[classifier] more interactions on consistencytracker
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@ -1,7 +1,8 @@
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import logging
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import numpy as np
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from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget, QPushButton, QGraphicsView, QSpinBox, QProgressBar, QGridLayout, QLabel
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from PySide6.QtWidgets import QWidget, QVBoxLayout, QTabWidget, QPushButton, QGraphicsView
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from PySide6.QtWidgets import QSpinBox, QProgressBar, QGridLayout, QLabel, QCheckBox
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from PySide6.QtCore import Signal, Slot, QRunnable, QObject, QThreadPool
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from PySide6.QtGui import QBrush, QColor
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import pyqtgraph as pg # needs to be imported after pyside to not import pyqt
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@ -13,12 +14,13 @@ class WorkerSignals(QObject):
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error = Signal(str)
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running = Signal(bool)
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progress = Signal(int, int, int)
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finished = Signal(bool)
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stopped = Signal(int)
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class ConsistencyWorker(QRunnable):
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signals = WorkerSignals()
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def __init__(self, positions, orientations, lengths, bendedness, frames, tracks, startframe=0) -> None:
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def __init__(self, positions, orientations, lengths, bendedness, frames, tracks,
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startframe=0, stoponerror=False) -> None:
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super().__init__()
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self.positions = positions
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self.orientations = orientations
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@ -28,25 +30,29 @@ class ConsistencyWorker(QRunnable):
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self.tracks = tracks
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self._startframe = startframe
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self._stoprequest = False
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self._stoponerror = stoponerror
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@Slot()
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def cancel(self):
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def stop(self):
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self._stoprequest = True
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@Slot()
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def run(self):
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last_pos = [self.positions[self.tracks == 1][0], self.positions[self.tracks == 2][0]]
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last_frame = [self.frames[self.tracks == 1][0], self.frames[self.tracks == 2][0]]
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last_angle = [self.orientations[self.tracks == 1][0], self.orientations[self.tracks == 2][0]]
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last_pos = [self.positions[(self.tracks == 1) & (self.frames <= self._startframe)][-1],
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self.positions[(self.tracks == 2) & (self.frames <= self._startframe)][-1]]
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last_frame = [self.frames[(self.tracks == 1) & (self.frames <= self._startframe)][-1],
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self.frames[(self.tracks == 2) & (self.frames <= self._startframe)][-1]]
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# last_angle = [self.orientations[self.tracks == 1][0], self.orientations[self.tracks == 2][0]]
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errors = 0
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processed = 0
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self._stoprequest = False
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maxframes = np.max(self.frames)
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steps = int((maxframes - self._startframe) // 100)
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processed = 1
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progress = 0
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assignment_error = False
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for f in range(self._startframe, np.max(self.frames), 1):
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processed += 1
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self._stoprequest = False
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maxframes = np.max(self.frames)
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startframe = np.max(last_frame)
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steps = int((maxframes - startframe) // 200)
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for f in range(startframe + 1, maxframes, 1):
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if self._stoprequest:
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break
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indices = np.where(self.frames == f)[0]
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@ -59,15 +65,17 @@ class ConsistencyWorker(QRunnable):
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self.tracks[idx] = 2
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last_frame[1] = f
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last_pos[1] = p
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last_angle[1] = self.orientations[idx]
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# last_angle[1] = self.orientations[idx]
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continue
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if f < last_frame[1]:
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last_frame[0] = f
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last_pos[0] = p
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last_angle[0] = self.orientations[idx]
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# last_angle[0] = self.orientations[idx]
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self.tracks[idx] = 1
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continue
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# else, we have already seen track one and track two entries
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if f - last_frame[0] == 0 or f - last_frame[1] == 0:
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print(f"framecount is zero! current frame {f}, last frame {last_frame[0]} and {last_frame[1]}")
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distance_to_trackone = np.linalg.norm(p - last_pos[0])/(f - last_frame[0])
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distance_to_tracktwo = np.linalg.norm(p - last_pos[1])/(f - last_frame[1])
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most_likely_track = np.argmin([distance_to_trackone, distance_to_tracktwo]) + 1
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@ -79,6 +87,8 @@ class ConsistencyWorker(QRunnable):
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logging.warning("frame %i: Issues assigning based on distances %s", f, str(distances))
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assignment_error = True
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errors += 1
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if self._stoponerror:
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break
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else:
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processed += 1
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for i, idx in enumerate(indices):
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@ -89,17 +99,16 @@ class ConsistencyWorker(QRunnable):
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last_pos[assignments[i]-1] = pp[i]
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last_frame[assignments[i]-1] = f
