def averageCompleted(self, averaged_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(averaged_array,
name=old_class.name.strip() +
' (Averaged)',
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 self.replaceTabCheckBox.isChecked():
new_class.name = old_class.name
self.parent.imageTabDisplay.replaceTab(tab_id, new_class)
self.parent.animationControl.setNFrames(new_class.n_frames)
# Create a new tab
else:
self.parent.imageTabDisplay.newTab(new_class)
# Close the window
self.close()
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 applyCrop(self):
# Get the final crop value
crop_size = int(self.sizeEntry.text())
# Crop the array
array = centerCrop(self.image_class.image.source,
self.image_class.trajectory, self.path_id)
new_array = cropImage(array, (crop_size, crop_size))
# Prepare the new array
new_name = self.image_class.name + ' (' + str(self.path_id) + ')'
space_scale = self.image_class.scale.space_scale
space_unit = self.image_class.scale.space_unit
frame_rate = self.image_class.scale.frame_rate
# Generate the class
new_class = ImageCollection(new_array,
name=new_name,
space_scale=space_scale,
space_unit=space_unit,
frame_rate=frame_rate)
# Open the new tab
self.parent.imageTabDisplay.newTab(new_class)
# Close the image
self.close()
def substackTab(self, tab_id=0):
# Get the user selection
_frame_text = """Enter a range (e.g. 2-14), a range with increment
(e.g. 1-100-2) or a list (e.g. 7,9,25,27)"""
selection, is_ok = qtw.QInputDialog.getText(self.parent,
'Substack Maker',
_frame_text,
text="")
if is_ok:
# Convert the input into a list of frames
selected_frames = getSubstackSelection(selection)
# Get the previous array
old_array = self.displayedTabs[tab_id].image_class.image.source
old_class = self.displayedTabs[tab_id].image_class
# Make the new frame selection
substack_array = makeSubstack(old_array, selected_frames)
# Get the new class name
old_name = old_class.name.strip() + " (substack)"
new_name, is_ok = qtw.QInputDialog.getText(self,
'Copy Tab',
'Enter the new name:',
text=old_name)
if not is_ok:
new_name = old_name
# Make a new class and replace the values
new_class = ImageCollection(substack_array, name=new_name)
new_class.scale = old_class.scale
new_class.zoom = old_class.zoom
new_class.contrast_limits = old_class.contrast_limits
new_class.bitness = old_class.bitness
# Prepare the image for display
new_class.rescaleForDisplay()
# Add the trajectory if needed
if old_class.trajectory is not None:
new_trajectory = substackTrajectory(old_class.trajectory,
selected_frames)
new_class.trajectory = new_trajectory
# Create the new tab
self.newTab(new_class)
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()
def cropImage(self):
# Raise an error if there is no selection
if self.selection_pointA is None or self.selection_pointB is None:
errorMessage("No Selection",
"A selection is required to crop the image.")
# Crop the image
else:
# Get the selection
selection = qtc.QRect(self.selection_pointA, self.selection_pointB)
origin = int(selection.x() / self.zoom), int(selection.y() /
self.zoom)
dimensions = int(selection.width() / self.zoom), int(
selection.height() / self.zoom)
# Get the current tab
tab_id = self.parent.imageTabDisplay.currentIndex()
old_class = self.parent.imageTabDisplay.displayedTabs[
tab_id].image_class
# Crop the array
new_array = cropImage(old_class.image.source,
dimensions,
origin=origin)
# Load the array in a file
new_class = ImageCollection(new_array,
name=old_class.name,
space_scale=self.parent.space_scale,
space_unit=self.parent.space_unit,
frame_rate=self.parent.frame_rate)
# Replace the array in the tab
self.parent.imageTabDisplay.replaceTab(tab_id, new_class)
# Close the image
self.close()
def loadImages(file_path,
name='Untitled',
open_range=None,
crop=False,
crop_size=152,
correct_sign=False,
space_scale=44.9,
space_unit="micron",
frame_rate=150):
# Open the image array
image_array = _open_image(file_path, open_range=open_range)
# Load the array in the class
image_instance = ImageCollection(image_array,
name=name,
crop=crop,
crop_size=crop_size,
correct_sign=correct_sign,
space_scale=space_scale,
space_unit=space_unit,
frame_rate=frame_rate)
return image_instance