def processing_labeling(self, new_tracks, new_labels, filename, acq):
freq = acq.GetAnalogFrequency()
self.button_save.hide()
self.button_processing_labeling.hide()
# Estimate bone lenght and mcp angles
filename_static = QtGui.QFileDialog.getOpenFileName(self, "Open Static File", "Users/jessicaabreu")
static_acq, static_data, static_labels = fp.open_c3d_data(str(filename_static[0]))
bone_labels, bone_lenghts, mcp_estatic_error, mcp_inner_angle, mcp_inner_angle_error, mcp_middle_angle, mcp_middle_angle_error, mcp_outer_angle = fp.hand_static_measurements(static_data, static_labels)
# wrist tracks
self.layout().itemAt(2).widget().deleteLater()
for i in range(6):
self.layout().itemAt(3).itemAt(i).widget().deleteLater()
check_box_w1 = QtGui.QGroupBox("Select W1 tracks")
check_box_w1_layout = QtGui.QGridLayout()
check_box_w1.setLayout(check_box_w1_layout)
check_box_w2 = QtGui.QGroupBox("Select W2 tracks")
check_box_w2_layout = QtGui.QGridLayout()
check_box_w2.setLayout(check_box_w2_layout)
check_box_w3 = QtGui.QGroupBox("Select W3 tracks")
check_box_w3_layout = QtGui.QGridLayout()
check_box_w3.setLayout(check_box_w3_layout)
for i in range(len(new_labels)):
column = i / 15
line = i % 15
check_item_w1 = QtGui.QCheckBox(new_labels[i], check_box_w1)
check_item_w1.setStyleSheet("font-size: 8px; font-weight: normal")
check_item_w2 = QtGui.QCheckBox(new_labels[i], check_box_w2)
check_item_w2.setStyleSheet("font-size: 8px; font-weight: normal")
check_item_w3 = QtGui.QCheckBox(new_labels[i], check_box_w3)
check_item_w3.setStyleSheet("font-size: 8px; font-weight: normal")
check_box_w1_layout.addWidget(check_item_w1, line, column)
check_box_w2_layout.addWidget(check_item_w2, line, column)
check_box_w3_layout.addWidget(check_item_w3, line, column)
self.layout().addWidget(check_box_w1, 2, 2)
self.layout().addWidget(check_box_w2, 2, 3)
self.layout().addWidget(check_box_w3, 2, 4)
button_ok_wrist = QtGui.QPushButton("Ok")
button_ok_wrist.clicked.connect(lambda: self.labelling(filename, acq, new_tracks, new_labels, freq, bone_lenghts, bone_labels, mcp_estatic_error, mcp_inner_angle, mcp_inner_angle_error, mcp_middle_angle, mcp_middle_angle_error, mcp_outer_angle))
self.layout().addWidget(button_ok_wrist, 3, 4)
def processing(self):
self.button_processing.hide()
filename1 = QtGui.QFileDialog.getOpenFileName(self, "Open File", "Users/jessicaabreu")
acq, data, headers = fp.open_c3d_data(str(filename1[0]))
split_labels, split_tracks = fp.split_wrong_tracks_by_gradient(data, headers, acq.GetAnalogFrequency())
new_tracks, new_labels = fp.join_equivalent_tracks(split_tracks, split_labels, acq.GetAnalogFrequency())
viewer = BiomecViewer(new_tracks, new_labels)
viewer_widget = viewer.edit_traits(parent=self, kind='subpanel').control
self.layout().addWidget(viewer_widget, 2, 1)
# making checkbox and plots
figurex = plt.figure()
canvasx = FigureCanvas(figurex)
toolbarx = NavigationToolbar(canvasx, None)
toolbarx.setIconSize(QtCore.QSize(12, 12))
toolbarx.setStyleSheet("background-color: #C0C0C0 ")
ax_x = figurex.add_subplot(111)
ax_x.cla()
plt.xlabel('Time (s)', fontsize=10)
plt.ylabel('Position (mm)', fontsize=10)
canvasx.draw()
figurey = plt.figure()
canvasy = FigureCanvas(figurey)
toolbary = NavigationToolbar(canvasy, None)
toolbary.setIconSize(QtCore.QSize(12, 12))
toolbary.setStyleSheet("background-color: #C0C0C0 ")
ax_y = figurey.add_subplot(111)
ax_y.cla()
plt.xlabel('Time (s)', fontsize=10)
plt.ylabel('Position (mm)', fontsize=10)
canvasy.draw()
figurez = plt.figure()
canvasz = FigureCanvas(figurez)
toolbarz = NavigationToolbar(canvasz, None)
toolbarz.setIconSize(QtCore.QSize(12, 12))
toolbarz.setStyleSheet("background-color: #C0C0C0 ")
ax_z = figurez.add_subplot(111)
ax_z.cla()
plt.xlabel('Time (s)', fontsize=10)
plt.ylabel('Position (mm)', fontsize=10)
