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/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "{}" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + 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. \ 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 new file mode 100644 index 0000000..5fa88df Binary files /dev/null and b/hd_gliomouse/__pycache__/__init__.cpython-36.pyc differ diff --git a/hd_gliomouse/__pycache__/hd_gliomouse_predict_folder.cpython-36.pyc b/hd_gliomouse/__pycache__/hd_gliomouse_predict_folder.cpython-36.pyc new file mode 100644 index 0000000..c2a4d98 Binary files /dev/null and b/hd_gliomouse/__pycache__/hd_gliomouse_predict_folder.cpython-36.pyc differ diff --git a/hd_gliomouse/__pycache__/paths.cpython-36.pyc b/hd_gliomouse/__pycache__/paths.cpython-36.pyc new file mode 100644 index 0000000..230158b Binary files /dev/null and b/hd_gliomouse/__pycache__/paths.cpython-36.pyc differ diff --git a/hd_gliomouse/__pycache__/setup_hd_gliomouse.cpython-36.pyc b/hd_gliomouse/__pycache__/setup_hd_gliomouse.cpython-36.pyc new file mode 100644 index 0000000..eb90ca6 Binary files /dev/null and b/hd_gliomouse/__pycache__/setup_hd_gliomouse.cpython-36.pyc differ diff --git a/hd_gliomouse/__pycache__/utils.cpython-36.pyc b/hd_gliomouse/__pycache__/utils.cpython-36.pyc new file mode 100644 index 0000000..21c1b76 Binary files /dev/null and b/hd_gliomouse/__pycache__/utils.cpython-36.pyc differ 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' + ] + ) +