simba-uw-tf-dev 5.3.4__tar.gz → 5.3.6__tar.gz

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: simba_uw_tf_dev
-Version: 5.3.4
+Version: 5.3.6
 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-5.3.4 → simba_uw_tf_dev-5.3.6}/setup.py

@@ -29,7 +29,7 @@ with open(GPU_REQUIREMENTS_PATH, "r") as f:
 # Setup configuration
 setuptools.setup(
     name="simba_uw_tf_dev",
-    version="5.3.4",
+    version="5.3.6",
     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-5.3.4 → simba_uw_tf_dev-5.3.6}/simba/__init__.py

@@ -2,6 +2,9 @@
 SimBA (Simple Behavioral Analysis)
 Toolkit for computer classification and analysis of behaviors in experimental animals
 """
+import matplotlib
+matplotlib.use("Agg")
+
 import multiprocessing
 
 from simba.utils.checks import is_wsl

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/simba/pose_importers/superanimal_import.py

@@ -1,197 +1,196 @@
-import os
-from typing import Dict, List, Optional, Union
-
-import numpy as np
-
-from simba.data_processors.interpolate import Interpolate
-from simba.data_processors.smoothing import Smoothing
-from simba.mixins.config_reader import ConfigReader
-from simba.mixins.pose_importer_mixin import PoseImporterMixin
-from simba.utils.checks import (check_if_dir_exists,
-                                check_if_keys_exist_in_dict, check_int,
-                                check_str, check_valid_lst)
-from simba.utils.enums import ConfigKey, Formats, TagNames
-from simba.utils.lookups import find_best_multi_animal_assignment_frame
-from simba.utils.printing import SimbaTimer, log_event, stdout_success
-from simba.utils.errors import InvalidInputError
-from simba.utils.read_write import (clean_superanimal_topview_filename,
-                                    find_all_videos_in_project,
-                                    find_files_of_filetypes_in_directory,
-                                    get_h5_frame_count,
-                                    get_video_meta_data,
-                                    read_dlc_superanimal_h5, write_df)
-
-
-class SuperAnimalTopViewImporter(PoseImporterMixin, ConfigReader):
-
-    """
-    Import SuperAnimal-TopView mouse data to SimBA
-
-    .. note::
-       For more information see the DeepLabCutModelZoo-SuperAnimal-TopViewMouse on huggingface https://huggingface.co/mwmathis/DeepLabCutModelZoo-SuperAnimal-TopViewMouse
-
-       Trackes 27 body-parts on one or more mice recorded from zenith.
-
-       Supports both DLC H5 layouts: the legacy TensorFlow backend (``df_with_missing`` /
-       ``table``) and the modern DLC 3.0+ PyTorch backend (HRNet, RTMPose), including
-       multi-animal tracked outputs ending in ``_el.h5`` / ``_full.h5``. H5 column order is
-       assumed to follow the SuperAnimal-TopView 27 body-part schema, with animals in the
-       order supplied via ``id_lst`` (positional mapping).
-
-    .. image:: _static/img/superanimal_topview.png
-       :width: 150
-       :align: center
-
-    :param config_path: path to SimBA project config file in Configparser format
-    :param str data_folder: Path to folder containing SuperAnimal data in ``.h5`` format.
-    :param List[str] id_lst: Names of animals.
-    :param Optional[Dict[str, str]] interpolation_setting: Dict defining the type and method to use to perform interpolation {'type': 'animals', 'method': 'linear'}.
-    :param Optional[Dict[str, Union[str, int]]] smoothing_settings: Dictionary defining the pose estimation smoothing method {'time_window': 500, 'method': 'gaussian'}.
-    :param Optional[int] initial_frame_no: Frame index at which to open the multi-animal
-        identity-assignment UI. Only used when ``len(id_lst) > 1``.
-
-        * If an integer is passed, it is used directly (and must be ``>= 0`` and strictly
-          less than the frame count of **every** H5 file in ``data_folder``; otherwise an
-          :class:`InvalidInputError` is raised by ``__init__``).
-        * If ``None`` (default) in multi-animal mode, the importer attempts to
-          auto-detect, **per video**, a frame where all ``len(id_lst)`` animals are
-          simultaneously tracked (via
-          :func:`simba.utils.lookups.find_best_multi_animal_assignment_frame`). The UI
-          opens on that frame, so the user only needs to press "c" once. If no such
-          frame exists (or detection fails for any reason) the UI falls back to frame 0
-          as in earlier SimBA versions.
-        * Single-animal imports ignore this argument entirely.
-
-    :references:
-        .. [1] Ye, Shaokai, Anastasiia Filippova, Jessy Lauer, et al. “SuperAnimal Pretrained Pose Estimation Models for Behavioral Analysis.” Nature Communications 15, no. 1 (2024): 5165. https://doi.org/10.1038/s41467-024-48792-2.
