def read_data1(self):
reading = Reading()
reading.update_output.connect(partial(self.updata_input_video,
label=0))
reading.read_video()
self.inputFileLineEdit1.setText(self.file_name_0)
def load_video(self):
self.reading = Reading()
self.reading.update_output.connect(self.updata_bg_video)
self.reading.read_video()
class BgCorrection_GUI(QtWidgets.QWidget):
output_Tab_bgCorrection = QtCore.Signal(object)
output_batchSize_Tab_bgCorrection = QtCore.Signal(int)
output_setting_Tab_bgCorrection = QtCore.Signal(object)
update_tab_index = QtCore.Signal(int)
def __init__(self, input_video, object_update_progressBar, parent=None):
super(BgCorrection_GUI, self).__init__(parent)
self.different_views = {}
self.input_video = input_video
self.object_update_progressBar = object_update_progressBar
self.setting_bg_correction = {}
self.flag_remove_box = True
self.flag_update_class = True
self.output = None
self.diff_video = None
self.original_video_bg = None
self.reconstruction_background = None
self.empty_value_box_flag = False
self.flag_no_warning = True
self.transform_algorithm = None
self.n_comp = None
self.n_iter = None
self.alpha = None
self.random_select = None
self.non_zero_coeff = None
self.patch_size = None
self.strides = None
self.resize(600, 600)
self.setWindowTitle('Background Correction')
self.combo_bg_filter = QtWidgets.QComboBox(self)
self.combo_bg_filter.addItem(
"-Select the background correction methods-")
self.combo_bg_filter.addItem("Differential rolling average")
self.combo_bg_filter.addItem("Spatial median Filter")
self.combo_bg_filter.addItem("Spatial gaussian Filter")
self.combo_bg_filter.addItem("Background correction temporal median")
self.combo_bg_filter.addItem("Flat field (Gaussian filter)")
self.combo_bg_filter.addItem(
"Flat field (mean background subtraction)")
self.combo_bg_filter.currentIndexChanged.connect(
self.layout_based_on_select_bg)
self.btn = QtWidgets.QPushButton("Update")
self.btn.setAutoDefault(False)
self.btn.clicked.connect(self.do_update)
self.btn.setFixedWidth(70)
self.btn.setFixedHeight(20)
self.grid = QtWidgets.QGridLayout()
self.grid.addWidget(self.combo_bg_filter, 0, 0)
self.grid.addWidget(self.createFirstExclusiveGroup(), 1, 0)
self.grid.addWidget(self.btn, 2, 0)
self.setLayout(self.grid)
def __del__(self):
print('Destructor called, Employee deleted.')
def createFirstExclusiveGroup(self):
self.groupBox_update = QtWidgets.QGroupBox(
"Background correction Setting:")
self.grid1 = QtWidgets.QGridLayout()
self.groupBox_update.setLayout(self.grid1)
return self.groupBox_update
def massage_filled(self):
self.flag_no_warning = False
self.msg_box1 = QtWidgets.QMessageBox()
self.msg_box1.setWindowTitle("Warning!")
self.msg_box1.setText("Please filled all parameters!")
