if not os.path.exists(imageDir):
continue
numfiles = len([name for name in os.listdir(imageDir)])
if numfiles >= 2:
fftOutputMosaic = "{0}/{1}.mosaic".format(testRoot, outputStem)
print("Calling fast fourier transform...")
print(" {0}".format(fftOutputMosaic))
try:
seg3d2.fftfilter(
layerid=layerid,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
tile_strategy=tileStrategy,
pixel_spacing=pixelSpacing,
directory=imageDir,
min_peak=minPeak,
peak_threshold=peakThreshold,
output_mosaic=fftOutputMosaic,
iterations_per_level=pyramidIterations,
pyramid_levels=pyramidLevels,
)
# refineGridMosaic="{0}/{1}g.mosaic".format(testRoot, outputStem)
# print("Calling refine grid filter...")
# print(" {0}".format(refineGridMosaic))
# print(refineGridMosaic)
# seg3d2.refinegridfilter(layerid=layerid, shrink_factor=shrinkFactor,
# pixel_spacing=pixelSpacing, iterations=refineGridIterations,
# input_mosaic=fftOutputMosaic, output_mosaic=refineGridMosaic,
# directory=imageDir, cell_size=cellSize)
for index in range(first, last + 1): # python loops over range first, last-1
outputName = "{0}_{1}".format(datasetName, index)
# build file names in order
files = []
for suffix in fileSuffixList:
filename = "%s%03d%s" % (filePrefix, index, suffix)
files.append(filename)
print("Tiling {0}".format(files))
fftMosaic = "{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
seg3d2.fftfilter(layerid=layerid,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
images=files,
directory=tilesDir,
output_mosaic=fftMosaic)
files = []
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):
testRoot2 = '{0}/test_vol'.format(testRoot)
outputVolumeDir = '{0}/vol'.format(testRoot2)
imageDirList = []
outputMosaicList = []
for index in range(firstIndex, mosaicLastIndex):
outputStem = 'mv{0}'.format(index)
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
outputName = "{0}_{1}".format(datasetName, index)
files = []
for suffix in fileSuffixList:
filename = "%s%03d%s" % (filePrefix, index, suffix)
files.append(filename)
print(files)
fftMosaic = "{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
seg3d2.fftfilter(layerid=layerid,
tile_strategy='top_left_book',
min_peak=minPeak,
peak_threshold=peakThreshold,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
pixel_spacing=pixelSpacing,
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
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 = []
layerid = "<none>"
testRoot2 = "{0}/test_vol".format(testRoot)
outputVolumeDir = "{0}/vol".format(testRoot2)
imageDirList = []
outputMosaicList = []
for index in range(firstIndex, mosaicLastIndex):
outputStem = "mv{0}".format(index)
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]
for index in range(rangeMin, mosaicRangeMax):
for suffix in fileSuffixList:
filename = "%s%03d%s" % (filePrefix, index, suffix)
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
############################################
if not os.path.exists(imageDir):
continue
numfiles = len([name for name in os.listdir(imageDir)])
if numfiles >= 2:
fftOutputMosaic = '{0}/{1}.mosaic'.format(testRoot, outputStem)
print("Calling fast fourier transform...")
print(" {0}".format(fftOutputMosaic))
try:
seg3d2.fftfilter(layerid=layerid,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
tile_strategy=tileStrategy,
pixel_spacing=pixelSpacing,
directory=imageDir,
min_peak=minPeak,
peak_threshold=peakThreshold,
output_mosaic=fftOutputMosaic,
iterations_per_level=pyramidIterations,
pyramid_levels=pyramidLevels)
#refineGridMosaic="{0}/{1}g.mosaic".format(testRoot, outputStem)
#print("Calling refine grid filter...")
#print(" {0}".format(refineGridMosaic))
#print(refineGridMosaic)
#seg3d2.refinegridfilter(layerid=layerid, shrink_factor=shrinkFactor,
# pixel_spacing=pixelSpacing, iterations=refineGridIterations,
# input_mosaic=fftOutputMosaic, output_mosaic=refineGridMosaic,
# directory=imageDir, cell_size=cellSize)
outputName = "{0}_{1}".format(datasetName, index)
files = []
for suffix in fileSuffixList:
filename = "%s%03d%s" % (filePrefix, index, suffix)
files.append(filename)
print(files)
fftMosaic="{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
seg3d2.fftfilter(layerid=layerid,
tile_strategy='top_left_book',
min_peak=minPeak,
peak_threshold=peakThreshold,
shrink_factor=shrinkFactor,
overlap_min=overlapMin,
overlap_max=overlapMax,
pixel_spacing=pixelSpacing,
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
first = 39
last = 247
for index in range(first, last+1): # python loops over range first, last-1
outputName = "{0}_{1}".format(datasetName, index)
# build file names in order
files = []
for suffix in fileSuffixList:
filename = "%s%03d%s" % (filePrefix, index, suffix)
files.append(filename)
print("Tiling {0}".format(files))
fftMosaic="{0}/{1}{2}".format(fftDir, outputName, mosaicExtension)
seg3d2.fftfilter(layerid=layerid, shrink_factor=shrinkFactor, overlap_min=overlapMin, overlap_max=overlapMax, images=files, directory=tilesDir, output_mosaic=fftMosaic)
files = []
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
