def get_setup():
''' Returns the drift correction mode and three image.
The order of return values is drift detection mode, pre-edge 1, pre-edge 2, post-edge.
'''
options = drift.get_options()
modes = drift.get_modes()
dialog = GenericDialog('3-window-method setup')
dialog.addMessage('Select the mode for drift correction\n' +
'and the images to process.')
dialog.addChoice('Mode:', options, options[0])
image_ids = WindowManager.getIDList()
if not image_ids or len(image_ids) < 2:
return [None]*4
image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
dialog.addMessage('Post-edge is divided by the pre-edge.')
dialog.addChoice('Pre-edge 1', image_titles, image_titles[0])
dialog.addChoice('Pre-edge 2', image_titles, image_titles[1])
dialog.addChoice('Post-edge', image_titles, image_titles[2])
dialog.showDialog()
if dialog.wasCanceled():
return [None]*4
mode = modes[dialog.getNextChoiceIndex()]
img1 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
img2 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
img3 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
return mode, img1, img2, img3
def correct_drift_gui():
"""
This function combines the image selection and drift correction.
There is no returned value.
"""
img1, img2 = select_images()
if img1 and img2:
drift.correct_drift(img1, img2, True)
def run_script():
'''Function to be run when this file is used as a script'''
selected_mode, img1_in, img2_in = get_setup()
if not selected_mode:
return
corrected_stack = drift.get_corrected_stack((img1_in, img2_in), mode=selected_mode)
img1, img2 = tools.stack_to_list_of_imp(corrected_stack)
img_ratio = ImageCalculator().run('Divide create', img2, img1)
img_ratio.setTitle('Jump-ratio [%s divided by %s]' % (img2.getShortTitle(),
img1.getShortTitle())
)
img_ratio.changes = True
img_ratio.copyScale(img1_in)
img_ratio.show()
IJ.run(img_ratio, 'Enhance Contrast', 'saturated=0.35')
# We want to optimise the lower displaylimit:
minimum = img_ratio.getProcessor().getMin()
maximum = img_ratio.getProcessor().getMax()
stat = img_ratio.getStatistics(Stats.MEAN + Stats.STD_DEV)
mean = stat.mean
stdv = stat.stdDev
if minimum < mean - stdv:
if mean - stdv >= 0:
img_ratio.getProcessor().setMinAndMax(mean - stdv, maximum)
else:
img_ratio.getProcessor().setMinAndMax(0, maximum)
img_ratio.updateAndDraw()
def run_script():
"""Function to be run when this file is used as a script"""
images = tools.get_images()
if not images:
return
elif len(images) >= 2:
corrected_stack = drift.get_corrected_stack(images, "SIFT")
corrected_stack.copyScale(images[0])
corrected_stack.show()
def run_script():
'''Function to be run when this file is used as a script'''
images = tools.get_images()
if not images:
return
elif len(images) >= 2:
corrected_stack = drift.get_corrected_stack_linear(images, 'CC')
corrected_stack.copyScale(images[0])
corrected_stack.show()
def get_setup():
''' Returns the drift correction mode and two image.'''
options = drift.get_options()
modes = drift.get_modes()
dialog = GenericDialog('Jump-ratio setup')
dialog.addMessage('Select the mode for drift correction\n' +
'and the images to process.')
dialog.addChoice('Mode:', options, options[0])
image_ids = WindowManager.getIDList()
if not image_ids or len(image_ids) < 2:
return [None]*3
image_titles = [WindowManager.getImage(id).getTitle() for id in image_ids]
dialog.addMessage('Post-edge is divided by the pre-edge.')
dialog.addChoice('Pre-edge', image_titles, image_titles[0])
dialog.addChoice('Post-edge', image_titles, image_titles[1])
dialog.showDialog()
if dialog.wasCanceled():
return [None]*3
mode = modes[dialog.getNextChoiceIndex()]
img1 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
img2 = WindowManager.getImage(image_ids[dialog.getNextChoiceIndex()])
return mode, img1, img2
def run_script():
'''Function to be run when this file is used as a script'''
selected_mode, pre1_in, pre2_in, post_in = get_setup()
if not selected_mode:
return
corrected_stack = drift.get_corrected_stack((pre1_in, pre2_in, post_in), mode=selected_mode)
pre1_imp, pre2_imp, post_imp = tools.stack_to_list_of_imp(corrected_stack)
mapping = ElementalMapping.ThreeWindow(pre1_imp, pre2_imp, post_imp)
map_imp, snr_imp, r_imp, lna_imp = mapping.get_result()
for imp in (map_imp, snr_imp, r_imp, lna_imp):
imp.copyScale(post_in)
show_imp(imp)