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()
