cleaner = cs.run("org.bonej.wrapperPlugins.tableTools.SharedTableCleaner", False)
for image in files:
for rep in reps:
for wa in was:
for maxShift in maxShifts:
for vectors in nVectors:
for ratio in skipRatios:
for iterations in maxIterations:
for filterB in filters:
for contact in contacts:
for step in steps:
f = open(logfilename, 'ab')
sourceName = workingDir+localDir+image
print(sourceName)
print(rep)
i = ImgOpener();
sourceImg = i.openImgs(sourceName).get(0)
axes = [Axes.X, Axes.Y, Axes.Z]
calibration = [1,1,1]
units = ["","",""]
source = ImgPlus(sourceImg,image,axes,calibration,units)
name = source.getName()
print("name: "+name)
imp = IJ.openImage(sourceName) # need for skeletonization
imp.show()
name = name+"-runs-"+str(rep)+"-weighted-"+str(wa)+"-maxShift-"+str(maxShift)+"-vectors-"+str(vectors)+"-ratio-"+str(ratio)+"-maxIts-"+str(iterations)+"-filter-"+str(filterB)+"-contact-"+str(contact)+"-step-"+str(step*1.0/2.3)
startTime = time.time()
wrapper = cs.run("org.bonej.wrapperPlugins.EllipsoidFactorWrapper",False,["inputImgPlus",source,"nVectors", vectors, "vectorIncrement", step*1.0/2.3, "skipRatio",ratio,"contactSensitivity",contact,"maxIterations",iterations, "maxDrift",maxShift*1.73,"minimumSemiAxis",filterB,"seedOnDistanceRidge",True,"seedOnTopologyPreserving",True,"showSecondaryImages",True,"runs",rep,"weightedAverageN",wa,"distanceThreshold",distanceThreshold])
wrapperInstance = wrapper.get()
outputs = wrapperInstance.getOutput("ellipsoidFactorOutputImages");
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from io.scif import SCIFIO
from io.scif.config import SCIFIOConfig
from io.scif.img import ImageRegion
from io.scif.img import ImgOpener
from io.scif.img import ImgSaver
from net.imagej.axis import Axes
imgDir = os.environ['IMG_ROOT']
relImg = "/test/ij/original-ome"
inImg = imgDir + relImg + ".tif"
ouImg = imgDir + relImg + "-cr.tif"
axes = [Axes.X, Axes.Y]
ranges = ["%i-%i" % (2, 15), "%i-%i" % (2, 25)]
config = SCIFIOConfig()
config.imgOpenerSetRegion(ImageRegion(axes, ranges))
opener = ImgOpener()
imps = opener.openImgs(inImg, config)
imp = imps[0]
saver = ImgSaver()
saver.saveImg(ouImg, imp)
print('Done')