def main(): #filename = sys.argv[1] #exportDir = sys.argv[2] inputDir = "/mnt/med-groups-lmu/ls1/users/l/lsalomie/" defaultName = "lif.lif" outputDir = "/home/hajaalin/tmp/lifexporttest" filename = OpenDialog("Choose LIF",inputDir,defaultName).getPath() if not filename: # user canceled dialog return chooser = DirectoryChooser("Choose export directory") chooser.setDefaultDirectory(outputDir) exportDir = chooser.getDirectory() if not exportDir: # user canceled dialog return # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 worker = EdfWorker(exportDir,params) iterateLif(filename,worker)
from edfgui import ExtendedDepthOfFieldHeadless from edfgui import Parameters imp = IJ.openImage("http://imagej.nih.gov/ij/images/mri-stack.zip"); imp.show() # remove for headless IJ.log("EDF: start...") parameters = Parameters() parameters.setQualitySettings(1) parameters.setTopologySettings(0) parameters.show3dView = False parameters.showTopology = False edfh = ExtendedDepthOfFieldHeadless(imp, parameters) impedf = edfh.processHeadless() IJ.log("EDF: done.") impedf.show() # remove for headless
import glob import os.path import sys from ij import IJ, ImagePlus, ImageStack, WindowManager from ij.io import DirectoryChooser from edfgui import ExtendedDepthOfField, Parameters file_in = sys.argv[1] file_out = sys.argv[2] # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 # read input image imp = ImagePlus(file_in) # make all-in-focus image edf = ExtendedDepthOfField(imp,params) edf.process() # save output imp = WindowManager.getCurrentImage() IJ.saveAsTiff(imp,file_out) imp.close()
import os.path import sys from ij import IJ, ImagePlus, ImageStack, WindowManager from edf import EdfComplexWavelets, PostProcessing, Tools from edfgui import ExtendedDepthOfField, Parameters from imageware import Builder, ImageWare from optparse import OptionParser # REAL_WAVELETS = 2 COMPLEX_WAVELETS = 3 # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 # # this is a reproduction of method "process" in edfgui.ExtendedDepthOfField. # def process(imp): isExtended = False waveletMethod = params.edfMethod == REAL_WAVELETS \ or params.edfMethod == COMPLEX_WAVELETS stackConverted = None impConverted = None impBW = imp
def process(dirIn, dirOut, expName, ps, pe, ts, te): jobid = commands.getoutput("echo $PBS_JOBID").split('.')[0] jobid = jobid.replace("[","_").replace("]","") # because the jobids look like 2356385[1] which causes problems print "job id: "+jobid jobdir = os.path.join("/tmp",str(jobid)+"_fiji") print "job dir: "+jobdir for p in range(ps,pe+1): pID = str(p); for t in range(ts,te+1): print "TIMEPOINT STARTING ***************" tID = "t"+str(t); print "time-point: "+tID; if os.path.isdir(jobdir): print "removing "+jobdir shutil.rmtree(jobdir) print "creating "+jobdir os.mkdir(jobdir) if stitching: fileOut = "rescaled_flipped_"; for z in range(zs,ze+1): zID = "z"+str(z); print "z-plane: "+zID; if bandpass: IJ.log("bandpass....") # load all images from same time point and same z-position fileID = expName+pID+"_b0"+tID+zID+"m.*"; IJ.log("opening images: "+os.path.join(dirIn,fileID)) IJ.run("Image Sequence...", "open=["+dirIn+"] starting=1 increment=1 scale=100 file=[] or=["+fileID+"] sort"); #selectWindow("im-2012-0007_Position35.tif_Files"); imp = IJ.getImage(); #imp.show(); imp.setTitle("Stack"); # illumination correction IJ.log("computing FFT..."); # run("Flip Horizontally", "stack"); impFFT = Duplicator().run(imp); for i in range(1, impFFT.getNSlices()+1): print "FFT of slice "+str(i) impFFT.setSlice(i) IJ.run(impFFT, "Bandpass Filter...", "filter_large=10000 filter_small=200 suppress=None tolerance=5 "); #impFFT.show() #stats = imp.getStatistics(Measurements.MEAN) #IJ.log("stats.mean = "+str(stats.mean)); # this is only the mean of one slice...is this a problem? print "dividing image stack by FFT stack..."; ic = ImageCalculator() impCorr = ic.run("Divide create 32-bit stack", imp, impFFT); #impCorr.show() def computeMean(pixels): return sum(pixels) / float(len(pixels)) print "multiplying each image by 128/mean for going back to 8 bit space..." stack = impCorr.getStack() for i in range(1, impCorr.getNSlices()+1): ip = stack.getProcessor(i).convertToFloat() mean = computeMean(ip.getPixels()) print "multiplying slice "+str(i)+" by "+str(float(128/mean)) ip.multiply(float(128/mean)) IJ.log("converting from 32-bit to 8-bit...") IJ.setMinAndMax(impCorr, 0, 255); IJ.run(impCorr,"8-bit",""); #IJ.saveAs(impCorr, "Tiff", "/Users/tischi/Documents/processed.tif"); #ff #impCorr.show() # save images IJ.log("saving bandpass corrected image sequence: "+os.path.join(jobdir,fileOut)) IJ.run(impCorr, "Image Sequence... ", "format=TIFF name=["+fileOut+"] start=1 digits=4 save=["+jobdir+"]"); if check: IJ.run(impCorr, "Image Sequence... ", "format=TIFF name=["+fileOut+"] start=1 digits=4 save=["+dirOut+"]"); #impCorr.close(); imp.close(); impFFT.hide(); # stitching IJ.log("STITCHING START **********") layoutFile = copyStitchingLayoutFile(dirIn,expName,jobdir,ps) ###layoutFile = makeStitchingLayoutFile(jobdir) createPreview = 0 computeOverlap = 0 fusion_method="Linear Blending" handleRGB = "Red, Green and Blue" showImage = 0 #fusion=1 regression=0.30 max/avg=2.50 absolute=3.50" st = Stitch_Image_Collection() st.alpha = 1 IJ.log("layout file: "+str(layoutFile)) impStitched = st.work(layoutFile, createPreview, computeOverlap, fusion_method, handleRGB, showImage) stitchedFile = os.path.join(jobdir,tID+zID+"_stitched.tif"); #impStitched.show() IJ.saveAs(impStitched,"Tiff", stitchedFile); if check: print os.path.join(dirOut,tID+zID+"_stitched.tif") stitchedFile = os.path.join(dirOut,tID+zID+"_stitched.tif"); IJ.saveAs(impStitched,"Tiff", stitchedFile); IJ.log("STITCHING END **********") if combine_z: IJ.log("combine z.....") ######### IJ.log("load stitched images into a stack...") for z in range(zs,ze+1): zID = "z"+str(z); stitchedFile = os.path.join(jobdir,tID+zID+"_stitched.tif"); IJ.log("opening "+stitchedFile) imp = IJ.openImage(stitchedFile) if z==zs: stack = ImageStack(imp.width,imp.height) stack.addSlice(imp.getProcessor()) imp = ImagePlus("stack", stack) #imp.show() ######## ######## IJ.log("cropping...") imp.setRoi(xs, ys, xe, ye); IJ.run(imp, "Crop", ""); #imp.show() ######## # the following normalisation should not be necessary, because they are already all 128/mean normalised #IJ.log("-- normalise intensity of all slices...") #stats = imp.getStatistics(Measurements.MEAN) #IJ.log("stats.mean = "+str(stats.mean)); # this is only the mean of one slice...is this a problem? #stack = imp.getStack() #for i in range(1, impFFT.getNSlices()+1): # ip = stack.getProcessor(i).convertToFloat() # ip.multiply(128/stats.mean) # #stack.setSlice(stack.getSliceLabel(i), ip) #run("Set Slice...", "slice="+1); #run("Set Measurements...", " mean redirect=None decimal=9"); #run("Select None"); #setBatchMode(true); #setMinAndMax(0, 255); run("32-bit"); #for(l=0; l<nSlices+1; l++) { ## run("Select All"); # run("Clear Results"); # run("Measure"); # picsum=getResult("Mean",0); # //if(l==0){picsum1=picsum;} # //int_ratio=picsum1/picsum; # int_ratio=128/picsum; # run("Select None"); # IJ.log("ratio ="+int_ratio); # run("Multiply...", "slice value="+int_ratio); # run("Next Slice [>]"); #} #setBatchMode(false); # stop here and try by hand #... #dfgfd #//stack-reg #//IJ.log("register xy...") #//run("StackReg", "transformation=Translation"); #// project into 1 plane .... #// run("Extended Depth of Field (Easy mode)..."); #//run("Z Project...", "start=["+1+"] stop=["+ze+"] projection=[Standard Deviation]"); doEDF = True if doEDF: IJ.log("EDF: start...") parameters = Parameters() parameters.setQualitySettings(1) parameters.setTopologySettings(0) parameters.show3dView = False parameters.showTopology = False edfh = ExtendedDepthOfFieldHeadless(imp, parameters) imp = edfh.processHeadless() IJ.log("EDF: done.") #imp.show() IJ.log("EDF: converting from 32-bit to 8-bit...") IJ.setMinAndMax(imp, 0, 255); IJ.run(imp,"8-bit",""); edfFile = os.path.join(dirOut,expName+pID+"-"+tID+"_EDOF_noTimeNorm.tif"); IJ.log("EDF save: "+edfFile) IJ.saveAs(imp,"Tiff", edfFile); IJ.log("EDF save: done.") #close(); // projection #close(); // stack print "TIMEPOINT FINISHED ***************" if os.path.isdir(jobdir): print "removing "+jobdir shutil.rmtree(jobdir)
from edfgui import ExtendedDepthOfField from edfgui import Parameters imp = WindowManager.getCurrentImage() # or imp = IJ.openImage(...) parameters = Parameters() # "quality='1' topology='0' show-view='on' show-topology='off'" quality = 1 topology = 0 showview = True showtopology= False parameters.setQualitySettings(quality) parameters.setTopologySettings(topology) parameters.show3dView = showview parameters.showTopology = showtopology if imp == None: IJ.error("The input image is not a z-stack of images.") else: if imp.getType() == ImagePlus.COLOR_RGB: parameters.outputColorMap = Parameters.COLOR_RGB edf = ExtendedDepthOfField(imp, parameters) edf.process() imp.show()