-        .. [2] mwmathis lab on huggingface - `https://huggingface.co/mwmathis/ <https://huggingface.co/mwmathis/>`_.
-
-    :example:
-    >>> importer = SuperAnimalTopViewImporter(config_path=r"C:\troubleshooting\super_animal_import\project_folder\project_config.ini", data_folder=r'C:\troubleshooting\super_animal_import\data_files', id_lst=['Animal_1'])
-    >>> importer.run()
-
-    :example multi-animal with a known good frame:
-    >>> importer = SuperAnimalTopViewImporter(config_path=r"...\project_config.ini", data_folder=r'...\data_files', id_lst=['mouse_1', 'mouse_2', 'mouse_3', 'mouse_4', 'mouse_5'], initial_frame_no=3313)
-    >>> importer.run()
-    """
-
-    def __init__(self,
-                 config_path: Union[str, os.PathLike],
-                 data_folder: Union[str, os.PathLike],
-                 id_lst: List[str],
-                 interpolation_settings: Optional[Dict[str, str]] = None,
-                 smoothing_settings: Optional[Dict[str, Union[int, str]]] = None,
-                 initial_frame_no: Optional[int] = None):
-
-
-        ConfigReader.__init__(self, config_path=config_path, read_video_info=False)
-        PoseImporterMixin.__init__(self)
-        check_if_dir_exists(in_dir=data_folder)
-        check_valid_lst(data=id_lst, source=f'{self.__class__.__name__} id_lst', valid_dtypes=(str,), min_len=1)
-        if interpolation_settings is not None:
-            check_if_keys_exist_in_dict(data=interpolation_settings, key=['method', 'type'], name=f'{self.__class__.__name__} interpolation_settings')
-            check_str(name=f'{self.__class__.__name__} interpolation_settings type', value=interpolation_settings['type'], options=('body-parts', 'animals'))
-            check_str(name=f'{self.__class__.__name__} interpolation_settings method', value=interpolation_settings['method'], options=('linear', 'quadratic', 'nearest'))
-        if smoothing_settings is not None:
-            check_if_keys_exist_in_dict(data=smoothing_settings, key=['method', 'time_window'], name=f'{self.__class__.__name__} smoothing_settings')
-            check_str(name=f'{self.__class__.__name__} smoothing_settings method', value=smoothing_settings['method'], options=('savitzky-golay', 'gaussian'))
-            check_int(name=f'{self.__class__.__name__} smoothing_settings time_window', value=smoothing_settings['time_window'], min_value=1)
-        if initial_frame_no is not None:
-            check_int(name=f'{self.__class__.__name__} initial_frame_no', value=initial_frame_no, min_value=0)
-
-        log_event(logger_name=str(__class__.__name__), log_type=TagNames.CLASS_INIT.value, msg=self.create_log_msg_from_init_args(locals=locals()))
-        self.interpolation_settings, self.smoothing_settings = (interpolation_settings, smoothing_settings)
-        self.initial_frame_no = initial_frame_no
-        self.data_folder, self.id_lst = data_folder, id_lst
-        self.import_log_path = os.path.join(self.logs_path, f"data_import_log_{self.datetime}.csv")
-        self.video_paths = find_all_videos_in_project(videos_dir=self.video_dir, raise_error=True if len(id_lst) > 1 else False)
-        self.input_data_paths = find_files_of_filetypes_in_directory(directory=self.data_folder, extensions=['.h5'], raise_error=True)
-        self.data_and_videos_lk = self.link_video_paths_to_data_paths(data_paths=self.input_data_paths, video_paths=self.video_paths, raise_error=True if len(id_lst) > 1 else False, filename_cleaning_func=clean_superanimal_topview_filename)
-        if initial_frame_no is not None:
-            offending = []
-            for h5_path in self.input_data_paths:
-                n_frames = get_h5_frame_count(path=h5_path)
-                if n_frames is not None and initial_frame_no >= n_frames:
-                    offending.append((h5_path, n_frames))
-            if offending:
-                details = "; ".join(f'{os.path.basename(p)} has {n} frames' for p, n in offending)
-                raise InvalidInputError(
-                    msg=(f'initial_frame_no={initial_frame_no} exceeds the frame count of '
-                         f'{len(offending)} of {len(self.input_data_paths)} H5 file(s) in the data '
-                         f'folder. Valid frame indices for a given file are [0, n_frames - 1]. '
-                         f'Offending file(s): {details}.'),
-                    source=self.__class__.__name__,
-                )
-        self.check_multi_animal_status()
-        self.config.set(ConfigKey.GENERAL_SETTINGS.value, ConfigKey.ANIMAL_CNT.value, str(len(self.id_lst)))
-        with open(self.config_path, "w") as f: self.config.write(f)
-        f.close()
