simba-uw-tf-dev 4.7.6__tar.gz → 4.7.7__tar.gz

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: simba_uw_tf_dev
-Version: 4.7.6
+Version: 4.7.7
 Summary: Toolkit for computer classification and analysis of behaviors in experimental animals
 Home-page: https://github.com/sgoldenlab/simba
 Author: Simon Nilsson, Jia Jie Choong, Sophia Hwang

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/setup.py

@@ -29,7 +29,7 @@ with open(GPU_REQUIREMENTS_PATH, "r") as f:
 # Setup configuration
 setuptools.setup(
     name="simba_uw_tf_dev",
-    version="4.7.6",
+    version="4.7.7",
     author="Simon Nilsson, Jia Jie Choong, Sophia Hwang",
     author_email="sronilsson@gmail.com",
     description="Toolkit for computer classification and analysis of behaviors in experimental animals",

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/assets/.recent_projects.txt

@@ -1,3 +1,4 @@
+E:/troubleshooting/mitra_pbn/mitra_pbn/project_folder/project_config.ini
 C:/troubleshooting/sleap_two_animals/project_folder/project_config.ini
 E:/troubleshooting/mitra_emergence/project_folder/project_config.ini
 C:/troubleshooting/meberled/project_folder/project_config.ini

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/assets/lookups/tooptips.json

@@ -5,7 +5,7 @@
   "batch_dropdown": "Number of frames processed at once. Larger batches speed up inference but require more GPU RAM.",
   "verbose_dropdown": "Toggle console printouts for progress and timings. Keep TRUE while tuning, FALSE for quiet runs.",
   "workers_dropdown": "How many CPU worker threads to use for pre/post-processing. Set <= available cores.",
-  "format_dropdown": "Model serialization format (None = auto-detect from file extension). Match the format used when exporting the weights.",
+  "format_dropdown": "Export/serialization format. Training: export the trained model to this format after training (None = PyTorch .pt only). Inference: match the format of your weights file, or None to auto-detect from file extension. Options: onnx, engine, torchscript, onnxsimplify, coreml, openvino, pb, tf, tflite, torch.",
   "img_size_dropdown": "Resize shorter image side to this many pixels before inference. Larger sizes improve accuracy but slow down processing.",
   "devices_dropdown": "Compute device to run on. Select CUDA device ID for GPU or CPU.",
   "interpolate_dropdown": "Fill missing detections by interpolating coordinates over time. Recommended for cleaner trajectories.",
@@ -43,5 +43,27 @@
   "KLEINBERG_GAMMA": "Higher values (e.g., 0.5-1.0) reduce total burst count by making downward transitions costly; lower values (e.g., 0.1-0.3) allow more flexible state changes",
   "KLEINBERG_HIERARCHY": "Hierarchy level to extract bursts from (0=lowest, higher=more selective).\n Level 0 captures all bursts; level 1-2 typically filters noise; level 3+ selects only the most prominent, sustained bursts.\nHigher levels yield fewer but more confident detections",
   "KLEINBERG_HIERARCHY_SEARCH": "If True, searches for target hierarchy level within detected burst periods,\n falling back to lower levels if target not found. If False, extracts only bursts at the exact specified hierarchy level.\n Recommended when target hierarchy may be sparse.",
-  "KLEINBERG_SAVE_ORIGINALS": "If True, saves the original data in a new sub-directory of \nthe project_folder/csv/machine_results directory"
+  "KLEINBERG_SAVE_ORIGINALS": "If True, saves the original data in a new sub-directory of \nthe project_folder/csv/machine_results directory",
+  "yolo_map_path": "Path to the YOLO dataset YAML file. Defines class names, paths to train/val images and labels, and number of keypoints.",
+  "yolo_initial_weights_path": "Optional path to pretrained weights (.pt) to start training from (e.g. yolo11n-pose.pt). Leave blank to train from scratch.",
+  "epochs_dropdown": "Number of training epochs. More epochs can improve accuracy but increase overfitting risk and training time.",
+  "plots_dropdown": "If TRUE, generate and save training curves (loss, mAP, etc.) in the save directory.",
+  "patience_dropdown": "Early-stopping patience: training stops if validation metric does not improve for this many epochs.",
+  "simba2yolo_config": "Path to the SimBA project configuration file (.ini). Defines project paths, body-parts, and animals.",
+  "simba2yolo_train_size": "Percentage of sampled frames to use for the YOLO training set. The remainder is used for validation. E.g. 70 means 70% train, 30% val.",
+  "simba2yolo_padding": "Extra margin (as a fraction of image size) added around the keypoint bounding box. Use a small value (e.g. 0.05–0.2) if the tight box cuts off body parts or you want more context in each crop; None or 0 = no padding.",
+  "simba2yolo_sample_size": "Maximum number of frames to sample per video for creating YOLO images and labels. Higher values give more data but increase processing time.",
+  "simba2yolo_grey": "If TRUE, extracted video frames are saved in greyscale. If FALSE, frames are saved in color.",
+  "simba2yolo_clahe": "If TRUE, apply CLAHE (Contrast Limited Adaptive Histogram Equalization) to frames before saving. Can improve keypoint visibility in low-contrast videos.",
+  "yolo_plot_line_thickness": "Thickness of the lines drawn between keypoints (skeleton). AUTO lets the plotter choose based on video size; or set 1–20 pixels.",
+  "yolo_plot_circle_size": "Radius of the circles drawn at each keypoint. AUTO lets the plotter choose based on video size; or set 1–20 pixels.",
+  "yolo_plot_tracks": "If TRUE, draw trajectory paths (tracks) for each detected instance over time. If FALSE, draw only keypoints and skeleton per frame.",
+  "yolo_plot_data_path": "Path to a single YOLO pose result CSV (output from YOLO pose inference). Must match the video you select.",
+  "yolo_plot_video_path": "Path to the video file to overlay pose results onto. Filename should match the data CSV (without extension).",
+  "yolo_plot_data_dir": "Directory containing YOLO pose result CSV files. Used for batch plotting; each CSV is matched to a video of the same name in the video directory.",
+  "SLEAP_DATA_DIR": "Directory containing SLEAP CSV prediction files. Each CSV should match a video filename (without extension).",
+  "ANIMAL_COUNT": "Number of animals (tracks) in the videos. Used to name classes (e.g. animal_1, animal_2) in the YOLO dataset.",
+  "sleap_remove_animal_ids": "If TRUE, merge all tracks into a single identity (animal_1). Use when animal IDs are not meaningful or for single-animal data.",
+  "sleap_threshold": "Minimum SLEAP instance confidence (the instance.score column in the CSV). Only pose predictions with score ≥ this value are used when building the YOLO dataset. E.g. 90 means keep instances where instance.score ≥ 0.9; lower values include more frames but may add noisy predictions.",
+  "SLEAP_SLP_DATA_DIR": "Directory containing SLEAP .SLP project/annotation files. Each .SLP file is converted to YOLO pose format."
 }

