uml

setup.py

@@ -17,7 +17,7 @@
 
 setuptools.setup(
     name="Simba-UW-tf-dev",
-    version="1.88.4",
+    version="1.88.5",
     author="Simon Nilsson, Jia Jie Choong, Sophia Hwang",
     author_email="sronilsson@gmail.com",
     description="Toolkit for computer classification of behaviors in experimental animals",

simba/SimBA.py

@@ -543,9 +543,11 @@ def __init__(self, config_path: str):
             processmovementdupLabel,
             text="SPONTANEOUS ALTERNATION",
             fg="navy",
-            command=lambda: SpontaneousAlternationPopUp(config_path=self.config_path),
+            command=lambda: threading.Thread(target=SpontaneousAlternationPopUp(config_path=self.config_path)).start(),
         )
 
+
+
         # organize
         processmovementdupLabel.grid(row=0, column=3, sticky=NW)
         analyze_distances_velocity_btn.grid(row=0, sticky=NW)

simba/data_processors/spontaneous_alternation_calculator.py

@@ -1,15 +1,15 @@
 import os
 import warnings
 from typing import List, Optional, Union
+import argparse
 
 import numpy as np
 import pandas as pd
 
 warnings.filterwarnings("ignore")
 
 from simba.mixins.config_reader import ConfigReader
-from simba.mixins.feature_extraction_supplement_mixin import \
-    FeatureExtractionSupplemental
+from simba.mixins.feature_extraction_supplement_mixin import FeatureExtractionSupplemental
 from simba.mixins.geometry_mixin import GeometryMixin
 from simba.utils.checks import (check_file_exist_and_readable, check_float,
                                 check_if_dir_exists, check_int, check_str,
@@ -20,6 +20,8 @@
 from simba.utils.read_write import (get_file_name_info_in_directory,
                                     get_fn_ext, read_df)
 from simba.utils.warnings import NoFileFoundWarning
+import platform
+import multiprocessing
 
 TAIL_END = "tail_end"
 
@@ -46,7 +48,7 @@ class SpontaneousAlternationCalculator(ConfigReader):
     :param Optional[float] threshold: Value between 0.0 and 1.0. Body-parts with detection probabilities below this value will be (if possible) filtered when constructing the animal geometry.
     :param Optional[int] buffer: Millimeters area for which the animal geometry should be increased in size. Useful if the animal geometry does not fully cover the animal.
     :param Optional[bool] detailed_data: If True, saves an additional CSV for each analyzed video with detailed data pertaining each error type and alternation sequence.
-    :param Optional[Union[str, os.PathLike]] data_path: Directory of path to the file sto be analyzed. If None, then ``project_folder/outlier_corrected_movement_location`` directory.
+    :param Optional[Union[str, os.PathLike]] data_path: Directory of path to the file to be analyzed. If None, then ``project_folder/outlier_corrected_movement_location`` directory.
 
     :example:
     >>> x = SpontaneousAlternationCalculator(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/spontenous_alternation/project_folder/project_config.ini', arm_names=['A', 'B', 'C'], center_name='Center', threshold=0.0, animal_area=100, buffer=2, detailed_data=True)
@@ -119,11 +121,7 @@ def __init__(
                 msg=f"{len(files_w_missing_rois)} file(s) at {data_path} are missing ROI definitions and will be skipped when performing spontaneous alternation calculations: {files_w_missing_rois}",
                 source=__class__.__name__,
             )
-        check_video_has_rois(
-            roi_dict=self.roi_dict,
-            video_names=self.files_w_rois,
-            roi_names=arm_names + [center_name],
-        )
+        check_video_has_rois(roi_dict=self.roi_dict, video_names=self.files_w_rois, roi_names=arm_names + [center_name],)
         self.file_paths = list(
             {file_paths[k] for k in self.files_w_rois if k in file_paths}
         )
@@ -148,9 +146,7 @@ def run(self):
             _, self.video_name, _ = get_fn_ext(filepath=file_path)
             _, px_per_mm, fps = self.read_video_info(video_name=self.video_name)
 
-            self.data_df = read_df(file_path=file_path, file_type=self.file_type).head(
-                5000
-            )
+            self.data_df = read_df(file_path=file_path, file_type=self.file_type)
             bp_df = self.data_df[
                 [
                     x
@@ -197,9 +193,8 @@ def run(self):
                 frames_in_roi = np.zeros(pct_overlap.shape)
                 frames_in_roi[np.argwhere(pct_overlap >= self.animal_area)] = 1
                 self.roi_df[geo_name] = frames_in_roi
-            self.video_results = FeatureExtractionSupplemental.spontaneous_alternations(
-                data=self.roi_df, arm_names=self.arm_names, center_name=self.center_name
-            )
+
+            self.video_results = FeatureExtractionSupplemental.spontaneous_alternations(data=self.roi_df, arm_names=self.arm_names, center_name=self.center_name)
             self.results[self.video_name] = self.video_results
 
     def save(self):
@@ -267,17 +262,47 @@ def save(self):
                 msg=f"Detailed spontaneous alternation data for {len(list(self.results.keys()))} video(s) saved at {save_dir}"
             )
 
