File size: 2,158 Bytes
e4b9a7b | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | # Copyright 2020 MONAI Consortium
# 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 os
import numpy as np
from monai.transforms import DivisiblePad
STRUCTURES = (
"BrainStem",
"Chiasm",
"Mandible",
"OpticNerve_L",
"OpticNerve_R",
"Parotid_L",
"Parotid_R",
"Submandibular_L",
"Submandibular_R",
)
def get_filenames(path, maskname=STRUCTURES):
"""
create file names according to the predefined folder structure.
Args:
path: data folder name
maskname: target structure names
"""
maskfiles = []
for seg in maskname:
if os.path.exists(os.path.join(path, "./structures/" + seg + "_crp_v2.npy")):
maskfiles.append(os.path.join(path, "./structures/" + seg + "_crp_v2.npy"))
else:
# the corresponding mask is missing seg, path.split("/")[-1]
maskfiles.append(None)
return os.path.join(path, "img_crp_v2.npy"), maskfiles
def load_data_and_mask(data, mask_data):
"""
Load data filename and mask_data (list of file names)
into a dictionary of {'image': array, "label": list of arrays, "name": str}.
"""
pad_xform = DivisiblePad(k=32)
img = np.load(data) # z y x
img = pad_xform(img[None])[0]
item = dict(image=img, label=[])
for maskfnm in mask_data:
if maskfnm is None:
ms = np.zeros(img.shape, np.uint8)
else:
ms = np.load(maskfnm).astype(np.uint8)
assert ms.min() == 0 and ms.max() == 1
mask = pad_xform(ms[None])[0]
item["label"].append(mask)
assert len(item["label"]) == 9
item["name"] = str(data)
return item
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