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/model/yolo_fit.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import urllib.request
 from contextlib import redirect_stderr, redirect_stdout
 
 os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
@@ -19,13 +20,19 @@ except ModuleNotFoundError:
 from simba.data_processors.cuda.utils import _is_cuda_available
 from simba.utils.checks import (check_file_exist_and_readable,
                                 check_if_dir_exists, check_int, check_str,
-                                check_valid_boolean, check_valid_device)
+                                check_valid_boolean, check_valid_device,
+                                check_valid_url)
 from simba.utils.enums import Options
 from simba.utils.errors import SimBAGPUError, SimBAPAckageVersionError
 from simba.utils.printing import stdout_information
 from simba.utils.read_write import find_core_cnt, get_current_time
 from simba.utils.yolo import load_yolo_model
 
+#YOLO_X_PATH = "https://huggingface.co/Ultralytics/YOLO11/resolve/main/yolo11x-pose.pt"
+
+YOLO_M_PATH = "https://huggingface.co/Ultralytics/YOLO11/resolve/main/yolo11m-pose.pt"
+
+
 
 class FitYolo():
 
@@ -74,9 +81,9 @@ class FitYolo():
     """
 
     def __init__(self,
-                 weights_path: Union[str, os.PathLike],
                  model_yaml: Union[str, os.PathLike],
                  save_path: Union[str, os.PathLike],
+                 weights_path: Optional[Union[str, os.PathLike]] = None,
                  epochs: int = 200,
                  batch: Union[int, float] = 16,
                  plots: bool = True,
@@ -92,7 +99,11 @@ class FitYolo():
             raise SimBAGPUError(msg='No GPU detected.', source=self.__class__.__name__)
         if YOLO is None:
             raise SimBAPAckageVersionError(msg='Ultralytics package not detected.', source=self.__class__.__name__)
-        check_file_exist_and_readable(file_path=weights_path)
+        if weights_path is not None:
+            check_file_exist_and_readable(file_path=weights_path)
+            self.weights_path = weights_path
+        else:
+            self._download_start_weights()
         check_file_exist_and_readable(file_path=model_yaml)
         check_valid_boolean(value=verbose, source=f'{__class__.__name__} verbose', raise_error=True)
         check_valid_boolean(value=plots, source=f'{__class__.__name__} plots', raise_error=True)
@@ -106,12 +117,19 @@ class FitYolo():
         check_valid_device(device=device)
         self.model_yaml, self.epochs, self.batch  = model_yaml, epochs, batch
         self.imgsz, self.device, self.workers, self.format = imgsz, device, workers, format
-        self.plots, self.save_path, self.verbose, self.weights_path, self.patience = plots, save_path, verbose, weights_path, patience
+        self.plots, self.save_path, self.verbose, self.patience = plots, save_path, verbose, patience
+
+    def _download_start_weights(self, url: str = YOLO_M_PATH, save_path: Union[str, os.PathLike] = "yolo11m-pose.pt"):
+        print(f'No start weights provided, downloading {save_path} from {url}...')
+        check_valid_url(url=url, raise_error=True, source=self.__class__.__name__)
+        if not os.path.isfile(save_path):
+            urllib.request.urlretrieve(url, save_path)
+            stdout_information(msg=f'Downloaded initial weights from {url}', source=self.__class__.__name__)
+        self.weights_path = save_path
+        print(self.weights_path)
 
 
     def run(self):
-        # Temporarily redirect stdout/stderr to terminal to ensure ultralytics output goes to terminal
-        # sys.__stdout__ and sys.__stderr__ are the original terminal streams
         stdout_information(msg=f'[{get_current_time()}] Please follow the YOLO pose model training in the terminal from where SimBA was launched ...', source=self.__class__.__name__)
         stdout_information(msg=f'[{get_current_time()}] Results will be stored in the {self.save_path} directory ..', source=self.__class__.__name__)
         with redirect_stdout(sys.__stdout__), redirect_stderr(sys.__stderr__):
@@ -133,7 +151,7 @@ class FitYolo():
 
 if __name__ == "__main__" and not hasattr(sys, 'ps1'):
     parser = argparse.ArgumentParser(description="Fit YOLO model using ultralytics package.")
-    parser.add_argument('--weights_path', type=str, required=True, help='Path to the trained YOLO model weights (e.g., yolo11n-pose.pt)')
+    parser.add_argument('--weights_path', type=str, default=None, help='Path to the trained YOLO model weights (e.g., yolo11n-pose.pt). Omit to download default starter weights.')
     parser.add_argument('--model_yaml', type=str, required=True, help='Path to map.yaml (model structure and label definitions)')
     parser.add_argument('--save_path', type=str, required=True, help='Directory where trained model and logs will be saved')
     parser.add_argument('--epochs', type=int, default=25, help='Number of epochs to train the model. Default is 25')
@@ -146,7 +164,6 @@ if __name__ == "__main__" and not hasattr(sys, 'ps1'):
     parser.add_argument('--workers', type=int, default=8, help='Number of data loader workers. Default is 8. Use -1 for max cores')
     parser.add_argument('--patience', type=int, default=100, help='Number of epochs to wait without improvement in validation metrics before early stopping the training. Default is 100')
 
