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import pydicom
import numpy as np
import scipy
class MRimage:
def __init__(self):
self.SeriesInstanceUID = ""
self.PatientInfo = {}
self.StudyInfo = {}
self.FrameOfReferenceUID = ""
self.ImgName = ""
self.SOPClassUID = ""
self.DcmFiles = []
self.isLoaded = 0
def print_MR_info(self, prefix=""):
print(prefix + "MR series: " + self.SeriesInstanceUID)
for mr_slice in self.DcmFiles:
print(prefix + " " + mr_slice)
def resample_MR(self, newvoxelsize):
mr = self.Image
# Rescaling to the newvoxelsize if given in parameter
source_shape = self.GridSize
voxelsize = self.PixelSpacing
VoxelX_source = self.ImagePositionPatient[0] + np.arange(source_shape[0])*voxelsize[0]
VoxelY_source = self.ImagePositionPatient[1] + np.arange(source_shape[1])*voxelsize[1]
VoxelZ_source = self.ImagePositionPatient[2] + np.arange(source_shape[2])*voxelsize[2]
target_shape = np.ceil(np.array(source_shape).astype(float)*np.array(voxelsize).astype(float)/newvoxelsize).astype(int)
VoxelX_target = self.ImagePositionPatient[0] + np.arange(target_shape[0])*newvoxelsize[0]
VoxelY_target = self.ImagePositionPatient[1] + np.arange(target_shape[1])*newvoxelsize[1]
VoxelZ_target = self.ImagePositionPatient[2] + np.arange(target_shape[2])*newvoxelsize[2]
print("source_shape",source_shape,"target_shape",target_shape)
if(all(source_shape == target_shape) and np.linalg.norm(np.subtract(voxelsize, newvoxelsize) < 0.001)):
print("Image does not need filtering")
else:
# anti-aliasing filter
sigma = [0, 0, 0]
if(newvoxelsize[0] > voxelsize[0]): sigma[0] = 0.4 * (newvoxelsize[0]/voxelsize[0])
if(newvoxelsize[1] > voxelsize[1]): sigma[1] = 0.4 * (newvoxelsize[1]/voxelsize[1])
if(newvoxelsize[2] > voxelsize[2]): sigma[2] = 0.4 * (newvoxelsize[2]/voxelsize[2])
if(sigma != [0, 0, 0]):
print("Image is filtered before downsampling")
mr = scipy.ndimage.gaussian_filter(mr, sigma)
xi = np.array(np.meshgrid(VoxelX_target, VoxelY_target, VoxelZ_target))
xi = np.rollaxis(xi, 0, 4)
xi = xi.reshape((xi.size // 3, 3))
# get resized mr
mr = scipy.interpolate.interpn((VoxelX_source,VoxelY_source,VoxelZ_source), mr, xi, method='linear', fill_value=0, bounds_error=False).reshape(target_shape).transpose(1,0,2)
self.PixelSpacing = newvoxelsize
self.GridSize = list(mr.shape)
self.NumVoxels = self.GridSize[0] * self.GridSize[1] * self.GridSize[2]
self.Image = mr
self.VoxelX = self.ImagePositionPatient[0] + np.arange(self.GridSize[0])*self.PixelSpacing[0]
self.VoxelY = self.ImagePositionPatient[1] + np.arange(self.GridSize[1])*self.PixelSpacing[1]
self.VoxelZ = self.ImagePositionPatient[2] + np.arange(self.GridSize[2])*self.PixelSpacing[2]
self.isLoaded = 1
def import_Dicom_MR(self):
if(self.isLoaded == 1):
print("Warning: CT series " + self.SeriesInstanceUID + " is already loaded")
return
images = []
SOPInstanceUIDs = []
SliceLocation = np.zeros(len(self.DcmFiles), dtype='float')
for i in range(len(self.DcmFiles)):
file_path = self.DcmFiles[i]
dcm = pydicom.dcmread(file_path)
if(hasattr(dcm, 'SliceLocation') and abs(dcm.SliceLocation - dcm.ImagePositionPatient[2]) > 0.001):
print("WARNING: SliceLocation (" + str(dcm.SliceLocation) + ") is different than ImagePositionPatient[2] (" + str(dcm.ImagePositionPatient[2]) + ") for " + file_path)
SliceLocation[i] = float(dcm.ImagePositionPatient[2])
images.append(dcm.pixel_array)# * dcm.RescaleSlope + dcm.RescaleIntercept)
SOPInstanceUIDs.append(dcm.SOPInstanceUID)
# sort slices according to their location in order to reconstruct the 3d image
sort_index = np.argsort(SliceLocation)
SliceLocation = SliceLocation[sort_index]
SOPInstanceUIDs = [SOPInstanceUIDs[n] for n in sort_index]
images = [images[n] for n in sort_index]
mr = np.dstack(images).astype("float32")
if mr.shape[0:2] != (dcm.Rows, dcm.Columns):
print("WARNING: GridSize " + str(mr.shape[0:2]) + " different from Dicom Rows (" + str(dcm.Rows) + ") and Columns (" + str(dcm.Columns) + ")")
MeanSliceDistance = (SliceLocation[-1] - SliceLocation[0]) / (len(images)-1)
if(abs(MeanSliceDistance - dcm.SliceThickness) > 0.001):
print("WARNING: MeanSliceDistance (" + str(MeanSliceDistance) + ") is different from SliceThickness (" + str(dcm.SliceThickness) + ")")
self.FrameOfReferenceUID = dcm.FrameOfReferenceUID
self.ImagePositionPatient = [float(dcm.ImagePositionPatient[0]), float(dcm.ImagePositionPatient[1]), SliceLocation[0]]
self.PixelSpacing = [float(dcm.PixelSpacing[0]), float(dcm.PixelSpacing[1]), MeanSliceDistance]
self.GridSize = list(mr.shape)
self.NumVoxels = self.GridSize[0] * self.GridSize[1] * self.GridSize[2]
self.Image = mr
self.SeriesDescription = dcm.SeriesDescription
self.SOPInstanceUIDs = SOPInstanceUIDs
self.VoxelX = self.ImagePositionPatient[0] + np.arange(self.GridSize[0])*self.PixelSpacing[0]
self.VoxelY = self.ImagePositionPatient[1] + np.arange(self.GridSize[1])*self.PixelSpacing[1]
self.VoxelZ = self.ImagePositionPatient[2] + np.arange(self.GridSize[2])*self.PixelSpacing[2]
self.isLoaded = 1
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