-        print(f"Importing {len(list(self.data_and_videos_lk.keys()))} SuperAnimal-TopView H5 file(s)...")
-
-    def _get_expected_column_names(self):
-        self.field_names, self.bp_names = [], []
-        for animal_id in self.id_lst:
-            animal_field_names = [f"{animal_id}_{s}" for s in Formats.SUPERANIMAL_TOPVIEW_BP_NAMES.value]
-            self.bp_names.extend((animal_field_names))
-            animal_field_names = [f"{s}{suffix}" for s in animal_field_names for suffix in ("_x", "_y", "_p")]
-            self.field_names.extend((animal_field_names))
-        with open(self.body_parts_path, "w") as f:
-            for name in self.bp_names:
-                f.write(name + "\n")
-        f.close()
-        ConfigReader.__init__(self, config_path=self.config_path, read_video_info=False, create_logger=False)
-        self.get_body_part_names()
-        self.animal_bp_dict = self.create_body_part_dictionary(self.multi_animal_status, self.id_lst, len(self.id_lst), self.x_cols, self.y_cols, self.p_cols, self.clr_lst)
-
-    def run(self):
-        self._get_expected_column_names()
-        for cnt, (video_name, video_data) in enumerate(self.data_and_videos_lk.items()):
-            video_timer = SimbaTimer(start=True)
-            self.add_spacer, self.frame_no, self.video_data, self.video_name = (2, 1, video_data, video_name)
-            print(f"Processing {video_name} ({cnt+1}/{len(self.input_data_paths)})...")
-            self.data_df = read_dlc_superanimal_h5(path=video_data['DATA'], col_names=self.field_names)
-            if self.animal_cnt > 1:
-                frame_to_use = self.initial_frame_no
-                if frame_to_use is None:
-                    n_bp = len(Formats.SUPERANIMAL_TOPVIEW_BP_NAMES.value)
-                    cascade = [max(1, int(round(n_bp * f))) for f in (0.75, 0.50, 0.25)] + [1]
-                    cascade = list(dict.fromkeys(cascade))
-                    matched_threshold = None
-                    for min_bp in cascade:
-                        try:
-                            candidate = find_best_multi_animal_assignment_frame(h5_path=video_data['DATA'], expected_animals=len(self.id_lst), min_bodyparts_per_animal=min_bp)
-                        except Exception as e:
-                            print(f"Auto-detection of a starting frame for {video_name} failed at min_bodyparts_per_animal={min_bp} ({type(e).__name__}: {e}); trying a lower threshold.")
-                            continue
-                        if candidate is not None:
-                            frame_to_use = candidate
-                            matched_threshold = min_bp
-                            break
-                    if frame_to_use is not None:
-                        print(f"Auto-selected starting frame {frame_to_use} for {video_name}: all {len(self.id_lst)} animals have >= {matched_threshold}/{n_bp} body-parts tracked. Press 'c' to accept and assign identities.")
-                    else:
-                        print(f"No frame in {video_name} has all {len(self.id_lst)} animals simultaneously tracked at any threshold; opening identity-assignment UI at frame 0 (use 'x' to step forward by 50 frames).")
-                self.initialize_multi_animal_ui(animal_bp_dict=self.animal_bp_dict, video_info=get_video_meta_data(video_data["VIDEO"]), data_df=self.data_df, video_path=video_data["VIDEO"], initial_frame_no=frame_to_use)
-                self.multianimal_identification()
-            else:
-                self.out_df = self.insert_multi_idx_columns(df=self.data_df.fillna(0))
-            self.save_path = os.path.join(os.path.join(self.input_csv_dir, f"{self.video_name}.{self.file_type}"))
-            self.out_df = self.out_df.replace([np.inf, -np.inf], np.nan).fillna(0)
-            self.out_df[self.out_df < 0] = 0
-            write_df(df=self.out_df, file_type=self.file_type, save_path=self.save_path, multi_idx_header=True)
-            if self.interpolation_settings is not None:
-                interpolator = Interpolate(config_path=self.config_path, data_path=self.save_path, type=self.interpolation_settings['type'], method=self.interpolation_settings['method'], multi_index_df_headers=True, copy_originals=False)
-                interpolator.run()
-            if self.smoothing_settings is not None:
-                smoother = Smoothing(config_path=self.config_path, data_path=self.save_path, time_window=self.smoothing_settings['time_window'], method=self.smoothing_settings['method'], multi_index_df_headers=True, copy_originals=False)
-                smoother.run()
-            video_timer.stop_timer()
-            stdout_success(msg=f"Video {video_name} data imported...", elapsed_time=video_timer.elapsed_time_str)
