[tracks] delegate functionality to widgets, cleanup

FixTracks.py

@@ -0,0 +1,80 @@
+"""
+pyside6-rcc resources.qrc -o resources.py
+
+"""
+import sys
+import logging
+import argparse
+import platform
+
+from PySide6.QtWidgets import QApplication
+from PySide6.QtCore import QSettings
+from PySide6.QtGui import QIcon, QPalette
+
+from fixtracks import info, mainwindow
+
+logging.basicConfig(level=logging.INFO, force=True)
+
+
+def is_dark_mode(app: QApplication) -> bool:
+    palette = app.palette()
+    # Check the brightness of the window text and base colors
+    text_color = palette.color(QPalette.ColorRole.WindowText)
+    base_color = palette.color(QPalette.ColorRole.Base)
+
+    # Calculate brightness (0 for dark, 255 for bright)
+    def brightness(color):
+        return (color.red() * 299 + color.green() * 587 + color.blue() * 114) // 1000
+
+    return brightness(base_color) < brightness(text_color)
+
+def set_logging(loglevel):
+    logging.basicConfig(level=loglevel, force=True)
+
+def main(args):
+    set_logging(logging.DEBUG)
+    if platform.system() == "Windows":
+        # from PySide6.QtWinExtras import QtWin
+        myappid = f"{info.organization_name}.{info.application_version}"
+        # QtWin.setCurrentProcessExplicitAppUserModelID(myappid)
+    settings = QSettings()
+    width = int(settings.value("app/width", 1024))
+    height = int(settings.value("app/height", 768))
+    x = int(settings.value("app/pos_x", 100))
+    y = int(settings.value("app/pos_y", 100))
+
+    app = QApplication(sys.argv)
+    app.setApplicationName(info.application_name)
+    app.setApplicationVersion(str(info.application_version))
+    app.setOrganizationDomain(info.organization_name)
+
+    # if platform.system() == 'Linux':
+    # icn = QIcon(":/icons/app_icon")
+    # app.setWindowIcon(icn)
+    # Create a Qt widget, which will be our window.
+    window = mainwindow.MainWindow(is_dark_mode(app))
+    window.setGeometry(100, 100, 1024, 768)
+    window.setWindowTitle("FixTracks")
+    window.setMinimumWidth(1024)
+    window.setMinimumHeight(768)
+    window.resize(width, height)
+    window.move(x, y)
+    window.show()
+
+    # Start the event loop.
+    app.exec()
+    pos = window.pos()
+    settings.setValue("app/width", window.width())
+    settings.setValue("app/height", window.height())
+    settings.setValue("app/pos_x", pos.x())
+    settings.setValue("app/pos_y", pos.y())
+
+
+if __name__ == "__main__":
+    levels = {"critical": logging.CRITICAL, "error": logging.ERROR, "warning":logging.WARNING, "info":logging.INFO, "debug":logging.DEBUG}
+    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"]
+
+    main(args)

fixtracks/mainwindow.py

@@ -144,8 +144,8 @@ class MainWindow(QMainWindow):
         about.show()
 
     def on_help(self, s):
-        help = HelpDialog(self)
+        help_dlg = HelpDialog(self)
-        help.show()
+        help_dlg.show()
 
     # @Slot(None)
     def exit_request(self):

fixtracks/utils/enums.py

@@ -1,7 +1,29 @@
 from enum import Enum
 
+from PySide6.QtGui import QColor
+
 class DetectionData(Enum):
     ID = 0
     FRAME = 1
     COORDINATES = 2
     TRACK_ID = 3
+
+class Tracks(Enum):
+    TRACKONE = 1
+    TRACKTWO = 2
+    UNASSIGNED = -1
+
+    def toColor(self):
+        track_colors = {
+            Tracks.TRACKONE: QColor.fromString("orange"),
+            Tracks.TRACKTWO: QColor.fromString("green"),
+            Tracks.UNASSIGNED: QColor.fromString("red")
+        }
+        return track_colors.get(self, QColor(128, 128, 128))  # Default to black if not found
+
+    @staticmethod
+    def fromValue(value):
+        for track in Tracks:
+            if track.value == value:
+                return track
+        return Tracks.UNASSIGNED

fixtracks/utils/trackingdata.py

@@ -5,6 +5,7 @@ import pandas as pd
 
 from PySide6.QtCore import QObject
 
+
 class TrackingData(QObject):
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -58,10 +59,15 @@ class TrackingData(QObject):
         self._start = start
         self._stop = stop
         self._selection_column = col
-        self._indices = np.where((self._data[col] >= self._start) & (self._data[col] < self._stop))[0]
+        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):
+    def selectedData(self, col:str):
-        return self._data[col][self._indices]
+        if col not in self.columns:
+            logging.error("TrackingData:selectedData: Invalid column name! %s", col)
+        return self[col][self._indices]
 