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assignment_error = False
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if f % steps == 0:
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if steps > 0 and f % steps == 0:
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progress += 1
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self.signals.progress.emit(progress, processed, errors)
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self.signals.finished.emit(True)
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self.signals.stopped.emit(f)
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class SizeClassifier(QWidget):
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apply = Signal()
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name = "SizeClassifier"
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name = "Size classifier"
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def __init__(self, parent=None):
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super().__init__(parent)
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@ -286,12 +295,12 @@ class NeighborhoodValidator(QWidget):
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class ConsistencyClassifier(QWidget):
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apply = Signal()
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name = "Consistency classifier"
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name = "Consistency tracker"
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def __init__(self, parent=None):
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super().__init__(parent)
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self._data = None
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self._all_cogs = None
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self._all_pos = None
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self._all_orientations = None
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self._all_lengths = None
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self._all_bendedness = None
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@ -299,41 +308,61 @@ class ConsistencyClassifier(QWidget):
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self._frames = None
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self._tracks = None
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self._worker = None
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self._processed_frames = 0
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self._errorlabel = QLabel()
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self._errorlabel.setStyleSheet("QLabel { color : red; }")
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self._assignedlabel = QLabel()
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self._maxframeslabel = QLabel()
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self._startframe_spinner = QSpinBox()
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self._startbtn = QPushButton("run")
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self._startbtn.clicked.connect(self.run)
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self._startbtn = QPushButton("start")
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self._startbtn.clicked.connect(self.start)
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self._startbtn.setEnabled(False)
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self._cancelbtn = QPushButton("cancel")
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self._cancelbtn.clicked.connect(self.cancel)
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self._cancelbtn.setEnabled(False)
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self._stopbtn = QPushButton("stop")
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self._stopbtn.clicked.connect(self.stop)
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self._stopbtn.setEnabled(False)
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self._proceedbtn = QPushButton("proceed")
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self._proceedbtn.clicked.connect(self.proceed)
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self._proceedbtn.setEnabled(False)
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self._refreshbtn = QPushButton("refresh")
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self._refreshbtn.clicked.connect(self.refresh)
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self._refreshbtn.setEnabled(True)
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self._apply_btn = QPushButton("apply")
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self._apply_btn.clicked.connect(lambda: self.apply.emit())
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self._apply_btn.setEnabled(False)
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self._progressbar = QProgressBar()
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self._progressbar.setMinimum(0)
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self._progressbar.setMaximum(100)
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self._apply_btn.clicked.connect(lambda: self.apply.emit())
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self._apply_btn.setEnabled(False)
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self._stoponerror = QCheckBox("Stop processing whenever an error is encountered")
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self._stoponerror.setToolTip("Stop process whenever ")
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self._stoponerror.setCheckable(True)
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self._stoponerror.setChecked(True)
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self.threadpool = QThreadPool()
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lyt = QGridLayout()
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lyt.addWidget(QLabel("Start frame:"), 0, 0 )
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lyt.addWidget(self._startframe_spinner, 0, 1 )
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lyt.addWidget(QLabel("assigned"), 1, 0)
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lyt.addWidget(self._assignedlabel, 1, 1)
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lyt.addWidget(QLabel("errors/issues"), 2, 0)
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lyt.addWidget(self._errorlabel, 2, 1)
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lyt.addWidget(self._startbtn, 3, 0)
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lyt.addWidget(self._cancelbtn, 3, 1)
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lyt.addWidget(self._progressbar, 4, 0, 1, 2)
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lyt.addWidget(self._apply_btn, 5, 0, 1, 2)
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lyt.addWidget(self._startframe_spinner, 0, 1, 1, 2)
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lyt.addWidget(QLabel("of"), 1, 1, 1, 1)
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lyt.addWidget(self._maxframeslabel, 1, 2, 1, 1)
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lyt.addWidget(self._stoponerror, 2, 0, 1, 3)
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lyt.addWidget(QLabel("assigned"), 3, 0)
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lyt.addWidget(self._assignedlabel, 3, 1)
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lyt.addWidget(QLabel("errors/issues"), 4, 0)
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lyt.addWidget(self._errorlabel, 4, 1)
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lyt.addWidget(self._startbtn, 5, 0)
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lyt.addWidget(self._stopbtn, 5, 1)
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lyt.addWidget(self._proceedbtn, 5, 2)
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lyt.addWidget(self._apply_btn, 6, 0, 1, 2)
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lyt.addWidget(self._refreshbtn, 6, 2, 1, 1)
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lyt.addWidget(self._progressbar, 7, 0, 1, 3)
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self.setLayout(lyt)
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def setData(self, data:TrackingData):
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@ -344,19 +373,23 @@ class ConsistencyClassifier(QWidget):
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data : Trackingdata
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The tracking data.
