video 1': '/Users/simon/Desktop/envs/troubleshooting/two_black_animals_14bp/project_folder/videos/Together_1.avi',
-#                                  'Video 2': '/Users/simon/Desktop/envs/troubleshooting/two_black_animals_14bp/project_folder/videos/Together_1.avi'},
-#                     video_height=640,
-#                     video_width=480,
-#                     concat_type='vertical') #horizontal, vertical, mosaic, mixed_mosaic
-#
-#
-
-
-# FrameMergererFFmpeg(config_path=None,
-#                     frame_types={'Video 1': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
-#                                  'Video 2': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
-#                                  'Video 3': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
-#                                  'Video 4': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4'},
-#                     video_height=640,
-#                     video_width=480,
-#                     concat_type='mixed_mosaic',
-#                     gpu=False) #horizontal, vertical, mosaic, mixed_mosaic
-#
+__author__ = "Simon Nilsson; sronilsson@gmail.com"
+
+import os
+import shutil
+from datetime import datetime
+from typing import List, Optional, Union
+
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal
+
+from simba.mixins.config_reader import ConfigReader
+from simba.utils.checks import (check_ffmpeg_available,
+                                check_file_exist_and_readable, check_int,
+                                check_nvidea_gpu_available, check_str,
+                                check_valid_boolean, check_valid_lst)
+from simba.utils.enums import Paths, TagNames
+from simba.utils.errors import FFMPEGCodecGPUError
+from simba.utils.printing import SimbaTimer, log_event, stdout_success
+from simba.utils.read_write import copy_files_to_directory, get_fn_ext
+from simba.video_processors.video_processing import (
+    horizontal_video_concatenator, mixed_mosaic_concatenator,
+    mosaic_concatenator, vertical_video_concatenator)
+
+HORIZONTAL = "horizontal"
+VERTICAL = "vertical"
+MOSAIC = "mosaic"
+MIXED_MOSAIC = "mixed_mosaic"
+ACCEPTED_TYPES = [HORIZONTAL, VERTICAL, MOSAIC, MIXED_MOSAIC]
+
+
+class FrameMergererFFmpeg(ConfigReader):
+    """
+    Merge separate visualizations of classifications, descriptive statistics etc., into  single video mosaic.
+
+    .. note::
+       `GitHub tutorial <https://github.com/sgoldenlab/simba/blob/master/docs/tutorial.md#step-12-merge-frames>`_.
+
+        .. image:: _static/img/mosaic_videos.gif
+          :width: 600
+          :align: center
+
+    :parameter str config_path: Optional path to SimBA project config file in Configparser format.
+    :parameter Literal["horizontal", "vertical", "mosaic", "mixed_mosaic"] concat_type: Type of concatenation. OPTIONS: 'horizontal', 'vertical', 'mosaic', 'mixed_mosaic'.
+    :parameter List[Union[str, os.PathLike]] video_paths: List with videos to concatenate.
+    :param int quality: Video quality (CRF value). Lower values = higher quality. Range 0-52. Default 23.
+    :parameter Optional[int] video_height: Optional height of the canatenated videos. Required if concat concat_type is not mixed_mosaic.
+    :parameter int video_width: Optional wisth of the canatenated videos. Required if concat concat_type is not mixed_mosaic.
+    :parameter Optional[bool] gpu: If True, use NVIDEA FFMpeg GPU codecs. Default False.
