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3 changed files with 10 additions and 180 deletions

View File

@ -1,134 +0,0 @@
import logging
import numpy as np
from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget,QPushButton
from PySide6.QtCore import Signal
from PySide6.QtGui import QBrush, QColor
import pyqtgraph as pg
class SizeClassifier(QWidget):
apply = Signal()
def __init__(self, parent=None):
super().__init__(parent)
self._t1_selection = None
self._t2_selection = None
self._coordinates = None
self._sizes = None
self._plot_widget = self.setupGraph()
self._apply_btn = QPushButton("apply")
self._apply_btn.clicked.connect(lambda: self.apply.emit())
layout = QVBoxLayout()
layout.addWidget(self._plot_widget)
layout.addWidget(self._apply_btn)
self.setLayout(layout)
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.setBrush(track1_brush)
self._t2_selection = pg.LinearRegionItem([300,400])
self._t2_selection.setZValue(-10) # what is that?
self._t2_selection.setBrush(track2_brush)
return plot_widget
def estimate_length(self, coords, bodyaxis =None):
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)
return dists
def estimate_histogram(self, dists, min_threshold=1., max_threshold=99.):
min_length = np.percentile(dists, min_threshold)
max_length = np.percentile(dists, max_threshold)
bins = np.linspace(0.5 * min_length, 1.5 * max_length, 100)
hist, edges = np.histogram(dists, bins=bins, density=True)
return hist, edges
def setCoordinates(self, coordinates):
self._coordinates = coordinates
self._sizes = self.estimate_length(coordinates)
n, e = self.estimate_histogram(self._sizes)
plot = self._plot_widget.addPlot()
bgi = pg.BarGraphItem(x0=e[:-1], x1=e[1:], height=n, pen='w', brush=(0,0,255,150))
plot.addItem(bgi)
plot.setLabel('left', "prob. density")
plot.setLabel('bottom', "bodylength", units="px")
plot.addItem(self._t1_selection)
plot.addItem(self._t2_selection)
def selections(self, track1=True):
if track1:
return self._t1_selection.getRegion()
else:
return self._t2_selection.getRegion()
def assignedTracks(self):
tracks = np.ones_like(self._sizes, dtype=int) * -1
t1lower, t1upper = self.selections()
t2lower, t2upper = self.selections(False)
tracks[(self._sizes >= t1lower) & (self._sizes < t1upper)] = 1
tracks[(self._sizes >= t2lower) & (self._sizes < t2upper)] = 2
return tracks
class ClassifierWidget(QTabWidget):
apply_sizeclassifier = Signal(np.ndarray)
def __init__(self, parent=None):
super().__init__(parent)
self._size_classifier = SizeClassifier()
self.addTab(self._size_classifier, "Size classifier")
self._size_classifier.apply.connect(self._on_applySizeClassifier)
def _on_applySizeClassifier(self):
tracks = self.size_classifier.assignedTracks()
self.apply_sizeclassifier.emit(tracks)
@property
def size_classifier(self):
return self._size_classifier
def main():
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)
coords = np.stack(df.keypoints.values,).astype(np.float32)[:,:,:]
app = QApplication([])
window = QWidget()
window.setMinimumSize(200, 200)
layout = QVBoxLayout()
win = SizeClassifier()
win.setCoordinates(coords)
btn = QPushButton("get bounds")
btn.clicked.connect(lambda: win.selections())
layout.addWidget(win)
layout.addWidget(btn)
window.setLayout(layout)
window.show()
app.exec()
if __name__ == "__main__":
main()