self.msg_box1.exec_()
@QtCore.Slot()
def do_update(self):
if self.btn.clicked:
if self.combo_bg_filter.currentText(
) == "Differential rolling average":
self.batch_size = self.le_batchSize.text()
if self.groupBox_FPNc.isChecked():
self.flag_FPN = True
if self.radio_axis_1.isChecked():
self.axis = 0
elif self.radio_axis_2.isChecked():
self.axis = 1
elif self.radio_axis_3.isChecked():
self.axis = 'Both'
if self.radio_cpFPN_mode.isChecked():
self.mode_FPN = 'cpFPN'
elif self.radio_wFPN_mode.isChecked():
self.mode_FPN = 'wFPN'
elif self.radio_FFT2D_FPN_mode.isChecked():
self.mode_FPN = 'fFPN'
elif self.radio_median_FPN_mode.isChecked():
self.mode_FPN = 'mFPN'
else:
self.flag_FPN = False
self.axis = 0
self.mode_FPN = 'fFPN'
if self.groupBox_PN.isChecked():
self.flag_power_normalization = True
try:
self.s_x_win_pn = int(self.start_win_size_x.text())
self.e_x_win_pn = int(self.end_win_size_x.text())
self.s_y_win_pn = int(self.start_win_size_y.text())
self.e_y_win_pn = int(self.end_win_size_y.text())
except:
self.s_x_win_pn = None
self.e_x_win_pn = None
self.s_y_win_pn = None
self.e_y_win_pn = None
else:
self.flag_power_normalization = False
self.s_x_win_pn = None
self.e_x_win_pn = None
self.s_y_win_pn = None
self.e_y_win_pn = None
if self.batch_size != '':
self.batch_size = int(self.batch_size)
self.output_batchSize_Tab_bgCorrection.emit(
self.batch_size)
dra_ = FUN_DRA(video=self.input_video,
object_update_progressBar=self.
object_update_progressBar)
dra_video = dra_.run_DRA_from_bgtabs(
mode_FPN=self.mode_FPN,
batch_size=self.batch_size,
flag_power_normalization=self.flag_power_normalization,
roi_x_pn=(self.s_x_win_pn, self.e_x_win_pn),
roi_y_pn=(self.s_y_win_pn, self.e_y_win_pn),
flag_FPN=self.flag_FPN,
axis=self.axis)
self.output = [dra_video, "DRA"]
self.output_Tab_bgCorrection.emit(self.output)
self.setting_bg_correction['mode_FPN'] = self.mode_FPN
self.setting_bg_correction[
'Batch_size (frames)'] = self.batch_size
self.setting_bg_correction[
'Power_Normalization'] = self.flag_power_normalization
self.setting_bg_correction['FPNc'] = self.flag_FPN
self.setting_bg_correction['FPNc_axis'] = self.axis
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
else:
self.msg_box = QtWidgets.QMessageBox()
self.msg_box.setWindowTitle("Warning!")
self.msg_box.setText("Please insert batch size!")
self.msg_box.exec_()
elif self.combo_bg_filter.currentText() == "Spatial median Filter":
median_size = self.line_edit1.text()
if median_size != '':
print("\nMedian is Applying--->", end='')
median_size = int(self.line_edit1.text())
blur = Filters(self.input_video)
blur_video = blur.median(median_size)
self.output = [blur_video, 'Spatial median Filter']
self.output_Tab_bgCorrection.emit(self.output)
self.setting_bg_correction[
'Spatial_median_kernel_size'] = median_size
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
self.output_batchSize_Tab_bgCorrection.emit(0)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Spatial gaussian Filter":
gaussian_sigma = self.line_edit2.text()
if gaussian_sigma != '':
print("\nGaussian is applying--->", end='')
gaussian_sigma = float(self.line_edit2.text())
blur = Filters(self.input_video)
blur_video = blur.gaussian(gaussian_sigma)
self.output = [blur_video, "Spatial gaussian Filter"]
self.output_Tab_bgCorrection.emit(self.output)
self.setting_bg_correction[
'Spatial_gaussian_sigma'] = gaussian_sigma
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
self.output_batchSize_Tab_bgCorrection.emit(0)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Background correction temporal median":
print("\nBackground correction temporal median--->", end='')
blur = Filters(self.input_video)
self.output = [
blur.temporal_median(),
"Background correction temporal median"
]
self.output_Tab_bgCorrection.emit(self.output)
self.output_batchSize_Tab_bgCorrection.emit(0)
print("Done!")