+
+    :example:
+    >>> video_paths = ['/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4', '/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4']
+    >>> merger = FrameMergererFFmpeg(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini', video_paths=videos, video_height=600, video_width=600, concat_type='mosaic')
+    >>> merger.run()
+    """
+
+    def __init__( self,
+                 concat_type: Literal["horizontal", "vertical", "mosaic", "mixed_mosaic"],
+                 video_paths: List[Union[str, os.PathLike]],
+                 video_height: Optional[int] = None,
+                 video_width: Optional[int] = None,
+                 config_path: Optional[str] = None,
+                 quality: int = 23,
+                 gpu: bool = False):
+
+        if gpu and not check_nvidea_gpu_available():
+            raise FFMPEGCodecGPUError(msg="NVIDEA GPU not available (as evaluated by nvidea-smi returning None", source=self.__class__.__name__)
+        check_ffmpeg_available()
+        check_str(name=f"{FrameMergererFFmpeg.__name__} concat_type", value=concat_type, options=ACCEPTED_TYPES)
+        check_valid_lst(data=video_paths, source=f"{self.__class__.__name__} video_paths", valid_dtypes=(str,), min_len=2)
+        check_valid_boolean(value=gpu, source=f'{self.__class__.__name__} gpu', raise_error=True)
+        self.quality = 23 if not check_int(name='quality', value=quality, min_value=0, max_value=52, raise_error=False)[0] else int(quality)
+        for i in video_paths:
+            check_file_exist_and_readable(file_path=i)
+        if concat_type != MIXED_MOSAIC:
+            check_int(name=f"{FrameMergererFFmpeg.__name__} video_height", value=video_height, min_value=0)
+            check_int(name=f"{FrameMergererFFmpeg.__name__} video_width", value=video_height, min_value=0)
+        if config_path is not None:
+            ConfigReader.__init__(self, config_path=config_path)
+            log_event(logger_name=str(__class__.__name__), log_type=TagNames.CLASS_INIT.value, msg=self.create_log_msg_from_init_args(locals=locals()))
+            self.output_dir = os.path.join(self.project_path, Paths.CONCAT_VIDEOS_DIR.value)
+            self.output_path = os.path.join(self.project_path, Paths.CONCAT_VIDEOS_DIR.value, f"merged_video_{self.datetime}.mp4")
+        else:
+            self.timer = SimbaTimer(start=True)
+            self.datetime = datetime.now().strftime("%Y%m%d%H%M%S")
+            self.output_dir, _, _ = get_fn_ext(filepath=video_paths[0])
+            self.output_path = os.path.join(self.output_dir, f"merged_video_{self.datetime}.mp4")
+
+        self.video_height, self.video_width, self.gpu = video_height, video_width, gpu
+        self.video_paths, self.concat_type = video_paths, concat_type
+        if not os.path.exists(self.output_dir): os.makedirs(self.output_dir)
+
+    def run(self):
+        if self.concat_type == HORIZONTAL:
+            _ = horizontal_video_concatenator(video_paths=self.video_paths, save_path=self.output_path, height_px=self.video_height, gpu=self.gpu, quality=self.quality, verbose=True)
+        elif self.concat_type == VERTICAL:
+            _ = vertical_video_concatenator(video_paths=self.video_paths, save_path=self.output_path, width_px=self.video_width, gpu=self.gpu, quality=self.quality, verbose=True)
+        elif self.concat_type == MOSAIC:
+            _ = mosaic_concatenator(video_paths=self.video_paths, save_path=self.output_path, width_px=self.video_width, height_px=self.video_height, gpu=self.gpu, quality=self.quality, verbose=True)
+        else:
+            _ = mixed_mosaic_concatenator(video_paths=self.video_paths, save_path=self.output_path, gpu=self.gpu, verbose=True)
+        self.timer.stop_timer()
+        stdout_success(msg=f"Merged video saved at {self.output_path}", source=self.__class__.__name__, elapsed_time=self.timer.elapsed_time_str)
+
+
+# videos = ['/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4', '/Users/simon/Desktop/envs/simba/troubleshooting/mouse_open_field/project_folder/videos/SI_DAY3_308_CD1_PRESENT_downsampled.mp4']
+#
+# merger = FrameMergererFFmpeg(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/project_config.ini',
+#                     video_paths=videos,
+#                     video_height=600,
+#                     video_width=600,
+#                     concat_type='vertical') #horizontal, vertical, mosaic, mixed_mosaic
+# merger.run()
+
+
+#
+# FrameMergererFFmpeg(config_path=None,
+#                     frame_types={'Video 1': '/Users/simon/Desktop/envs/troubleshooting/two_black_animals_14bp/project_folder/videos/Together_1.avi',
+#                                  'Video 2': '/Users/simon/Desktop/envs/troubleshooting/two_black_animals_14bp/project_folder/videos/Together_1.avi'},
+#                     video_height=640,
+#                     video_width=480,
+#                     concat_type='vertical') #horizontal, vertical, mosaic, mixed_mosaic
+#
+#
+
+
+# FrameMergererFFmpeg(config_path=None,
+#                     frame_types={'Video 1': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
+#                                  'Video 2': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
+#                                  'Video 3': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4',
+#                                  'Video 4': r'C:\Users\Nape_Computer_2\Desktop\test_videos\Box1_PM2_day_5_20211104T171021.mp4'},
+#                     video_height=640,
+#                     video_width=480,
+#                     concat_type='mixed_mosaic',
+#                     gpu=False) #horizontal, vertical, mosaic, mixed_mosaic
+#