def load_series(pet_paths, pct_paths):
pet_series = {}
pct_series = {}
for key, value in pet_paths.items():
pet_series[key] = ImageReg.load_series_no_write(value)
pct_series[key] = ImageReg.load_series_no_write(pct_paths[key])
return pet_series, pct_series
def write_nifty(pet_paths, pct_paths):
pet_series = {}
pct_series = {}
for key, value in pet_paths.items():
pet_series[key] = ImageReg.load_series(value, 'PET\\{}'.format(key))
pct_series[key] = ImageReg.load_series(pct_paths[key], 'PlanningCT\\{}'.format(key))
return pet_series, pct_series
def main(argv=None):
# read_dicom(".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\1-REGCTsim-CTPET-CT-43961\\000000.dcm")
# ImageReg.load_series(".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\112161818-kVCT Image Set-62659\\", "pct_series")
# ImageReg.load_series(".\\Patients\\HN-CHUM-001\\08-27-1885-PANC. avec C.A. SPHRE ORL tte et cou -TP-74220\\3-StandardFull-07232\\", "petct_series")
fixed = ImageReg.image_info("pct_series.mha")
moving = ImageReg.image_info("petct_series.mha")
dvf = sitk.ReadImage("dvf.mhd")
vis = ImageReg.resample_image(fixed, moving, dvf)
print(type(vis))
ImageReg.myshow(vis, fixed)
print("Done Loading Patient Info")
def write_nifty(pet_paths, pct_paths):
# Function that writes image series to .nii format
pet_series = {}
pct_series = {}
for key, value in pet_paths.items():
try:
pet_series[key] = ImageReg.load_series(value, pet_outdir, key)
pct_series[key] = ImageReg.load_series(pct_paths[key], planning_outdir, key)
except RuntimeError:
print("RuntimeError Ignored")
pass
return pet_series, pct_series
def main(argv=None):
# read_dicom(".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\1-REGCTsim-CTPET-CT-43961\\000000.dcm")
# ImageReg.load_series(
# ".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\112161818-kVCT Image Set-62659\\", "pct_series")
# ImageReg.load_series(
# ".\\Patients\\HN-CHUM-001\\08-27-1885-PANC. avec C.A. SPHRE ORL tte et cou -TP-74220\\3-StandardFull-07232\\", "petct_series")
fixed = ImageReg.image_info("pct_series.mha")
moving = ImageReg.image_info("petct_series.mha")
dvf = sitk.ReadImage("dvf.mhd", sitk.sitkVectorFloat64)
small_dvf = ImageReg.resize_image(dvf, fixed)
small_moving = ImageReg.resize_image(moving, fixed)
transform_img = ImageReg.resample_image(small_moving, fixed, small_dvf)
ImageReg.myshow(transform_img)
print("Done Loading Patient Info")
def main(argv=None):
# read_dicom(".\\Patients\\HN-CHUM-001\\08-27-1885-PANC. avec C.A. SPHRE ORL tte et cou -TP-74220\\3-StandardFull-07232\\000000.dcm")
# ImageReg.load_series(
# ".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\112161818-kVCT Image Set-62659\\", "pct_series")
# ImageReg.load_series(
# ".\\Patients\\HN-CHUM-001\\08-27-1885-PANC. avec C.A. SPHRE ORL tte et cou -TP-74220\\3-StandardFull-07232\\", "test_series")
fixed = ImageReg.image_info("pct_series.mha")
moving = ImageReg.image_info("petct_series.mha")
dvf = sitk.ReadImage("dvf.mhd", sitk.sitkVectorFloat64)
# small_dvf = ImageReg.resize_image(dvf, fixed)
# small_moving = ImageReg.resize_image(movsng, fixed)
pre_def, post_def = ImageReg.get_rigid_transforms(dvf_path)
transform = ImageReg.define_transform(pre_def, post_def, dvf)
transform_img = ImageReg.resample_image(moving, fixed, transform)
ImageReg.myshow(transform_img)
print("Done Loading Patient Info")
from imageReg import ImageReg
from interact import Interact
import SimpleITK as sitk
# Change working directory such that it can access data
os.chdir("..")
# Print current working directory
cwd = os.getcwd()
print(cwd)
# Paths
pct_path = ".\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\112161818-kVCT Image Set-62659\\000000.dcm"
dvf_path = "E:\\Mphys\\ElastixReg\\DVF\\HN-CHUM-001\\deformationField.nii"
petct_path = ".\\Patients\\HN-CHUM-001\\08-27-1885-PANC. avec C.A. SPHRE ORL tte et cou -TP-74220\\3-StandardFull-07232"
struct_path = '.\\Patients\\HN-CHUM-001\\08-27-1885-TomoTherapy Patient Disease-00441\\114120634-TomoTherapy Structure Set-68567\\000000.dcm'
ReadData = ReadData()
ImageReg = ImageReg()
Interact = Interact()
def read_dicom(dicom_path):
# Function that reads a dicom file and writes to a text file
dataset = ReadData.read_dicom(dicom_path)
# vector_grid = dataset.DeformableRegistrationSequence[1].DeformableRegistrationGridSequence[0].VectorGridData
# vector_grid = np.array(vector_grid).astype(np.float64)
#
# with open("dvf.raw", "wb") as f:
# f.write(vector_grid)
ReadData.write_dicom(dataset, "image_test")
def load_patients_array():
def show_image(image_array):
data = np.asarray(image_array).astype(np.float64)
image = sitk.GetImageFromArray(data)
ImageReg.myshow(image)
sitk.WriteImage(image, "imagetest.mha")
def pretransformed_pet(pet_series, pct_series):
transformed_pet_series = {}
for key, petvalue in pet_series.items():
transformed_pet_series[key] = ImageReg.initial_transform(pct_series[key], petvalue)
return transformed_pet_series
def main(argv=None):
slice_array(planning_path, start, end)
slice_image = sitk.ReadImage("sliced_pct.mha")
ImageReg.myshow(slice_image)