def write_masks(patient_dir,
contour_path,
image_path,
index,
img_format='nii'):
for folder, path in contour_path.items():
print(contour_path[folder])
if contour_path[folder] is not None:
ReadMasks.create_image_mask_files(folder, contour_path[folder][0],
image_path[folder], index,
img_format)
else:
print("No Structure Set found")
print("Done Writing masks")
"""
Script that loads PETCT and Planning CT and writes to .nii such that registration
can be performed.
"""
import os
import pydicom
import shutil
from imageReg import ImageReg
from readMasks import ReadMasks
ImageReg = ImageReg()
ReadMasks = ReadMasks()
patient_dir = "E:\\Mphys\\Patients\\"
#pet_outdir = "E:\\Mphys\\NiftyPatients\\PET\\"
#planning_outdir = "E:\\Mphys\\NiftyPatients\\PlanningCT\\"
def load_files(patient_dir):
"""
Function that takes the patient directory and navigates through the
tree to find relevant files
File paths are returned as dict with key = Patient filename
and value = path to scan folders
"""
pet_paths = {}
pct_paths = {}
struct_path = {}
for f in os.listdir(patient_dir):
try: