intermediate state

fixtracks/utils/trackingdata.py

@@ -157,6 +157,32 @@ class TrackingData(QObject):
         center_of_gravity = np.sum(weighted_coords, axis=1) / sum_scores
         return center_of_gravity
 
+    def animalLength(self, bodyaxis=None):
+        if bodyaxis is None:
+            bodyaxis = [0, 1, 2, 5]
+        bodycoords = self.coordinates()[:, bodyaxis, :]
+        lengths = np.sum(np.sqrt(np.sum(np.diff(bodycoords, axis=1)**2, axis=2)), axis=1)
+        return lengths
+
+    def orientation(self, head_node=1, tail_node=5):
+        bodycoords = self.coordinates()[:, [head_node, tail_node], :]
+        vectors = bodycoords[:, 1, :] - bodycoords[:, 0, :]
+        orientations = np.arctan2(vectors[:, 1], vectors[:, 0])
+        return orientations
+
+    def bendedness(self, bodyaxis=None):
+        if bodyaxis is None:
+            bodyaxis = [0, 1, 2, 5]
+        bodycoords = self.coordinates()[:, bodyaxis, :]
+        head_tail_vector = bodycoords[:, -1, :] - bodycoords[:, 0, :]
+        head_tail_length = np.linalg.norm(head_tail_vector, axis=1, keepdims=True)
+        normalized_head_tail_vector = head_tail_vector / head_tail_length
+
+        projections = np.einsum('ijk,ij->ik', bodycoords - bodycoords[:, 0, np.newaxis, :], normalized_head_tail_vector)
+        distances = np.linalg.norm(bodycoords - (bodycoords[:, 0, np.newaxis, :] + projections[:, :, np.newaxis] * normalized_head_tail_vector[:, np.newaxis, :]), axis=2)
+        deviation = np.mean(distances, axis=1)
+        return deviation
+
     def __getitem__(self, key):
         return self._data[key]
 
@@ -174,7 +200,6 @@ def main():
     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}
@@ -208,6 +233,13 @@ def main():
     data = TrackingData()
     data.setData(as_dict(df))
     all_cogs = data.centerOfGravity()
+    orientations = data.orientation()
+    lengths = data.animalLength()
+    frames = data["frame"]
+    tracks = data["track"]
+    bendedness = data.bendedness()
+
+    embed()
     tracks = data["track"]
     cogs = all_cogs[tracks==1]
     all_dists = neighborDistances(cogs, 2, False)

fixtracks/widgets/classifier.py

@@ -1,10 +1,10 @@
 import logging
 import numpy as np
-import pyqtgraph as pg
 
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget,QPushButton, QGraphicsView
 from PySide6.QtCore import Signal
 from PySide6.QtGui import QBrush, QColor
+import pyqtgraph as pg  # needs to be imported after pyside to not import pyqt
 
 from fixtracks.utils.trackingdata import TrackingData
 
@@ -38,10 +38,10 @@ class SizeClassifier(QWidget):
 
         self._t1_selection = pg.LinearRegionItem([100, 200])
         self._t1_selection.setZValue(-10)
-        self._t1_selection.setBrush(track1_brush)
+        self._t1_selection.setBrush("orange")
         self._t2_selection = pg.LinearRegionItem([300,400])
         self._t2_selection.setZValue(-10)
-        self._t2_selection.setBrush(track2_brush)
+        self._t2_selection.setBrush("green")
         return plot_widget
 
     def estimate_length(self, coords, bodyaxis =None):
@@ -94,6 +94,7 @@ class NeighborhoodValidator(QWidget):
         self._positions = None
         self._distances = None
         self._tracks = None
+        self._frames = None
         self._plot = None
 
         self._plot_widget = self.setupGraph()
@@ -116,8 +117,10 @@ class NeighborhoodValidator(QWidget):
     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)
+        print(min_dist, max_dist)
         if log:
             bins = np.logspace(min_dist, max_dist, bin_count, base=10)
+        else:
             bins = np.linspace(min_dist, max_dist, bin_count)
         hist, edges = np.histogram(dists, bins=bins, density=True)
         return hist, edges
@@ -157,9 +160,12 @@ class NeighborhoodValidator(QWidget):
         frames : np.ndarray
             respective frame.
         """
-        def mouseClicked(self, event):
+        def mouseClicked(event):
-            print("mouse clicked at", event.pos())
+            pos = event.pos()
-
+            if self._plot.sceneBoundingRect().contains(pos):
+                mousePoint = vb.mapSceneToView(pos)
+                print("mouse clicked at", mousePoint)
+                vLine.setPos(mousePoint.x())
         track2_brush = QBrush(QColor.fromString("green"))
         track1_brush = QBrush(QColor.fromString("orange"))
         self._positions = positions
@@ -172,11 +178,12 @@ class NeighborhoodValidator(QWidget):
         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()
+        vb = self._plot.vb
+        n, e = self.estimate_histogram(t1_distances[1:], 1, 95, bin_count=100, log=False)
         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)
+        n, e = self.estimate_histogram(t2_distances[1:], 1, 95, 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)
@@ -187,7 +194,45 @@ class NeighborhoodValidator(QWidget):
         # plot.addItem(self._threshold)
         vLine = pg.InfiniteLine(pos=10, angle=90, movable=False)
         self._plot.addItem(vLine, ignoreBounds=True)
-        vb = self._plot.vb
+
+
+class ConsistencyClassifier(QWidget):
+    apply = Signal()
+    name = "Consistency classifier"
+
+    def __init__(self, parent=None):
+        super().__init__(parent)
+
+
+    def setData(self, keypoints, 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(event):
+            pos = event.pos()
+            if self._plot.sceneBoundingRect().contains(pos):
+                mousePoint = vb.mapSceneToView(pos)
+                print("mouse clicked at", mousePoint)
+                vLine.setPos(mousePoint.x())
+        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)
 
 
 
@@ -226,7 +271,7 @@ def main():
     import pickle
     from fixtracks.info import PACKAGE_ROOT
     
-    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)

fixtracks/widgets/detectiontimeline.py

@@ -32,15 +32,29 @@ class Window(QGraphicsRectItem):
         self.signals.windowMoved.emit()
 
     def setWindowWidth(self, newwidth):
-        logging.debug("timeline.window: update window width to %.3f", newwidth)
+        logging.debug("timeline.window: update window width to %f", newwidth)
         self._width = newwidth
         r = self.rect()
         r.setWidth(newwidth)
         self.setRect(r)
         self.signals.windowMoved.emit()
 
-    def setWindow(self, newx, newwidth):
+    def setWindow(self, newx:float, newwidth:float):
-        logging.debug("timeline.window: update window to range %.3f to %.3f", newx, newwidth)
+        def setWindow(self, newx: float, newwidth: float):
+            """
+            Update the window to the specified range.
+            Parameters
+            ----------
+            newx : float
+                The new x-coordinate of the window.
+            newwidth : float
+                The new width of the window.
+            Returns
+            -------
+            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())
@@ -62,7 +76,6 @@ class Window(QGraphicsRectItem):
             self.setX(self.scene().width() - self._width)
         if r.y() != self._y:
             self.setY(self._y)
-        print(self.sceneBoundingRect())
         super().mouseReleaseEvent(event)
         self.signals.windowMoved.emit()
 
@@ -80,7 +93,7 @@ class DetectionTimeline(QWidget):
         self._data = detectiondata
         self._rangeStart = 0.0
         self._rangeStop = 0.005
-        self.total_width = 2000
+        self._total_width = 2000
         self._stepCount = 200
         self._bg_brush = QBrush(QColor(20, 20, 20, 255))
         transparent_brush = QBrush(QColor(200, 200, 200, 64))
@@ -101,7 +114,7 @@ class DetectionTimeline(QWidget):
         self._window = Window(0, 0, 100, 60, axis_pen, transparent_brush)
         self._window.signals.windowMoved.connect(self.on_windowMoved)
 
