def imageStackOpened(self):
# Add in a new tab
self.parent.imageTabDisplay.newTab(self.image_class)
# Do background correction if required
if self.backgroundCorrectionCheckBox.isChecked():
# Open the progress window
openWindow(self.parent, ImageCorrectionProgressBarWindow,
'progress_bar')
# Get the settings in memory
do_median = self.parent.config.background_type == 'Median'
do_division = self.parent.config.correction_type == 'Division'
do_intensity_correction = self.parent.config.correct_intensity
replace_tab = not self.parent.config.correct_newtab
# Apply the background correction
corrected_array = backgroundCorrection(
self.image_class.image.source,
median=do_median,
divide=do_division)
# Apply the intensity fluctuation correction - if required
if do_intensity_correction:
_intensity_correction_type = self.parent.config.intensity_correction_type.lower(
)
corrected_array = intensityCorrection(
corrected_array, correction=_intensity_correction_type)
# Load the array in a file
new_class = ImageCollection(corrected_array,
name=self.image_class.name.strip() +
' (Corrected)',
space_scale=self.parent.space_scale,
space_unit=self.parent.space_unit,
frame_rate=self.parent.frame_rate)
# Update the current tab
if replace_tab:
# Get the current tab
tab_id = self.parent.imageTabDisplay.currentIndex()
# Update the tab
new_class.name = self.image_class.name
self.parent.imageTabDisplay.replaceTab(tab_id, new_class)
# Create a new tab
else:
self.parent.imageTabDisplay.newTab(new_class)
# Close the progress window
self.parent.subWindows['progress_bar'].close()
self.parent.application.processEvents()
# Close the current window
self.close()
def processImage(self):
# Retrieve the user selection
do_division = self.correctionTypeComboBox.currentText() == 'Division'
do_median = self.backgroundTypeComboBox.currentText() == 'Median'
do_intensity_correction = self.correctFluctuationsCheckBox.isChecked()
do_crop = self.cropCheckBox.isChecked()
crop_size = int(self.cropSizeEntry.text())
do_bit_correction = self.signCorrectionCheckBox.isChecked()
replace_tab = self.replaceTabCheckBox.isChecked()
# Crop the image - if required
if do_crop:
self.image_array = cropImage(self.image_array, (crop_size,crop_size))
# Correct signed bits image - if required
if do_bit_correction:
self.image_array = correctSignedBits(self.image_array)
# Open the progress window
openWindow(self.parent, ImageCorrectionProgressBarWindow, 'progress_bar')
# Apply the background correction
self.image_array = backgroundCorrection(self.image_array, median=do_median, divide=do_division)
# Apply the intensity fluctuation correction - if required
if do_intensity_correction:
self.image_array = intensityCorrection(self.image_array)
# Get the current tab
tab_id = self.parent.imageTabDisplay.currentIndex()
old_class = self.parent.imageTabDisplay.displayedTabs[tab_id].image_class
# Load the array in a file
new_class = ImageCollection(self.image_array, name=old_class.name.strip()+' (Corrected)', space_scale=old_class.scale.space_scale, space_unit=old_class.scale.space_unit, frame_rate=old_class.scale.frame_rate)
# Update the current tab
if replace_tab:
new_class.name = old_class.name
self.parent.imageTabDisplay.replaceTab(tab_id, new_class)
# Create a new tab
else:
self.parent.imageTabDisplay.newTab(new_class)
# Close the progress window
self.parent.subWindows['progress_bar'].close()
self.parent.application.processEvents()
# Close the window
self.close()
def correctFluctuations(self):
# Get the settings
correction_type = self.correctionSelectionBox.currentText().lower()
# Check the fluctuations values
do_correction = True
if self.variations_value < 0.01:
do_correction = warningProceedMessage(
'Low intensity fluctuations',
'The measured intensity fluctuations are below 0.01% of the mean intensity. Performing a correction might not improve the quality of the signal. Proceed anyway?'
)
# Do the correction if accepted
if do_correction:
# Open the progress window
openWindow(self.parent, ImageCorrectionProgressBarWindow,
'progress_bar')
self.image_array = intensityCorrection(self.image_array,
correction=correction_type)
# Get the current tab
tab_id = self.parent.imageTabDisplay.currentIndex()
use_name = self.parent.imageTabDisplay.displayedTabs[
tab_id].image_class.name
# Load the array in a file
new_class = ImageCollection(self.image_array,
name=use_name,
space_scale=self.parent.space_scale,
space_unit=self.parent.space_unit,
frame_rate=self.parent.frame_rate)
# Refresh the tab
self.parent.imageTabDisplay.replaceTab(tab_id, new_class)
# Close the progress window
self.parent.subWindows['progress_bar'].close()
self.parent.application.processEvents()
# Close the window
self.close()