-
     args = parser.parse_args()
 
     yolo_fitter = FitYolo(weights_path=args.weights_path,
@@ -159,11 +176,27 @@ if __name__ == "__main__" and not hasattr(sys, 'ps1'):
                           format=args.format,
                           device=int(args.device) if args.device != 'cpu' else 'cpu',
                           verbose=args.verbose,
-                          workers=args.workers)
+                          workers=args.workers,
+                          patience=args.patience)
     yolo_fitter.run()
 
 
 
+
+
+# fitter = FitYolo(weights_path=r"D:\maplight_tg2576_yolo\yolo_mdl\original_weight_oct\best.pt",
+#                  model_yaml=r"D:\maplight_tg2576_yolo\yolo_mdl\map.yaml",
+#                  save_path=r"D:\maplight_tg2576_yolo\yolo_mdl\mdl",
+#                  epochs=1500,
+#                  batch=22,
+#                  format=None,
+#                  device=0,
+#                  imgsz=640)
+# fitter.run()
+
+
+
+
 # fitter = FitYolo(weights_path=r"E:\yolo_resident_intruder\mdl\train3\weights\best.pt",
 #                  model_yaml=r"E:\maplight_videos\yolo_mdl\map.yaml",
 #                  save_path=r"E:\maplight_videos\yolo_mdl\mdl",

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/third_party_label_appenders/transform/coco_keypoints_to_yolo.py

@@ -75,7 +75,7 @@ class COCOKeypoints2Yolo:
                  img_dir: Union[str, os.PathLike],
                  save_dir: Union[str, os.PathLike],
                  train_size: float = 0.7,
-                 flip_idx: Tuple[int, ...] = (0, 2, 1, 3, 5, 4, 6, 7, 8),
+                 flip_idx: Tuple[int, ...] = (0, 2, 1, 5, 4, 3, 6),
                  verbose: bool = True,
                  greyscale: bool = False,
                  clahe: bool = False,
@@ -175,7 +175,6 @@ class COCOKeypoints2Yolo:
         missing = [x for x in list(range(shapes[0])) if x not in self.flip_idx]
         if len(missing) > 0:
             raise InvalidInputError(msg=f'keypoints contains index values not in flip_idx ({missing}).', source=self.__class__.__name__)
-
         create_yolo_keypoint_yaml(path=self.save_dir, train_path=self.train_img_dir, val_path=self.val_img_dir, names=self.map_dict, save_path=self.map_path, kpt_shape=(int(shapes[0]), 3), flip_idx=self.flip_idx)
         timer.stop_timer()
         if self.verbose: stdout_success(msg=f'COCO keypoints to YOLO conversion complete. Data saved in directory {self.save_dir}.', elapsed_time=timer.elapsed_time_str)

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/third_party_label_appenders/transform/sleap_csv_to_yolo.py

@@ -19,10 +19,10 @@ from simba.utils.checks import (check_float, check_if_dir_exists, check_int,
                                 check_valid_dataframe, check_valid_tuple)
 from simba.utils.enums import Options
 from simba.utils.errors import NoFilesFoundError
-from simba.utils.printing import SimbaTimer, stdout_success
+from simba.utils.printing import SimbaTimer, stdout_success, stdout_information
 from simba.utils.read_write import (create_directory,
                                     find_files_of_filetypes_in_directory,
-                                    get_video_meta_data, read_frm_of_video)
+                                    get_video_meta_data, read_frm_of_video, copy_files_to_directory, clean_sleap_filenames_in_directory, remove_a_folder)
 from simba.utils.yolo import keypoint_array_to_yolo_annotation_str
 
 
@@ -70,11 +70,16 @@ class Sleap2Yolo:
                  padding: float = 0.00,
                  single_id: Optional[str] = None):
 
