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 drift_vector_from_drift_matrix(drift_matrix):
''' Returns a list of tuples that represents the optimized drift vector.
:param drift_matrix: A NxN matrix that contains the measured drift between N images.
'''
barycenters = [tools.mean_of_list_of_tuples(row) for row in drift_matrix]
# print 'List of centers: ', centers
mod_matrix = [[tuple(map(operator.sub, cell, barycenters[i]))
for cell in row]
for i, row in enumerate(drift_matrix)]
# print 'Modified drift matrix:'
# pprint.pprint(mod_matrix)
rot_matrix = [list(x) for x in zip(*mod_matrix)]
# print 'Rotated matrix:'
# pprint.pprint(rot_matrix)
drift_vector = [tup
for tup in [tools.mean_of_list_of_tuples(row)
for row in rot_matrix
]
]
return drift_vector
def get_corrected_stack_using_vector(images, drift_vector, suffix=''):
''' Returns a drift corrected stack using the given drift vector.
:param images: A list of length N containing ImagePlus objects.
:param drift_matrix: A list of length N that contains the measured drift.
'''
shift_vector = shift_vector_from_drift_vector(drift_vector)
stack = tools.stack_from_list_of_imp(shift_images(images, shift_vector))
title = 'Drift corrected stack'
if suffix:
title += ' (%s)' % (suffix)
corrected_stack = ImagePlus(title, stack)
return corrected_stack
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)