elif self.combo_bg_filter.currentText(
) == "Flat field (Gaussian filter)":
sigma = self.line_edit5.text()
if sigma != '':
print("\nBackground correction Flat Field--->", end='')
sigma = int(self.line_edit5.text())
blur = Filters(self.input_video)
self.output = [
blur.flat_field(sigma=sigma),
"Flat field (Gaussian filter)"
]
self.output_Tab_bgCorrection.emit(self.output)
self.setting_bg_correction['Flat_field_sigma'] = sigma
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
self.output_batchSize_Tab_bgCorrection.emit(0)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Flat field (mean background subtraction)":
if self.original_video_bg is not None:
print("\nBackground correction Flat Field back ground--->",
end='')
if self.original_video_bg.shape[1] == self.input_video.shape[1] and self.original_video_bg.shape[2] == \
self.input_video.shape[2]:
self.output = np.divide(
self.input_video,
np.mean(self.original_video_bg, axis=0))
self.output_Tab_bgCorrection.emit([
self.output,
"Flat field (mean background subtraction)"
])
self.output_batchSize_Tab_bgCorrection.emit(0)
print("Done!")
else:
self.flag_no_warning = False
self.msg_box1 = QtWidgets.QMessageBox()
self.msg_box1.setWindowTitle("Warning!")
self.msg_box1.setText(
"The size of these two videos is not the same!")
self.msg_box1.exec_()
else:
self.massage_filled()
else:
self.msg_box = QtWidgets.QMessageBox()
self.msg_box.setWindowTitle("Warning!")
self.msg_box.setText("Continuing without using any filter!")
self.msg_box.exec_()
self.output = self.input_video
self.output_Tab_bgCorrection.emit([self.output, 'RAW'])
self.output_batchSize_Tab_bgCorrection.emit(0)
self.update_tab_index.emit(1)
def on_select(self):
self.transform_algorithm = self.combo.currentText()
self.create_como_values()
def axis_selection(self):
if self.radio_cpFPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_wFPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_median_FPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_FFT2D_FPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
def layout_based_on_select_bg(self):
if self.combo_bg_filter.currentText(
) == "Differential rolling average":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.groupBatchSize = QtWidgets.QGroupBox("Batch size:")
self.le_batchSize = QtWidgets.QLineEdit()
self.le_batchSize.setPlaceholderText('radius')
self.le_batchSize_label = QtWidgets.QLabel("Batch size (frames):")
self.le_batchSize.setFixedWidth(50)
self.groupBox_PN = QtWidgets.QGroupBox(
"Laser Power normalization:")
self.groupBox_PN.setCheckable(True)
self.groupBox_PN.setChecked(False)
self.start_win_size_x = QtWidgets.QLineEdit()
self.start_win_size_x.setPlaceholderText('ROI X start')
self.start_win_size_x_label = QtWidgets.QLabel(
"start width pixel:")
self.end_win_size_x = QtWidgets.QLineEdit()
self.end_win_size_x.setPlaceholderText('ROI X end')
self.end_win_size_x_label = QtWidgets.QLabel("end width pixel:")
self.start_win_size_y = QtWidgets.QLineEdit()
self.start_win_size_y.setPlaceholderText('ROI Y start')
self.start_win_size_y_label = QtWidgets.QLabel(
"start hight pixel:")
self.end_win_size_y = QtWidgets.QLineEdit()
self.end_win_size_y.setPlaceholderText('ROI X end')
self.end_win_size_y_label = QtWidgets.QLabel("start hight pixel:")
self.selected_frame = QtWidgets.QLineEdit()
self.selected_frame.setPlaceholderText('selected frame')
self.selected_frame_label = QtWidgets.QLabel(
"selected preview frame:")
self.selected_frame.setText('0')
self.preview_roi = QtWidgets.QPushButton("ROI preview")
self.preview_roi.setAutoDefault(False)
self.preview_roi.clicked.connect(self.preview_roi_plot)
self.preview_roi.setFixedHeight(20)
self.preview_roi.setFixedWidth(100)
grid_pn = QtWidgets.QGridLayout()