+        check_if_dir_exists(in_dir=save_dir)
         self.data_paths = find_files_of_filetypes_in_directory(directory=data_dir, extensions=['.csv'], as_dict=True, raise_error=True)
+        self.data_temp_dir = os.path.join(data_dir, '.temp')
+        create_directory(paths=self.data_temp_dir, overwrite=True, verbose=True)
+        copy_files_to_directory(file_paths=list(self.data_paths.values()), dir=self.data_temp_dir, verbose=False, integer_save_names=False)
+        clean_sleap_filenames_in_directory(dir=self.data_temp_dir, verbose=True)
+        self.data_paths = find_files_of_filetypes_in_directory(directory=self.data_temp_dir, extensions=['.csv'], as_dict=True, raise_error=True)
         self.video_paths = find_files_of_filetypes_in_directory(directory=video_dir, extensions=Options.ALL_VIDEO_FORMAT_OPTIONS.value, as_dict=True, raise_error=True)
         missing_video_paths = [x for x in self.video_paths.keys() if x not in self.data_paths.keys()]
         missing_data_paths = [x for x in self.data_paths.keys() if x not in self.video_paths.keys()]
-        check_if_dir_exists(in_dir=save_dir)
         self.img_dir, self.lbl_dir = os.path.join(save_dir, 'images'), os.path.join(save_dir, 'labels')
         self.img_train_dir, self.img_val_dir = os.path.join(save_dir, 'images', 'train'), os.path.join(save_dir, 'images', 'val')
         self.lbl_train_dir, self.lb_val_dir = os.path.join(save_dir, 'labels', 'train'), os.path.join(save_dir, 'labels', 'val')
@@ -92,15 +97,15 @@ class Sleap2Yolo:
         if frms_cnt is not None:
             check_int(name=f'{self.__class__.__name__} frms_cnt', value=frms_cnt, min_value=1, raise_error=True)
         if len(missing_video_paths) > 0:
-            raise NoFilesFoundError(msg=f'Video(s) {missing_video_paths} could not be found in {video_dir} directory', source=self.__class__.__name__)
+            remove_a_folder(folder_dir=self.data_temp_dir, ignore_errors=True)
+            raise NoFilesFoundError(msg=f'{len(missing_video_paths)} video(s) {missing_video_paths} (of {len(self.data_paths.keys())} expected) could not be found in {video_dir} directory', source=self.__class__.__name__)
         if len(missing_data_paths) > 0:
-            raise NoFilesFoundError(msg=f'CSV data for {missing_data_paths} could not be found in {data_dir} directory', source=self.__class__.__name__)
+            remove_a_folder(folder_dir=self.data_temp_dir, ignore_errors=True)
+            raise NoFilesFoundError(msg=f'{len(missing_data_paths)} CSV data for {missing_data_paths} (of {len(self.video_paths.keys())} could not be found in {data_dir} directory', source=self.__class__.__name__)
         self.verbose, self.instance_threshold, self.frms_cnt = verbose, instance_threshold, frms_cnt
         self.names, self.greyscale, self.train_size, self.clahe = names, greyscale, train_size, clahe
         self.padding, self.flip_idx, self.save_dir, self.single_id = padding, flip_idx, save_dir, single_id
 
-
-
     def run(self):
         dfs, timer, bp_cols = [], SimbaTimer(start=True), []
         for file_cnt, (file_name, file_path) in enumerate(self.data_paths.items()):
@@ -115,6 +120,7 @@ class Sleap2Yolo:
             dfs.append(df)
 
         dfs = pd.concat(dfs, axis=0)
+        dfs['track'] = dfs['track'].fillna(-1)
         unique_tracks_lk = {v: k for k, v in enumerate(dfs['track'].unique())}
         if self.names is not None:
             check_valid_tuple(x=self.names, source=f'{self.__class__.__name__} names', valid_dtypes=(str,), accepted_lengths=(len(list(unique_tracks_lk.keys())),))
@@ -125,14 +131,13 @@ class Sleap2Yolo:
         train_idx = random.sample(list(dfs['id'].unique()), int(len(dfs['frame_idx'].unique()) * self.train_size))
         if self.flip_idx is None:
             self.flip_idx = get_yolo_keypoint_flip_idx(x=list(dict.fromkeys([x[:-2] for x in bp_cols])))
-
         for frm_cnt, frm_id in enumerate(dfs['id'].unique()):
             frm_data = dfs[dfs['id'] == frm_id]
             video_path = list(frm_data['video'])[0]
             frm_idx = list(frm_data['frame_idx'])[0]
             video_meta = get_video_meta_data(video_path=video_path)
             if self.verbose:
-                print(f'Processing frame: {frm_cnt + 1}/{len(list(dfs["id"].unique()))} ...')
+                stdout_information(msg=f'Processing frame: {frm_cnt + 1}/{len(list(dfs["id"].unique()))} ...', source=self.__class__.__name__)
             img = read_frm_of_video(video_path=video_path, frame_index=frm_idx, greyscale=self.greyscale, clahe=self.clahe)
             img_h, img_w = img.shape[0], img.shape[1]
             if list(frm_data['id'])[0] in train_idx:
@@ -155,12 +160,13 @@ class Sleap2Yolo:
 
         create_yolo_keypoint_yaml(path=self.save_dir, train_path=self.img_train_dir, val_path=self.img_val_dir, names=map_dict, save_path=self.map_path, kpt_shape=(len(self.flip_idx), 3), flip_idx=tuple(self.flip_idx))
         timer.stop_timer()
+        remove_a_folder(folder_dir=self.data_temp_dir, ignore_errors=True)
         stdout_success(msg=f'YOLO formated data saved in {self.save_dir} directory', source=self.__class__.__name__, elapsed_time=timer.elapsed_time_str)
 
 
-# DATA_DIR = r'D:\ares\data\ant\sleap_csv'
-# VIDEO_DIR = r'D:\ares\data\ant\sleap_video'
-# SAVE_DIR = r"D:\imgs\sleap_csv"
+# DATA_DIR = r'E:\troubleshooting\mitra_pbn\raw_data\yolo\tracking'
+# VIDEO_DIR = r'E:\troubleshooting\mitra_pbn\raw_data\yolo\videos'
+# SAVE_DIR = r"E:\troubleshooting\mitra_pbn\raw_data\yolo\data"
 #
 # runner = Sleap2Yolo(data_dir=DATA_DIR, video_dir=VIDEO_DIR, frms_cnt=50, train_size=0.8, instance_threshold=0.9, save_dir=SAVE_DIR, single_id='ant')
 # runner.run()