     def setUserSelection(self, ids):
         """
@@ -84,14 +90,20 @@ class TrackingData(QObject):
         userFlag : bool
             Should the "userlabeled" state of the detections be set to True or False? 
         """
-        self._data["track"][self._user_selections] = track_id
+        self["track"][self._user_selections] = track_id
         self.setAssignmentStatus(userFlag)
 
     def setAssignmentStatus(self, isTrue: bool):
-        self._data["userlabeled"][self._user_selections] = isTrue
+        logging.debug("TrackingData:Re-setting assignment status of user selected data to %s", str(isTrue))
+        self["userlabeled"][self._user_selections] = isTrue
 
     def revertAssignmentStatus(self):
-        self._data["userlabeled"][:] = False
+        logging.debug("TrackingData:Un-setting assignment status of all data!")
+        self["userlabeled"][:] = False
+
+    def revertTrackAssignments(self):
+        logging.debug("TrackingData: Reverting all track assignments!")
+        self["track"][:] = -1
 
     def deleteDetections(self):
         # from IPython import embed
@@ -102,21 +114,21 @@ class TrackingData(QObject):
         # embed()
         pass
 
-    def assignTracks(self, tracks):
+    def assignTracks(self, tracks:np.ndarray):
-        """assignTracks _summary_
+        """assigns the given tracks to the user-selected detections. If the sizes of 
+        provided tracks and the user selection do not match and error is logged and the tracks are not set.
 
         Parameters
         ----------
-        tracks : _type_
+        tracks : np.ndarray
-            _description_
+            The track information.
 
         Returns
         -------
-        _type_
+        None
-            _description_
         """
         if len(tracks) != self.numDetections:
-            logging.error("DataController: Size of passed tracks does not match data!")
+            logging.error("Trackingdata: Size of passed tracks does not match data!")
             return
         self._data["track"] = tracks
 
@@ -142,11 +154,13 @@ class TrackingData(QObject):
                         and M is number of keypoints
         """
         if selection:
-            return np.stack(self._data["keypoints"][self._start:self._stop, :, :]).astype(np.float32)
+            if len(self._indices) < 1:
-        else:
+                logging.info("TrackingData.coordinates returns empty array, not detections in range!")
-            return np.stack(self._data["keypoints"]).astype(np.float32)
+                return np.ndarray([])
+            return np.stack(self._data["keypoints"][self._indices]).astype(np.float32)
+        return np.stack(self._data["keypoints"]).astype(np.float32)
 
-    def keypointScores(self):
+    def keypointScores(self, selection=False):
         """
         Returns the keypoint scores as a NumPy array of type float32.
 
@@ -156,9 +170,14 @@ class TrackingData(QObject):
             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.
         """ 
+        if selection:
+            if len(self._indices) < 1:
+                logging.info("TrackingData.scores returns empty array, not detections in range!")
+                return np.ndarray([])
+            return np.stack(self._data["keypoint_score"][self._indices]).astype(np.float32)
         return np.stack(self._data["keypoint_score"]).astype(np.float32)
 
-    def centerOfGravity(self, threshold=0.8):
+    def centerOfGravity(self, selection=False, threshold=0.8, nodes=[0,1,2]):
         """
         Calculate the center of gravity of keypoints weighted by their scores. Ignores keypoints that have a score
         less than threshold.
@@ -166,16 +185,19 @@ class TrackingData(QObject):
         Parameters:
         -----------
         threshold: float 
-        keypoints with a score less than threshold are ignored
+            nodes with a score less than threshold are ignored
+        nodes: list
+            nodes/keypoints to consider for estimation. Defaults to [0,1,2]
 
         Returns:
         --------
         np.ndarray: 
         A NumPy array of shape (N, 2) containing the center of gravity for each detection.
         """
-        scores = self.keypointScores()
+        scores = self.keypointScores(selection)
         scores[scores < threshold] = 0.0
-        weighted_coords = self.coordinates() * scores[:, :, np.newaxis]
+        scores[:, np.setdiff1d(np.arange(scores.shape[1]), nodes)] = 0.0
+        weighted_coords = self.coordinates(selection=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
@@ -279,19 +301,19 @@ def main():
     frames = data["frame"]
     tracks = data["track"]
     bendedness = data.bendedness()
-    positions = data.coordinates()[[160388, 160389]]
+    # positions = data.coordinates()[[160388, 160389]]
 
     embed()
     tracks = data["track"]
     cogs = all_cogs[tracks==1]
     all_dists = neighborDistances(cogs, 2, False)
-    plt.hist(all_dists[1:, 0], bins=1000)
+    # plt.hist(all_dists[1:, 0], bins=1000)
-    print(np.percentile(all_dists[1:, 0], 99))
+    # print(np.percentile(all_dists[1:, 0], 99))
-    print(np.percentile(all_dists[1:, 0], 1))
+    # print(np.percentile(all_dists[1:, 0], 1))
-    plt.gca().set_xscale("log")
+    # plt.gca().set_xscale("log")
-    plt.gca().set_yscale("log")
+    # plt.gca().set_yscale("log")
     # plt.hist(all_dists[1:, 1], bins=100)
-    plt.show()
+    # plt.show()
     # def compute_neighbor_distances(cogs, window=10):
     #     distances = []
     #     for i in range(len(cogs)):
@@ -303,9 +325,6 @@ def main():
     #     return distances
     # print("estimating neighorhood distances")
     # neighbor_distances = compute_neighbor_distances(cogs)
-    embed()
-
-
 
 if __name__ == "__main__":
     main()

fixtracks/widgets/classifier.py

@@ -34,6 +34,9 @@ class ConsitencyDataLoader(QRunnable):
 