grid_pn.addWidget(self.start_win_size_x_label, 0, 0)
grid_pn.addWidget(self.start_win_size_x, 0, 1)
grid_pn.addWidget(self.end_win_size_x_label, 0, 2)
grid_pn.addWidget(self.end_win_size_x, 0, 3)
grid_pn.addWidget(self.start_win_size_y_label, 1, 0)
grid_pn.addWidget(self.start_win_size_y, 1, 1)
grid_pn.addWidget(self.end_win_size_y_label, 1, 2)
grid_pn.addWidget(self.end_win_size_y, 1, 3)
grid_pn.addWidget(self.selected_frame_label, 2, 0)
grid_pn.addWidget(self.selected_frame, 2, 1)
grid_pn.addWidget(self.preview_roi, 2, 2)
self.groupBox_PN.setLayout(grid_pn)
grid_batch = QtWidgets.QGridLayout()
grid_batch.addWidget(self.le_batchSize_label, 0, 0)
grid_batch.addWidget(self.le_batchSize, 0, 1)
self.groupBatchSize.setLayout(grid_batch)
self.groupBox_FPNc = QtWidgets.QGroupBox("FPNc:")
self.groupBox_FPNc.setCheckable(True)
self.groupBox_FPNc.setChecked(False)
self.FPN_mode_group = QtWidgets.QButtonGroup()
self.radio_wFPN_mode = QtWidgets.QRadioButton("Wavelet FPNc")
self.radio_cpFPN_mode = QtWidgets.QRadioButton(
"Column_projection FPNc")
self.radio_median_FPN_mode = QtWidgets.QRadioButton("Median FPNc")
self.radio_FFT2D_FPN_mode = QtWidgets.QRadioButton("FFT2D FPNc")
self.FPN_mode_group.addButton(self.radio_wFPN_mode)
self.FPN_mode_group.addButton(self.radio_cpFPN_mode)
self.FPN_mode_group.addButton(self.radio_FFT2D_FPN_mode)
self.FPN_mode_group.addButton(self.radio_median_FPN_mode)
self.radio_wFPN_mode.toggled.connect(self.axis_selection)
self.radio_cpFPN_mode.toggled.connect(self.axis_selection)
self.radio_FFT2D_FPN_mode.toggled.connect(self.axis_selection)
self.radio_median_FPN_mode.toggled.connect(self.axis_selection)
self.axis_group = QtWidgets.QButtonGroup()
self.radio_axis_1 = QtWidgets.QRadioButton("FPNc in axis 0")
self.radio_axis_2 = QtWidgets.QRadioButton("FPNc in axis 1")
self.radio_axis_3 = QtWidgets.QRadioButton("FPNc in Both axis")
self.radio_axis_2.setChecked(True)
self.radio_cpFPN_mode.setChecked(True)
self.axis_group.addButton(self.radio_axis_1)
self.axis_group.addButton(self.radio_axis_2)
self.axis_group.addButton(self.radio_axis_3)
grid = QtWidgets.QGridLayout()
grid.addWidget(self.radio_cpFPN_mode, 0, 0)
grid.addWidget(self.radio_median_FPN_mode, 1, 0)
grid.addWidget(self.radio_wFPN_mode, 2, 0)
grid.addWidget(self.radio_FFT2D_FPN_mode, 3, 0)
grid.addWidget(self.radio_axis_1, 0, 1)
grid.addWidget(self.radio_axis_2, 1, 1)
# grid.addWidget(self.radio_axis_3, 2, 1)
self.groupBox_FPNc.setLayout(grid)
self.grid1.addWidget(self.groupBatchSize, 1, 0)
self.grid1.addWidget(self.groupBox_PN, 2, 0)
self.grid1.addWidget(self.groupBox_FPNc, 3, 0)
elif self.combo_bg_filter.currentText() == "Spatial median Filter":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit1 = QtWidgets.QLineEdit(self)
self.line_edit1_label = QtWidgets.QLabel("Neighborhood size (px):")
self.line_edit1.setFixedWidth(50)
self.grid1.addWidget(self.line_edit1_label, 2, 0)
self.grid1.addWidget(self.line_edit1, 2, 1)
elif self.combo_bg_filter.currentText() == "Spatial gaussian Filter":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit2 = QtWidgets.QLineEdit(self)
self.line_edit2_label = QtWidgets.QLabel("Sigma (px):")
self.line_edit2.setFixedWidth(50)
self.grid1.addWidget(self.line_edit2_label, 2, 0)
self.grid1.addWidget(self.line_edit2, 2, 1)
elif self.combo_bg_filter.currentText(
) == "Background correction temporal median":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
elif self.combo_bg_filter.currentText(
) == "Flat field (Gaussian filter)":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit5 = QtWidgets.QLineEdit(self)
self.line_edit5_label = QtWidgets.QLabel("Sigma (px):")
self.line_edit5.setFixedWidth(50)
self.grid1.addWidget(self.line_edit5_label, 2, 0)