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/ui/create_project_ui.py

@@ -66,7 +66,7 @@ class ProjectCreatorPopUp():
         self.settings_frm = CreateLabelFrameWithIcon(parent=self.create_project_tab, header="SETTINGS", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.CREATE_PROJECT.value)
         self.general_settings_frm = CreateLabelFrameWithIcon(parent=self.settings_frm, header="GENERAL PROJECT SETTINGS", icon_name='settings', icon_link=Links.CREATE_PROJECT.value, padx=5, pady=5, relief='solid')
         self.project_dir_select = FolderSelect(self.general_settings_frm, "PROJECT DIRECTORY:", lblwidth=35, entry_width=35, font=Formats.FONT_REGULAR.value, lbl_icon='browse')
-        self.project_name_eb = Entry_Box(self.general_settings_frm, "PROJECT NAME:", labelwidth=35, entry_box_width=35, img='id_card_2')
+        self.project_name_eb = Entry_Box(self.general_settings_frm, "PROJECT NAME:", labelwidth=35, entry_box_width=35, img='id_card_2', justify='center')
         self.file_type_dropdown = SimBADropDown(parent=self.general_settings_frm, dropdown_options=Options.WORKFLOW_FILE_TYPE_OPTIONS.value, label='WORKFLOW FILE TYPE:', label_width=35, dropdown_width=35, value=Options.WORKFLOW_FILE_TYPE_OPTIONS.value[0], img='file_type')
 
         self.ml_settings_frm = GetMLSettingsFrame(parent=self.create_project_tab, lbl_width=35, bx_width=22)

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/ui/pop_ups/batch_preprocess_pop_up.py

@@ -21,7 +21,7 @@ class BatchPreProcessPopUp(PopUpMixin):
         PopUpMixin.__init__(self, title="BATCH PROCESS VIDEO", size=(600, 400), icon='stack')
         selections_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="SELECTIONS", icon_name=Keys.DOCUMENTATION.value, icon_link=Links.BATCH_PREPROCESS.value,)
         self.input_folder_select = FolderSelect(selections_frm, "INPUT VIDEO DIRECTORY:", title="Select Folder with Input Videos", lblwidth=30, lbl_icon='folder')
-        self.output_folder_select = FolderSelect(selections_frm, "OUTPUT VIDEO DIRECTORY:", title="Select Folder for Output videos", lblwidth=30, lbl_icon='folder')
+        self.output_folder_select = FolderSelect(selections_frm, "OUTPUT VIDEO DIRECTORY:", title="Select Folder for Output videos", lblwidth=30, lbl_icon='folder_2')
 
         confirm_btn = SimbaButton(parent=selections_frm, txt="CONFIRM", img='tick', txt_clr='blue', font=Formats.FONT_REGULAR.value, cmd=self.run)
         selections_frm.grid(row=0, column=0, sticky=NW)

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/ui/pop_ups/simba_to_yolo_keypoints_popup.py

