Added support for accessing livermask as python package [no ci]
Browse files- livermask/livermask.py +9 -60
- livermask/utils/__init__.py +0 -2
- livermask/utils/run.py +64 -0
- setup.py +1 -7
livermask/livermask.py
CHANGED
@@ -1,70 +1,13 @@
|
|
1 |
-
import numpy as np
|
2 |
-
import os
|
3 |
import sys
|
4 |
-
|
5 |
-
import nibabel as nib
|
6 |
-
from nibabel.processing import resample_to_output, resample_from_to
|
7 |
-
from scipy.ndimage import zoom
|
8 |
-
from tensorflow.python.keras.models import load_model
|
9 |
-
from skimage.morphology import remove_small_holes, binary_dilation, binary_erosion, ball
|
10 |
-
from skimage.measure import label, regionprops
|
11 |
import warnings
|
12 |
import argparse
|
13 |
-
import pkg_resources
|
14 |
-
import tensorflow as tf
|
15 |
-
import logging as log
|
16 |
-
import chainer
|
17 |
-
import math
|
18 |
-
from .utils.unet3d import UNet3D
|
19 |
-
import yaml
|
20 |
-
from tensorflow.keras import backend as K
|
21 |
-
from numba import cuda
|
22 |
-
from .utils.process import liver_segmenter_wrapper, vessel_segmenter, intensity_normalization
|
23 |
-
from .utils.utils import verboseHandler
|
24 |
-
import logging as log
|
25 |
-
from .utils.utils import get_model, get_vessel_model
|
26 |
|
27 |
|
28 |
os.environ['TF_FORCE_GPU_ALLOW_GROWTH'] = 'true' # due to this: https://github.com/tensorflow/tensorflow/issues/35029
|
29 |
warnings.filterwarnings('ignore', '.*output shape of zoom.*') # mute some warnings
|
30 |
|
31 |
|
32 |
-
def func(path, output, cpu, verbose, vessels, extension):
|
33 |
-
# enable verbose or not
|
34 |
-
log = verboseHandler(verbose)
|
35 |
-
|
36 |
-
cwd = "/".join(os.path.realpath(__file__).replace("\\", "/").split("/")[:-1]) + "/"
|
37 |
-
name = cwd + "model.h5"
|
38 |
-
name_vessel = cwd + "model-hepatic_vessel.npz"
|
39 |
-
|
40 |
-
# get models
|
41 |
-
get_model(name)
|
42 |
-
|
43 |
-
if vessels:
|
44 |
-
get_vessel_model(name_vessel)
|
45 |
-
|
46 |
-
if not os.path.isdir(path):
|
47 |
-
paths = [path]
|
48 |
-
else:
|
49 |
-
paths = [path + "/" + p for p in os.listdir(path)]
|
50 |
-
|
51 |
-
multiple_flag = len(paths) > 1
|
52 |
-
if multiple_flag:
|
53 |
-
os.makedirs(output + "/", exist_ok=True)
|
54 |
-
|
55 |
-
for curr in tqdm(paths, "CT:"):
|
56 |
-
# check if current file is a nifti file, if not, skip
|
57 |
-
if curr.endswith(".nii") or curr.endswith(".nii.gz"):
|
58 |
-
# perform liver parenchyma segmentation, launch it in separate process to properly clear memory
|
59 |
-
pred = liver_segmenter_wrapper(curr, output, cpu, verbose, multiple_flag, name, extension)
|
60 |
-
|
61 |
-
if vessels:
|
62 |
-
# perform liver vessel segmentation
|
63 |
-
vessel_segmenter(curr, output, cpu, verbose, multiple_flag, pred, name_vessel, extension)
|
64 |
-
else:
|
65 |
-
log.info("Unsuported file: " + curr)
|
66 |
-
|
67 |
-
|
68 |
def main():
|
69 |
parser = argparse.ArgumentParser()
|
70 |
parser.add_argument('-i', '--input', type=str, nargs='?',
|
@@ -79,7 +22,11 @@ def main():
|
|
79 |
help="segment vessels.")
|
80 |
parser.add_argument('-e', '--extension', type=str, default=".nii",
|
81 |
help="define the output extension. (default: .nii)")
|
82 |
-
ret = parser.parse_args(sys.argv[1:])
|
|
|
|
|
|
|
|
|
83 |
|
84 |
if ret.cpu:
|
85 |
os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
|
@@ -114,7 +61,9 @@ def main():
|
|
114 |
if ret.extension not in [".nii", ".nii.gz"]:
|
115 |
raise ValueError("Extension not supported. Expected: .nii or .nii.gz")
|
116 |
|
117 |
-
|
|
|
|
|
118 |
|
119 |
|
120 |
if __name__ == "__main__":
|
|
|
|
|
|
|
1 |
import sys
|
2 |
+
import os
|
|
|
|
|
|
|
|
|
|
|
|
|
3 |
import warnings
|
4 |
import argparse
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
5 |
|
6 |
|
7 |
os.environ['TF_FORCE_GPU_ALLOW_GROWTH'] = 'true' # due to this: https://github.com/tensorflow/tensorflow/issues/35029
|
8 |
warnings.filterwarnings('ignore', '.*output shape of zoom.*') # mute some warnings
|
9 |
|
10 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
11 |
def main():
|
12 |
parser = argparse.ArgumentParser()
|
13 |
parser.add_argument('-i', '--input', type=str, nargs='?',
|
|
|
22 |
help="segment vessels.")
