dicom_to_nii.py

import pydicom
import sys
import os
import numpy as np
import nibabel as nib
import scipy


def convert_transform_mr_to_nii(dir_mr_dicom, tranform_mr, dir_nii, outputname, CT):
    Patients = PatientList()
    Patients.list_dicom_files(dir_mr_dicom, 1)
    patient = Patients.list[0]
    patient_name = patient.PatientInfo.PatientName
    patient.import_patient_data(CT.PixelSpacing)
    MR = patient.MRimages[0]
    image_position_patient =  CT.ImagePositionPatient
    voxelsize = np.array(CT.PixelSpacing)
    save_images(dst_dir=os.path.join(dir_nii), voxelsize=voxelsize,
                image_position_patient=image_position_patient, image=tranform_mr.imageArray, outputname=outputname)
    return MR

def convert_mr_dicom_to_nii(dir_dicom, dir_nii, outputname, newvoxelsize=None):
    Patients = PatientList()  # initialize list of patient data
    # search dicom files in the patient data folder, stores all files in the attributes (all CT images, dose file, struct file)
    Patients.list_dicom_files(dir_dicom, 1)
    patient = Patients.list[0]
    patient_name = patient.PatientInfo.PatientName
    patient.import_patient_data(newvoxelsize)
    MR = patient.MRimages[0]
    image_position_patient = MR.ImagePositionPatient
    voxelsize = np.array(MR.PixelSpacing)
    save_images(dst_dir=os.path.join(dir_nii), voxelsize=voxelsize,
                image_position_patient=image_position_patient, image=MR.Image, outputname=outputname)
    return MR

    
def convert_ct_dicom_to_nii(dir_dicom, dir_nii, outputname, newvoxelsize=None):
    Patients = PatientList()  # initialize list of patient data
    # search dicom files in the patient data folder, stores all files in the attributes (all CT images, dose file, struct file)
    Patients.list_dicom_files(dir_dicom, 1)
    patient = Patients.list[0]
    patient_name = patient.PatientInfo.PatientName
    patient.import_patient_data(newvoxelsize)
    CT = patient.CTimages[0]
    image_position_patient = CT.ImagePositionPatient
    voxelsize = np.array(CT.PixelSpacing)
    save_images(dst_dir=os.path.join(dir_nii), voxelsize=voxelsize,
                image_position_patient=image_position_patient, image=CT.Image, outputname=outputname)
    return CT


def save_images(dst_dir, voxelsize, image_position_patient, image, outputname):

    # encode in nii  and save at dst_dir
    # IMPORTANT I NEED TO CONFIRM THE SIGNS OF THE ENTRIES IN THE AFFINE,
    # ALTHOUGH MAYBE AT THE END THE IMPORTANCE IS HOW WE WILL USE THIS DATA ....
    # also instead of changing field by field, the pixdim and affine can be encoded
    # using the set_sform method --> info here: https://nipy.org/nibabel/nifti_images.html

    # IMAGE (CT, MR ...)
    image_shape = image.shape
    # Separate Conversion from preprocessing
    # image = overwrite_ct_threshold(image)
    # for Nifti1 header, change for a Nifti2 type of header
    image_nii = nib.Nifti1Image(image, affine=np.eye(4))
    # Update header fields
    image_nii = set_header_info(image_nii, voxelsize, image_position_patient)
    
    # Save  nii    
    nib.save(image_nii, os.path.join(dst_dir, outputname))
    
    # nib.save(image_nii, os.path.join(dst_dir, 'ct.nii.gz'))


# def overwrite_ct_threshold(ct_image, body, artefact=None, contrast=None):
#     # Change the HU out of the body to air: -1000
#     ct_image[body == 0] = -1000
#     if artefact is not None:
#         # Change the HU to muscle: 14
#         ct_image[artefact == 1] = 14
#     if contrast is not None:
#         # Change the HU to water: 0 Houndsfield Unit: CT unit
#         ct_image[contrast == 1] = 0
#     # Threshold above 1560HU
#     ct_image[ct_image > 1560] = 1560
#     return ct_image


def set_header_info(nii_file, voxelsize, image_position_patient, contours_exist=None):
    nii_file.header['pixdim'][1] = voxelsize[0]
    nii_file.header['pixdim'][2] = voxelsize[1]
    nii_file.header['pixdim'][3] = voxelsize[2]

