def create_pickle_for_patient(in_dir, out_dir):
scan_id = os.path.basename(in_dir)
image_folder = os.path.join(in_dir, "sa", "images")
con_file = os.path.join(in_dir, "sa", "contours.con")
meta_txt = os.path.join(in_dir, "meta.txt")
if not os.path.isdir(image_folder):
logger.error("Could not find image folder for: {}".format(scan_id))
return
if not os.path.isfile(con_file):
logger.error("Could not find .con file for: {}".format(scan_id))
return
if not os.path.isfile(meta_txt):
logger.error("Could not find meta.txt file for: {}".format(scan_id))
return
dr = DCMreaderVM(image_folder)
if dr.num_frames == 0 and dr.num_frames == 0 or dr.broken:
logger.error("Could not create pickle file for {}".format(scan_id))
return
cr = CONreaderVM(con_file)
contours = left_ventricle_contours(cr.get_hierarchical_contours())
frame_slice_dict = collect_contour_slices_by_frames(contours)
if not (len(frame_slice_dict) == 2):
logger.error("Too many contour frames for {}".format(scan_id))
return
pickle_file_path = os.path.join(out_dir, scan_id + ".p")
create_path_for_file(pickle_file_path)
diastole_frame = frame_of_diastole(frame_slice_dict, contours)
sampling_slices = calculate_sampling_slices(frame_slice_dict,
diastole_frame)
sampling_contours = []
for slice_index in sampling_slices:
shape = dr.get_image(slice_index, diastole_frame).shape
sampling_contours.append(contours[slice_index][diastole_frame])
pathology = read_pathology(meta_txt)
shape = dr.get_image(sampling_slices[0], diastole_frame).shape
contour_diff_matricies = create_contour_diff_matricies(
sampling_contours, shape)
print(type(contour_diff_matricies))
patient_data = PatientData(scan_id, pathology, cr.get_volume_data(),
contour_diff_matricies)
with (open(pickle_file_path, "wb")) as pickleFile:
pickle.dump(patient_data, pickleFile)
def contours2images(patient_folder):
image_folder = pjoin(patient_folder, 'sa', 'images')
con_file = pjoin(patient_folder, 'sa', 'contours.con')
# reading the dicom files
dr = DCMreaderVM(image_folder)
# reading the contours
cr = CONreaderVM(con_file)
contours = cr.get_hierarchical_contours()
# drawing the contours for the images
for slc in contours:
for frm in contours[slc]:
image = dr.get_image(slc, frm) # numpy array
cntrs = []
rgbs = []
for mode in contours[slc][frm]:
# choose color
if mode == 'ln': # left endocardium -> red
rgb = [1, 0, 0]
elif mode == 'lp': # left epicardium -> green
rgb = [0, 1, 0]
elif mode == 'rn': # right endocardium -> yellow
rgb = [1, 1, 0]
else:
rgb = None
if rgb is not None:
cntrs.append(contours[slc][frm][mode])
rgbs.append(rgb)
if len(cntrs) > 0:
draw(image, cntrs, rgbs)
image_folder = 'C:\\dev\\LHYP\\sample\\13457546AMR801\\sa\\images'
con_file = 'C:\\dev\\LHYP\\sample\\13457546AMR801\\sa\\contours.con'
# reading the dicom files
dr = DCMreaderVM(image_folder)
# reading the contours
cr = CONreaderVM(con_file)
contours = cr.get_hierarchical_contours()
# drawing the contours for the images
for slc in contours:
for frm in contours[slc]:
image = dr.get_image(slc, frm) # numpy array
cntrs = []
rgbs = []
for mode in contours[slc][frm]:
# choose color
if mode == 'ln':
rgb = [1, 0, 0]
elif mode == 'lp':
rgb = [0, 1, 0]
elif mode == 'rn':
rgb = [1, 1, 0]
else:
rgb = None
if rgb is not None:
cntrs.append(contours[slc][frm][mode])
rgbs.append(rgb)