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
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)