def getIsotropicImgs(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))
# 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)
# 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.resampleImage(img_cor, [0.5, 0.5, 0.5], sitk.sitkLinear,0)
# resample sagittal to tra_HR and obtain mask (voxels that are defined in sagittal image )
sag_toTraHR = utils.resampleImage(img_sag, [0.5, 0.5, 0.5], sitk.sitkLinear,0)
return tra_HR, cor_toTraHR, sag_toTraHR
def getROIFromOriginalTra(original_tra, size, start):
tra = original_tra
tra = utils.resampleImage(tra, [0.5,0.5,3], sitk.sitkLinear,0)
tra = utils.sizeCorrectionImage(tra, factor=6, imgSize=28)
print('tra size: ', tra.GetSize())
tra = sitk.RegionOfInterest(tra, [size[0], size[1], int(size[2]/6)],
[start[0], start[1], int(start[2]/6)])
return tra
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
def segment(inputDirectory, outputDirectory, multistream=True):
# load images
files = os.listdir(inputDirectory)
for file in files:
if 'tra' in file:
img_tra = sitk.ReadImage(inputDirectory + '/' + file)
if 'cor' in file:
img_cor = sitk.ReadImage(inputDirectory + '/' + file)
if 'sag' in file:
img_sag = sitk.ReadImage(inputDirectory + '/' + file)
# make directory of the output
if not os.path.exists(outputDirectory):
os.makedirs(outputDirectory)
# save original and upsampled version of transversal image
img_tra_original = img_tra
img_tra_HR = utils.resampleImage(img_tra, [0.5, 0.5, 0.5], sitk.sitkLinear,
0)
img_tra_HR = utils.sizeCorrectionImage(img_tra_HR, 6, 168)
sitk.WriteImage(img_tra_HR, outputDirectory + '/tra_HR.nrrd')
# save upsampled version of coronal image
cor_toTraHR = utils.resampleToReference(img_cor, img_tra_HR,
sitk.sitkLinear, 0)
sitk.WriteImage(cor_toTraHR, outputDirectory + '/cor_HR.nrrd')
# save upsampled version of sagittal image
sag_toTraHR = utils.resampleToReference(img_sag, img_tra_HR,
sitk.sitkLinear, 0)
sitk.WriteImage(sag_toTraHR, outputDirectory + '/sag_HR.nrrd')
# preprocess and save to numpy array
print('... preprocess images and save to array...')
img_tra, img_cor, img_sag, startROI, sizeROI = preprocessing.getCroppedIsotropicImgs(
outputDirectory, img_tra, img_cor, img_sag)
input_array = preprocessing.createInputArray(multistream, img_tra, img_cor,
img_sag)
#TODO: delete directory with cropped images?
# get net and model
if multistream:
weightFile = 'weights/weights_multiStream.h5'
model = UNET3D.get_net_multiPlane()
else:
weightFile = 'weights/weights_singleStream.h5'
model = UNET3D.get_net_singlePlane()
#TODO: compile network here
print('... load weights into model...')
model.load_weights(weightFile)
# predict image with CNN (either multistream or single stream)
print('... predict image ...')
if multistream:
img_labels = model.predict([
input_array[0:1, :, :, :, 0:1], input_array[0:1, :, :, :, 1:2],
input_array[0:1, :, :, :, 2:3]
],
verbose=1)
else:
img_labels = model.predict([input_array[0:1, :, :, :, 0:1]], verbose=1)
pred_img = sitk.GetImageFromArray(img_labels[0, :, :, :, 0])
pred_img = utils.binaryThresholdImage(pred_img, 0.5)
pred_img = utils.getLargestConnectedComponents(pred_img)
pred_img.SetSpacing(img_tra.GetSpacing())
pred_img.SetOrigin(img_tra.GetOrigin())
pred_img.SetDirection(img_tra.GetDirection())
print('... save predicted image...')
# transform prediction back to original and upsampled transversal input space
# upsampled transversal space
output_predicted_original = sitk.Image(img_tra_HR.GetSize(),
sitk.sitkUInt8)
arr = sitk.GetArrayFromImage(output_predicted_original)
arr[startROI[2]:startROI[2] + sizeROI[2],
startROI[1]:startROI[1] + sizeROI[1],
startROI[0]:startROI[0] + sizeROI[0]] = img_labels[0, :, :, :, 0]
output_predicted = sitk.GetImageFromArray(arr)
output_predicted.SetOrigin(img_tra_HR.GetOrigin())
output_predicted.SetDirection(img_tra_HR.GetDirection())
output_predicted.SetSpacing(img_tra_HR.GetSpacing())
sitk.WriteImage(output_predicted, outputDirectory + '/predicted_HR.nrrd')
# original transversal space (high slice thickness), transform perdiction with shape-based interpolation (via distance transformation)
segm_dis = sitk.SignedMaurerDistanceMap(output_predicted,
insideIsPositive=True,
squaredDistance=False,
useImageSpacing=False)
segm_dis = utils.resampleToReference(segm_dis, img_tra_original,
sitk.sitkLinear, -1)
#smoothed = sitk.DiscreteGaussian(gt_traHR, variance=1.0)
thresholded = utils.binaryThresholdImage(segm_dis, 0)
sitk.WriteImage(thresholded,
outputDirectory + '/predicted_transversal_space.nrrd')
K.clear_session()
tf.reset_default_graph()