self.grid1.addWidget(self.line_edit5, 2, 1)
elif self.combo_bg_filter.currentText(
) == "Flat field (mean background subtraction)":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.btn_read_file = QtWidgets.QPushButton("load")
self.btn_read_file.setAutoDefault(False)
self.btn_read_file.clicked.connect(self.load_video)
self.btn_read_file.setFixedHeight(20)
self.btn_read_file.setFixedWidth(50)
self.grid1.addWidget(self.btn_read_file, 1, 0)
def remove_widgets(self):
for i_ in range(0, 7, 1):
for j_ in range(0, 7, 1):
if i_ == 0 and j_ == 0:
pass
else:
layout = self.grid1.itemAtPosition(i_, j_)
if layout is not None:
layout.widget().deleteLater()
self.grid1.removeItem(layout)
self.flag_remove_box = False
def load_video(self):
self.reading = Reading()
self.reading.update_output.connect(self.updata_bg_video)
self.reading.read_video()
def updata_bg_video(self, video_in):
self.original_video_bg = video_in[0]
def preview_roi_plot(self, selected_frame):
if self.groupBox_PN.isChecked():
self.flag_power_normalization = True
try:
self.s_x_win_pn = int(self.start_win_size_x.text())
self.e_x_win_pn = int(self.end_win_size_x.text())
self.s_y_win_pn = int(self.start_win_size_y.text())
self.e_y_win_pn = int(self.end_win_size_y.text())
selected_frame = int(self.selected_frame.text())
img_ = self.input_video[selected_frame, :, :]
roi_img_ = img_[self.s_x_win_pn:self.e_x_win_pn,
self.s_y_win_pn:self.e_y_win_pn]
fig, ax = plt.subplots()
ax.imshow(img_, cmap='gray')
rect = patches.Rectangle((self.s_x_win_pn, self.s_y_win_pn),
roi_img_.shape[0],
roi_img_.shape[1],
linewidth=2,
edgecolor='r',
facecolor='none')
ax.add_patch(rect)
plt.show()
except:
self.msg_box1 = QtWidgets.QMessageBox()
self.msg_box1.setWindowTitle("Warning!")
self.msg_box1.setText("The ROI is not defined!")
self.msg_box1.exec_()
def closeEvent(self, event):
QtCore.QCoreApplication.instance().quit()
def read_data(self):
reading = Reading()
reading.update_output.connect(self.updata_input_setting)
reading.load_batch_data()
class BgCorrection_GUI(QtWidgets.QWidget):
output_setting_Tab_bgCorrection = QtCore.Signal(object)
update_tab_index = QtCore.Signal(int)
def __init__(self, parent=None):
super(BgCorrection_GUI, self).__init__(parent)
self.different_views = {}
self.setting_bg_correction = {}
self.flag_remove_box = True
self.flag_update_class = True
self.flag_hotPixels = False
self.empty_value_box_flag = False
self.flag_no_warning = True
self.transform_algorithm = None
self.n_comp = None
self.n_iter = None
self.alpha = None
self.random_select = None
self.non_zero_coeff = None
self.patch_size = None
self.strides = None
self.resize(600, 600)
self.setWindowTitle('Background Correction')
self.combo_bg_filter = QtWidgets.QComboBox(self)
self.combo_bg_filter.addItem(
"-Select the background correction methods-")
self.combo_bg_filter.addItem("Differential rolling average")
self.combo_bg_filter.addItem("Spatial median Filter")
self.combo_bg_filter.addItem("Spatial gaussian Filter")
self.combo_bg_filter.addItem("Background correction temporal median")
self.combo_bg_filter.addItem("Flat field (Gaussian filter)")
self.combo_bg_filter.addItem(
"Flat field (mean background subtraction)")
self.combo_bg_filter.currentIndexChanged.connect(
self.layout_based_on_select_bg)
self.btn = QtWidgets.QPushButton("Next")
self.btn.setAutoDefault(False)
self.btn.clicked.connect(self.do_update)
self.btn.setFixedWidth(70)
self.btn.setFixedHeight(20)
self.grid = QtWidgets.QGridLayout()
self.grid.addWidget(self.combo_bg_filter, 0, 0)
self.grid.addWidget(self.createFirstExclusiveGroup(), 1, 0)
self.grid.addWidget(self.btn, 2, 0)
self.setLayout(self.grid)
def __del__(self):
print('Destructor called, Employee deleted.')