@@ -1,96 +1,96 @@
-__author__ = "Simon Nilsson; sronilsson@gmail.com"
-
-from tkinter import *
-
-import numpy as np
-
-from simba.mixins.config_reader import ConfigReader
-from simba.mixins.pop_up_mixin import PopUpMixin
-from simba.third_party_label_appenders.transform.simba_to_yolo import \
-    SimBA2Yolo
-from simba.third_party_label_appenders.transform.utils import (
-    get_yolo_keypoint_bp_id_idx, get_yolo_keypoint_flip_idx)
-from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, FileSelect,
-                                        FolderSelect, SimBADropDown)
-from simba.utils.read_write import str_2_bool
-
-TRAIN_SIZE_OPTIONS = np.arange(10, 110, 10)
-SAMPLE_SIZE_OPTIONS = list(np.arange(50, 650, 50))
-
-THRESHOLD_OPTIONS = list(np.arange(0.1, 1.1, 0.1))
-
-PADDING_OPTIONS = list(np.round(np.arange(0.01, 10.05, 0.05),2).astype(str))
-PADDING_OPTIONS = list(np.insert(PADDING_OPTIONS, 0, 'None'))
-
-class SimBA2YoloKeypointsPopUp(PopUpMixin):
-
-    """
-    :example:
-    >>> SimBA2YoloKeypointsPopUp()
-    """
-    def __init__(self):
-        PopUpMixin.__init__(self, title="SIMBA TO YOLO KEYPOINTS", icon='SimBA_logo_3_small')
-        settings_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="SETTINGS", icon_name='settings')
-        self.config_select = FileSelect(parent=settings_frm, fileDescription='SIMBA PROJECT CONFIG (.INI): ', lblwidth=35, file_types=[("INI FILE", (".ini", ".INI",))], entry_width=40, initialdir=r"C:\troubleshooting\mitra\project_folder", lbl_icon='ini')
-        self.save_dir = FolderSelect(settings_frm, folderDescription="SAVE DIRECTORY:", lblwidth=35, entry_width=40, initialdir=r'C:\troubleshooting\mitra\yolo', lbl_icon='folder')
-        self.train_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=TRAIN_SIZE_OPTIONS, label="TRAIN SIZE (%): ", label_width=35, dropdown_width=40, value=70, img='pct_2')
-        self.verbose_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="VERBOSE: ", label_width=35, dropdown_width=40, value='TRUE', img='verbose')
-        self.padding_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=PADDING_OPTIONS, label="PADDING: ", label_width=35, dropdown_width=40, value='None', img='size_black')
-        self.sample_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=SAMPLE_SIZE_OPTIONS, label="FRAME SAMPLES PER VIDEO: ", label_width=35, dropdown_width=40, value=100, img='frames')
-        self.threshold_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=THRESHOLD_OPTIONS, label="CONFIDENCE THRESHOLD: ", label_width=35, dropdown_width=40, value='None', img='threshold')
-        self.grey_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="GREYSCALE: ", label_width=35, dropdown_width=40, value='FALSE', img='grey')
-        self.clahe_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="CLAHE: ", label_width=35, dropdown_width=40, value='FALSE', img='clahe')
-
-        settings_frm.grid(row=0, column=0, sticky=NW)
-        self.config_select.grid(row=0, column=0, sticky=NW)
-        self.save_dir.grid(row=1, column=0, sticky=NW)
-        self.train_size_dropdown.grid(row=2, column=0, sticky=NW)
-
-        self.verbose_dropdown.grid(row=3, column=0, sticky=NW)
-        self.padding_dropdown.grid(row=4, column=0, sticky=NW)
-        self.sample_size_dropdown.grid(row=5, column=0, sticky=NW)
-        self.threshold_dropdown.grid(row=6, column=0, sticky=NW)
-        self.grey_dropdown.grid(row=7, column=0, sticky=NW)
-        self.clahe_dropdown.grid(row=8, column=0, sticky=NW)
-
-        self.create_run_frm(run_function=self.run)
-        self.main_frm.mainloop()
-
-
-    def run(self):
-        config_path = self.config_select.file_path
-        config = ConfigReader(config_path=config_path)
-        animal_names = list(config.animal_bp_dict.keys())
-        bps = [x[:-2] for x in config.animal_bp_dict[animal_names[0]]['X_bps']]
-        flip_idx = get_yolo_keypoint_flip_idx(x=bps)
-        #map_dict = {c: k for c, k in enumerate(animal_names)}
-        bp_id_idx = None
-        if len(animal_names) > 1:
-            bp_id_idx = get_yolo_keypoint_bp_id_idx(animal_bp_dict=config.animal_bp_dict)
-        train_size = int(self.train_size_dropdown.get_value()) / 100
-        verbose = str_2_bool(self.verbose_dropdown.get_value())
-        save_dir = self.save_dir.folder_path
-        padding = float(self.padding_dropdown.get_value()) if self.padding_dropdown.get_value() != 'None' else 0.0
-        sample_size = int(self.sample_size_dropdown.get_value())
-        grey = str_2_bool(self.grey_dropdown.get_value())
-        clahe = str_2_bool(self.clahe_dropdown.get_value())
-        threshold = float(self.threshold_dropdown.get_value())
-
-        runner = SimBA2Yolo(config_path=config_path,
-                            save_dir=save_dir,
-                            data_dir=None,
-                            train_size=train_size,
-                            threshold=threshold,
-                            verbose=verbose,
-                            greyscale=grey,
-                            padding=padding,
-                            flip_idx=flip_idx,
-                            names=tuple(animal_names),
-                            sample_size=sample_size,
-                            bp_id_idx=bp_id_idx,
-                            clahe=clahe)
-        runner.run()
-
-
-#SimBA2YoloKeypointsPopUp()
-#simba_to_yolo_keypoints(config_path=r"C:\troubleshooting\mitra\project_folder\project_config.ini", save_dir=r'C:\troubleshooting\mitra\yolo', sample_size=150, verbose=True)
+__author__ = "Simon Nilsson; sronilsson@gmail.com"
+
+from tkinter import *
+
+import numpy as np
+
+from simba.mixins.config_reader import ConfigReader
+from simba.mixins.pop_up_mixin import PopUpMixin
+from simba.third_party_label_appenders.transform.simba_to_yolo import \
+    SimBA2Yolo
+from simba.third_party_label_appenders.transform.utils import (
+    get_yolo_keypoint_bp_id_idx, get_yolo_keypoint_flip_idx)
+from simba.ui.tkinter_functions import (CreateLabelFrameWithIcon, FileSelect,
+                                        FolderSelect, SimBADropDown)
+from simba.utils.read_write import str_2_bool
+
+TRAIN_SIZE_OPTIONS = np.arange(10, 110, 10)
+SAMPLE_SIZE_OPTIONS = list(np.arange(50, 650, 50))
+
+THRESHOLD_OPTIONS = [round(x, 2) for x in np.arange(0.1, 1.1, 0.1)]
+
+PADDING_OPTIONS = list(np.round(np.arange(0.01, 10.05, 0.05),2).astype(str))
+PADDING_OPTIONS = list(np.insert(PADDING_OPTIONS, 0, 'None'))
+
+class SimBA2YoloKeypointsPopUp(PopUpMixin):
+
+    """
+    :example:
+    >>> SimBA2YoloKeypointsPopUp()
+    """
+    def __init__(self):
+        PopUpMixin.__init__(self, title="SIMBA TO YOLO KEYPOINTS", icon='SimBA_logo_3_small')
+        settings_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="SETTINGS", icon_name='settings')
+        self.config_select = FileSelect(parent=settings_frm, fileDescription='SIMBA PROJECT CONFIG (.INI): ', lblwidth=35, file_types=[("INI FILE", (".ini", ".INI",))], entry_width=40, initialdir=r"C:\troubleshooting\mitra\project_folder", lbl_icon='ini', tooltip_key='simba2yolo_config')
+        self.save_dir = FolderSelect(settings_frm, folderDescription="SAVE DIRECTORY:", lblwidth=35, entry_width=40, initialdir=r'C:\troubleshooting\mitra\yolo', lbl_icon='folder', tooltip_key='SAVE_DIR')
+        self.train_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=TRAIN_SIZE_OPTIONS, label="TRAIN SIZE (%): ", label_width=35, dropdown_width=40, value=70, img='pct_2', tooltip_key='simba2yolo_train_size')
+        self.verbose_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="VERBOSE: ", label_width=35, dropdown_width=40, value='TRUE', img='verbose', tooltip_key='verbose_dropdown')
+        self.padding_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=PADDING_OPTIONS, label="PADDING: ", label_width=35, dropdown_width=40, value='None', img='size_black', tooltip_key='simba2yolo_padding')
+        self.sample_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=SAMPLE_SIZE_OPTIONS, label="FRAME SAMPLES PER VIDEO: ", label_width=35, dropdown_width=40, value=100, img='frames', tooltip_key='simba2yolo_sample_size')
+        self.threshold_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=THRESHOLD_OPTIONS, label="CONFIDENCE THRESHOLD: ", label_width=35, dropdown_width=40, value='None', img='threshold', tooltip_key='threshold_dropdown')
+        self.grey_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="GREYSCALE: ", label_width=35, dropdown_width=40, value='FALSE', img='grey', tooltip_key='simba2yolo_grey')
+        self.clahe_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="CLAHE: ", label_width=35, dropdown_width=40, value='FALSE', img='clahe', tooltip_key='simba2yolo_clahe')
+
+        settings_frm.grid(row=0, column=0, sticky=NW)
+        self.config_select.grid(row=0, column=0, sticky=NW)
+        self.save_dir.grid(row=1, column=0, sticky=NW)
+        self.train_size_dropdown.grid(row=2, column=0, sticky=NW)
+
+        self.verbose_dropdown.grid(row=3, column=0, sticky=NW)
+        self.padding_dropdown.grid(row=4, column=0, sticky=NW)
+        self.sample_size_dropdown.grid(row=5, column=0, sticky=NW)
+        self.threshold_dropdown.grid(row=6, column=0, sticky=NW)
+        self.grey_dropdown.grid(row=7, column=0, sticky=NW)
+        self.clahe_dropdown.grid(row=8, column=0, sticky=NW)
+
+        self.create_run_frm(run_function=self.run)
+        self.main_frm.mainloop()
+
+
+    def run(self):
+        config_path = self.config_select.file_path
+        config = ConfigReader(config_path=config_path)
+        animal_names = list(config.animal_bp_dict.keys())
+        bps = [x[:-2] for x in config.animal_bp_dict[animal_names[0]]['X_bps']]
+        flip_idx = get_yolo_keypoint_flip_idx(x=bps)
+        #map_dict = {c: k for c, k in enumerate(animal_names)}
+        bp_id_idx = None
+        if len(animal_names) > 1:
+            bp_id_idx = get_yolo_keypoint_bp_id_idx(animal_bp_dict=config.animal_bp_dict)
+        train_size = int(self.train_size_dropdown.get_value()) / 100
+        verbose = str_2_bool(self.verbose_dropdown.get_value())
+        save_dir = self.save_dir.folder_path
+        padding = float(self.padding_dropdown.get_value()) if self.padding_dropdown.get_value() != 'None' else 0.0
+        sample_size = int(self.sample_size_dropdown.get_value())
+        grey = str_2_bool(self.grey_dropdown.get_value())
+        clahe = str_2_bool(self.clahe_dropdown.get_value())
+        threshold = float(self.threshold_dropdown.get_value())
+
+        runner = SimBA2Yolo(config_path=config_path,
+                            save_dir=save_dir,
+                            data_dir=None,
+                            train_size=train_size,
+                            threshold=threshold,
+                            verbose=verbose,
+                            greyscale=grey,
+                            padding=padding,
+                            flip_idx=flip_idx,
+                            names=tuple(animal_names),
+                            sample_size=sample_size,
+                            bp_id_idx=bp_id_idx,
+                            clahe=clahe)
+        runner.run()
+
+
+#SimBA2YoloKeypointsPopUp()
+#simba_to_yolo_keypoints(config_path=r"C:\troubleshooting\mitra\project_folder\project_config.ini", save_dir=r'C:\troubleshooting\mitra\yolo', sample_size=150, verbose=True)

