[timeline] renaming stuff

allow deletion of entries

FixTracks.py

@@ -32,7 +32,7 @@ def set_logging(loglevel):
     logging.basicConfig(level=loglevel, force=True)
 
 def main(args):
-    set_logging(logging.DEBUG)
+    set_logging(args.loglevel)
     if platform.system() == "Windows":
         # from PySide6.QtWinExtras import QtWin
         myappid = f"{info.organization_name}.{info.application_version}"
@@ -75,6 +75,6 @@ if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="FixTracks. Tools for fixing animal tracking")
     parser.add_argument("-ll", "--loglevel", type=str, default="INFO", help=f"The log level that should be used. Valid levels are {[str(k) for k in levels.keys()]}")
     args = parser.parse_args()
-    args.loglevel = levels[args.loglevel if args.loglevel.lower() in levels else "info"]
+    args.loglevel = levels[args.loglevel.lower() if args.loglevel.lower() in levels else "info"]
 
     main(args)

fixtracks/utils/trackingdata.py

@@ -7,21 +7,16 @@ from PySide6.QtCore import QObject
 
 
 class TrackingData(QObject):
-    def __init__(self, parent=None):
+    def __init__(self, datadict, parent=None):
         super().__init__(parent)
-        self._data = None
-        self._columns = []
-        self._start = 0
-        self._stop = 0
-        self._indices = None
-        self._selection_column = None
-        self._user_selections = None
-
-    def setData(self, datadict):
         assert isinstance(datadict, dict)
         self._data = datadict
+        if "userlabeled" not in self._data.keys():
             self._data["userlabeled"] = np.zeros_like(self["frame"], dtype=bool)
         self._columns = [k for k in self._data.keys()]
+        self._indices = self["index"]
+        self._selection = np.asarray([])
+        self._selected_ids = None
 
     @property
     def data(self):
@@ -42,60 +37,77 @@ class TrackingData(QObject):
     def numDetections(self):
         return self._data["track"].shape[0]
 
-    @property
+    def _find(self, ids):
-    def selectionRange(self):
+        ids = np.sort(ids)
-        return self._start, self._stop
+        indexes = np.ones_like(ids, dtype=int) * -1
-
+        j = 0
-    @property
+        for idx, i in enumerate(self._indices):
-    def selectionRangeColumn(self):
+            if i == ids[j]:
-        return self._selection_column
+                indexes[j] = idx
+                j += 1
+            if j == len(indexes):
+                break
+        indexes = indexes[indexes >= 0]
+        return indexes
 
     @property
     def selectionIndices(self):
-        return self._indices
+        return self._selection
 
     def setSelectionRange(self, col, start, stop):
         logging.debug("Trackingdata: set selection range based on column %s to %.2f - %.2f", col, start, stop)
-        self._start = start
+        col_indices = np.where((self[col] >= start) & (self[col] < stop))[0]
-        self._stop = stop
+        self._selection = self._indices[col_indices]
-        self._selection_column = col
-        col_indices = np.where((self._data[col] >= self._start) & (self._data[col] < self._stop))[0]
-        self._indices = self["index"][col_indices]
         if len(col_indices) < 1:
             logging.warning("TrackingData: Selection range is empty!")
 
     def selectedData(self, col:str):
         if col not in self.columns:
             logging.error("TrackingData:selectedData: Invalid column name! %s", col)
-        return self[col][self._indices]
+        return self[col][self._selection]
 
-    def setUserSelection(self, ids):
+    def setSelection(self, ids):
         """
-        Set the user selections. That is, e.g. when the user selected a number of detection ids (aka the index of the original data frame entries).
+        Set the selection based on the detection 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)
+        self._selection = self._find(ids)
+        self._selected_ids = ids
 
-    def assignUserSelection(self, track_id:int, userFlag:bool=True)-> None:
+    def setTrack(self, track_id:int, setUserLabeled:bool=True)-> None:
         """Assign a new track_id to the user-selected detections
 
         Parameters
         ----------
         track_id : int
             The new track id for the user-selected detections
-        userFlag : bool
+        setUserLabeled : bool
-            Should the "userlabeled" state of the detections be set to True or False? 
+            Should the "userlabeled" state of the detections be set to True? Otherwise they will be left untouched.
         """
         self["track"][self._user_selections] = track_id
-        self.setAssignmentStatus(userFlag)
+        if setUserLabeled:
+            self.setUserLabeledStatus(True, True)
 
