diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..8d82ac6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,113 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+
+*.memmap
+*.png
+*.zip
+*.npz
+*.npy
+*.jpg
+*.jpeg
+.idea
+.idea/*
+*.png
+*.nii.gz
+*.nii
+*.tif
+*.bmp
+*.pkl
+*.xml
+*.pkl
+*.pdf
+*.png
+*.jpg
+*.jpeg
+
+*.model
\ No newline at end of file
diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000..5c98b42
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,2 @@
+# Default ignored files
+/workspace.xml
\ No newline at end of file
diff --git a/.idea/hd-gliomouse.iml b/.idea/hd-gliomouse.iml
new file mode 100644
index 0000000..6711606
--- /dev/null
+++ b/.idea/hd-gliomouse.iml
@@ -0,0 +1,11 @@
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000..105ce2d
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..7508464
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+
+
+
+
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..40dc87f
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..94a25f7
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..9c8f3ea
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,201 @@
+ Apache License
+ Version 2.0, January 2004
+ http://www.apache.org/licenses/
+
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\ No newline at end of file
diff --git a/hd_gliomouse/__init__.py b/hd_gliomouse/__init__.py
new file mode 100644
index 0000000..33a12e3
--- /dev/null
+++ b/hd_gliomouse/__init__.py
@@ -0,0 +1,15 @@
+from __future__ import absolute_import
+from . import utils
+from . import paths
+from . import setup_hd_gliomouse
+
+print("\n########################")
+print("If you are using hd-bet, please cite the following papers:\n")
+print("Kickingereder P, Isensee F, Tursunova I, Petersen J, Neuberger U, Bonekamp D, Brugnara G, Schell M, Kessler T, "
+ "Foltyn M, Harting I, Sahm F, Prager M, Nowosielski M, Wick A, Nolden M, Radbruch A, Debus J, Schlemmer HP, "
+ "Heiland S, Platten M, von Deimling A, van den Bent MJ, Gorlia T, Wick W, Bendszus M, Maier-Hein KH. Automated "
+ "quantitative tumour response assessment of MRI in neuro-oncology with artificial neural networks: a "
+ "multicentre, retrospective study. Lancet Oncol. 2019 May;20(5):728-740. "
+ "https://doi.org/10.1016/S1470-2045(19)30098-1\n")
+print("Isensee, Fabian, et al. \"nnU-Net: Breaking the Spell on Successful Medical Image Segmentation.\" "
+ "arXiv preprint arXiv:1904.08128 (2019). (https://arxiv.org/abs/1904.08128)\n")
diff --git a/hd_gliomouse/__pycache__/__init__.cpython-36.pyc b/hd_gliomouse/__pycache__/__init__.cpython-36.pyc
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diff --git a/hd_gliomouse/__pycache__/hd_gliomouse_predict_folder.cpython-36.pyc b/hd_gliomouse/__pycache__/hd_gliomouse_predict_folder.cpython-36.pyc
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diff --git a/hd_gliomouse/__pycache__/paths.cpython-36.pyc b/hd_gliomouse/__pycache__/paths.cpython-36.pyc
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diff --git a/hd_gliomouse/__pycache__/utils.cpython-36.pyc b/hd_gliomouse/__pycache__/utils.cpython-36.pyc
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diff --git a/hd_gliomouse/hd_gliomouse_predict.py b/hd_gliomouse/hd_gliomouse_predict.py
new file mode 100644
index 0000000..90dbdfc
--- /dev/null
+++ b/hd_gliomouse/hd_gliomouse_predict.py
@@ -0,0 +1,55 @@
+# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+# 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.
+
+from hd_gliomouse.utils import blockPrint, enablePrint
+blockPrint()
+from nnunet.inference.predict import predict_cases
+enablePrint()
+import argparse
+from hd_gliomouse.paths import folder_with_parameter_files
+from hd_gliomouse.setup_hd_gliomouse import maybe_download_weights
+
+
+def main():
+ parser = argparse.ArgumentParser(description="This script will allow you to predict a single case with hd_glio. "
+ "If you have multiple cases, please use hd_glio_predict_folder (this one "
+ "will be substantially faster for multiple cases because we can "
+ "interleave preprocessing, GPU prediction and nifti export."
+ "\n"
+ "IMPORTANT!\n"
+ "The input files must be brain extracted with the non-brain region being "
+ "0 (you can achieve that by using hd-bet "
+ "(https://github.com/MIC-DKFZ/HD-BET). Furthermore, the input files "
+ "must be co-registered and in the same co-ordinate system (pixels "
+ "arrays must be aligned)\n"
+ "All input files must be niftis (.nii.gz)")
+
+ parser.add_argument("-i", type=str, required=True,
+ help="input file")
+ parser.add_argument("-o", "--output_file", type=str, required=True,
+ help="output filename. Must end with .nii.gz")
+
+ args = parser.parse_args()
+ inp = args.i
+ output_file = args.output_file
+
+ maybe_download_weights()
+
+ predict_cases(folder_with_parameter_files, [[inp, ]], [output_file], (0, 1, 2, 3, 4), False, 1, 1, None, True,
+ None, True)
+
+
+if __name__ == "__main__":
+ main()
+
diff --git a/hd_gliomouse/hd_gliomouse_predict_folder.py b/hd_gliomouse/hd_gliomouse_predict_folder.py
new file mode 100644
index 0000000..a7dffd3
--- /dev/null
+++ b/hd_gliomouse/hd_gliomouse_predict_folder.py
@@ -0,0 +1,60 @@
+# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+# 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.