-        self._scene = QGraphicsScene(QRectF(0, 0, self.total_width, 55.))
+        self._scene = QGraphicsScene(QRectF(0, 0, self._total_width, 55.))
         self._scene.setBackgroundBrush(self._bg_brush)
         self._scene.addItem(self._window)
 
@@ -147,6 +160,7 @@ class DetectionTimeline(QWidget):
         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
         if isinstance(self._data, pd.DataFrame):
             maxframe = np.max(self._data.frame.values)
 
@@ -178,9 +192,9 @@ class DetectionTimeline(QWidget):
             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)
 
-    def updatePosition(self):
+    def updatePositionLabel(self):
-        start = np.round(self._rangeStart * 100, 1)
+        start = np.round(self._rangeStart * 100, 4)
-        stop = np.round(self._rangeStop * 100, 1)
+        stop = np.round(self._rangeStop * 100, 4)
         self._position_label.setText(f"Current position: {start}% to {stop}% of data.")
 
     @property
@@ -202,10 +216,10 @@ class DetectionTimeline(QWidget):
 
     def on_windowMoved(self):
         scene_width = self._scene.width()
-        self._rangeStart = np.round(self._window.sceneBoundingRect().left() / scene_width, 3)
+        self._rangeStart = self._window.sceneBoundingRect().left() / scene_width
-        self._rangeStop = np.round(self._window.sceneBoundingRect().right() / scene_width, 3)
+        self._rangeStop = self._window.sceneBoundingRect().right() / scene_width
         logging.debug("Timeline: WindowUpdated positions start: %.3f end: %.3f", self.rangeStart, self.rangeStop)
-        self.updatePosition()
+        self.updatePositionLabel()
         self.signals.windowMoved.emit()
 
     def setWindowPos(self, newx: float):
@@ -220,8 +234,8 @@ class DetectionTimeline(QWidget):
             newx = 0.0
         elif newx > 1.0:
             newx = 1.0
-        logging.debug("Set window x tp new position %.3f", newx)
+        logging.debug("Timeline:setWindow to new position %.4f", newx)
-        x_rel = np.round(newx * self.total_width)
+        x_rel = np.round(newx * self._total_width)
         self._window.setWindowX(x_rel)
 
     def setWindowWidth(self, width: float):
@@ -232,17 +246,30 @@ class DetectionTimeline(QWidget):
         width : float
             The width in a range 0.0 to 1.0 (aka 0% to 100% of the span.)
         """
-        logging.debug("Set window width to new value %.3f of %i total width", width, self.total_width)
+        logging.debug("Set window width to new value %.5f of %i total width", width, self._total_width)
-        span = np.round(width * self.total_width)
+        span = np.round(width * self._total_width)
-        self._window.setWindowWidth(span)
+        self._window.setWindowWidth(np.round(span))
 
-    def setWindow(self, xpos, width):
+    def setWindow(self, xpos:float, width:float):
-        span = np.round(width * self.total_width)
+        """
+        Set the window position and width.
+        Parameters
+        ----------
+        xpos : float
+            The x position of the window as a fraction of the total data. 
+            Must be between 0.0 and 1.0. Values outside this range will be clamped.
+        width : float
+            The width of the window as a fraction of the total data.
+        Returns
+        -------
+        None
+        """
         if xpos < 0.0:
             xpos = 0.0
         elif xpos > 1.0:
             xpos = 1.0
-        xstart = np.round(xpos * self.total_width)
+        xstart = xpos * self._total_width
+        span = width * self._total_width
         self._window.setWindow(xstart, span)
 
     def windowBounds(self):