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sgoldenlab · Apr 25, 2024 · 3bd67e1 · 3bd67e1
1 parent 501f4a5
commit 3bd67e1
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Showing 23 changed files with 3,429 additions and 1,102 deletions.
diff --git a/simba/data_processors/directing_other_animals_calculator.py b/simba/data_processors/directing_other_animals_calculator.py
diff --git a/simba/mixins/config_reader.py b/simba/mixins/config_reader.py
@@ -225,8 +225,12 @@ def read_roi_data(self) -> None:
                 source=self.__class__.__name__,
             )
         else:
-            self.rectangles_df = pd.read_hdf(self.roi_coordinates_path, key=Keys.ROI_RECTANGLES.value)
-            if ("Center_X" in self.rectangles_df.columns) and (self.rectangles_df["Center_X"].isnull().values.any()):
+            self.rectangles_df = pd.read_hdf(
+                self.roi_coordinates_path, key=Keys.ROI_RECTANGLES.value
+            )
+            if ("Center_X" in self.rectangles_df.columns) and (
+                self.rectangles_df["Center_X"].isnull().values.any()
+            ):
                 for idx, row in self.rectangles_df.iterrows():
                     self.rectangles_df.loc[idx]["Center_X"] = row["Tags"]["Center tag"][
                         0
@@ -264,11 +268,23 @@ def read_roi_data(self) -> None:
             self.roi_types_names_lst = list(self.roi_types_names_lst)
             for shape_type, shape_data in self.roi_dict.items():
                 if shape_type == Keys.ROI_CIRCLES.value:
-                    self.roi_dict[Keys.ROI_CIRCLES.value]["Center_X"] = self.roi_dict[ Keys.ROI_CIRCLES.value]["centerX"]
-                    self.roi_dict[Keys.ROI_CIRCLES.value]["Center_Y"] = self.roi_dict[Keys.ROI_CIRCLES.value]["centerY"]
+                    self.roi_dict[Keys.ROI_CIRCLES.value]["Center_X"] = self.roi_dict[
+                        Keys.ROI_CIRCLES.value
+                    ]["centerX"]
+                    self.roi_dict[Keys.ROI_CIRCLES.value]["Center_Y"] = self.roi_dict[
+                        Keys.ROI_CIRCLES.value
+                    ]["centerY"]
                 elif shape_type == Keys.ROI_RECTANGLES.value:
-                    self.roi_dict[Keys.ROI_RECTANGLES.value]["Center_X"] = self.roi_dict[Keys.ROI_RECTANGLES.value]["Bottom_right_X"] - (self.roi_dict[Keys.ROI_RECTANGLES.value]["width"] / 2)
-                    self.roi_dict[Keys.ROI_RECTANGLES.value]["Center_Y"] = self.roi_dict[Keys.ROI_RECTANGLES.value]["Bottom_right_Y"] - (self.roi_dict[Keys.ROI_RECTANGLES.value]["height"] / 2)
+                    self.roi_dict[Keys.ROI_RECTANGLES.value][
+                        "Center_X"
+                    ] = self.roi_dict[Keys.ROI_RECTANGLES.value]["Bottom_right_X"] - (
+                        self.roi_dict[Keys.ROI_RECTANGLES.value]["width"] / 2
+                    )
+                    self.roi_dict[Keys.ROI_RECTANGLES.value][
+                        "Center_Y"
+                    ] = self.roi_dict[Keys.ROI_RECTANGLES.value]["Bottom_right_Y"] - (
+                        self.roi_dict[Keys.ROI_RECTANGLES.value]["height"] / 2
+                    )
                 elif shape_type == Keys.ROI_POLYGONS.value:
                     try:
                         self.roi_dict[Keys.ROI_POLYGONS.value]["Center_X"] = (

diff --git a/simba/mixins/feature_extraction_supplement_mixin.py b/simba/mixins/feature_extraction_supplement_mixin.py
@@ -740,14 +740,31 @@ def distance_and_velocity(
         >>> sum_movement, avg_velocity = FeatureExtractionSupplemental.distance_and_velocity(x=x, fps=10, pixels_per_mm=10, centimeters=True)
         """
 
-        check_valid_array(data=x, source=FeatureExtractionSupplemental.distance_and_velocity.__name__, accepted_ndims=(1, 2), accepted_dtypes=(np.float32, np.float64, np.int32, np.int64, int, float))
-        check_float(name=f"{FeatureExtractionSupplemental.distance_and_velocity.__name__} fps",value=fps,min_value=1)
-        check_float(name=f"{FeatureExtractionSupplemental.distance_and_velocity.__name__} pixels_per_mm",value=pixels_per_mm,min_value=10e-6)
+        check_valid_array(
+            data=x,
+            source=FeatureExtractionSupplemental.distance_and_velocity.__name__,
+            accepted_ndims=(1, 2),
+            accepted_dtypes=(np.float32, np.float64, np.int32, np.int64, int, float),
+        )
+        check_float(
+            name=f"{FeatureExtractionSupplemental.distance_and_velocity.__name__} fps",
+            value=fps,
+            min_value=1,
+        )
+        check_float(
+            name=f"{FeatureExtractionSupplemental.distance_and_velocity.__name__} pixels_per_mm",
+            value=pixels_per_mm,
+            min_value=10e-6,
+        )
         if x.ndim == 2:
-            check_valid_array(data=x, source=FeatureExtractionSupplemental.distance_and_velocity.__name__, accepted_axis_1_shape=(2,))
+            check_valid_array(
+                data=x,
+                source=FeatureExtractionSupplemental.distance_and_velocity.__name__,
+                accepted_axis_1_shape=(2,),
+            )
             t = np.full((x.shape[0]), 0.0)
             for i in range(1, x.shape[0]):
-                t[i] = np.linalg.norm(x[i] - x[i-1])
+                t[i] = np.linalg.norm(x[i] - x[i - 1])
             x = np.copy(t) / pixels_per_mm
         movement = np.sum(x) / pixels_per_mm
         v = []
@@ -761,11 +778,12 @@ def distance_and_velocity(
 
 
 x = np.random.randint(0, 100, (100, 2))
-FeatureExtractionSupplemental.distance_and_velocity(x=x, fps=10, pixels_per_mm=10, centimeters=True)
+FeatureExtractionSupplemental.distance_and_velocity(
+    x=x, fps=10, pixels_per_mm=10, centimeters=True
+)
 # # sum_movement, avg_velocity =
 
 
-
 # df = read_df(file_path='/Users/simon/Desktop/envs/simba/troubleshooting/two_black_animals_14bp/project_folder/csv/targets_inserted/Together_1.csv', file_type='csv')
 #
 # df = pd.DataFrame(np.random.randint(0, 2, (100, 2)), columns=['Attack', 'Sniffing'])