     @Slot()
     def run(self):
+        if self.data is None:
+            logging.error("ConsistencyTracker.DataLoader failed. No Data!")
+            return
         self.positions = self.data.centerOfGravity()
         self.orientations = self.data.orientation()
         self.lengths = self.data.animalLength()
@@ -464,9 +467,6 @@ class ConsistencyClassifier(QWidget):
         self.setEnabled(False)
         self._progressbar.setRange(0,0)
         self._data = data
-        self._dataworker = ConsitencyDataLoader(self._data)
-        self._dataworker.signals.stopped.connect(self.data_processed)
-        self.threadpool.start(self._dataworker)
 
     @Slot()
     def data_processed(self):
@@ -482,6 +482,7 @@ class ConsistencyClassifier(QWidget):
             self._frames = self._dataworker.frames
             self._tracks = self._dataworker.tracks
             self._maxframes = np.max(self._frames)
+            # FIXME the following line causes an error when there are no detections in the range
             min_frame = max([self._frames[self._tracks == 1][0], self._frames[self._tracks == 2][0]]) + 1
             self._maxframeslabel.setText(str(self._maxframes))
             self._startframe_spinner.setMinimum(min_frame)
@@ -525,7 +526,9 @@ class ConsistencyClassifier(QWidget):
         self.start()
 
     def refresh(self):
-        self.setData(self._data)
+        self._dataworker = ConsitencyDataLoader(self._data)
+        self._dataworker.signals.stopped.connect(self.data_processed)
+        self.threadpool.start(self._dataworker)
 
     def worker_progress(self, progress, processed, errors):
         self._progressbar.setValue(progress)
@@ -556,7 +559,8 @@ class ClassifierWidget(QTabWidget):
         self._consistency_tracker = ConsistencyClassifier()
         self.addTab(self._size_classifier, SizeClassifier.name)
         self.addTab(self._consistency_tracker, ConsistencyClassifier.name)
-        self.tabBarClicked.connect(self.update)
+        # self.tabBarClicked.connect(self.update)
+        self.currentChanged.connect(self.tabChanged)
         self._size_classifier.apply.connect(self._on_applySizeClassifier)
         self._consistency_tracker.apply.connect(self._on_applyConsistencyTracker)
 
@@ -576,12 +580,21 @@ class ClassifierWidget(QTabWidget):
     def consistency_tracker(self):
         return self._consistency_tracker
 
+    @Slot()
+    def tabChanged(self):
+        if isinstance(self.currentWidget(), ConsistencyClassifier):
+            self.consistency_tracker.refresh()
+
     @Slot()
     def update(self):
-        self.consistency_tracker.setData(self._data)
+        if isinstance(self.currentWidget(), ConsistencyClassifier):
+            self.consistency_tracker.refresh()
 
     def setData(self, data:TrackingData):
         self._data = data
+        self.consistency_tracker.setData(data)
+        coordinates = self._data.coordinates()
+        self._size_classifier.setCoordinates(coordinates)
 
 def as_dict(df):
     d = {c: df[c].values for c in df.columns}

fixtracks/widgets/detectiontimeline.py

@@ -1,13 +1,14 @@
 import logging
 import numpy as np
-import pandas as pd
+
 from PySide6.QtCore import Qt
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QSizePolicy, QLabel
-from PySide6.QtWidgets import QGraphicsView, QGraphicsScene, QGraphicsItem, QGraphicsRectItem, QGraphicsLineItem
+from PySide6.QtWidgets import QGraphicsView, QGraphicsScene, QGraphicsItem, QGraphicsRectItem, QGraphicsLineItem, QGraphicsEllipseItem
 from PySide6.QtCore import Qt, QRectF, QRectF
 from PySide6.QtGui import QBrush, QColor, QPen, QFont
 
 from fixtracks.utils.signals import DetectionTimelineSignals
+from fixtracks.utils.trackingdata import TrackingData
 
 
 class Window(QGraphicsRectItem):
@@ -40,24 +41,23 @@ class Window(QGraphicsRectItem):
         self.signals.windowMoved.emit()
 
