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)