-    def setAssignmentStatus(self, isTrue: bool):
+    def setUserLabeledStatus(self, new_status: bool, selection=True):
-        logging.debug("TrackingData:Re-setting assignment status of user selected data to %s", str(isTrue))
+        """Sets the status of the "userlabeled" column to a given value (True|False). This can done for ALL data in one go, or only for the UserSelection.
-        self["userlabeled"][self._user_selections] = isTrue
+
+        Parameters
+        ----------
+        new_status : bool
+            The new status, TRUE, if the detections are confirmed by the user (human observer) and can be treated as correct
+        selection : bool, optional
+            Whether the new status should be set for the selection only (True, default) ore not (False)
+        """
+        logging.debug("TrackingData: (Re-)setting assignment status of %s to %s", 
+                      "user selected data" if selection else " ALL", str(new_status))
+        if selection:
+            self["userlabeled"][self._selection] = new_status
+        else:
+            self["userlabeled"][:] = new_status
 
     def revertAssignmentStatus(self):
         logging.debug("TrackingData:Un-setting assignment status of all data!")
@@ -105,14 +117,15 @@ class TrackingData(QObject):
         logging.debug("TrackingData: Reverting all track assignments!")
         self["track"][:] = -1
 
-    def deleteDetections(self):
+    def deleteDetections(self, ids=None):
-        # from IPython import embed
+        if ids is not None:
-        # if self._user_selections is not None:
+            del_indices = self._find(ids)
-        #     ids = self._user_selections
+        else:
-        #     for c in self.columns:
+            del_indices = self._indices
-        #     pass
+        for c in self._columns:
-        # embed()
+            self._data[c] = np.delete(self._data[c], del_indices, axis=0)
-        pass
+        self._indices = self["index"]
+        self._selected_ids = np.setdiff1d(self._selected_ids, del_indices)
 
     def assignTracks(self, tracks:np.ndarray):
         """assigns the given tracks to the user-selected detections. If the sizes of 
@@ -154,11 +167,11 @@ class TrackingData(QObject):
                         and M is number of keypoints
         """
         if selection:
-            if len(self._indices) < 1:
+            if len(self._selection) < 1:
                 logging.info("TrackingData.coordinates returns empty array, not detections in range!")
                 return np.ndarray([])
-            return np.stack(self._data["keypoints"][self._indices]).astype(np.float32)
+            return np.stack(self["keypoints"][self._selection]).astype(np.float32)
-        return np.stack(self._data["keypoints"]).astype(np.float32)
+        return np.stack(self["keypoints"]).astype(np.float32)
 
     def keypointScores(self, selection=False):
         """
@@ -171,11 +184,11 @@ class TrackingData(QObject):
             with N the number of detections and M the number of keypoints.
         """
         if selection:
-            if len(self._indices) < 1:
+            if len(self._selection) < 1:
                 logging.info("TrackingData.scores returns empty array, not detections in range!")
-                return np.ndarray([])
+                return None
-            return np.stack(self._data["keypoint_score"][self._indices]).astype(np.float32)
+            return np.stack(self["keypoint_score"][self._selection]).astype(np.float32)
-        return np.stack(self._data["keypoint_score"]).astype(np.float32)
+        return np.stack(self["keypoint_score"]).astype(np.float32)
 
     def centerOfGravity(self, selection=False, threshold=0.8, nodes=[0,1,2]):
         """
@@ -195,12 +208,17 @@ class TrackingData(QObject):
         A NumPy array of shape (N, 2) containing the center of gravity for each detection.
         """
         scores = self.keypointScores(selection)
+        if scores is None:
+            return None
         scores[scores < threshold] = 0.0
         scores[:, np.setdiff1d(np.arange(scores.shape[1]), nodes)] = 0.0
-        weighted_coords = self.coordinates(selection=selection) * scores[:, :, np.newaxis]
+        weighted_coords = self.coordinates(selection) * 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
+        cogs = np.zeros((weighted_coords.shape[0], 2))
+        val_ids = np.where(sum_scores > 0.0)[0]
+        cogs[val_ids] = np.sum(weighted_coords[val_ids], axis=1) / sum_scores[val_ids]
+        return cogs
 
     def animalLength(self, bodyaxis=None):
         if bodyaxis is None:
@@ -288,22 +306,26 @@ def main():
             plt.plot([positions[si, 0], positions[ei, 0]],
                      [positions[si, 1], positions[ei, 1]], color="tab:green")
 