     def setWindow(self, newx:float, newwidth:float):
-        def setWindow(self, newx: float, newwidth: float):
+        """
-            """
+        Update the window to the specified range.
-            Update the window to the specified range.
+        Parameters
-            Parameters
+        ----------
-            ----------
+        newx : float
-            newx : float
+            The new x-coordinate of the window.
-                The new x-coordinate of the window.
+        newwidth : float
-            newwidth : float
+            The new width of the window.
-                The new width of the window.
+        Returns
-            Returns
+        -------
-            -------
+        None
-            None
+        """
-            """
-
         logging.debug("timeline.window: update window to range %.5f to %.5f", newx, newwidth)
         self._width = newwidth
         r = self.rect()
         self.setRect(newx, r.y(), self._width, r.height())
+        self.update()
         self.signals.windowMoved.emit()
 
     def mouseMoveEvent(self, event):
@@ -86,40 +86,44 @@ class Window(QGraphicsRectItem):
 class DetectionTimeline(QWidget):
     signals = DetectionTimelineSignals()
 
-    def __init__(self, detectiondata=None, trackone_id=1, tracktwo_id=2, parent=None):
+    def __init__(self, trackone_id=1, tracktwo_id=2, parent=None):
         super().__init__(parent)
         self._trackone = trackone_id
         self._tracktwo = tracktwo_id
-        self._data = detectiondata
+        self._data = None
         self._rangeStart = 0.0
         self._rangeStop = 0.005
         self._total_width = 2000
-        self._stepCount = 300
+        self._stepCount = 1000
         self._bg_brush = QBrush(QColor(20, 20, 20, 255))
         transparent_brush = QBrush(QColor(200, 200, 200, 64))
         self._white_pen = QPen(QColor.fromString("white"))
         self._white_pen.setWidth(0.1)
         self._t1_pen = QPen(QColor.fromString("orange"))
-        self._t1_pen.setWidth(2)
+        self._t1_pen.setWidth(1)
         self._t2_pen = QPen(QColor(0, 255, 0, 255))
-        self._t2_pen.setWidth(2)
+        self._t2_pen.setWidth(1)
         self._other_pen = QPen(QColor.fromString("red"))
-        self._other_pen.setWidth(2)
+        self._other_pen.setWidth(1)
-        axis_pen = QPen(QColor.fromString("white"))
+        window_pen = QPen(QColor.fromString("white"))
-        axis_pen.setWidth(2)
+        window_pen.setWidth(2)
+        self._user_brush = QBrush(QColor.fromString("white"))
+        user_pen = QPen(QColor.fromString("white"))
+        user_pen.setWidth(2)
+
         font = QFont()
         font.setPointSize(15)
-        font.setBold(False)
+        font.setBold(True)
 
-        self._window = Window(0, 0, 100, 60, axis_pen, transparent_brush)
+        self._window = Window(0, 0, 100, 60, window_pen, transparent_brush)
         self._window.signals.windowMoved.connect(self.on_windowMoved)
 
-        self._scene = QGraphicsScene(QRectF(0, 0, self._total_width, 65.))
+        self._scene = QGraphicsScene(QRectF(0, 0, self._total_width, 85.))
         self._scene.setBackgroundBrush(self._bg_brush)
         self._scene.addItem(self._window)
 
         self._view = QGraphicsView()
-        # self._view.setRenderHints(QPainter.RenderHint.Antialiasing | QPainter.RenderHint.SmoothPixmapTransform);
+        # self._view.setRenderHints(QPainter.RenderHint.Antialiasing | QPainter.RenderHint.SmoothPixmapTransform)
         self._view.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
         self._view.setScene(self._scene)
         self._view.fitInView(self._scene.sceneRect(), aspectRadioMode=Qt.AspectRatioMode.KeepAspectRatio)
@@ -136,6 +140,10 @@ class DetectionTimeline(QWidget):
         other_label.setFont(font)
         other_label.setDefaultTextColor(self._other_pen.color())
         other_label.setPos(200, 50)
+        user_label = self._scene.addText("user-labeled", font)
+        user_label.setFont(font)
+        user_label.setDefaultTextColor(user_pen.color())
+        user_label.setPos(350, 50)
 
         self._position_label = QLabel("")
         f = self._position_label.font()
@@ -146,51 +154,48 @@ class DetectionTimeline(QWidget):
         layout.addWidget(self._view)
         layout.addWidget(self._position_label, Qt.AlignmentFlag.AlignRight)
         self.setLayout(layout)
-
-        if self._data is not None:
-            self.draw_coverage()
         # self.setMaximumHeight(100)
         # self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Fixed)
 
