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 process_pi_signal(path, position, unsynchronized=True): if unsynchronized: path_signal = path + "\\pi" path_signal_before = path_signal + "\\before" path_signal_after = path_signal + "\\after" path_signal_merged = path_signal + "\\merged" path_imp_before = path_signal_before + "\\pi_in-focusxy%sc1.tif" % position path_imp_after = path_signal_after + "\\pixy%sc1.tif" % position path_imp_merged = path_signal_merged + "\\merged.tif" path_imp_merged_sub = path_signal_merged + "\\merged_sub.tif" imp1 = IJ.openImage(path_imp_before) imp1.show() imp2 = IJ.openImage(path_imp_after) imp2.show() zp1 = ZProjector(imp1) zp1.setMethod(ZProjector.AVG_METHOD) zp1.doProjection() zpimp1 = zp1.getProjection() zp2 = ZProjector(imp2) zp2.setMethod(ZProjector.AVG_METHOD) zp2.doProjection() zpimp2 = zp2.getProjection() imp_sub1 = ImageCalculator().run("Subtract create stack", imp1, zpimp1) imp_sub1.show() imp_sub2 = ImageCalculator().run("Subtract create stack", imp2, zpimp2) imp_sub2.show() concatenate_files(imp1, imp2, path_imp_merged) concatenate_files(imp_sub1, imp_sub2, path_imp_merged_sub) else: path_signal = path + "\\pi\\seq0002xy%sc1.tif" % position path_sub = path + "\\pi\\sub.tif" imp = IJ.openImage(path_signal) imp.show() zp = ZProjector(imp) zp.setMethod(ZProjector.AVG_METHOD) zp.doProjection() zpimp = zp.getProjection() imp_sub = ImageCalculator().run("Subtract create stack", imp, zpimp) imp_sub.show() IJ.saveAs(imp_sub, "Tiff", path_sub) imp.changes = False imp.close() zpimp.changes = False zpimp.close() imp_sub.changes = False imp_sub.close()
def process_caspase_signal(path_signal, path_imp, path_imp_out): path_imp = path_signal + path_imp imp = IJ.openImage(path_imp) imp.show() zp = ZProjector(imp) zp.setMethod(ZProjector.AVG_METHOD) zp.doProjection() zpimp = zp.getProjection() imp_sub = ImageCalculator().run("Subtract create stack", imp, zpimp) imp_sub.show() IJ.saveAs(imp_sub, "Tiff", path_signal + path_imp_out) imp.changes = False imp.close() imp_sub.changes = False imp_sub.close()
IJ.run(imp, "Duplicate...", "title=wy") #create wy by rotating wx by 90 degrees IJ.run("Rotate 90 Degrees Left") imp2 = IJ.getImage() imp2.changes = False #integration in the phase domain by shifting Pi/2, see equation 21 in Frankot-Chellapa A = ImageCalculator().run("Multiply create 32-bit stack", DZDX, imp) B = ImageCalculator().run("Multiply create 32-bit stack", DZDY, imp2) # numerator of C = ImageCalculator().run("Add create 32-bit stack", A, B) # eq 21 D = ImageCalculator().run("Multiply create 32-bit", imp, imp) # square wx E = ImageCalculator().run("Multiply create 32-bit", imp2, imp2) # square wy F = ImageCalculator().run("Add create 32-bit", D, E) # demnominator of eq 21 Z = ImageCalculator().run("Divide create 32-bit stack", C, F) # solve eq 21 Z.show() IJ.run("Inverse FFT") #results of integration IJ.run( "Stack to Images" ) #separate real and imaginary... why does imaginary produce result? more reading needed. #clean-up by closing un-necessary images imp2.close() DZDX.close() DZDY.close() imp.changes = False imp.close() A.changes = False A.close() Z.close()