|
23 |
parser.add_argument('-e', '--extension', type=str, default=".nii",
|
24 |
help="define the output extension. (default: .nii)")
|
25 |
+
ret = parser.parse_args(sys.argv[1:])
|
26 |
+
print(ret)
|
27 |
+
|
28 |
+
# only now do we call tensorflow, if necessary (to avoid redundant imports for livermask -h call)
|
29 |
+
import tensorflow as tf
|
30 |
|
31 |
if ret.cpu:
|
32 |
os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
|
|
|
61 |
if ret.extension not in [".nii", ".nii.gz"]:
|
62 |
raise ValueError("Extension not supported. Expected: .nii or .nii.gz")
|
63 |
|
64 |
+
# finally, import run_analysis method with relevant imports and run analysis
|
65 |
+
from .utils.run import run_analysis
|
66 |
+
run_analysis(*vars(ret).values())
|
67 |
|
68 |
|
69 |
if __name__ == "__main__":
|
livermask/utils/__init__.py
CHANGED
@@ -1,2 +0,0 @@
|
|
1 |
-
|
2 |
-
|
|
|
|
|
|
livermask/utils/run.py
ADDED
@@ -0,0 +1,64 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
import numpy as np
|
2 |
+
import os
|
3 |
+
import sys
|
4 |
+
from tqdm import tqdm
|
5 |
+
import nibabel as nib
|
6 |
+
from nibabel.processing import resample_to_output, resample_from_to
|
7 |
+
from scipy.ndimage import zoom
|
8 |
+
from tensorflow.python.keras.models import load_model
|
9 |
+
from skimage.morphology import remove_small_holes, binary_dilation, binary_erosion, ball
|
10 |
+
from skimage.measure import label, regionprops
|
11 |
+
import warnings
|
12 |
+
import argparse
|
13 |
+
import pkg_resources
|
14 |
+
import tensorflow as tf
|
15 |
+
import logging as log
|
16 |
+
import math
|
17 |
+
from .unet3d import UNet3D
|
18 |
+
import yaml
|
19 |
+
from tensorflow.keras import backend as K
|
20 |
+
from numba import cuda
|
21 |
+
from .process import liver_segmenter_wrapper, vessel_segmenter, intensity_normalization
|
22 |
+
from .utils import verboseHandler
|
23 |
+
import logging as log
|
24 |
+
from .utils import get_model, get_vessel_model
|
25 |
+
|
26 |
+
|
27 |
+
def run_analysis(path, output, cpu, verbose, vessels, extension):
|
28 |
+
# fix paths (necessary if called as a package and not CLI)
|
29 |
+
path = path.replace("\\", "/")
|
30 |
+
output = output.replace("\\", "/")
|
31 |
+
|
32 |
+
# enable verbose or not
|
33 |
+
log = verboseHandler(verbose)
|
34 |
+
|
35 |
+
cwd = "/".join(os.path.realpath(__file__).replace("\\", "/").split("/")[:-1]) + "/"
|
36 |
+
name = cwd + "model.h5"
|
37 |
+
name_vessel = cwd + "model-hepatic_vessel.npz"
|
38 |
+
|
39 |
+
# get models
|
40 |
+
get_model(name)
|
41 |
+
|
42 |
+
if vessels:
|
43 |
+
get_vessel_model(name_vessel)
|
44 |
+
|
45 |
+
if not os.path.isdir(path):
|
46 |
+
paths = [path]
|
47 |
+
else:
|
48 |
+
paths = [path + "/" + p for p in os.listdir(path)]
|
49 |
+
|
50 |
+
multiple_flag = len(paths) > 1
|
51 |
+
if multiple_flag:
|
52 |
+
os.makedirs(output + "/", exist_ok=True)
|
53 |
+
|
54 |
+
for curr in tqdm(paths, "CT:"):
|
55 |
+
# check if current file is a nifti file, if not, skip
|
56 |
+
if curr.endswith(".nii") or curr.endswith(".nii.gz"):
|
57 |
+
# perform liver parenchyma segmentation, launch it in separate process to properly clear memory
|
58 |
+
pred = liver_segmenter_wrapper(curr, output, cpu, verbose, multiple_flag, name, extension)
|
59 |
+
|
60 |
+
if vessels:
|
61 |
+
# perform liver vessel segmentation
|
62 |
+
vessel_segmenter(curr, output, cpu, verbose, multiple_flag, pred, name_vessel, extension)
|
63 |
+
else:
|
64 |
+
log.info("Unsuported file: " + curr)
|
setup.py
CHANGED
@@ -19,13 +19,7 @@ setup(
|
|
19 |
long_description_content_type="text/markdown",
|
20 |
url="https://github.com/andreped/livermask",
|
21 |
include_package_data=True,
|
22 |
-
packages=find_packages(
|
23 |
-
include=[
|
24 |
-
'livermask',
|
25 |
-
'livermask.utils',
|
26 |
-
'livermask.configs',
|
27 |
-
]
|
28 |
-
),
|
29 |
entry_points={
|
30 |
'console_scripts': [
|
31 |
'livermask = livermask.livermask:main',
|
|
|
19 |
long_description_content_type="text/markdown",
|
20 |
url="https://github.com/andreped/livermask",
|
21 |
include_package_data=True,
|
22 |
+
packages=find_packages(exclude=('figures')),
|
|
|
|
|
|
|
|
|
|
|
|
|
23 |
entry_points={
|
24 |
'console_scripts': [
|
25 |
'livermask = livermask.livermask:main',
|