-    def setDetectionData(self, data):
+    def clear(self):
-        self._data = data
         for i in self._scene.items():
-            if isinstance(i, QGraphicsLineItem):
+            if isinstance(i, (QGraphicsLineItem, QGraphicsEllipseItem)):
                 self._scene.removeItem(i)
+
+    def setData(self, data:TrackingData):
+        logging.debug("Timeline: setData!")
+        self._data = data
+        self.update()
+
+    def update(self):
+        self.clear()
         self.draw_coverage()
 
     def draw_coverage(self):
-        # FIXME this must be disentangled. timeline should not have to deal with two different ways of data storage
+        logging.debug("Timeline: drawCoverage!")
-        if isinstance(self._data, pd.DataFrame):
+        if isinstance(self._data, TrackingData):
-            maxframe = np.max(self._data.frame.values)
-
-            bins = np.linspace(0, maxframe, self._stepCount)
-            pos = np.linspace(0, self._scene.width(), self._stepCount)
-            track1_frames = self._data.frame.values[self._data.track == self._trackone]
-            track2_frames = self._data.frame.values[self._data.track == self._tracktwo]
-            other_frames = self._data.frame.values[(self._data.track != self._trackone) &
-                                                   (self._data.track != self._tracktwo)]
-        elif isinstance(self._data, dict):
             maxframe = np.max(self._data["frame"])
             bins = np.linspace(0, maxframe, self._stepCount)
-            pos = np.linspace(0, self._scene.width(), self._stepCount)
+            pos = np.linspace(0, self._scene.width(), self._stepCount)  # of the vertical dashes is this correct?
             track1_frames = self._data["frame"][self._data["track"] == self._trackone]
             track2_frames = self._data["frame"][self._data["track"] == self._tracktwo]
             other_frames = self._data["frame"][(self._data["track"] != self._trackone) &
                                                (self._data["track"] != self._tracktwo)]
+            userlabeled = self._data["frame"][self._data["userlabeled"]]
         else:
+            print("Data is not trackingdata")
             return
         t1_coverage, _ = np.histogram(track1_frames, bins=bins)
-        t1_coverage = t1_coverage > 0
         t2_coverage, _ = np.histogram(track2_frames, bins=bins)
-        t2_coverage = t2_coverage > 0
         other_coverage, _ = np.histogram(other_frames, bins=bins)
-        other_coverage = other_coverage > 0
+        labeled_coverage, _ = np.histogram(userlabeled, bins=bins)
 
-        for i in range(len(t1_coverage)-1):
+        for i in range(len(bins)-1):
             if t1_coverage[i]: self._scene.addLine(pos[i], 0, pos[i], 15., pen=self._t1_pen)
             if t2_coverage[i]: self._scene.addLine(pos[i], 17, pos[i], 32., pen=self._t2_pen)
             if other_coverage[i]: self._scene.addLine(pos[i], 34, pos[i], 49., pen=self._other_pen)
+            if other_coverage[i]: self._scene.addLine(pos[i], 34, pos[i], 49., pen=self._other_pen)
+            if labeled_coverage[i]: self._scene.addEllipse(pos[i]-2, 52, 4, 4, brush=self._user_brush)
 
     def updatePositionLabel(self):
         start = np.round(self._rangeStart * 100, 4)
@@ -207,6 +212,7 @@ class DetectionTimeline(QWidget):
 
     def fit_scene_to_view(self):
         """Scale the image to fit the QGraphicsView."""
+        logging.debug("Timeline: fit scene to view")
         self._view.fitInView(self._scene.sceneRect(), Qt.KeepAspectRatio)
 
     def resizeEvent(self, event):
@@ -289,6 +295,11 @@ def main():
         view.setWindowPos(0.0)
         print(view.windowBounds())
 
+    def as_dict(df):
+        d = {c: df[c].values for c in df.columns}
+        d["index"] = df.index.values
+        return d
+
     import pickle
     import numpy as np
     from PySide6.QtWidgets import QApplication, QPushButton, QHBoxLayout
@@ -298,13 +309,18 @@ def main():
     datafile = PACKAGE_ROOT / "data/merged_small.pkl"
     with open(datafile, "rb") as f:
         df = pickle.load(f)
-
+    data = TrackingData()
+    data.setData(as_dict(df))
+    data.setUserSelection(np.arange(0,100, 1))
+    data.setAssignmentStatus(True)
     start_x = 0.1
     app = QApplication([])
     window = QWidget()
     window.setMinimumSize(200, 75)
 
-    view = DetectionTimeline(df)
+    view = DetectionTimeline()
+    view.setData(data)
+
     fwdBtn = QPushButton(">>")
     fwdBtn.clicked.connect(lambda: fwd(0.5))
     zeroBtn = QPushButton("0->|")

fixtracks/widgets/detectionview.py

@@ -3,12 +3,12 @@ import numpy as np
 
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QSizePolicy, QGraphicsView, QGraphicsScene, QGraphicsEllipseItem, QGraphicsRectItem
 from PySide6.QtCore import Qt, QPointF, QRectF, QPointF
-from PySide6.QtGui import QPixmap, QBrush, QColor, QImage
+from PySide6.QtGui import QPixmap, QBrush, QColor, QImage, QPen
 