View File

@ -10,11 +10,9 @@ from fixtracks.widgets.detectionview import DetectionData
class Skeleton(QGraphicsRectItem):
skeleton_grid = [(0, 1), (1, 2), (1, 3), (1, 4), (2, 5)]
bodyaxis = [0, 1, 2, 5]
def __init__(self, x, y, width, height, keypoint_coordinates, brush):
super().__init__(x, y, width, height)
self._keypoints = keypoint_coordinates
skeleton_pen = QPen(brush.color())
skeleton_pen.setWidthF(1.0)
skeleton_marker = 5
@ -39,12 +37,6 @@ class Skeleton(QGraphicsRectItem):
# self.setAcceptHoverEvents(True) # Enable hover events if needed
self.setFlags(QGraphicsRectItem.ItemIsSelectable)
@property
def length(self):
bodykps = self._keypoints[self.bodyaxis, :]
dist = np.sum(np.sqrt(np.sum(np.diff(bodykps, axis=0)**2, axis=1)), axis=0)
return dist
# def mousePressEvent(self, event):
# self.signals.clicked.emit(self.data(0), QPointF(event.scenePos().x(), event.scenePos().y()))
@ -90,11 +82,7 @@ class SkeletonWidget(QWidget):
def updateInfo(self, index):
if index > -1:
s = self._skeletons[index]
l = s.length
i = s.data(DetectionData.ID.value)
t = s.data(DetectionData.TRACK_ID.value)
f = s.data(DetectionData.FRAME.value)
self._info_label.setText(f"Id {i}, track {t} on frame {f}, length {l:.1f} px")
self._info_label.setText(f"Detection id {s.data(DetectionData.ID.value)}, track {s.data(DetectionData.TRACK_ID.value)} on frame {s.data(DetectionData.FRAME.value)}")
else:
self._info_label.setText("")
@ -131,8 +119,6 @@ class SkeletonWidget(QWidget):
def addSkeleton(self, coords, detection_id, frame, track, brush, update=True):
def check_extent(x, y, w, h):
if x == 0 and y == 0:
return
if len(self._skeletons) == 0:
self._minx = x
self._maxx = x + w
@ -200,9 +186,14 @@ def main():
df = pickle.load(f)
focus_brush = QBrush(QColor.fromString("red"))
second_brush = QBrush(QColor.fromString("blue"))
scnd_coords = np.stack(df.keypoints[(df.track == 2)].values,).astype(np.float32)[:,:,:]
scnd_tracks = df.track[df.track == 2].values
scnd_ids = df.track[(df.track == 2)].index.values
focus_coords = np.stack(df.keypoints[df.track == 1].values,).astype(np.float32)[:,:,:]
focus_tracks = df.track[df.track == 1].values
focus_frames = df.track[df.track == 1].values
focus_ids = df.track[(df.track == 2)].index.values
app = QApplication([])
@ -218,8 +209,7 @@ def main():
layout.addWidget(btn)
# view.addSkeleton(focus_coords[10,:,:], focus_ids[10], focus_brush)
count = 100
view.addSkeletons(focus_coords[:count,:,:], focus_ids[:count],
focus_frames[:count], focus_tracks[:count], focus_brush)
view.addSkeletons(focus_coords[:count,:,:], focus_ids[:count], focus_brush)
# view.addSkeletons(scnd_coords[:count,:,:], scnd_ids[:count], second_brush)
# view.addSkeletons(focus_coords[:10,:,:], focus_ids[:10], focus_brush)

View File

@ -14,8 +14,6 @@ from fixtracks.utils.writer import PickleWriter
from fixtracks.widgets.detectionview import DetectionView, DetectionData
from fixtracks.widgets.detectiontimeline import DetectionTimeline
from fixtracks.widgets.skeleton import SkeletonWidget
from fixtracks.widgets.classifier import ClassifierWidget
class PoseTableModel(QAbstractTableModel):
column_header = ["frame", "track"]
@ -261,10 +259,6 @@ class DataController(QObject):
logging.error("Column %s not in dictionary", col)
return np.nan
@property
def numDetections(self):
return self._data["track"].shape[0]
@property
def selectionRange(self):
return self._start, self._stop
@ -292,12 +286,6 @@ class DataController(QObject):
def assignUserSelection(self, track_id):
self._data["track"][self._user_selections] = track_id
def assignTracks(self, tracks):
if len(tracks) != self.numDetections:
logging.error("DataController: Size of passed tracks does not match data!")
return
self._data["track"] = tracks
def save(self, filename):
export_columns = self._columns.copy()
export_columns.remove("index")
@ -311,8 +299,6 @@ class DataController(QObject):
return 0
return self._data["keypoints"][0].shape[0]
def coordinates(self):
return np.stack(self._data["keypoints"]).astype(np.float32)
class FixTracks(QWidget):
back = Signal()
@ -405,13 +391,9 @@ class FixTracks(QWidget):
btnBox.addWidget(self._progress_bar)
btnBox.addWidget(self._saveBtn)
self._classifier = ClassifierWidget()
self._classifier.apply_sizeclassifier.connect(self.on_classifyBySize)
self._classifier.setMaximumWidth(500)
cntrlBox = QHBoxLayout()
cntrlBox.addWidget(self._classifier)
cntrlBox.addItem(QSpacerItem(200, 100, QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Expanding))
cntrlBox.addWidget(self._controls_widget, alignment=Qt.AlignmentFlag.AlignCenter)
cntrlBox.addItem(QSpacerItem(300, 100, QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Expanding))
vbox = QVBoxLayout()
vbox.addLayout(timelinebox)
@ -430,12 +412,6 @@ class FixTracks(QWidget):
layout.addWidget(splitter)
self.setLayout(layout)
def on_classifyBySize(self, tracks):
self._data.setSelectionRange("index", 0, self._data.numDetections)
self._data.assignTracks(tracks)
self._timeline.setDetectionData(self._data.data)
self.update()
def on_dataSelection(self):
filename = self._data_combo.currentText()
if "please select" in filename.lower() or len(filename.strip()) == 0:
@ -533,8 +509,6 @@ class FixTracks(QWidget):
maxframes = self._data.max("frame")
rel_width = self._windowspinner.value() / maxframes
self._timeline.setWindowWidth(rel_width)
coordinates = self._data.coordinates()
self._classifier.size_classifier.setCoordinates(coordinates)
self.update()
self._saveBtn.setEnabled(True)