# if os.path.getsize(refineGridMosaic) == 0:
# print("Refine grid failed for {0}. Using fft mosaic {1} instead.".format(
# refineGridMosaic, fftOutputMosaic))
# refineGridMosaic = fftOutputMosaic
refineGridMosaic = fftOutputMosaic
assmblOutImg = "{0}/{1}{2}".format(testRoot, outputStem, outputImageExtension)
############################################
# Assembling of images
############################################
print("Assembling image...")
print(" {0}".format(assmblOutImg))
seg3d2.assemblefilter(
layerid=layerid,
input_mosaic=refineGridMosaic,
output_image=assmblOutImg,
directory=imageDir,
shrink_factor=1,
)
imageDirList.append(imageDir)
outputMosaicList.append(assmblOutImg) # refineGridMosaic)
sliceNums.append(index)
except:
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]
seg3d2.fftfilter(layerid=layerid,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
pixel_spacing=pixelSpacing,
images=files,
directory=enhancedDir,
output_mosaic=fftMosaic,
iterations_per_level=pyramidIterations,
pyramid_levels=pyramidLevels)
imageOutputFile = "{0}/{1}{2}".format(resultsDir, outputName,
outputImageExtension)
seg3d2.assemblefilter(layerid=layerid,
shrink_factor=shrinkFactor,
pixel_spacing=pixelSpacing,
input_mosaic=fftMosaic,
output_image=imageOutputFile,
directory=testRoot)
files = []
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)
print(fftOutputMosaic)
outputMosaicList.append(fftOutputMosaic)
seg3d2.fftfilter(layerid=layerid,
directory=imageDir,
output_mosaic=fftOutputMosaic,
shrink_factor=shrinkFactor)
assembleOutputImage = '{0}/results/{1}{2}'.format(testOutputRoot,
outputStem,
outputImageExtension)
print(assembleOutputImage)
seg3d2.assemblefilter(layerid=layerid,
input_mosaic=fftOutputMosaic,
output_image=assembleOutputImage,
directory=imageDir,
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)
#iterations_per_level=pyramidIterations, pyramid_levels=pyramidLevels
#refineGridMosaic="{0}/{1}{2}".format(refineGridDir, outputName, mosaicExtension)
#seg3d2.refinegridfilter(layerid=layerid, shrink_factor=shrinkFactor, pixel_spacing=pixelSpacing, iterations=refineGridIterations, input_mosaic=fftMosaic, output_mosaic=refineGridMosaic, directory=testRoot, cell_size=cellSize)
# in case refine grid failed:
#if os.path.getsize(refineGridMosaic) == 0:
# print("Refine grid failed for {0}. Using fft mosaic {1} instead.".format(refineGridMosaic, fftMosaic))
refineGridMosaic = fftMosaic
imageOutputFile = "{0}/{1}{2}".format(resultsDir, outputName,
outputImageExtension)
seg3d2.assemblefilter(layerid=layerid,
shrink_factor=1,
pixel_spacing=pixelSpacing,
input_mosaic=refineGridMosaic,
output_image=imageOutputFile,
directory=testRoot,
feathering=blendEdges)
files = []
#sys.exit()
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
imageDir = "{0}/{1}".format(testRoot, index)
imageDirList.append(imageDir)
testOutputRoot = "{0}/test".format(imageDir)
fftOutputMosaic = "{0}/fft/{1}.mosaic".format(testOutputRoot, outputStem)
print(fftOutputMosaic)
outputMosaicList.append(fftOutputMosaic)
seg3d2.fftfilter(layerid=layerid, directory=imageDir, output_mosaic=fftOutputMosaic, shrink_factor=shrinkFactor)
assembleOutputImage = "{0}/results/{1}{2}".format(testOutputRoot, outputStem, outputImageExtension)
print(assembleOutputImage)
seg3d2.assemblefilter(
layerid=layerid,
input_mosaic=fftOutputMosaic,
output_image=assembleOutputImage,
directory=imageDir,
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)
files.append(filename)
print(files)
for f in files:
inputImage = "{0}/{1}".format(testRoot, f)
outputImage = "{0}/{1}".format(enhancedDir, f)
seg3d2.clahefilter(layerid=layerid, shrink_factor=claheShrinkFactor, input_image=inputImage, output_image=outputImage, window_x=window[0], window_y=window[1])
outputName = "{0}_{1}".format(datasetName, index)
fftMosaic = "{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
seg3d2.fftfilter(layerid=layerid, shrink_factor=shrinkFactor, overlap_min=overlapMin, overlap_max=overlapMax, pixel_spacing=pixelSpacing, images=files, directory=enhancedDir, output_mosaic=fftMosaic, iterations_per_level=pyramidIterations, pyramid_levels=pyramidLevels)
imageOutputFile = "{0}/{1}{2}".format(resultsDir, outputName, outputImageExtension)
seg3d2.assemblefilter(layerid=layerid, shrink_factor=shrinkFactor, pixel_spacing=pixelSpacing, input_mosaic=fftMosaic, output_image=imageOutputFile, directory=testRoot)
files = []
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
#if os.path.getsize(refineGridMosaic) == 0:
# print("Refine grid failed for {0}. Using fft mosaic {1} instead.".format(
# refineGridMosaic, fftOutputMosaic))
# refineGridMosaic = fftOutputMosaic
refineGridMosaic = fftOutputMosaic
assmblOutImg = '{0}/{1}{2}'.format(testRoot, outputStem,
outputImageExtension)
############################################
#Assembling of images
############################################
print('Assembling image...')
print(" {0}".format(assmblOutImg))
seg3d2.assemblefilter(layerid=layerid,
input_mosaic=refineGridMosaic,
output_image=assmblOutImg,
directory=imageDir,
shrink_factor=1)
imageDirList.append(imageDir)
outputMosaicList.append(assmblOutImg) #refineGridMosaic)
sliceNums.append(index)
except:
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]
images=files,
directory=testRoot,
output_mosaic=fftMosaic)
#iterations_per_level=pyramidIterations, pyramid_levels=pyramidLevels
#refineGridMosaic="{0}/{1}{2}".format(refineGridDir, outputName, mosaicExtension)
#seg3d2.refinegridfilter(layerid=layerid, shrink_factor=shrinkFactor, pixel_spacing=pixelSpacing, iterations=refineGridIterations, input_mosaic=fftMosaic, output_mosaic=refineGridMosaic, directory=testRoot, cell_size=cellSize)
# in case refine grid failed:
#if os.path.getsize(refineGridMosaic) == 0:
# print("Refine grid failed for {0}. Using fft mosaic {1} instead.".format(refineGridMosaic, fftMosaic))
refineGridMosaic = fftMosaic
imageOutputFile="{0}/{1}{2}".format(resultsDir, outputName, outputImageExtension)
seg3d2.assemblefilter(layerid=layerid, shrink_factor=1, pixel_spacing=pixelSpacing, input_mosaic=refineGridMosaic, output_image=imageOutputFile, directory=testRoot, feathering=blendEdges)
files = []
#sys.exit()
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