 from fixtracks.info import PACKAGE_ROOT
 from fixtracks.utils.signals import DetectionSignals, DetectionViewSignals, DetectionSceneSignals
-from ..utils.enums import DetectionData
+from fixtracks.utils.enums import DetectionData, Tracks
-
+from fixtracks.utils.trackingdata import TrackingData
 
 class Detection(QGraphicsEllipseItem):
     signals = DetectionSignals()
@@ -79,6 +79,7 @@ class DetectionView(QWidget):
     def __init__(self, parent=None):
         super().__init__(parent)
         self._img = None
+        self._data = None
         self._pixmapitem = None
         self._scene = DetectionScene()
         # self.setRenderHint(QGraphicsView.RenderFlag.Ren Antialiasing)
@@ -90,7 +91,6 @@ class DetectionView(QWidget):
         self._minZoom = 0.1
         self._maxZoom = 10
         self._currentZoom = 1.0
-
         lyt = QVBoxLayout()
         lyt.addWidget(self._view)
         self.setLayout(lyt)
@@ -116,6 +116,9 @@ class DetectionView(QWidget):
         self._view.setScene(self._scene)
         self._view.fitInView(self._scene.sceneRect(), aspectRadioMode=Qt.AspectRatioMode.KeepAspectRatio)
 
+    def setData(self, data:TrackingData):
+        self._data = data
+
     def clearDetections(self):
         items = self._scene.items()
         if items is not None:
@@ -124,23 +127,34 @@ class DetectionView(QWidget):
                     self._scene.removeItem(it)
                     del it
 
-    def addDetections(self, coordinates:np.array, track_ids:np.array, detection_ids:np.array, frames: np.array,
+    def updateDetections(self, keypoint=-1):
-                      keypoint:int, brush:QBrush):
+        self.clearDetections()
+        if self._data is None:
+            return
+        frames = self._data.selectedData("frame")
+        tracks = self._data.selectedData("track")
+        coordinates = self._data.coordinates(selection=True)
+        centercoordinates = self._data.centerOfGravity(selection=True)
+        userlabeled = self._data.selectedData("userlabeled")
+        indices = self._data.selectedData("index")
         image_rect = self._pixmapitem.boundingRect() if self._pixmapitem is not None else QRectF(0,0,0,0)
-        num_detections = coordinates.shape[0]
+
-        for i in range(num_detections):
+        for i, idx in enumerate(indices):
-            x = coordinates[i, keypoint, 0]
+            t = tracks[i]
-            y = coordinates[i, keypoint, 1]
+            c = Tracks.fromValue(t).toColor()
-            c = brush.color()
+            if keypoint >= 0:
-            c.setAlpha(int(i * 255 / num_detections))
+                x = coordinates[i, keypoint, 0]
-            brush.setColor(c)
+                y = coordinates[i, keypoint, 1]
-            item = Detection(image_rect.left() + x, image_rect.top() + y, 20, 20, brush=brush)
+            else:
-            item.setData(DetectionData.TRACK_ID.value, track_ids[i])
+                x = centercoordinates[i, 0]
-            item.setData(DetectionData.ID.value, detection_ids[i])
+                y = centercoordinates[i, 1]
+
+            item = Detection(image_rect.left() + x, image_rect.top() + y, 20, 20, brush=QBrush(c))
+            item.setData(DetectionData.TRACK_ID.value, tracks[i])
+            item.setData(DetectionData.ID.value, idx)
             item.setData(DetectionData.COORDINATES.value, coordinates[i, :, :])
             item.setData(DetectionData.FRAME.value, frames[i])
             item = self._scene.addItem(item)
-        # logging.debug("DetectionView: Number of items in scene: %i", len(self._scene.items()))
 
     def fit_image_to_view(self):
         """Scale the image to fit the QGraphicsView."""
@@ -159,7 +173,7 @@ class DetectionView(QWidget):
 def main():
     def items_selected(items):
         print("items selected")
-
+    # FIXME The following code will no longer work...
     import pickle
     import numpy as np
     from IPython import embed

fixtracks/widgets/selection_control.py

@@ -117,6 +117,7 @@ class SelectionControls(QWidget):
         deleteBtn.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
         deleteBtn.setStyleSheet(pushBtnStyle("red"))
         deleteBtn.setToolTip(f"DANGERZONE! Delete current selection of detections!")
+        deleteBtn.setEnabled(False)
         deleteBtn.clicked.connect(self.on_Delete)
 
         revertBtn = QPushButton("revert assignments")

fixtracks/widgets/tracks.py

@@ -2,8 +2,8 @@ import logging
 import numpy as np
 import pandas as pd
 
-from PySide6.QtCore import Qt, QThreadPool, Signal, QSize, QObject
+from PySide6.QtCore import Qt, QThreadPool, Signal
-from PySide6.QtGui import QImage, QBrush, QColor, QFont
+from PySide6.QtGui import QImage, QBrush, QColor
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QHBoxLayout, QLabel, QPushButton, QSizePolicy, QComboBox
 from PySide6.QtWidgets import QSpinBox, QSpacerItem, QProgressBar, QSplitter, QGridLayout, QFileDialog, QGridLayout
 