-        self.timer.stop_timer()
-        stdout_success(msg=f"All SuperAnimal-TopView H5 data files imported to {self.input_csv_dir} directory", elapsed_time=self.timer.elapsed_time_str)
-
-
-# importer = SuperAnimalTopViewImporter(config_path=r"C:\troubleshooting\super_animal_import\project_folder\project_config.ini",
-#                            data_folder=r'C:\troubleshooting\super_animal_import\data_files',
-#                            id_lst=['Animal_1'])
+import os
+from typing import Dict, List, Optional, Union
+
+import numpy as np
+
+from simba.data_processors.interpolate import Interpolate
+from simba.data_processors.smoothing import Smoothing
+from simba.mixins.config_reader import ConfigReader
+from simba.mixins.pose_importer_mixin import PoseImporterMixin
+from simba.utils.checks import (check_if_dir_exists,
+                                check_if_keys_exist_in_dict, check_int,
+                                check_str, check_valid_lst)
+from simba.utils.enums import ConfigKey, Formats, TagNames
+from simba.utils.errors import InvalidInputError
+from simba.utils.lookups import find_best_multi_animal_assignment_frame
+from simba.utils.printing import SimbaTimer, log_event, stdout_success
+from simba.utils.read_write import (clean_superanimal_topview_filename,
+                                    find_all_videos_in_project,
+                                    find_files_of_filetypes_in_directory,
+                                    get_h5_frame_count, get_video_meta_data,
+                                    read_dlc_superanimal_h5, write_df)
+
+
+class SuperAnimalTopViewImporter(PoseImporterMixin, ConfigReader):
+
+    """
+    Import SuperAnimal-TopView mouse data to SimBA
+
+    .. note::
+       For more information see the DeepLabCutModelZoo-SuperAnimal-TopViewMouse on huggingface https://huggingface.co/mwmathis/DeepLabCutModelZoo-SuperAnimal-TopViewMouse
+
+       Trackes 27 body-parts on one or more mice recorded from zenith.
+
+       Supports both DLC H5 layouts: the legacy TensorFlow backend (``df_with_missing`` /
+       ``table``) and the modern DLC 3.0+ PyTorch backend (HRNet, RTMPose), including
+       multi-animal tracked outputs ending in ``_el.h5`` / ``_full.h5``. H5 column order is
+       assumed to follow the SuperAnimal-TopView 27 body-part schema, with animals in the
+       order supplied via ``id_lst`` (positional mapping).
+
+    .. image:: _static/img/superanimal_topview.png
+       :width: 150
+       :align: center
+
+    :param config_path: path to SimBA project config file in Configparser format
+    :param str data_folder: Path to folder containing SuperAnimal data in ``.h5`` format.
+    :param List[str] id_lst: Names of animals.
+    :param Optional[Dict[str, str]] interpolation_setting: Dict defining the type and method to use to perform interpolation {'type': 'animals', 'method': 'linear'}.
+    :param Optional[Dict[str, Union[str, int]]] smoothing_settings: Dictionary defining the pose estimation smoothing method {'time_window': 500, 'method': 'gaussian'}.
+    :param Optional[int] initial_frame_no: Frame index at which to open the multi-animal
+        identity-assignment UI. Only used when ``len(id_lst) > 1``.
+
+        * If an integer is passed, it is used directly (and must be ``>= 0`` and strictly
+          less than the frame count of **every** H5 file in ``data_folder``; otherwise an
+          :class:`InvalidInputError` is raised by ``__init__``).
+        * If ``None`` (default) in multi-animal mode, the importer attempts to
+          auto-detect, **per video**, a frame where all ``len(id_lst)`` animals are
+          simultaneously tracked (via
+          :func:`simba.utils.lookups.find_best_multi_animal_assignment_frame`). The UI
+          opens on that frame, so the user only needs to press "c" once. If no such
+          frame exists (or detection fails for any reason) the UI falls back to frame 0
+          as in earlier SimBA versions.
+        * Single-animal imports ignore this argument entirely.
+
+    :references:
+        .. [1] Ye, Shaokai, Anastasiia Filippova, Jessy Lauer, et al. “SuperAnimal Pretrained Pose Estimation Models for Behavioral Analysis.” Nature Communications 15, no. 1 (2024): 5165. https://doi.org/10.1038/s41467-024-48792-2.
+        .. [2] mwmathis lab on huggingface - `https://huggingface.co/mwmathis/ <https://huggingface.co/mwmathis/>`_.
+
+    :example:
+    >>> importer = SuperAnimalTopViewImporter(config_path=r"C:\troubleshooting\super_animal_import\project_folder\project_config.ini", data_folder=r'C:\troubleshooting\super_animal_import\data_files', id_lst=['Animal_1'])
+    >>> importer.run()
+
+    :example multi-animal with a known good frame:
