e = sys.exc_info()[0]
print("Error: {0}".format(e))
# sys.exit()
outputStosList = []
for i in range(len(sliceNums) - 1):
index = sliceNums[i]
nextIndex = sliceNums[i + 1]
inputFixed = outputMosaicList[i]
inputMoving = outputMosaicList[i + 1]
print("Assembling Volume with slice: {0}".format(inputMoving))
outputStos = "{0}/{1}-{2}.stos".format(testRoot, index, nextIndex)
print(outputStos)
outputStosList.append(outputStos)
seg3d2.slicetoslicebrutefilter(
layerid=layerid,
input_fixed=inputFixed,
input_moving=inputMoving,
output_stos=outputStos,
shrink_factor=shrinkFactor,
)
outputVolumeDir = "{0}/vol".format(testRoot)
seg3d2.slicetovolumefilter(
layerid=layerid,
input_files=outputStosList,
output_prefixes=[outputVolumeDir],
image_dirs=imageDirList,
shrink_factor=1,
)
shrink_factor=shrinkFactor,
feathering="blend")
fixedIndex = 1
inputFixed = outputMosaicList[0]
print(inputFixed)
outputStosList = []
for index in range(firstIndex, lastIndex):
nextIndex = index + 1
inputMoving = outputMosaicList[index]
print(inputMoving)
outputStos = '{0}/stos/mv{1}{2}.stos'.format(testRoot2, fixedIndex,
nextIndex)
print(outputStos)
outputStosList.append(outputStos)
seg3d2.slicetoslicebrutefilter(layerid=layerid,
input_fixed=inputFixed,
input_moving=inputMoving,
output_stos=outputStos,
shrink_factor=shrinkFactor)
print(imageDirList)
seg3d2.slicetovolumefilter(layerid=layerid,
input_files=outputStosList,
output_prefixes=[outputVolumeDir],
image_dirs=imageDirList,
shrink_factor=shrinkFactor,
load_volume=True)
if not os.path.isfile(mosaicMoving):
break
stosOutputStos = "{0}/{1}_{2}_{3}{4}".format(stosDir, datasetName, index,
nextIndex, stosExtension)
seg3d2.slicetoslicebrutefilter(layerid=layerid,
shrink_factor=shrinkFactor,
input_fixed=mosaicFixed,
input_moving=mosaicMoving,
output_stos=stosOutputStos)
stosfiles = []
for f in os.listdir(stosDir):
if f.endswith(stosExtension):
stosPath = "%s/%s" % (stosDir, f)
stosfiles.append(stosPath)
# Full resolution volume.
#volumeShrinkFactor = 1
volumeShrinkFactor = 8
# There is a hard limit on image size in Seg3D in the renderer: no dimension can be > 4096
seg3d2.slicetovolumefilter(layerid=layerid,
input_files=stosfiles,
output_prefixes=[volumeDir],
image_dirs=[tilesDir],
shrink_factor=volumeShrinkFactor,
load_volume=True)
print("Volume written to {0}.".format(volumeDir))
break
mosaicMoving = "{0}/{1}{2}".format(fftDir, nextOutputName, mosaicExtension)
if not os.path.isfile(mosaicMoving):
break
stosOutputStos = "{0}/{1}_{2}_{3}{4}".format(stosDir, datasetName, index,
next_index, stosExtension)
seg3d2.slicetoslicebrutefilter(layerid=layerid,
shrink_factor=shrinkFactor,
input_fixed=mosaicFixed,
input_moving=mosaicMoving,
output_stos=stosOutputStos)
stosfiles = []
for f in os.listdir(stosDir):
if f.endswith(stosExtension):
stosPath = "%s/%s" % (stosDir, f)
stosfiles.append(stosPath)
# TODO: error, make test
#stosfiles.append(f)
print(stosfiles)
prefix = [volumeDir]
imageDirs = [testRoot]
seg3d2.slicetovolumefilter(layerid=layerid,
input_files=stosfiles,
output_prefixes=prefix,
image_dirs=imageDirs,
shrink_factor=volumeShrinkFactor)
for index in range(rangeMin, stosRangeMax):
next_index = index + 1
print('index={0}, next_index={1}'.format(index, next_index))
outputName = "{0}_{1}".format(datasetName, index)
nextOutputName = "{0}_{1}".format(datasetName, next_index)
mosaicFixed = "{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
if not os.path.isfile(mosaicFixed):
break
mosaicMoving = "{0}/{1}{2}".format(fftDir, nextOutputName, mosaicExtension)
if not os.path.isfile(mosaicMoving):
break
stosOutputStos = "{0}/{1}_{2}_{3}{4}".format(stosDir, datasetName, index, next_index, stosExtension)
seg3d2.slicetoslicebrutefilter(layerid=layerid, shrink_factor=shrinkFactor, input_fixed=mosaicFixed, input_moving=mosaicMoving, output_stos=stosOutputStos)
stosfiles = []
for f in os.listdir(stosDir):
if f.endswith(stosExtension):
stosPath = "%s/%s" % (stosDir, f)
stosfiles.append(stosPath)
# TODO: error, make test
#stosfiles.append(f)
print(stosfiles)
prefix = [volumeDir]
imageDirs = [testRoot]
seg3d2.slicetovolumefilter(layerid=layerid, input_files=stosfiles, output_prefixes=prefix, image_dirs=imageDirs, shrink_factor=volumeShrinkFactor)
for index in range(first, last):
nextIndex = index + 1
print('slice to slice registration: index={0}, nextIndex={1}'.format(index, nextIndex))
outputName = "{0}_{1}".format(datasetName, index)
nextOutputName = "{0}_{1}".format(datasetName, nextIndex)
mosaicFixed="{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
if not os.path.isfile(mosaicFixed):
break
mosaicMoving="{0}/{1}{2}".format(fftDir, nextOutputName, mosaicExtension)
if not os.path.isfile(mosaicMoving):
break
stosOutputStos="{0}/{1}_{2}_{3}{4}".format(stosDir, datasetName, index, nextIndex, stosExtension)
seg3d2.slicetoslicebrutefilter(layerid=layerid, shrink_factor=shrinkFactor, input_fixed=mosaicFixed, input_moving=mosaicMoving, output_stos=stosOutputStos)
stosfiles=[]
for f in os.listdir(stosDir):
if f.endswith(stosExtension):
stosPath = "%s/%s" % (stosDir, f)
stosfiles.append(stosPath)
# Full resolution volume.
#volumeShrinkFactor = 1
volumeShrinkFactor = 8
# There is a hard limit on image size in Seg3D in the renderer: no dimension can be > 4096
seg3d2.slicetovolumefilter(layerid=layerid, input_files=stosfiles, output_prefixes=[volumeDir], image_dirs=[tilesDir], shrink_factor=volumeShrinkFactor, load_volume=True)
print("Volume written to {0}.".format(volumeDir))