def getROI(inputDir):
files = os.listdir(inputDir)
for file in files:
# load images
if 'tra.nrrd' in file:
img_tra = sitk.ReadImage(os.path.join(inputDir, file))
if 'cor.nrrd' in file:
img_cor = sitk.ReadImage(os.path.join(inputDir, file))
if 'sag.nrrd' in file:
img_sag = sitk.ReadImage(os.path.join(inputDir, file))
# preprocess and save to numpy array
print('... preprocess images and save to array...')
roi_tra, roi_cor, roi_sag, start, size = getCroppedIsotropicImgs(img_tra,
img_cor, img_sag)
#### included for zone segmentation (not upsampled transversal image as input)
tra_orig_roi = getROIFromOriginalTra(img_tra, size=size, start=start)
print('... normalize intensities ...')
tra_orig_roi = utils.normalizeIntensitiesPercentile(tra_orig_roi)[0]
# pad z-axis of transversal image to size of 32
filter = sitk.ConstantPadImageFilter()
filter.SetPadLowerBound([0, 0, 2])
filter.SetPadUpperBound([0, 0, 2])
filter.SetConstant(0)
tra_orig_roi = filter.Execute(tra_orig_roi)
# save image
sitk.WriteImage(tra_orig_roi, os.path.join(inputDir, 'roi_tra.nrrd'))
return tra_orig_roi
def getCroppedIsotropicImgs(outputDirectory, *imgs):
img_tra = imgs[0]
img_cor = imgs[1]
img_sag = imgs[2]
# normalize intensities
print('... normalize intensities ...')
img_tra, img_cor, img_sag = utils.normalizeIntensitiesPercentile(
img_tra, img_cor, img_sag)
# get intersecting region (bounding box)
print('... get intersecting region (ROI) ...')
# upsample transversal image to isotropic voxel size (isotropic transversal image coordinate system is used as reference coordinate system)
tra_HR = utils.resampleImage(img_tra, [0.5, 0.5, 0.5], sitk.sitkLinear, 0)
tra_HR = utils.sizeCorrectionImage(tra_HR, factor=6, imgSize=168)
# resample coronal and sagittal to tra_HR space
# resample coronal to tra_HR and obtain mask (voxels that are defined in coronal image )
cor_toTraHR = utils.resampleToReference(img_cor, tra_HR, sitk.sitkLinear,
-1)
cor_mask = utils.binaryThresholdImage(cor_toTraHR, 0)
tra_HR_Float = utils.castImage(tra_HR, sitk.sitkFloat32)
cor_mask_Float = utils.castImage(cor_mask, sitk.sitkFloat32)
# mask transversal volume (set voxels, that are defined only in transversal image but not in coronal image, to 0)
coronal_masked_traHR = sitk.Multiply(tra_HR_Float, cor_mask_Float)
# resample sagittal to tra_HR and obtain mask (voxels that are defined in sagittal image )
sag_toTraHR = utils.resampleToReference(img_sag, tra_HR, sitk.sitkLinear,
-1)
sag_mask = utils.binaryThresholdImage(sag_toTraHR, 0)
# mask sagittal volume
sag_mask_Float = utils.castImage(sag_mask, sitk.sitkFloat32)
# masked image contains voxels, that are defined in tra, cor and sag images
maskedImg = sitk.Multiply(sag_mask_Float, coronal_masked_traHR)
boundingBox = utils.getBoundingBox(maskedImg)
# correct the size and start position of the bounding box according to new size
start, size = sizeCorrectionBoundingBox(boundingBox, newSize=168, factor=6)
start[2] = 0
size[2] = tra_HR.GetSize()[2]
# resample cor and sag to isotropic transversal image space
cor_traHR = utils.resampleToReference(img_cor, tra_HR, sitk.sitkLinear, -1)
sag_traHR = utils.resampleToReference(img_sag, tra_HR, sitk.sitkLinear, -1)
## extract bounding box for all planes
region_tra = sitk.RegionOfInterest(tra_HR, [size[0], size[1], size[2]],
[start[0], start[1], start[2]])
maxVal = utils.getMaximumValue(region_tra)
region_tra = utils.thresholdImage(region_tra, 0, maxVal, 0)
region_cor = sitk.RegionOfInterest(cor_traHR, [size[0], size[1], size[2]],
[start[0], start[1], start[2]])
maxVal = utils.getMaximumValue(region_cor)
region_cor = utils.thresholdImage(region_cor, 0, maxVal, 0)
region_sag = sitk.RegionOfInterest(sag_traHR, [size[0], size[1], size[2]],
[start[0], start[1], start[2]])
maxVal = utils.getMaximumValue(region_sag)
region_sag = utils.thresholdImage(region_sag, 0, maxVal, 0)
# save cropped images to output directory
# if not os.path.exists(outputDirectory+ '/ROI/'):
# os.makedirs(outputDirectory+ '/ROI/')
#
# sitk.WriteImage(region_tra, outputDirectory + '/ROI/'+ 'croppedIsotropic_tra.nrrd')
# sitk.WriteImage(region_cor, outputDirectory + '/ROI/'+ 'croppedIsotropic_cor.nrrd')
# sitk.WriteImage(region_sag, outputDirectory + '/ROI/'+ 'croppedIsotropic_sag.nrrd')
return region_tra, region_cor, region_sag, start, size