+
+from batchgenerators.utilities.file_and_folder_operations import subfiles, join
+from hd_gliomouse.utils import blockPrint, enablePrint
+blockPrint()
+from nnunet.inference.predict import predict_cases
+enablePrint()
+import argparse
+from hd_gliomouse.paths import folder_with_parameter_files
+from hd_gliomouse.setup_hd_gliomouse import maybe_download_weights
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument("-i", "--input_folder", type=str, required=True,
+ help="folder with input files. All .nii.gz files in this folder will be processed.")
+ parser.add_argument("-o", "--output_folder", type=str, required=True,
+ help="output folder. This is there the resulting segmentations will be saved. Cannot be the "
+ "same folder as the input folder. If output_folder does not exist "
+ "it will be created")
+ parser.add_argument("-p", "--processes", default=4, type=str, required=False,
+ help="number of processes for data preprocessing and nifti export. You should not have to "
+ "touch this. So don't unless there is a clear indication that it is required. Default: 4")
+ parser.add_argument('--overwrite_existing', default=True, type=str, required=False,
+ help="set to False to keep segmentations in output_folder and continue where you left off "
+ "(useful if something crashes). If True then all segmentations that may already be "
+ "present in output_folder will be overwritten. Default: True")
+
+ args = parser.parse_args()
+ input_folder = args.input_folder
+ output_folder = args.output_folder
+ processes = args.processes
+ overwrite_existing = args.overwrite_existing
+
+ maybe_download_weights()
+
+ # we must generate a list of input filenames
+ nii_files = subfiles(input_folder, suffix='.nii.gz', join=False)
+ input_list_of_lists = [[join(input_folder, i)] for i in nii_files]
+
+ output_filenames = [join(output_folder, i) for i in nii_files]
+
+ predict_cases(folder_with_parameter_files, input_list_of_lists, output_filenames, (0, 1, 2, 3, 4), False, processes,
+ processes, None, True, None, overwrite_existing, False, 2, None, 3, 0)
+
+
+if __name__ == "__main__":
+ main()
diff --git a/hd_gliomouse/paths.py b/hd_gliomouse/paths.py
new file mode 100644
index 0000000..1d798d8
--- /dev/null
+++ b/hd_gliomouse/paths.py
@@ -0,0 +1,4 @@
+import os
+
+# please refer to the readme on where to get the parameters. Save them in this folder:
+folder_with_parameter_files = os.path.join(os.path.expanduser('~'), 'hd_gliomouse_params')
diff --git a/hd_gliomouse/setup_hd_gliomouse.py b/hd_gliomouse/setup_hd_gliomouse.py
new file mode 100644
index 0000000..1e67f3b
--- /dev/null
+++ b/hd_gliomouse/setup_hd_gliomouse.py
@@ -0,0 +1,51 @@
+# Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+# 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.
+
+from urllib.request import urlopen
+from batchgenerators.utilities.file_and_folder_operations import *
+from hd_gliomouse.paths import folder_with_parameter_files
+import shutil
+import zipfile
+
+
+def maybe_download_weights():
+ # check if models are available
+ all_good = True
+ for f in range(5):
+ if not isfile(join(folder_with_parameter_files, 'fold_%d' % f, "model_final_checkpoint.model")) or not \
+ isfile(join(folder_with_parameter_files, 'fold_%d' % f, "model_final_checkpoint.model.pkl")):
+ all_good = False
+ break
+ if all_good:
+ return
+
+ import http.client
+ http.client.HTTPConnection._http_vsn = 10
+ http.client.HTTPConnection._http_vsn_str = 'HTTP/1.0'
+
+ if isdir(folder_with_parameter_files):
+ shutil.rmtree(folder_with_parameter_files)
+ maybe_mkdir_p(folder_with_parameter_files)
+
+ out_filename = join(folder_with_parameter_files, "parameters.zip")
+
+ url = "https://zenodo.org/record/3738243/files/hd-glio-mouse.zip?download=1"
+ print("Downloading", url, "...")
+ data = urlopen(url).read()
+ with open(out_filename, 'wb') as f:
+ f.write(data)
+
+ zipfile.ZipFile(out_filename).extractall(path=folder_with_parameter_files)
+ os.remove(out_filename)
+
diff --git a/hd_gliomouse/utils.py b/hd_gliomouse/utils.py
new file mode 100644
index 0000000..92cadd7
--- /dev/null
+++ b/hd_gliomouse/utils.py
@@ -0,0 +1,9 @@
+import sys, os
+
+
+def blockPrint():
+ sys.stdout = open(os.devnull, 'w')
+
+
+def enablePrint():
+ sys.stdout = sys.__stdout__
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..a0e8912
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,33 @@
+from setuptools import setup
+
+
+setup(name='hd_gliomouse',
+ version='1.0',
+ packages=["hd_gliomouse"],
+ description='Tool for brain tumor segmentation in mice. This is the result of a joint project between the Department of '
+ 'Neuroradiology at the Heidelberg University Hospital and the Division of Medical Image Computing at '
+ 'the German Cancer Research Center (DKFZ). See readme.md for more information',
+ url='https://github.com/NeuroAI-HD/HD-GLIOMOUSE',
+ python_requires='>=3.5',
+ author='Fabian Isensee',
+ author_email='f.isensee@dkfz.de',
+ license='Apache 2.0',
+ zip_safe=False,
+ install_requires=[
+ 'torch',
+ 'nnunet>1.0', 'batchgenerators'
+ ],
+ entry_points={
+ 'console_scripts': [
+ 'hd_gliomouse_predict = hd_gliomouse.hd_gliomouse_predict:main',
+ 'hd_gliomouse_predict_folder = hd_gliomouse.hd_gliomouse_predict_folder:main',
+ ],
+ },
+ classifiers=[
+ 'Intended Audience :: Science/Research',
+ 'Programming Language :: Python',
+ 'Topic :: Scientific/Engineering',
+ 'Operating System :: Unix'
+ ]
+ )
+