{simba_uw_tf_dev-4.7.6 → simba_uw_tf_dev-4.7.7}/simba/ui/pop_ups/sleap_annotations_to_yolo_popup.py

@@ -20,8 +20,9 @@ from simba.utils.read_write import (find_files_of_filetypes_in_directory,
 TRAIN_SIZE_OPTIONS = list(np.arange(10, 110, 10))
 SAMPLE_SIZE_OPTIONS = list(np.arange(50, 650, 50))
 
-PADDING_OPTIONS = list(np.round(np.arange(0.01, 10.05, 0.05),2).astype(str))
-PADDING_OPTIONS = list(np.insert(PADDING_OPTIONS, 0, 'None'))
+_padding_arr = np.concatenate([[0.01], np.arange(0.05, 10.05, 0.05)])
+PADDING_OPTIONS = [f"{x:.2f}" for x in np.round(_padding_arr, 2)]
+PADDING_OPTIONS = ['None'] + PADDING_OPTIONS
 
 
 
@@ -37,26 +38,28 @@ class SLEAPAnnotations2YoloPopUp(PopUpMixin):
     def __init__(self):
         PopUpMixin.__init__(self, title="SLEAP ANNOTATIONS TO YOLO POSE ESTIMATION ANNOTATIONS", icon='sleap_small')
         settings_frm = CreateLabelFrameWithIcon(parent=self.main_frm, header="SETTINGS", icon_name='settings')
-        self.sleap_dir = FolderSelect(settings_frm, folderDescription="SLEAP DATA DIRECTORY (.SLP):", lblwidth=35, entry_width=40, initialdir=r"D:\troubleshooting\two_animals_sleap\import_data", lbl_icon='folder')
-        self.save_dir = FolderSelect(settings_frm, folderDescription="SAVE DIRECTORY:", lblwidth=35, entry_width=40, initialdir=r"D:\troubleshooting\two_animals_sleap\yolo_kpts_2", lbl_icon='folder')
+        self.sleap_dir = FolderSelect(settings_frm, folderDescription="SLEAP DATA DIRECTORY (.SLP):", lblwidth=35, entry_width=40, lbl_icon='folder', tooltip_key='SLEAP_SLP_DATA_DIR')
+        self.video_dir = FolderSelect(settings_frm, folderDescription="VIDEO DIRECTORY:", lblwidth=35, entry_width=40, lbl_icon='folder_video', tooltip_key='VIDEO_DIR')
+        self.save_dir = FolderSelect(settings_frm, folderDescription="SAVE DIRECTORY:", lblwidth=35, entry_width=40, initialdir=r"D:\troubleshooting\two_animals_sleap\yolo_kpts_2", lbl_icon='folder', tooltip_key='SAVE_DIR')
 