    # affine - voxelsize
    nii_file.affine[0][0] = voxelsize[0]
    nii_file.affine[1][1] = voxelsize[1]
    nii_file.affine[2][2] = voxelsize[2]
    # affine - imagecorner
    nii_file.affine[0][3] = image_position_patient[0]
    nii_file.affine[1][3] = image_position_patient[1]
    nii_file.affine[2][3] = image_position_patient[2]
    if contours_exist:
        nii_file.header.extensions.append(
            nib.nifti1.Nifti1Extension(0, bytearray(contours_exist)))
    return nii_file


class PatientList:

    def __init__(self):
        self.list = []

    def find_CT_image(self, display_id):
        count = -1
        for patient_id in range(len(self.list)):
            for ct_id in range(len(self.list[patient_id].CTimages)):
                if (self.list[patient_id].CTimages[ct_id].isLoaded == 1):
                    count += 1
                if (count == display_id):
                    break
            if (count == display_id):
                break

        return patient_id, ct_id

    def find_dose_image(self, display_id):
        count = -1
        for patient_id in range(len(self.list)):
            for dose_id in range(len(self.list[patient_id].RTdoses)):
                if (self.list[patient_id].RTdoses[dose_id].isLoaded == 1):
                    count += 1
                if (count == display_id):
                    break
            if (count == display_id):
                break

        return patient_id, dose_id

    def find_contour(self, ROIName):
        for patient_id in range(len(self.list)):
            for struct_id in range(len(self.list[patient_id].RTstructs)):
                if (self.list[patient_id].RTstructs[struct_id].isLoaded == 1):
                    for contour_id in range(len(self.list[patient_id].RTstructs[struct_id].Contours)):
                        if (self.list[patient_id].RTstructs[struct_id].Contours[contour_id].ROIName == ROIName):
                            return patient_id, struct_id, contour_id

    def list_dicom_files(self, folder_path, recursive):
        file_list = os.listdir(folder_path)
        # print("len file_list", len(file_list), "folderpath",folder_path)
        for file_name in file_list:
            file_path = os.path.join(folder_path, file_name)

            # folders
            if os.path.isdir(file_path):
                if recursive == True:
                    subfolder_list = self.list_dicom_files(file_path, True)
                    # join_patient_lists(Patients, subfolder_list)

            # files
            elif os.path.isfile(file_path):

                try:
                    dcm = pydicom.dcmread(file_path)
                except:
                    print("Invalid Dicom file: " + file_path)
                    continue

                patient_id = next((x for x, val in enumerate(
                    self.list) if val.PatientInfo.PatientID == dcm.PatientID), -1)

                if patient_id == -1:
                    Patient = PatientData()
                    Patient.PatientInfo.PatientID = dcm.PatientID
                    Patient.PatientInfo.PatientName = str(dcm.PatientName)
                    Patient.PatientInfo.PatientBirthDate = dcm.PatientBirthDate
                    Patient.PatientInfo.PatientSex = dcm.PatientSex
                    self.list.append(Patient)
                    patient_id = len(self.list) - 1

                # Dicom CT
                if dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.2":
                    ct_id = next((x for x, val in enumerate(
                        self.list[patient_id].CTimages) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
                    if ct_id == -1:
                        CT = CTimage()
                        CT.SeriesInstanceUID = dcm.SeriesInstanceUID
                        CT.SOPClassUID == "1.2.840.10008.5.1.4.1.1.2"
                        CT.PatientInfo = self.list[patient_id].PatientInfo
                        CT.StudyInfo = StudyInfo()
                        CT.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
                        CT.StudyInfo.StudyID = dcm.StudyID
                        CT.StudyInfo.StudyDate = dcm.StudyDate
                        CT.StudyInfo.StudyTime = dcm.StudyTime
                        if (hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""):
                            CT.ImgName = dcm.SeriesDescription
                        else:
                            CT.ImgName = dcm.SeriesInstanceUID
                        self.list[patient_id].CTimages.append(CT)
                        ct_id = len(self.list[patient_id].CTimages) - 1

                    self.list[patient_id].CTimages[ct_id].DcmFiles.append(
                        file_path)
                elif dcm.SOPClassUID == "1.2.840.10008.5.1.4.1.1.4":
                        mr_id = next((x for x, val in enumerate(self.list[patient_id].MRimages) if val.SeriesInstanceUID == dcm.SeriesInstanceUID), -1)
                        if mr_id == -1:
                            MR = MRimage()
                            MR.SeriesInstanceUID = dcm.SeriesInstanceUID
                            MR.SOPClassUID == "1.2.840.10008.5.1.4.1.1.4"
                            MR.PatientInfo = self.list[patient_id].PatientInfo
                            MR.StudyInfo = StudyInfo()
                            MR.StudyInfo.StudyInstanceUID = dcm.StudyInstanceUID
                            MR.StudyInfo.StudyID = dcm.StudyID
                            MR.StudyInfo.StudyDate = dcm.StudyDate
                            MR.StudyInfo.StudyTime = dcm.StudyTime
                            if(hasattr(dcm, 'SeriesDescription') and dcm.SeriesDescription != ""): MR.ImgName = dcm.SeriesDescription
                            else: MR.ImgName = dcm.SeriesInstanceUID
                            self.list[patient_id].MRimages.append(MR)
                            mr_id = len(self.list[patient_id].MRimages) - 1