def createFirstExclusiveGroup(self):
self.groupBox_update = QtWidgets.QGroupBox(
"Background correction Setting:")
self.grid1 = QtWidgets.QGridLayout()
self.groupBox_update.setLayout(self.grid1)
return self.groupBox_update
def massage_filled(self):
self.flag_no_warning = False
self.msg_box1 = QtWidgets.QMessageBox()
self.msg_box1.setWindowTitle("Warning!")
self.msg_box1.setText("Please filled all parameters!")
self.msg_box1.exec_()
@QtCore.Slot()
def do_update(self):
if self.btn.clicked:
if self.combo_bg_filter.currentText(
) == "Differential rolling average":
self.batch_size = self.le_batchSize.text()
if self.groupBox_FPNc.isChecked():
self.flag_FPN = True
if self.radio_axis_1.isChecked():
self.axis = 0
elif self.radio_axis_2.isChecked():
self.axis = 1
elif self.radio_axis_3.isChecked():
self.axis = 'Both'
if self.radio_cpFPN_mode.isChecked():
self.mode_FPN = 'cpFPN'
elif self.radio_wFPN_mode.isChecked():
self.mode_FPN = 'wFPN'
elif self.radio_FFT2D_FPN_mode.isChecked():
self.mode_FPN = 'fFPN'
elif self.radio_median_FPN_mode.isChecked():
self.mode_FPN = 'mFPN'
else:
self.flag_FPN = False
self.axis = 0
self.mode_FPN = 'fFPN'
if self.checkbox_power_normalization.isChecked():
self.flag_power_normalization = True
else:
self.flag_power_normalization = False
if self.checkbox_hotPixels.isChecked():
self.flag_hotPixels = True
else:
self.flag_hotPixels = False
if self.batch_size != '':
self.batch_size = int(self.batch_size)
self.setting_bg_correction['type_BGc'] = 'DRA'
self.setting_bg_correction['mode_FPN'] = self.mode_FPN
self.setting_bg_correction[
'Batch_size (frames)'] = self.batch_size
self.setting_bg_correction[
'Power_Normalization'] = self.flag_power_normalization
self.setting_bg_correction['FPNc'] = self.flag_FPN
self.setting_bg_correction['FPNc_axis'] = self.axis
self.setting_bg_correction[
'filter_hotPixels'] = self.flag_hotPixels
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
else:
self.msg_box = QtWidgets.QMessageBox()
self.msg_box.setWindowTitle("Warning!")
self.msg_box.setText("Please insert batch size!")
self.msg_box.exec_()
elif self.combo_bg_filter.currentText() == "Spatial median Filter":
median_size = self.line_edit1.text()
if median_size != '':
print("\nMedian is Applying--->", end='')
median_size = int(self.line_edit1.text())
self.setting_bg_correction[
'type_BGc'] = 'Spatial median Filter'
self.setting_bg_correction[
'Spatial_median_kernel_size'] = median_size
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Spatial gaussian Filter":
gaussian_sigma = self.line_edit2.text()
if gaussian_sigma != '':
print("\nGaussian is applying--->", end='')
gaussian_sigma = float(self.line_edit2.text())
self.setting_bg_correction[
'type_BGc'] = 'Spatial gaussian Filter'
self.setting_bg_correction[
'Spatial_gaussian_sigma'] = gaussian_sigma
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Background correction temporal median":
print("\nBackground correction temporal median--->", end='')
self.setting_bg_correction[
'type_BGc'] = 'Background correction temporal median'
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
print("Done!")