-        self.verbose_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="VERBOSE: ", label_width=35, dropdown_width=40, value='TRUE', img='verbose')
-        self.train_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=TRAIN_SIZE_OPTIONS, label="TRAIN SIZE (%): ", label_width=35, dropdown_width=40, value=70, img='pct_2')
-        self.grey_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="GREYSCALE: ", label_width=35, dropdown_width=40, value='FALSE', img='grey')
-        self.padding_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=PADDING_OPTIONS, label="PADDING: ", label_width=35, dropdown_width=40, value='None', img='size_black')
-        self.clahe_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="CLAHE: ", label_width=35, dropdown_width=40, value='FALSE', img='clahe')
-        self.single_id_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="REMOVE ANIMAL ID'S", label_width=35, dropdown_width=40, value='FALSE', img='mouse_head')
+        self.verbose_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="VERBOSE: ", label_width=35, dropdown_width=40, value='TRUE', img='verbose', tooltip_key='verbose_dropdown')
+        self.train_size_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=TRAIN_SIZE_OPTIONS, label="TRAIN SIZE (%): ", label_width=35, dropdown_width=40, value=70, img='pct_2', tooltip_key='simba2yolo_train_size')
+        self.grey_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="GREYSCALE: ", label_width=35, dropdown_width=40, value='FALSE', img='grey', tooltip_key='simba2yolo_grey')
+        self.padding_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=PADDING_OPTIONS, label="PADDING: ", label_width=35, dropdown_width=40, value='None', img='size_black', tooltip_key='simba2yolo_padding')
+        self.clahe_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="CLAHE: ", label_width=35, dropdown_width=40, value='FALSE', img='clahe', tooltip_key='simba2yolo_clahe')
+        self.single_id_dropdown = SimBADropDown(parent=settings_frm, dropdown_options=['TRUE', 'FALSE'], label="REMOVE ANIMAL ID'S", label_width=35, dropdown_width=40, value='FALSE', img='mouse_head', tooltip_key='sleap_remove_animal_ids')
 
         settings_frm.grid(row=0, column=0, sticky=NW)
         self.sleap_dir .grid(row=0, column=0, sticky=NW)
-        self.save_dir.grid(row=1, column=0, sticky=NW)
+        self.video_dir.grid(row=1, column=0, sticky=NW)
+        self.save_dir.grid(row=2, column=0, sticky=NW)
 
-        self.verbose_dropdown.grid(row=2, column=0, sticky=NW)
-        self.train_size_dropdown.grid(row=3, column=0, sticky=NW)
-        self.grey_dropdown.grid(row=4, column=0, sticky=NW)
-        self.clahe_dropdown.grid(row=5, column=0, sticky=NW)
-        self.padding_dropdown.grid(row=6, column=0, sticky=NW)
-        self.single_id_dropdown.grid(row=7, column=0, sticky=NW)
+        self.verbose_dropdown.grid(row=3, column=0, sticky=NW)
+        self.train_size_dropdown.grid(row=4, column=0, sticky=NW)
+        self.grey_dropdown.grid(row=5, column=0, sticky=NW)
+        self.clahe_dropdown.grid(row=6, column=0, sticky=NW)
+        self.padding_dropdown.grid(row=7, column=0, sticky=NW)
+        self.single_id_dropdown.grid(row=8, column=0, sticky=NW)
 
         self.create_run_frm(run_function=self.run)
         self.main_frm.mainloop()
@@ -65,9 +68,12 @@ class SLEAPAnnotations2YoloPopUp(PopUpMixin):
     def run(self):
         sleap_dir = self.sleap_dir.folder_path
         save_dir = self.save_dir.folder_path
+        video_dir = self.video_dir.folder_path
 
         check_if_dir_exists(in_dir=sleap_dir, source=f'{self.__class__.__name__} SLEAP DATA DIRECTORY', raise_error=True)
         check_if_dir_exists(in_dir=save_dir, source=f'{self.__class__.__name__} SAVE DIRECTORY', raise_error=True)
+        video_dir_exist = check_if_dir_exists(in_dir=video_dir, source=f'{self.__class__.__name__} VIDEO DIRECTORY', raise_error=False)
+        video_dir = video_dir if video_dir_exist else None
         _ = find_files_of_filetypes_in_directory(directory=sleap_dir, extensions=['.slp'], raise_error=True)
 
         grey = str_2_bool(self.grey_dropdown.get_value())
@@ -77,7 +83,15 @@ class SLEAPAnnotations2YoloPopUp(PopUpMixin):
         padding = float(self.padding_dropdown.get_value()) if self.padding_dropdown.get_value() != 'None' else 0.0
         single_id = 'animal_1' if str_2_bool(self.single_id_dropdown.get_value()) else None
 
-        runner = SleapAnnotations2Yolo(sleap_dir=sleap_dir, save_dir=save_dir, padding=padding, train_size=train_size, verbose=verbose, greyscale=grey, clahe=clahe, single_id=single_id)
+        runner = SleapAnnotations2Yolo(sleap_dir=sleap_dir,
+                                       save_dir=save_dir,
+                                       video_dir=video_dir,
+                                       padding=padding,
+                                       train_size=train_size,
+                                       verbose=verbose,
+                                       greyscale=grey,
+                                       clahe=clahe,
+                                       single_id=single_id)
         runner.run()