+    >>> importer = SuperAnimalTopViewImporter(config_path=r"...\project_config.ini", data_folder=r'...\data_files', id_lst=['mouse_1', 'mouse_2', 'mouse_3', 'mouse_4', 'mouse_5'], initial_frame_no=3313)
+    >>> importer.run()
+    """
+
+    def __init__(self,
+                 config_path: Union[str, os.PathLike],
+                 data_folder: Union[str, os.PathLike],
+                 id_lst: List[str],
+                 interpolation_settings: Optional[Dict[str, str]] = None,
+                 smoothing_settings: Optional[Dict[str, Union[int, str]]] = None,
+                 initial_frame_no: Optional[int] = None):
+
+
+        ConfigReader.__init__(self, config_path=config_path, read_video_info=False)
+        PoseImporterMixin.__init__(self)
+        check_if_dir_exists(in_dir=data_folder)
+        check_valid_lst(data=id_lst, source=f'{self.__class__.__name__} id_lst', valid_dtypes=(str,), min_len=1)
+        if interpolation_settings is not None:
+            check_if_keys_exist_in_dict(data=interpolation_settings, key=['method', 'type'], name=f'{self.__class__.__name__} interpolation_settings')
+            check_str(name=f'{self.__class__.__name__} interpolation_settings type', value=interpolation_settings['type'], options=('body-parts', 'animals'))
+            check_str(name=f'{self.__class__.__name__} interpolation_settings method', value=interpolation_settings['method'], options=('linear', 'quadratic', 'nearest'))
+        if smoothing_settings is not None:
+            check_if_keys_exist_in_dict(data=smoothing_settings, key=['method', 'time_window'], name=f'{self.__class__.__name__} smoothing_settings')
+            check_str(name=f'{self.__class__.__name__} smoothing_settings method', value=smoothing_settings['method'], options=('savitzky-golay', 'gaussian'))
+            check_int(name=f'{self.__class__.__name__} smoothing_settings time_window', value=smoothing_settings['time_window'], min_value=1)
+        if initial_frame_no is not None:
+            check_int(name=f'{self.__class__.__name__} initial_frame_no', value=initial_frame_no, min_value=0)
+
+        log_event(logger_name=str(__class__.__name__), log_type=TagNames.CLASS_INIT.value, msg=self.create_log_msg_from_init_args(locals=locals()))
+        self.interpolation_settings, self.smoothing_settings = (interpolation_settings, smoothing_settings)
+        self.initial_frame_no = initial_frame_no
+        self.data_folder, self.id_lst = data_folder, id_lst
+        self.import_log_path = os.path.join(self.logs_path, f"data_import_log_{self.datetime}.csv")
+        self.video_paths = find_all_videos_in_project(videos_dir=self.video_dir, raise_error=True if len(id_lst) > 1 else False)
+        self.input_data_paths = find_files_of_filetypes_in_directory(directory=self.data_folder, extensions=['.h5'], raise_error=True)
+        self.data_and_videos_lk = self.link_video_paths_to_data_paths(data_paths=self.input_data_paths, video_paths=self.video_paths, raise_error=True if len(id_lst) > 1 else False, filename_cleaning_func=clean_superanimal_topview_filename)
+        if initial_frame_no is not None:
+            offending = []
+            for h5_path in self.input_data_paths:
+                n_frames = get_h5_frame_count(path=h5_path)
+                if n_frames is not None and initial_frame_no >= n_frames:
+                    offending.append((h5_path, n_frames))
+            if offending:
+                details = "; ".join(f'{os.path.basename(p)} has {n} frames' for p, n in offending)
+                raise InvalidInputError(
+                    msg=(f'initial_frame_no={initial_frame_no} exceeds the frame count of '
+                         f'{len(offending)} of {len(self.input_data_paths)} H5 file(s) in the data '
+                         f'folder. Valid frame indices for a given file are [0, n_frames - 1]. '
+                         f'Offending file(s): {details}.'),
+                    source=self.__class__.__name__,
+                )
+        self.check_multi_animal_status()
+        self.config.set(ConfigKey.GENERAL_SETTINGS.value, ConfigKey.ANIMAL_CNT.value, str(len(self.id_lst)))
+        with open(self.config_path, "w") as f: self.config.write(f)
+        f.close()
+        print(f"Importing {len(list(self.data_and_videos_lk.keys()))} SuperAnimal-TopView H5 file(s)...")
+
+    def _get_expected_column_names(self):
+        self.field_names, self.bp_names = [], []
+        for animal_id in self.id_lst:
+            animal_field_names = [f"{animal_id}_{s}" for s in Formats.SUPERANIMAL_TOPVIEW_BP_NAMES.value]
+            self.bp_names.extend((animal_field_names))
+            animal_field_names = [f"{s}{suffix}" for s in animal_field_names for suffix in ("_x", "_y", "_p")]
