예제 #1
0
def scaleandfilter(infile,outfile,scalex,scaley):
	
	print ("infile is: "+infile)
	
	imp = Opener().openImage(infile)
	print imp
	print "scalex = %f; scaley = %f" % (scalex,scaley)
	# Rescale
	ip = imp.getProcessor()
	ip.setInterpolate(True)
	sp = StackProcessor(imp.getStack(),ip);
	sp2=sp.resize(int(round(ip.width * scalex)), int(round(ip.height *scaley)));
	imp.setStack(imp.getTitle(),sp2);
	
	cal = imp.getCalibration()
	cal.pixelWidth /= scalex
	cal.pixelHeight /= scaley

	IJ.run(imp, "8-bit","")
	
	intif=infile+".tif"
	outtif=infile+"-filtered.tif"
	print("saving input file as "+intif)
	f=FileSaver(imp)
	f.saveAsTiffStack(intif)
	imp.close()

	# anisotropic filtering
	anisopts="-scanrange:10 -tau:2 -nsteps:2 -lambda:0.1 -ipflag:0 -anicoeff1:1 -anicoeff2:0 -anicoeff3:0"
	anisopts=anisopts+" -dx:%f -dy:%f -dz:%f" % (cal.pixelWidth,cal.pixelHeight,cal.pixelDepth)
	
	if sys.version_info > (2, 4):
		#for testing
		# subprocess.check_call(["cp",intif,outtif])
		subprocess.check_call(["anisofilter"]+anisopts.split(' ')+[intif,outtif])
	else:
		os.system(" ".join(["anisofilter"]+anisopts.split(' ')+[intif,outtif]))

	# Hessian (tubeness)
	print("Opening output tif: "+outtif)
	imp = Opener().openImage(outtif)
	imp.setCalibration(cal)
	print("Running tubeness on tif: "+outtif)
	IJ.run(imp,"Tubeness", "sigma=1")
	IJ.run(imp, "8-bit","")

	# Save to PIC
	print("Saving as PIC: "+outfile)
	# IJ.saveAs("tiff","outtif")
	IJ.run(imp,"Biorad ...", "biorad="+outfile)