elif self.combo_bg_filter.currentText(
) == "Flat field (Gaussian filter)":
sigma = self.line_edit5.text()
if sigma != '':
print("\nBackground correction Flat Field--->", end='')
sigma = int(self.line_edit5.text())
self.setting_bg_correction[
'type_BGc'] = 'Flat field (Gaussian filter)'
self.setting_bg_correction['Flat_field_sigma'] = sigma
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
print("Done!")
else:
self.massage_filled()
elif self.combo_bg_filter.currentText(
) == "Flat field (mean background subtraction)":
if self.original_video_bg is not None:
print("\nBackground correction Flat Field back ground--->",
end='')
self.setting_bg_correction[
'type_BGc'] = 'Flat field (mean background subtraction)"'
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
print("Done!")
else:
self.massage_filled()
else:
self.msg_box = QtWidgets.QMessageBox()
self.msg_box.setWindowTitle("Warning!")
self.msg_box.setText("Continuing without using any filter!")
self.msg_box.exec_()
self.setting_bg_correction['type_BGc'] = 'RAW'
self.output_setting_Tab_bgCorrection.emit(
self.setting_bg_correction)
self.update_tab_index.emit(2)
def on_select(self):
self.transform_algorithm = self.combo.currentText()
self.create_como_values()
def axis_selection(self):
if self.radio_cpFPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_wFPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_median_FPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
elif self.radio_FFT2D_FPN_mode.isChecked():
self.radio_axis_1.setEnabled(True)
self.radio_axis_2.setEnabled(True)
self.radio_axis_3.setEnabled(True)
def layout_based_on_select_bg(self):
if self.combo_bg_filter.currentText(
) == "Differential rolling average":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.groupBatchSize = QtWidgets.QGroupBox("Batch size:")
self.le_batchSize = QtWidgets.QLineEdit()
self.le_batchSize.setPlaceholderText('radius')
self.le_batchSize_label = QtWidgets.QLabel("Batch size (frames):")
self.le_batchSize.setFixedWidth(50)
self.checkbox_power_normalization = QtWidgets.QCheckBox(
"Laser power normalization", self)
self.checkbox_hotPixels = QtWidgets.QCheckBox(
"Hot pixels correction", self)
grid_batch = QtWidgets.QGridLayout()
grid_batch.addWidget(self.le_batchSize_label, 0, 0)
grid_batch.addWidget(self.le_batchSize, 0, 1)
grid_batch.addWidget(self.checkbox_power_normalization, 1, 0)
grid_batch.addWidget(self.checkbox_hotPixels, 2, 0)
self.groupBatchSize.setLayout(grid_batch)
self.groupBox_FPNc = QtWidgets.QGroupBox("FPNc:")
self.groupBox_FPNc.setCheckable(True)
self.groupBox_FPNc.setChecked(False)
self.FPN_mode_group = QtWidgets.QButtonGroup()
self.radio_wFPN_mode = QtWidgets.QRadioButton("Wavelet FPNc")
self.radio_cpFPN_mode = QtWidgets.QRadioButton(
"Column_projection FPNc")
self.radio_median_FPN_mode = QtWidgets.QRadioButton("Median FPNc")
self.radio_FFT2D_FPN_mode = QtWidgets.QRadioButton("FFT2D FPNc")
self.FPN_mode_group.addButton(self.radio_wFPN_mode)
self.FPN_mode_group.addButton(self.radio_cpFPN_mode)
self.FPN_mode_group.addButton(self.radio_FFT2D_FPN_mode)
self.FPN_mode_group.addButton(self.radio_median_FPN_mode)
self.radio_wFPN_mode.toggled.connect(self.axis_selection)