+            self.field_names.extend((animal_field_names))
+        with open(self.body_parts_path, "w") as f:
+            for name in self.bp_names:
+                f.write(name + "\n")
+        f.close()
+        ConfigReader.__init__(self, config_path=self.config_path, read_video_info=False, create_logger=False)
+        self.get_body_part_names()
+        self.animal_bp_dict = self.create_body_part_dictionary(self.multi_animal_status, self.id_lst, len(self.id_lst), self.x_cols, self.y_cols, self.p_cols, self.clr_lst)
+
+    def run(self):
+        self._get_expected_column_names()
+        for cnt, (video_name, video_data) in enumerate(self.data_and_videos_lk.items()):
+            video_timer = SimbaTimer(start=True)
+            self.add_spacer, self.frame_no, self.video_data, self.video_name = (2, 1, video_data, video_name)
+            print(f"Processing {video_name} ({cnt+1}/{len(self.input_data_paths)})...")
+            self.data_df = read_dlc_superanimal_h5(path=video_data['DATA'], col_names=self.field_names)
+            if self.animal_cnt > 1:
+                frame_to_use = self.initial_frame_no
+                if frame_to_use is None:
+                    n_bp = len(Formats.SUPERANIMAL_TOPVIEW_BP_NAMES.value)
+                    cascade = [max(1, int(round(n_bp * f))) for f in (0.75, 0.50, 0.25)] + [1]
+                    cascade = list(dict.fromkeys(cascade))
+                    matched_threshold = None
+                    for min_bp in cascade:
+                        try:
+                            candidate = find_best_multi_animal_assignment_frame(h5_path=video_data['DATA'], expected_animals=len(self.id_lst), min_bodyparts_per_animal=min_bp)
+                        except Exception as e:
+                            print(f"Auto-detection of a starting frame for {video_name} failed at min_bodyparts_per_animal={min_bp} ({type(e).__name__}: {e}); trying a lower threshold.")
+                            continue
+                        if candidate is not None:
+                            frame_to_use = candidate
+                            matched_threshold = min_bp
+                            break
+                    if frame_to_use is not None:
+                        print(f"Auto-selected starting frame {frame_to_use} for {video_name}: all {len(self.id_lst)} animals have >= {matched_threshold}/{n_bp} body-parts tracked. Press 'c' to accept and assign identities.")
+                    else:
+                        print(f"No frame in {video_name} has all {len(self.id_lst)} animals simultaneously tracked at any threshold; opening identity-assignment UI at frame 0 (use 'x' to step forward by 50 frames).")
+                self.initialize_multi_animal_ui(animal_bp_dict=self.animal_bp_dict, video_info=get_video_meta_data(video_data["VIDEO"]), data_df=self.data_df, video_path=video_data["VIDEO"], initial_frame_no=frame_to_use)
+                self.multianimal_identification()
+            else:
+                self.out_df = self.insert_multi_idx_columns(df=self.data_df.fillna(0))
+            self.save_path = os.path.join(os.path.join(self.input_csv_dir, f"{self.video_name}.{self.file_type}"))
+            self.out_df = self.out_df.replace([np.inf, -np.inf], np.nan).fillna(0)
+            self.out_df[self.out_df < 0] = 0
+            write_df(df=self.out_df, file_type=self.file_type, save_path=self.save_path, multi_idx_header=True)
+            if self.interpolation_settings is not None:
+                interpolator = Interpolate(config_path=self.config_path, data_path=self.save_path, type=self.interpolation_settings['type'], method=self.interpolation_settings['method'], multi_index_df_headers=True, copy_originals=False)
+                interpolator.run()
+            if self.smoothing_settings is not None:
+                smoother = Smoothing(config_path=self.config_path, data_path=self.save_path, time_window=self.smoothing_settings['time_window'], method=self.smoothing_settings['method'], multi_index_df_headers=True, copy_originals=False)
+                smoother.run()
+            video_timer.stop_timer()
+            stdout_success(msg=f"Video {video_name} data imported...", elapsed_time=video_timer.elapsed_time_str)
+        self.timer.stop_timer()
+        stdout_success(msg=f"All SuperAnimal-TopView H5 data files imported to {self.input_csv_dir} directory", elapsed_time=self.timer.elapsed_time_str)
+
+
+# importer = SuperAnimalTopViewImporter(config_path=r"C:\troubleshooting\super_animal_import\project_folder\project_config.ini",
+#                            data_folder=r'C:\troubleshooting\super_animal_import\data_files',
+#                            id_lst=['Animal_1'])
 # importer.run()