                        self.list[patient_id].MRimages[mr_id].DcmFiles.append(file_path)
                else:
                    print("Unknown SOPClassUID " +
                          dcm.SOPClassUID + " for file " + file_path)
            # other
            else:
                print("Unknown file type " + file_path)

    def print_patient_list(self):
        print("")
        for patient in self.list:
            patient.print_patient_info()

        print("")


class PatientData:

    def __init__(self):
        self.PatientInfo = PatientInfo()
        self.CTimages = []
        self.MRimages = []

    def print_patient_info(self, prefix=""):
        print("")
        print(prefix + "PatientName: " + self.PatientInfo.PatientName)
        print(prefix + "PatientID: " + self.PatientInfo.PatientID)

        for ct in self.CTimages:
            print("")
            ct.print_CT_info(prefix + "   ")
            
        for mr in self.MRimages:
            print("")
            mr.print_MR_info(prefix + "  ")

    def import_patient_data(self, newvoxelsize=None):
        # import CT images
        for i, ct in enumerate(self.CTimages):
            if (ct.isLoaded == 1):
                continue
            ct.import_Dicom_CT()
        # Resample CT images
        for i, ct in enumerate(self.CTimages):
            ct.resample_CT(newvoxelsize)
            
        # import MR images
        for i, mr in enumerate(self.MRimages):
            if (mr.isLoaded == 1):
                continue
            mr.import_Dicom_MR(newvoxelsize)
        # Resample MR images
        # for i,mr in enumerate(self.MRimages):
        #     mr.resample_MR(newvoxelsize)

class PatientInfo:

    def __init__(self):
        self.PatientID = ''
        self.PatientName = ''
        self.PatientBirthDate = ''
        self.PatientSex = ''


class StudyInfo:

    def __init__(self):
        self.StudyInstanceUID = ''
        self.StudyID = ''
        self.StudyDate = ''
        self.StudyTime = ''


class CTimage:

    def __init__(self):
        self.SeriesInstanceUID = ""
        self.PatientInfo = {}
        self.StudyInfo = {}
        self.FrameOfReferenceUID = ""
        self.ImgName = ""
        self.SOPClassUID = ""
        self.DcmFiles = []
        self.isLoaded = 0

    def print_CT_info(self, prefix=""):
        print(prefix + "CT series: " + self.SeriesInstanceUID)
        for ct_slice in self.DcmFiles:
            print(prefix + "   " + ct_slice)

    def resample_CT(self, newvoxelsize):
        ct = self.Image
        # Rescaling to the newvoxelsize if given in parameter
        if newvoxelsize is not None:
            source_shape = self.GridSize
            voxelsize = self.PixelSpacing
            # print("self.ImagePositionPatient",self.ImagePositionPatient, "source_shape",source_shape,"voxelsize",voxelsize)
            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")
                    ct = scipy.ndimage.gaussian_filter(ct, 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 ct
                ct = scipy.interpolate.interpn((VoxelX_source, VoxelY_source, VoxelZ_source), ct, xi, method='linear',
                                               fill_value=-1000, bounds_error=False).reshape(target_shape).transpose(1, 0, 2)

            self.PixelSpacing = newvoxelsize
        self.GridSize = list(ct.shape)
        self.NumVoxels = self.GridSize[0] * self.GridSize[1] * self.GridSize[2]
        self.Image = ct
        # print("self.ImagePositionPatient",self.ImagePositionPatient, "self.GridSize[0]",self.GridSize[0],"self.PixelSpacing",self.PixelSpacing)

        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_CT(self):

        if (self.isLoaded == 1):
            print("Warning: CT serries " +
                  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]
        ct = np.dstack(images).astype("float32")

        if ct.shape[0:2] != (dcm.Rows, dcm.Columns):
            print("WARNING: GridSize " + str(ct.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(ct.shape)
        self.NumVoxels = self.GridSize[0] * self.GridSize[1] * self.GridSize[2]
        self.Image = ct
        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

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 import_Dicom_MR(self, newvoxelsize):
    
    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) + ")")
    
    # Rescaling to the newvoxelsize if given in parameter
    if newvoxelsize is not None:
      source_shape = list(mr.shape)
      
      voxelsize = [float(dcm.PixelSpacing[0]), float(dcm.PixelSpacing[1]), MeanSliceDistance]
      VoxelX_source = dcm.ImagePositionPatient[0] + np.arange(source_shape[0])*voxelsize[0]
      VoxelY_source = dcm.ImagePositionPatient[1] + np.arange(source_shape[1])*voxelsize[1]
      VoxelZ_source = dcm.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 = dcm.ImagePositionPatient[0] + np.arange(target_shape[0])*newvoxelsize[0]
      VoxelY_target = dcm.ImagePositionPatient[1] + np.arange(target_shape[1])*newvoxelsize[1]
      VoxelZ_target = dcm.ImagePositionPatient[2] + np.arange(target_shape[2])*newvoxelsize[2]
      
      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)
        else:
            print("Image does not need filtering")
                
            
        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 ct
        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.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] if newvoxelsize is None else newvoxelsize
    self.GridSize = list(mr.shape)
    self.NumVoxels = self.GridSize[0] * self.GridSize[1] * self.GridSize[2]
    self.Image = mr
    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