[trackingdata] improvements, some docstrings

fixtracks/utils/trackingdata.py

@@ -1,10 +1,10 @@
 import pickle
 import logging
 import numpy as np
+import pandas as pd
 
 from PySide6.QtCore import QObject
 
-
 class TrackingData(QObject):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -62,12 +62,39 @@ class TrackingData(QObject):
         return self._data[col][self._indices]
 
     def setUserSelection(self, ids):
+        """
+        Set the user selections. That is, e.g. when the user selected a number of ids.
+        Parameters
+        ----------
+        ids : array-like
+            An array-like object containing the IDs to be set as user selections. 
+            The IDs will be converted to integers.
+        """
         self._user_selections = ids.astype(int)
 
-    def assignUserSelection(self, track_id):
+    def assignUserSelection(self, track_id:int)-> None:
+        """Assign a new track_id to the user-selected detections
+
+        Parameters
+        ----------
+        track_id : int
+            The new track id for the user-selected detections
+        """
         self._data["track"][self._user_selections] = track_id
 
     def assignTracks(self, tracks):
+        """assignTracks _summary_
+
+        Parameters
+        ----------
+        tracks : _type_
+            _description_
+
+        Returns
+        -------
+        _type_
+            _description_
+        """
         if len(tracks) != self.numDetections:
             logging.error("DataController: Size of passed tracks does not match data!")
             return
@@ -87,8 +114,54 @@ class TrackingData(QObject):
         return self._data["keypoints"][0].shape[0]
 
     def coordinates(self):
-        return  np.stack(self._data["keypoints"]).astype(np.float32)
+        """
+        Returns the coordinates of all keypoints as a NumPy array.
+
+        Returns:
+            np.ndarray: A NumPy array of shape (N, M, 2) where N is the number of detections, 
+                        and M is number of keypoints
+        """
+        return np.stack(self._data["keypoints"]).astype(np.float32)
+
+    def keypointScores(self):
+        """
+        Returns the keypoint scores as a NumPy array of type float32.
+
+        Returns
+        -------
+        numpy.ndarray
+            A NumPy array of type float32 containing the keypoint scores of the shape (N, M) 
+            with N the number of detections and M the number of keypoints.
+        """
+        return np.stack(self._data["keypoint_score"]).astype(np.float32)
 
+    def centerOfGravity(self, threshold=0.8):
+        """
+        Calculate the center of gravity of keypoints weighted by their scores. Ignores keypoints that have a score
+        less than threshold.
+
+        Parameters:
+        -----------
+        threshold: float 
+        keypoints with a score less than threshold are ignored
+
+        Returns:
+        --------
+        np.ndarray: 
+        A NumPy array of shape (N, 2) containing the center of gravity for each detection.
+        """
+        scores = self.keypointScores()
+        scores[scores < threshold] = 0.0
+        weighted_coords = self.coordinates() * scores[:, :, np.newaxis]
+        sum_scores = np.sum(scores, axis=1, keepdims=True)
+        center_of_gravity = np.sum(weighted_coords, axis=1) / sum_scores
+        return center_of_gravity
+
+    def __getitem__(self, key):
+        return self._data[key]
+
+    # def __setitem__(self, key, value):
+    #     self._data[key] = value
         """ 
          self._data.setSelectionRange("index", 0, self._data.numDetections)
         self._data.assignTracks(tracks)
@@ -99,22 +172,65 @@ class TrackingData(QObject):
 def main():
     import pandas as pd
     from IPython import embed
+    import matplotlib.pyplot as plt
     from fixtracks.info import PACKAGE_ROOT
+    from scipy.spatial.distance import cdist
 
     def as_dict(df:pd.DataFrame):
         d = {c: df[c].values for c in df.columns}
         d["index"] = df.index.values
         return d
 
+
+    def neighborDistances(x, n=5, symmetric=True):
+        pad_shape = list(x.shape)
+        pad_shape[0] = 5
+        pad = np.zeros(pad_shape)
+        if symmetric:
+            padded_x = np.vstack((pad, x, pad))
+        else:
+            padded_x = np.vstack((pad, x))
+        dists = np.zeros((padded_x.shape[0], 2*n))
+        count = 0
+        r = range(-n, n+1) if symmetric else range(-n, 0)
+        for i in r:
+            if i == 0:
+                continue
+            shifted_x = np.roll(padded_x, i)
+            dists[:, count] = np.sqrt(np.sum((padded_x - shifted_x)**2, axis=1))
+            count += 1
+        return dists
+
     datafile = PACKAGE_ROOT / "data/merged_small.pkl"
     with open(datafile, "rb") as f:
         df = pickle.load(f)
 
     data = TrackingData()
     data.setData(as_dict(df))
+    all_cogs = data.centerOfGravity()
+    tracks = data["track"]
+    cogs = all_cogs[tracks==1]
+    all_dists = neighborDistances(cogs, 2, False)
+    plt.hist(all_dists[1:, 0], bins=1000)
+    print(np.percentile(all_dists[1:, 0], 99))
+    print(np.percentile(all_dists[1:, 0], 1))
+    plt.gca().set_xscale("log")
+    plt.gca().set_yscale("log")
+    # plt.hist(all_dists[1:, 1], bins=100)
+    plt.show()
+    # def compute_neighbor_distances(cogs, window=10):
+    #     distances = []
+    #     for i in range(len(cogs)):
+    #         start = max(0, i - window)
+    #         stop = min(len(cogs), i + window + 1)
+    #         neighbors = cogs[start:stop]
+    #         dists = cdist([cogs[i]], neighbors)[0]
+    #         distances.append(dists)
+    #     return distances
+    # print("estimating neighorhood distances")
+    # neighbor_distances = compute_neighbor_distances(cogs)
     embed()
 
-    pass
 
 
 if __name__ == "__main__":