+# if __name__ == "__main__":
+#     parser = argparse.ArgumentParser(description='SimBA Custom Feature Extractor')
+#     parser.add_argument('--config_path', type=str, help='SimBA project config path')
+#     parser.add_argument('--arm_names', nargs='+', help='List of ROI arm names')
+#     parser.add_argument('--center_name', type=str, help='Name of ROI center')
+#     parser.add_argument('--animal_area', type=int, default=80, help='Size of animal geometry required for scored entry/exit')
+#     parser.add_argument('--threshold', type=float, default=0.0, help='Body-part threshold')
+#     parser.add_argument('--buffer', type=int, default=2, help='Added buffer to animal geometry')
+#     parser.add_argument('--verbose', type=bool, default=False, help='If process print outs')
+#     parser.add_argument('--detailed_data', default=False, type=bool, help='If to create additional detailed data')
+#     parser.add_argument('--data_path', type=bool, default=None, help='Path to directory or file.')
+#     args = parser.parse_args()
+#     x = SpontaneousAlternationCalculator(config_path=args.config_path,
+#                                          arm_names=args.arm_names,
+#                                          center_name=args.center_name,
+#                                          threshold=args.threshold,
+#                                          animal_area=args.animal_area,
+#                                          buffer=args.buffer,
+#                                          verbose=args.verbose,
+#                                          detailed_data=args.detailed_data,
+#                                          data_path=args.data_path)
+#     x.run()
+#     x.save()
+
 
-# x = SpontaneousAlternationCalculator(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/spontenous_alternation/project_folder/project_config.ini',
-#                                      arm_names=['A', 'B', 'C'],
-#                                      center_name='Center',
-#                                      threshold=0.0,
-#                                      animal_area=100,
-#                                      buffer=2,
-#                                      detailed_data=True)
+# config_path = '/Users/simon/Desktop/envs/simba/troubleshooting/spontenous_alternation/project_folder/project_config.ini'
+# arm_names = ['A', 'B', 'C']
+# center_name = 'Center'
+# threshold = 0.0
+# animal_area = 60
+# buffer = 2
+# verbose = True
 #
+# x = SpontaneousAlternationCalculator(config_path=config_path,
+#                                      arm_names=arm_names,
+#                                      center_name=center_name,
+#                                      threshold=threshold,
+#                                      animal_area=animal_area,
+#                                      buffer=buffer,
+#                                      verbose=verbose)
 # x.run()
 # x.save()
 
-# spontaneous_alternations(config_path='/Users/simon/Desktop/envs/simba/troubleshooting/spontenous_alternation/project_folder/project_config.ini',
-#                          roi_names=['A', 'B', 'C'], body_part='Center')
+

simba/mixins/feature_extraction_supplement_mixin.py

@@ -472,18 +472,8 @@ def spontaneous_alternations(
         >>> spontanous_alternations = FeatureExtractionSupplemental.spontaneous_alternations(data=df, shape_names=['left', 'top', 'right', 'bottom'])
         """
 
-        def get_sliding_alternation(
-            data: np.ndarray,
-        ) -> Tuple[
-            Union[
-                Dict[int, List[int]], Dict[int, List[int]], Dict[Tuple[int], List[int]]
-            ]
-        ]:
-            stride, same_arm_return_cnt, alternate_arm_return_cnt = (
-                len(arm_names) - 1,
-                0,
-                0,
-            )
+        def get_sliding_alternation(data: np.ndarray) -> Tuple[Union[Dict[int, List[int]], Dict[int, List[int]], Dict[Tuple[int], List[int]]]]:
+            stride, same_arm_return_cnt, alternate_arm_return_cnt = (len(arm_names) - 1, 0, 0)
             alternation_cnt = 0
             alternations, same_arm_returns, alternate_arm_returns = {}, {}, {}
             for i in list(itertools.permutations(arm_names)):
@@ -571,6 +561,7 @@ def get_sliding_alternation(
             same_arm_return_cnt,
             alternation_cnt,
         ) = get_sliding_alternation(data=arm_entry_sequence)
+
         pct_alternation = alternation_cnt / (
             arm_entry_sequence.shape[0] - (len(arm_names) - 1)
         )