@@ -28,15 +28,11 @@ class FixTracks(QWidget):
         self._threadpool = QThreadPool()
         self._reader = None
         self._image = None
-        self._clear_detections = True
         self._currentWindowPos = 0  # in frames
         self._currentWindowWidth = 0  # in frames
         self._maxframes = 0
         self._data = TrackingData()
-        self._brushes = {"assigned_left": QBrush(QColor.fromString("orange")),
+
-                         "assigned_right": QBrush(QColor.fromString("green")),
-                         "unassigned": QBrush(QColor.fromString("red"))
-        }
         self._detectionView = DetectionView()
         self._detectionView.signals.itemsSelected.connect(self.on_detectionsSelected)
         self._skeleton = SkeletonWidget()
@@ -60,7 +56,7 @@ class FixTracks(QWidget):
         self._windowspinner.setSingleStep(50)
         self._windowspinner.setValue(500)
         self._windowspinner.valueChanged.connect(self.on_windowSizeChanged)
-        # self._timeline.setWindowWidth(0.01)
+
         self._keypointcombo = QComboBox()
         self._keypointcombo.currentIndexChanged.connect(self.on_keypointSelected)
 
@@ -143,7 +139,7 @@ class FixTracks(QWidget):
     def on_autoClassify(self, tracks):
         self._data.setSelectionRange("index", 0, self._data.numDetections)
         self._data.assignTracks(tracks)
-        self._timeline.setDetectionData(self._data.data)
+        self._timeline.update()
         self.update()
 
     def on_dataSelection(self):
@@ -163,40 +159,15 @@ class FixTracks(QWidget):
         self._detectionView.setImage(img)
 
     def update(self):
-        def update_detectionView(df, name):
-            if len(df) == 0:
-                return
-            keypoint = self._keypointcombo.currentIndex()
-            coords = np.stack(df["keypoints"].values).astype(np.float32)[:, :,:]
-            tracks = df["track"].values.astype(int)
-            ids = df.index.values.astype(int)
-            frames = df["frame"].values.astype(int)
-            self._detectionView.addDetections(coords, tracks, ids, frames, keypoint, self._brushes[name])
-
         start_frame = self._currentWindowPos
         stop_frame = start_frame + self._currentWindowWidth
-        self._controls_widget.setWindow(start_frame, stop_frame)
         logging.debug("Tracks:update: Updating View for detection range %i, %i frames", start_frame, stop_frame)
         self._data.setSelectionRange("frame", start_frame, stop_frame)
-        frames = self._data.selectedData("frame")
+
-        tracks = self._data.selectedData("track")
+        self._controls_widget.setWindow(start_frame, stop_frame)
-        keypoints = self._data.selectedData("keypoints")
+        kp = self._keypointcombo.currentText().lower()
-        index = self._data.selectedData("index")
+        kpi = -1 if "center" in kp else int(kp)
-
+        self._detectionView.updateDetections(kpi)
-        df = pd.DataFrame({"frame": frames,
-                           "track": tracks,
-                           "keypoints": keypoints},
-                            index=index)
-        assigned_left = df[(df.track == self.trackone_id)]
-        assigned_right = df[(df.track == self.tracktwo_id)]
-        unassigned = df[(df.track != self.trackone_id) & (df.track != self.tracktwo_id)]
-
-        if self._clear_detections:
-            self._detectionView.clearDetections()
-        update_detectionView(unassigned, "unassigned")
-        update_detectionView(assigned_left, "assigned_left")
-        update_detectionView(assigned_right, "assigned_right")
-        self._classifier.setData(self._data)
 
     @property
     def fileList(self):
@@ -223,6 +194,7 @@ class FixTracks(QWidget):
 
     def populateKeypointCombo(self, num_keypoints):
         self._keypointcombo.clear()
+        self._keypointcombo.addItem("Center")
         for i in range(num_keypoints):
             self._keypointcombo.addItem(str(i))
         self._keypointcombo.setCurrentIndex(0)
@@ -238,17 +210,13 @@ class FixTracks(QWidget):
             self._currentWindowWidth = self._windowspinner.value()
             self._maxframes = self._data.max("frame")
             self.populateKeypointCombo(self._data.numKeypoints())
-            self._timeline.setDetectionData(self._data.data)
+            self._timeline.setData(self._data)
             self._timeline.setWindow(self._currentWindowPos / self._maxframes,
                                      self._currentWindowWidth / self._maxframes)
-            coordinates = self._data.coordinates()
+            self._detectionView.setData(self._data)
-            positions = self._data.centerOfGravity()
+            self._classifier.setData(self._data)
-            tracks = self._data["track"]
-            frames = self._data["frame"]
-            self._classifier.size_classifier.setCoordinates(coordinates)
-            self._classifier.consistency_tracker.setData(self._data)
             self.update()
-            logging.info("Finished loading data: %i frames, %i detections", self._maxframes, len(positions))
+            logging.info("Finished loading data: %i frames", self._maxframes)
 
