/
dataset_utils.py
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/
dataset_utils.py
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# Copyright 2017 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import SimpleITK as sitk
import os
from multiprocessing import pool
import cPickle
import numpy as np
from skimage.transform import resize
def resize_image(image, old_spacing, new_spacing, order=3):
new_shape = (int(np.round(old_spacing[0]/new_spacing[0]*float(image.shape[0]))),
int(np.round(old_spacing[1]/new_spacing[1]*float(image.shape[1]))),
int(np.round(old_spacing[2]/new_spacing[2]*float(image.shape[2]))))
return resize(image, new_shape, order=order, mode='edge')
str_to_ind = {'DCM':0, 'HCM':1, 'MINF':2, 'NOR':3, 'RV':4}
ind_to_str = {}
for k in str_to_ind.keys():
ind_to_str[str_to_ind[k]] = k
def view_patient_raw_data(patient, width=400, height=400):
import batchviewer
a = []
a.append(patient['ed_data'][None])
a.append(patient['ed_gt'][None])
a.append(patient['es_data'][None])
a.append(patient['es_gt'][None])
batchviewer.view_batch(np.vstack(a), width, height)
def convert_to_one_hot(seg):
vals = np.unique(seg)
res = np.zeros([len(vals)] + list(seg.shape), seg.dtype)
for c in range(len(vals)):
res[c][seg == c] = 1
return res
def preprocess_image(itk_image, is_seg=False, spacing_target=(1, 0.5, 0.5), keep_z_spacing=False):
spacing = np.array(itk_image.GetSpacing())[[2, 1, 0]]
image = sitk.GetArrayFromImage(itk_image).astype(float)
if keep_z_spacing:
spacing_target = list(spacing_target)
spacing_target[0] = spacing[0]
if not is_seg:
order_img = 3
if not keep_z_spacing:
order_img = 1
image = resize_image(image, spacing, spacing_target, order=order_img).astype(np.float32)
image -= image.mean()
image /= image.std()
else:
tmp = convert_to_one_hot(image)
vals = np.unique(image)
results = []
for i in range(len(tmp)):
results.append(resize_image(tmp[i].astype(float), spacing, spacing_target, 1)[None])
image = vals[np.vstack(results).argmax(0)]
return image
def load_dataset(ids=range(101), root_dir="/home/fabian/drives/E132-Projekte/ACDC/new_dataset_preprocessed_for_2D_v2/"):
with open(os.path.join(root_dir, "patient_info.pkl"), 'r') as f:
patient_info = cPickle.load(f)
data = {}
for i in ids:
if os.path.isfile(os.path.join(root_dir, "pat_%03.0d.npy"%i)):
a = np.load(os.path.join(root_dir, "pat_%03.0d.npy"%i), mmap_mode='r')
data[i] = {}
data[i]['height'] = patient_info[i]['height']
data[i]['weight'] = patient_info[i]['weight']
data[i]['pathology'] = patient_info[i]['pathology']
data[i]['ed_data'] = a[0, :]
data[i]['ed_gt'] = a[1, :]
data[i]['es_data'] = a[2, :]
data[i]['es_gt'] = a[3, :]
return data
def process_patient(args):
id, patient_info, folder, folder_out, keep_z_spc = args
#print id
# if id in [286, 288]:
# return
patient_folder = os.path.join(folder, "patient%03.0d"%id)
if not os.path.isdir(patient_folder):
return
images = {}
fname = os.path.join(patient_folder, "patient%03.0d_frame%02.0d.nii.gz" % (id, patient_info[id]['ed']))
if os.path.isfile(fname):
images["ed"] = sitk.ReadImage(fname)
fname = os.path.join(patient_folder, "patient%03.0d_frame%02.0d_gt.nii.gz" % (id, patient_info[id]['ed']))
if os.path.isfile(fname):
images["ed_seg"] = sitk.ReadImage(fname)
fname = os.path.join(patient_folder, "patient%03.0d_frame%02.0d.nii.gz" % (id, patient_info[id]['es']))
if os.path.isfile(fname):
images["es"] = sitk.ReadImage(fname)
fname = os.path.join(patient_folder, "patient%03.0d_frame%02.0d_gt.nii.gz" % (id, patient_info[id]['es']))
if os.path.isfile(fname):
images["es_seg"] = sitk.ReadImage(fname)
print id, images["es_seg"].GetSpacing()
for k in images.keys():
#print k
images[k] = preprocess_image(images[k], is_seg=(k == "ed_seg" or k == "es_seg"),
spacing_target=(10, 1.25, 1.25), keep_z_spacing=keep_z_spc)
img_as_list = []
for k in ['ed', 'ed_seg', 'es', 'es_seg']:
if k not in images.keys():
print id, "has missing key:", k
img_as_list.append(images[k][None])
try:
all_img = np.vstack(img_as_list)
except:
print id, "has a problem with spacings"
np.save(os.path.join(folder_out, "pat_%03.0d" % id), all_img.astype(np.float32))
def generate_patient_info(folder):
patient_info={}
for id in range(151):
fldr = os.path.join(folder, 'patient%03.0d'%id)
if not os.path.isdir(fldr):
print "could not find dir of patient ", id
continue
nfo = np.loadtxt(os.path.join(fldr, "Info.cfg"), dtype=str, delimiter=': ')
patient_info[id] = {}
patient_info[id]['ed'] = int(nfo[0, 1])
patient_info[id]['es'] = int(nfo[1, 1])
patient_info[id]['height'] = float(nfo[3, 1])
patient_info[id]['pathology'] = nfo[2, 1]
patient_info[id]['weight'] = float(nfo[5, 1])
return patient_info
def run_preprocessing(folder="/media/fabian/My Book/datasets/ACDC/training/",
folder_out = "/media/fabian/DeepLearningData/datasets/ACDC_forReal_orig_Z/", keep_z_spacing=True):
patient_info = generate_patient_info(folder)
if not os.path.isdir(folder_out):
os.mkdir(folder_out)
with open(os.path.join(folder_out, "patient_info.pkl"), 'w') as f:
cPickle.dump(patient_info, f)
# beware of z spacing!!! see process_patient for more info!
ids = range(101)
p = pool.Pool(8)
p.map(process_patient, zip(ids, [patient_info]*101, [folder]*101, [folder_out]*101, [keep_z_spacing]*101))
p.close()
p.join()
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-i", help="folder where the extracted training data is", type=str)
parser.add_argument("-out2d", help="folder where to save the data for the 2d network", type=str)
parser.add_argument("-out3d", help="folder where to save the data for the 3d network", type=str)
args = parser.parse_args()
run_preprocessing(args.i, args.out2d, True)
run_preprocessing(args.i, args.out3d, False)