canvasz.draw()
check_box = QtGui.QGroupBox("Plot Tracks")
check_box_layout = QtGui.QGridLayout()
check_box.setLayout(check_box_layout)
for i in range(len(new_labels)):
column = i / 5
line = i % 5
check_item = QtGui.QCheckBox(new_labels[i])
check_item.setStyleSheet("font-size: 8px; font-weight: normal")
check_item.stateChanged.connect(self.wrapper_plot(ax_x, ax_y, ax_z, new_tracks[i, :, :],
new_labels[i], check_item, figurex,
figurey, figurez, canvasx, canvasy,
canvasz, acq
))
check_box_layout.addWidget(check_item, line, column)
plot_layout = QtGui.QVBoxLayout()
plot_layout.addWidget(canvasx)
plot_layout.addWidget(toolbarx)
plot_layout.addWidget(canvasy)
plot_layout.addWidget(toolbary)
plot_layout.addWidget(canvasz)
plot_layout.addWidget(toolbarz)
self.layout().addWidget(check_box, 1, 2)
self.layout().addLayout(plot_layout, 2, 2)
self.button_processing_labeling.show()
self.button_processing_labeling.clicked.connect(lambda: self.processing_labeling(new_tracks, new_labels, filename1[0], acq))
self.button_save.show()
self.button_save.clicked.connect(lambda: self.save(new_tracks, new_labels, filename1[0], acq, "pre_processed"))
def wrist_labelling(self, tracks, labels, freq):
'''
Uses UI input to label wrist trajectories. Adjusts UI after input is given.
Receives:
tracks: numpy array with marker trajectories. Shape (marker_number, frames, 3)
labels: list with marker labels
freq: acquisition frequency
Returns:
wrist_tracks: numpy array with wrist tracks joined and gaps interpolated with constrined cubic spline
wrist_labels: list with wrist labels
other_tracks: tracks excludind wrist tracks
other_labels: other_tracks labels
'''
list_w1 = []
list_w2 = []
list_w3 = []
indexes_wrist = []
# w1
w1_track = np.empty((tracks.shape[1], 3))
w1_track.fill(np.nan)
for check_item in self.layout().itemAt(3).widget().findChildren(QtGui.QCheckBox):
if check_item.isChecked():
track_index = labels.index(str(check_item.text()))
indexes_wrist.append(track_index)
track = tracks[track_index, :, :]
index_values = np.where(np.isfinite(track[:, 0]))[0]
w1_track[index_values[0]: index_values[-1] + 1, :] = track[index_values[0]: index_values[-1] + 1, :]
w1 = fp.interp_constrained_spline(w1_track, freq)
# w2
w2_track = np.empty((tracks.shape[1], 3))
w2_track.fill(np.nan)
for check_item in self.layout().itemAt(4).widget().findChildren(QtGui.QCheckBox):
if check_item.isChecked():
track_index = labels.index(str(check_item.text()))
indexes_wrist.append(track_index)
track = tracks[track_index, :, :]
index_values = np.where(np.isfinite(track[:, 0]))[0]
w2_track[index_values[0]: index_values[-1] + 1, :] = track[index_values[0]: index_values[-1] + 1, :]
w2 = fp.interp_constrained_spline(w2_track, freq)
# w3
w3_track = np.empty((tracks.shape[1], 3))
w3_track.fill(np.nan)
for check_item in self.layout().itemAt(5).widget().findChildren(QtGui.QCheckBox):
if check_item.isChecked():
track_index = labels.index(str(check_item.text()))
indexes_wrist.append(track_index)
track = tracks[track_index, :, :]
index_values = np.where(np.isfinite(track[:, 0]))[0]
w3_track[index_values[0]: index_values[-1] + 1, :] = track[index_values[0]: index_values[-1] + 1, :]
w3 = fp.interp_constrained_spline(w3_track, freq)
# stacking
wrist_tracks = np.dstack((w1.T, w2.T, w3.T)).T
wrist_labels = ['W1', 'W2', 'W3']
other_tracks = np.delete(tracks, indexes_wrist, axis=0)
other_labels = list(np.delete(np.array(labels), indexes_wrist))
# adjusting ui
for i in range (4):
self.layout().itemAt(6-i).widget().deleteLater()
return wrist_tracks, wrist_labels, other_tracks, other_labels
from file_processing import FileProcessing
if __name__ == '__main__':
rows_number = int(input("Please enter the number of rows: \n"))
file_p = FileProcessing(rows_number)
file_p.input_file()
file_p.output_file()