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/simba/roi_tools/ROI_directing_analyzer.py

@@ -192,7 +192,6 @@ class DirectingROIAnalyzer(ConfigReader,
             video_timer = SimbaTimer(start=True)
             stdout_information(msg=f"Analyzing ROI directionality in video {self.video_name}...")
             data_df = read_df(file_path=file_path, file_type=self.file_type)
-            data_df.columns = [x.lower() for x in data_df.columns]
             video_roi_dict, shape_names = slice_roi_dict_for_video(data=self.roi_dict, video_name=self.video_name)
             if len(shape_names) == 0:
                 stdout_warning(msg=f'Skipping video {self.video_name}: No ROIs drawn for video {self.video_name} detected.')

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/simba/roi_tools/ROI_feature_analyzer.py

@@ -93,7 +93,7 @@ class ROIFeatureCreator(ConfigReader, FeatureExtractionMixin):
             self.bp_lk[cnt] = [animal, bp, [f'{bp}_{"x"}', f'{bp}_{"y"}', f'{bp}_{"p"}']]
         if self.roi_directing_viable:
             print("Directionality calculations are VIABLE.")
-            self.directing_analyzer = DirectingROIAnalyzer(config_path=config_path, data_path=self.data_paths)
+            self.directing_analyzer = DirectingROIAnalyzer(config_path=config_path, data_path=data_path)
             self.directing_analyzer.run()
             self.dr = self.directing_analyzer.results_df
         else:

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/simba/utils/data.py

@@ -3,20 +3,24 @@ __author__ = "Simon Nilsson; sronilsson@gmail.com"
 import ast
 import configparser
 import gc
+import importlib.util
+import inspect
 import io
 import os
 import platform
 import subprocess
+import sys
 from copy import deepcopy
 from datetime import datetime
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
 import h5py
+import matplotlib
 import numpy as np
 import pandas as pd
+from matplotlib import cm
 from numba import jit, njit, prange, typed
-from pylab import *
 from scipy import stats
 from scipy.interpolate import interp1d
 from scipy.signal import savgol_filter

{simba_uw_tf_dev-5.3.4 → simba_uw_tf_dev-5.3.6}/simba_uw_tf_dev.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: simba-uw-tf-dev
-Version: 5.3.4
+Version: 5.3.6
 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