[tracks, classifier] include neighborhood classifier, not yet doing

anything

fixtracks/widgets/classifier.py

@@ -1,15 +1,17 @@
 import logging
 import numpy as np
+import pyqtgraph as pg
 
-from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget,QPushButton
+from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget,QPushButton, QGraphicsView
 from PySide6.QtCore import Signal
 from PySide6.QtGui import QBrush, QColor
 
-import pyqtgraph as pg
+from fixtracks.utils.trackingdata import TrackingData
 
 
 class SizeClassifier(QWidget):
     apply = Signal()
+    name = "SizeClassifier"
 
     def __init__(self, parent=None):
         super().__init__(parent)
@@ -29,17 +31,16 @@ class SizeClassifier(QWidget):
 
     def setupGraph(self):
         track1_brush = QBrush(QColor.fromString("orange"))
-        track1_brush.color().setAlphaF(0.5)
         track2_brush = QBrush(QColor.fromString("green"))
 
         pg.setConfigOptions(antialias=True)
         plot_widget = pg.GraphicsLayoutWidget(show=False)
 
         self._t1_selection = pg.LinearRegionItem([100, 200])
-        self._t1_selection.setZValue(-10)  # what is that?
+        self._t1_selection.setZValue(-10)
         self._t1_selection.setBrush(track1_brush)
         self._t2_selection = pg.LinearRegionItem([300,400])
-        self._t2_selection.setZValue(-10)  # what is that?
+        self._t2_selection.setZValue(-10)
         self._t2_selection.setBrush(track2_brush)
         return plot_widget
 
@@ -47,8 +48,8 @@ class SizeClassifier(QWidget):
         if bodyaxis is None:
             bodyaxis = [0, 1, 2, 5]
         bodycoords = coords[:, bodyaxis, :]
-        dists = np.sum(np.sqrt(np.sum(np.diff(bodycoords, axis=1)**2, axis=2)), axis=1)
+        lengths = np.sum(np.sqrt(np.sum(np.diff(bodycoords, axis=1)**2, axis=2)), axis=1)
-        return dists
+        return lengths
 
     def estimate_histogram(self, dists, min_threshold=1., max_threshold=99.):
         min_length = np.percentile(dists, min_threshold)
@@ -83,6 +84,112 @@ class SizeClassifier(QWidget):
         tracks[(self._sizes >= t2lower) & (self._sizes < t2upper)] = 2
         return tracks
 
+class NeighborhoodValidator(QWidget):
+    apply = Signal()
+    name = "Neighborhood Validator"
+
+    def __init__(self, parent = None):
+        super().__init__(parent)
+        self._threshold = None
+        self._positions = None
+        self._distances = None
+        self._tracks = None
+        self._plot = None
+
+        self._plot_widget = self.setupGraph()
+        self._apply_btn = QPushButton("apply")
+        self._apply_btn.clicked.connect(lambda: self.apply.emit())
+
+        layout = QVBoxLayout()
+        print(isinstance(self._plot_widget, QGraphicsView))
+        layout.addWidget(self._plot_widget)
+        layout.addWidget(self._apply_btn)
+        self.setLayout(layout)
+
+    def setupGraph(self):
+        pg.setConfigOptions(antialias=True)
+        plot_widget = pg.GraphicsLayoutWidget(show=False)
+        self._threshold = pg.LineSegmentROI([[10, 64], [120,64]], pen='r')
+        self._threshold.setZValue(-10)  # what is that?
+        return plot_widget
+
+    def estimate_histogram(self, dists, min_threshold=1., max_threshold=99., bin_count=100, log=False):
+        min_dist = np.percentile(dists, min_threshold)
+        max_dist = np.percentile(dists, max_threshold)
+        if log:
+            bins = np.logspace(min_dist, max_dist, bin_count, base=10)
+        bins = np.linspace(min_dist, max_dist, bin_count)
+        hist, edges = np.histogram(dists, bins=bins, density=True)
+        return hist, edges
+
+    def neighborDistances(self, x, frames, n=5, symmetric=True):
+        logging.debug("classifier:NeighborhoodValidator neighborDistance")
+        pad_shape = list(x.shape)
+        pad_shape[0] = n
+        pad = np.atleast_2d(np.zeros(pad_shape))
+        if symmetric:
+            padded_x = np.vstack((pad, x, pad))
+            dists = np.zeros((x.shape[0]-1, 2*n))
+        else:
+            padded_x = np.vstack((pad, x))
+            dists = np.zeros((x.shape[0]-1, 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, axis=0)
+            dist = np.sqrt(np.sum((padded_x - shifted_x)**2, axis=1))
+            dists[:, count] = dist[n+1:]/np.diff(frames)
+            count += 1
+        return dists
+
+    def setData(self, positions, tracks, frames):
+        """Set the data, the classifier/should be working on.
+
+        Parameters
+        ----------
+        positions : np.ndarray
+            The position estimates, e.g. the center of gravity for each detection
+        tracks : np.ndarray
+            The current track assignment.
+        frames : np.ndarray
+            respective frame.
+        """
+        def mouseClicked(self, event):
+            print("mouse clicked at", event.pos())
+
+        track2_brush = QBrush(QColor.fromString("green"))
+        track1_brush = QBrush(QColor.fromString("orange"))
+        self._positions = positions
+        self._tracks = tracks
+        self._frames = frames
+        t1_positions = self._positions[self._tracks == 1]
+        t1_frames = self._frames[self._tracks == 1]
+        t1_distances = self.neighborDistances(t1_positions, t1_frames, 1, False)
+        t2_positions = self._positions[self._tracks == 2]
+        t2_frames = self._frames[self._tracks == 2]
+        t2_distances = self.neighborDistances(t2_positions, t2_frames, 1, False)
+
+        n, e = self.estimate_histogram(t1_distances[1:], bin_count=100, log=False)
+        self._plot = self._plot_widget.addPlot()
+        bgi1 = pg.BarGraphItem(x0=e[:-1], x1=e[1:], height=n, pen='w', brush=track1_brush)
+        self._plot.addItem(bgi1)
+        n, e = self.estimate_histogram(t2_distances[1:], bin_count=100, log=False)
+        bgi2 = pg.BarGraphItem(x0=e[:-1], x1=e[1:], height=n, pen='w', brush=track2_brush)
+        self._plot.addItem(bgi2)
+        self._plot.scene().sigMouseClicked.connect(mouseClicked)
+        self._plot.setLogMode(x=False, y=True)
+        # plot.setXRange(np.min(t1_distances), np.max(t1_distances))
+        self._plot.setLabel('left', "prob. density")
+        self._plot.setLabel('bottom', "distance", units="px/frame")
+        # plot.addItem(self._threshold)
+        vLine = pg.InfiniteLine(pos=10, angle=90, movable=False)
+        self._plot.addItem(vLine, ignoreBounds=True)
+        vb = self._plot.vb
+
+    
 