     def on_keypointSelected(self):
         self.update()
@@ -280,38 +248,43 @@ class FixTracks(QWidget):
     def on_assignOne(self):
         logging.debug("Assigning user selection to track One")
         self._data.assignUserSelection(self.trackone_id)
-        self._timeline.setDetectionData(self._data.data)
+        self._timeline.update()
         self.update()
 
     def on_assignTwo(self):
         logging.debug("Assigning user selection to track Two")
         self._data.assignUserSelection(self.tracktwo_id)
-        self._timeline.setDetectionData(self._data.data)
+        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._timeline.setDetectionData(self._data.data)
+        self._timeline.update()
         self.update()
 
     def on_setUserFlag(self):
         self._data.setAssignmentStatus(True)
+        self._timeline.update()
         self.update()
 
     def on_unsetUserFlag(self):
         logging.debug("Tracks:unsetUserFlag")
         self._data.setAssignmentStatus(False)
+        self._timeline.update()
         self.update()
 
     def on_revertUserFlags(self):
-        logging.debug("Tracks:revert ALL UserFlags")
+        logging.debug("Tracks:revert ALL UserFlags and track assignments")
         self._data.revertAssignmentStatus()
+        self._data.revertTrackAssignments()
+        self._timeline.update()
         self.update()
 
     def on_deleteDetection(self):
-        logging.debug("Tracks:delete detections")
+        logging.warning("Tracks:delete detections is currently not supported!")
         # self._data.deleteDetections()
+        self._timeline.update()
         self.update()
 
     def on_windowChanged(self):
@@ -354,7 +327,6 @@ class FixTracks(QWidget):
         self.update()
 
     def moveWindow(self, stepsize):
-        self._clear_detections = True
         step = np.round(stepsize * (self._currentWindowWidth))
         new_start_frame = self._currentWindowPos + step
         self._timeline.setWindowPos(new_start_frame / self._maxframes)

main.py

@@ -1,65 +0,0 @@
-"""
-pyside6-rcc resources.qrc -o resources.py
-
-"""
-import sys
-import platform
-import logging
-from PySide6.QtWidgets import QApplication
-from PySide6.QtCore import QSettings
-from PySide6.QtGui import QIcon, QPalette
-
-from fixtracks import fixtracks, info
-
-logging.basicConfig(level=logging.INFO, force=True)
-
-
-def is_dark_mode(app: QApplication) -> bool:
-    palette = app.palette()
-    # Check the brightness of the window text and base colors
-    text_color = palette.color(QPalette.ColorRole.WindowText)
-    base_color = palette.color(QPalette.ColorRole.Base)
-
-    # Calculate brightness (0 for dark, 255 for bright)
-    def brightness(color):
-        return (color.red() * 299 + color.green() * 587 + color.blue() * 114) // 1000
-
-    return brightness(base_color) < brightness(text_color)
-
-
-# import resources  # needs to be imported somewhere in the project to be picked up by qt
-
-if platform.system() == "Windows":
-    # from PySide6.QtWinExtras import QtWin
-    myappid = f"{info.organization_name}.{info.application_version}"
-    # QtWin.setCurrentProcessExplicitAppUserModelID(myappid)
-settings = QSettings()
-width = int(settings.value("app/width", 1024))
-height = int(settings.value("app/height", 768))
-x = int(settings.value("app/pos_x", 100))
-y = int(settings.value("app/pos_y", 100))
-app = QApplication(sys.argv)
-app.setApplicationName(info.application_name)
-app.setApplicationVersion(str(info.application_version))
-app.setOrganizationDomain(info.organization_name)
-
-# if platform.system() == 'Linux':
-# icn = QIcon(":/icons/app_icon")
-# app.setWindowIcon(icn)
-# Create a Qt widget, which will be our window.
-window = fixtracks.MainWindow(is_dark_mode(app))
-window.setGeometry(100, 100, 1024, 768)
-window.setWindowTitle("FixTracks")
-window.setMinimumWidth(1024)
-window.setMinimumHeight(768)
-window.resize(width, height)
-window.move(x, y)
-window.show()
-
-# Start the event loop.
-app.exec()
-pos = window.pos()
-settings.setValue("app/width", window.width())
-settings.setValue("app/height", window.height())
-settings.setValue("app/pos_x", pos.x())
-settings.setValue("app/pos_y", pos.y())

pyproject.toml

@@ -2,7 +2,7 @@
 name = "fixtracks"
 version = "0.1.0"
 description = "A project to fix track metadata"
-authors = ["Your Name <your.email@example.com>"]
+authors = ["Your Name <jan.grewe@uni-tuebingen.de>"]
 license = "MIT"
 
 [tool.poetry.dependencies]