self.radio_cpFPN_mode.toggled.connect(self.axis_selection)
self.radio_FFT2D_FPN_mode.toggled.connect(self.axis_selection)
self.radio_median_FPN_mode.toggled.connect(self.axis_selection)
self.axis_group = QtWidgets.QButtonGroup()
self.radio_axis_1 = QtWidgets.QRadioButton("FPNc in axis 0")
self.radio_axis_2 = QtWidgets.QRadioButton("FPNc in axis 1")
self.radio_axis_3 = QtWidgets.QRadioButton("FPNc in Both axis")
self.radio_axis_2.setChecked(True)
self.radio_cpFPN_mode.setChecked(True)
self.axis_group.addButton(self.radio_axis_1)
self.axis_group.addButton(self.radio_axis_2)
self.axis_group.addButton(self.radio_axis_3)
grid = QtWidgets.QGridLayout()
grid.addWidget(self.radio_cpFPN_mode, 0, 0)
grid.addWidget(self.radio_median_FPN_mode, 1, 0)
grid.addWidget(self.radio_wFPN_mode, 2, 0)
grid.addWidget(self.radio_FFT2D_FPN_mode, 3, 0)
grid.addWidget(self.radio_axis_1, 0, 1)
grid.addWidget(self.radio_axis_2, 1, 1)
grid.addWidget(self.radio_axis_3, 2, 1)
self.groupBox_FPNc.setLayout(grid)
self.grid1.addWidget(self.groupBatchSize, 1, 0)
self.grid1.addWidget(self.groupBox_FPNc, 2, 0)
elif self.combo_bg_filter.currentText() == "Spatial median Filter":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit1 = QtWidgets.QLineEdit(self)
self.line_edit1_label = QtWidgets.QLabel("Neighborhood size (px):")
self.line_edit1.setFixedWidth(50)
self.grid1.addWidget(self.line_edit1_label, 2, 0)
self.grid1.addWidget(self.line_edit1, 2, 1)
elif self.combo_bg_filter.currentText() == "Spatial gaussian Filter":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit2 = QtWidgets.QLineEdit(self)
self.line_edit2_label = QtWidgets.QLabel("Sigma (px):")
self.line_edit2.setFixedWidth(50)
self.grid1.addWidget(self.line_edit2_label, 2, 0)
self.grid1.addWidget(self.line_edit2, 2, 1)
elif self.combo_bg_filter.currentText(
) == "Background correction temporal median":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
elif self.combo_bg_filter.currentText(
) == "Flat field (Gaussian filter)":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.line_edit5 = QtWidgets.QLineEdit(self)
self.line_edit5_label = QtWidgets.QLabel("Sigma (px):")
self.line_edit5.setFixedWidth(50)
self.grid1.addWidget(self.line_edit5_label, 2, 0)
self.grid1.addWidget(self.line_edit5, 2, 1)
elif self.combo_bg_filter.currentText(
) == "Flat field (mean background subtraction)":
while self.flag_remove_box:
self.remove_widgets()
self.flag_remove_box = True
self.btn_read_file = QtWidgets.QPushButton("load")
self.btn_read_file.setAutoDefault(False)
self.btn_read_file.clicked.connect(self.load_video)
self.btn_read_file.setFixedHeight(20)
self.btn_read_file.setFixedWidth(50)
self.grid1.addWidget(self.btn_read_file, 1, 0)
def remove_widgets(self):
for i_ in range(0, 7, 1):
for j_ in range(0, 7, 1):
if i_ == 0 and j_ == 0:
pass
else:
layout = self.grid1.itemAtPosition(i_, j_)
if layout is not None:
layout.widget().deleteLater()
self.grid1.removeItem(layout)
self.flag_remove_box = False
def load_video(self):
self.reading = Reading()
self.reading.update_output.connect(self.updata_bg_video)
self.reading.read_video()
def closeEvent(self, event):
QtCore.QCoreApplication.instance().quit()