 class ClassifierWidget(QTabWidget):
     apply_sizeclassifier = Signal(np.ndarray)
@@ -90,7 +197,9 @@ class ClassifierWidget(QTabWidget):
     def __init__(self, parent=None):
         super().__init__(parent)
         self._size_classifier = SizeClassifier()
-        self.addTab(self._size_classifier, "Size classifier")
+        self._neigborhood_validator = NeighborhoodValidator()
+        self.addTab(self._size_classifier, SizeClassifier.name)
+        self.addTab(self._neigborhood_validator, NeighborhoodValidator.name)
         self._size_classifier.apply.connect(self._on_applySizeClassifier)
 
     def _on_applySizeClassifier(self):
@@ -101,48 +210,51 @@ class ClassifierWidget(QTabWidget):
     def size_classifier(self):
         return self._size_classifier
 
+    @property
+    def neighborhood_validator(self):
+        return self._neigborhood_validator
 
 
-def test_sizeClassifier(coords):
+def as_dict(df):
-    app = QApplication([])
+    d = {c: df[c].values for c in df.columns}
-    window = QWidget()
+    d["index"] = df.index.values
-    window.setMinimumSize(200, 200)
+    return d
-    layout = QVBoxLayout()
-    win = SizeClassifier()
-    win.setCoordinates(coords)
-
-    layout.addWidget(win)
-    window.setLayout(layout)
-    window.show()
-    app.exec()
-
-
-def test_neighborhoodClassifier(coords):
-    app = QApplication([])
-    window = QWidget()
-    window.setMinimumSize(200, 200)
-    layout = QVBoxLayout()
-    win = SizeClassifier()
-    win.setCoordinates(coords)
-    layout.addWidget(win)
-    window.setLayout(layout)
-    window.show()
-    app.exec()
 
 
 def main():
+    test_size = False
     import pickle
     from fixtracks.info import PACKAGE_ROOT
-    from PySide6.QtWidgets import QApplication
+    
     datafile = PACKAGE_ROOT / "data/merged_small.pkl"
-    print(datafile)
+
     with open(datafile, "rb") as f:
         df = pickle.load(f)
+    data = TrackingData()
+    data.setData(as_dict(df))
 
-    coords = np.stack(df.keypoints.values,).astype(np.float32)
+    positions = data.centerOfGravity()
-    frames = df.frame.values
+    tracks = data["track"]
-    test_sizeClassifier(coords)
+    frames = data["frame"]
+    coords = data.coordinates()
+
+    app = QApplication([])
+    window = QWidget()
+    window.setMinimumSize(200, 200)
+    # if test_size:
+    #     win = SizeClassifier()
+    #     win.setCoordinates(coords)
+    # else:
+    w = ClassifierWidget()
+    w.neighborhood_validator.setData(positions, tracks, frames)
+
+    layout = QVBoxLayout()
+    layout.addWidget(w)
+    window.setLayout(layout)
+    window.show()
+    app.exec()
 
 
 if __name__ == "__main__":
+    from PySide6.QtWidgets import QApplication
     main()

fixtracks/widgets/tracks.py

@@ -378,7 +378,11 @@ class FixTracks(QWidget):
             rel_width = self._windowspinner.value() / maxframes
             self._timeline.setWindowWidth(rel_width)
             coordinates = self._data.coordinates()
+            positions = self._data.centerOfGravity()
+            tracks = self._data["track"]
+            frames = self._data["frame"]
             self._classifier.size_classifier.setCoordinates(coordinates)
+            self._classifier.neighborhood_validator.setData(positions, tracks, frames)
             self.update()
             self._saveBtn.setEnabled(True)