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"""
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self._all_cogs = data.centerOfGravity()
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self._data = data
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self._all_pos = data.centerOfGravity()
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self._all_orientations = data.orientation()
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self._all_lengths = data.animalLength()
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self._all_bendedness = data.bendedness()
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self._all_scores = data["confidence"] # ignore for now, let's see how far this carries.
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self._frames = data["frame"]
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self._tracks = data["track"]
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self._maxframes = np.max(self._frames)
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min_frame = max([self._frames[self._tracks == 1][0], self._frames[self._tracks == 2][0]]) + 1
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self._maxframeslabel.setText(str(self._maxframes))
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self._startframe_spinner.setMinimum(min_frame)
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self._startframe_spinner.setMaximum(self._frames[-1])
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self._startframe_spinner.setValue(self._frames[0] + 1)
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self._startbtn.setEnabled(True)
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self._assignedlabel.setText("0")
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self._errorlabel.setText("0")
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self._worker = None
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@Slot(float)
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@ -364,30 +397,44 @@ class ConsistencyClassifier(QWidget):
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if self._progressbar is not None:
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self._progressDialog.setValue(int(value * 100))
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def cancel(self):
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def stop(self):
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if self._worker is not None:
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self._worker.cancel()
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self._worker.stop()
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self._startbtn.setEnabled(True)
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self._cancelbtn.setEnabled(False)
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self._proceedbtn.setEnabled(True)
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self._stopbtn.setEnabled(False)
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self._refreshbtn.setEnabled(True)
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def run(self):
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def start(self):
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self._startbtn.setEnabled(False)
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self._cancelbtn.setEnabled(True)
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self._worker = ConsistencyWorker(self._all_cogs, self._all_orientations, self._all_lengths,
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self._all_bendedness, self._frames, self._tracks, self._startframe_spinner.value())
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self._worker.signals.finished.connect(self.worker_done)
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self._refreshbtn.setEnabled(False)
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self._stopbtn.setEnabled(True)
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self._worker = ConsistencyWorker(self._all_pos, self._all_orientations, self._all_lengths,
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self._all_bendedness, self._frames, self._tracks,
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self._startframe_spinner.value(), self._stoponerror.isChecked())
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self._worker.signals.stopped.connect(self.worker_stopped)
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self._worker.signals.progress.connect(self.worker_progress)
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self.threadpool.start(self._worker)
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def proceed(self):
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self.start()
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def refresh(self):
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self.setData(self._data)
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def worker_progress(self, progress, processed, errors):
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self._progressbar.setValue(progress)
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self._errorlabel.setText(str(errors))
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self._assignedlabel.setText(str(processed))
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def worker_done(self):
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def worker_stopped(self, frame):
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self._apply_btn.setEnabled(True)
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self._startbtn.setEnabled(True)
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self._cancelbtn.setEnabled(False)
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self._stopbtn.setEnabled(False)
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self._startframe_spinner.setValue(frame-1)
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self._proceedbtn.setEnabled(bool(frame < self._maxframes-1))
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self._refreshbtn.setEnabled(True)
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self._processed_frames = frame
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def assignedTracks(self):
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return self._tracks
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@ -441,7 +488,7 @@ def main():
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from IPython import embed
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from fixtracks.info import PACKAGE_ROOT
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datafile = PACKAGE_ROOT / "data/merged_small_tracked.pkl"
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datafile = PACKAGE_ROOT / "data/merged_small.pkl"
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with open(datafile, "rb") as f:
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df = pickle.load(f)
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