strPath = strImgRoot + strRel umPerPx = 0.0368365 strUmPerPx = str(umPerPx) strCal = "channels=1 slices=1 frames=1 unit=micron pixel_width=" strCal += strUmPerPx strCal += " pixel_height=" strCal += strUmPerPx strCal += " voxel_depth=1.0000000 frame=[0 sec] origin=0,0" # print strPath for file in os.listdir(strPath): print file sFile = os.path.join(strPath, file) imp = IJ.openImage(sFile) imp.show() IJ.run(imp, "Properties...", strCal) IJ.run("16-bit") imp.show() strRpt = Tools.split(imp.getTitle(), ".")[0] + "-ij.csv" strCmd = "min=200 max=999999 top/bottom=5 lo=0.25 med=0.50 hi=0.75 log=0 path=" strCmd += strRptPath + " report=" + strRpt IJ.run("Analyze Line", strCmd) IJ.selectWindow(imp.getTitle()) strImgOut = strPngPath + Tools.split(imp.getTitle(), ".")[0] + ".png" IJ.saveAs("PNG", strImgOut) IJ.run("Close")
#filelist = os.listdir(filedir) for root, directories, filenames in os.walk(filedir): print directories for filename in filenames: if filename.lower().endswith('.lif'): print filedir print "..." + filename filebase = splitext(filename)[0] imps = getImps(os.path.join(filedir, filename)) printInfo(imps) for (counter, item) in enumerate(imps): #outimp = zproj(item) outimp = makeComposite(item) #outimp.show() #outname = filedir + filebase + "/" + "s" + str(counter) + ".tif" subname = ijtool.split(item.getTitle(), " - ")[1] #outname = filedir + filebase + "/" + subname + "_ZP.tif" outdir = os.path.join(filedir, "processed") outname = os.path.join(outdir, filebase + "_" + subname + "_" + str(counter) + "_Composite") print outname if not os.path.isdir(outdir): os.mkdir(outdir) fs = FileSaver(outimp) fs.saveAsTiffStack(outname+".tif") fs.saveAsJpeg(outname+".jpg") #outimp = zproject(filepath) #outimp.show()
import os strGitHome = os.environ['GIT_HOME'] strImgDir = "/OSImageAnalysis/ImageJ/Analyze_Line/std/" umPerPx = 0.0368365 # should not need to change below here... strImage = strGitHome + strImgDir + "line.tif" strUmPerPx = str(umPerPx) strRptPath = strGitHome + strImgDir strCal = "channels=1 slices=1 frames=1 unit=micron pixel_width=" strCal += strUmPerPx strCal += " pixel_height=" strCal += strUmPerPx strCal += " voxel_depth=1.0000000 frame=[0 sec] origin=0,0" imp = IJ.openImage(strImage) IJ.run(imp, "Properties...", strCal) imp.show() IJ.run("16-bit") imp.show() strRpt = Tools.split(imp.getTitle(), ".")[0] + "-ij.csv" strCmd = "min=200 max=999999 top/bottom=5 lo=0.25 med=0.50 hi=0.75 log=0 path=" strCmd += strRptPath + " report=" + strRpt IJ.run("Analyze Line", strCmd)