-    datafile = PACKAGE_ROOT / "data/merged_small.pkl"
+    datafile = PACKAGE_ROOT / "data/merged_small_tracked.pkl"
     with open(datafile, "rb") as f:
         df = pickle.load(f)
 
+    data = TrackingData(as_dict(df))
+    test_indices = [32, 88, 99, 2593]
+    data.deleteDetections(test_indices)
     
-    data = TrackingData()
+    embed()
-    data.setData(as_dict(df))
+    data.deleteDetections(test_indices)
+    data.setSelection(test_indices)
     all_cogs = data.centerOfGravity()
     orientations = data.orientation()
     lengths = data.animalLength()
     frames = data["frame"]
     tracks = data["track"]
     bendedness = data.bendedness()
+    indices = data._indices
     # positions = data.coordinates()[[160388, 160389]]
 
-    embed()
     tracks = data["track"]
     cogs = all_cogs[tracks==1]
     all_dists = neighborDistances(cogs, 2, False)

fixtracks/widgets/detectiontimeline.py

@@ -311,8 +311,8 @@ def main():
         df = pickle.load(f)
     data = TrackingData()
     data.setData(as_dict(df))
-    data.setUserSelection(np.arange(0,100, 1))
+    data.setSelection(np.arange(0,100, 1))
-    data.setAssignmentStatus(True)
+    data.setUserLabeledStatus(True)
     start_x = 0.1
     app = QApplication([])
     window = QWidget()

fixtracks/widgets/tracks.py

@@ -31,7 +31,7 @@ class FixTracks(QWidget):
         self._currentWindowPos = 0  # in frames
         self._currentWindowWidth = 0  # in frames
         self._maxframes = 0
-        self._data = TrackingData()
+        self._data = None
 
         self._detectionView = DetectionView()
         self._detectionView.signals.itemsSelected.connect(self.on_detectionsSelected)
@@ -204,7 +204,7 @@ class FixTracks(QWidget):
         self._progress_bar.setRange(0, 100)
         self._progress_bar.setValue(0)
         if state and self._reader is not None:
-            self._data.setData(self._reader.asdict)
+            self._data = TrackingData(self._reader.asdict)
             self._saveBtn.setEnabled(True)
             self._currentWindowPos = 0
             self._currentWindowWidth = self._windowspinner.value()
@@ -247,30 +247,30 @@ class FixTracks(QWidget):
 
     def on_assignOne(self):
         logging.debug("Assigning user selection to track One")
-        self._data.assignUserSelection(self.trackone_id)
+        self._data.setTrack(self.trackone_id)
         self._timeline.update()
         self.update()
 
     def on_assignTwo(self):
         logging.debug("Assigning user selection to track Two")
-        self._data.assignUserSelection(self.tracktwo_id)
+        self._data.setTrack(self.tracktwo_id)
         self._timeline.update()
         self.update()
 
     def on_assignOther(self):
         logging.debug("Assigning user selection to track Other")
-        self._data.assignUserSelection(self.trackother_id, False)
+        self._data.setTrack(self.trackother_id, False)
         self._timeline.update()
         self.update()
 
     def on_setUserFlag(self):
-        self._data.setAssignmentStatus(True)
+        self._data.setUserLabeledStatus(True)
         self._timeline.update()
         self.update()
 
     def on_unsetUserFlag(self):
         logging.debug("Tracks:unsetUserFlag")
-        self._data.setAssignmentStatus(False)
+        self._data.setUserLabeledStatus(False)
         self._timeline.update()
         self.update()
 
@@ -320,7 +320,7 @@ class FixTracks(QWidget):
             ids[i] = d.data(DetectionData.ID.value)
             frames[i] = d.data(DetectionData.FRAME.value)
             coordinates[i, :, :] = d.data(DetectionData.COORDINATES.value)
-        self._data.setUserSelection(ids)
+        self._data.setSelection(ids)
         self._controls_widget.setSelectedTracks(tracks)
         self._skeleton.clear()
         self._skeleton.addSkeletons(coordinates, ids, frames, tracks, QBrush(QColor(10, 255, 65, 255)))