diff --git a/bin/hyppopy_exe.py b/bin/hyppopy_exe.py index c0f4383..6dc44e8 100644 --- a/bin/hyppopy_exe.py +++ b/bin/hyppopy_exe.py @@ -1,72 +1,76 @@ #!/usr/bin/env python # # DKFZ # # # Copyright (c) German Cancer Research Center, # Division of Medical and Biological Informatics. # All rights reserved. # # This software is distributed WITHOUT ANY WARRANTY; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR # A PARTICULAR PURPOSE. # # See LICENSE.txt or http://www.mitk.org for details. # # Author: Sven Wanner (s.wanner@dkfz.de) +import os +import sys +ROOT = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) +sys.path.append(ROOT) from hyppopy.projectmanager import ProjectManager from hyppopy.workflows.unet_usecase.unet_usecase import unet_usecase from hyppopy.workflows.svc_usecase.svc_usecase import svc_usecase from hyppopy.workflows.randomforest_usecase.randomforest_usecase import randomforest_usecase from hyppopy.workflows.imageregistration_usecase.imageregistration_usecase import imageregistration_usecase import os import sys import argparse def print_warning(msg): print("\n!!!!! WARNING !!!!!") print(msg) sys.exit() def args_check(args): if not args.workflow: print_warning("No workflow specified, check --help") if not args.config: print_warning("Missing config parameter, check --help") if not os.path.isfile(args.config): print_warning(f"Couldn't find configfile ({args.config}), please check your input --config") if __name__ == "__main__": parser = argparse.ArgumentParser(description='UNet Hyppopy UseCase Example Optimization.') parser.add_argument('-w', '--workflow', type=str, help='workflow to be executed') parser.add_argument('-c', '--config', type=str, help='config filename, .xml or .json formats are supported.' 'pass a full path filename or the filename only if the' 'configfile is in the data folder') args = parser.parse_args() args_check(args) ProjectManager.read_config(args.config) if args.workflow == "svc_usecase": uc = svc_usecase() elif args.workflow == "randomforest_usecase": uc = randomforest_usecase() elif args.workflow == "unet_usecase": uc = unet_usecase() elif args.workflow == "imageregistration_usecase": uc = imageregistration_usecase() else: print("No workflow called {} found!".format(args.workflow)) sys.exit() uc.run() print(uc.get_results()) diff --git a/requirements.txt b/requirements.txt index 074b8cb..aeccb6e 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,13 +1,18 @@ dicttoxml==1.7.4 hyperopt==0.1.1 matplotlib==3.0.2 numpy==1.16.0 Optunity==1.1.1 pytest==4.1.1 scikit-learn==0.20.2 scipy==1.2.0 sklearn==0.0 Sphinx==1.8.3 xmlrunner==1.7.7 xmltodict==0.11.0 Yapsy==1.11.223 +pandas==0.24.1 +trixi==0.1.1.6 +torch==1.0.0 +medpy==0.3.0 +batchgenerators==0.18.1 \ No newline at end of file diff --git a/requirements_withunet.txt b/requirements_withunet.txt deleted file mode 100644 index 99da379..0000000 --- a/requirements_withunet.txt +++ /dev/null @@ -1,113 +0,0 @@ -alabaster==0.7.12 -atomicwrites==1.3.0 -attrs==18.2.0 -babel==2.6.0 -backcall==0.1.0 -batchgenerators==0.18.1 -bleach==3.1.0 -bz2file==0.98 -certifi==2018.11.29 -chardet==3.0.4 -Click==7.0 -cloudpickle==0.7.0 -colorama==0.4.1 -colorlover==0.3.0 -cycler==0.10.0 -dask==1.1.1 -decorator==4.3.2 -dicttoxml==1.7.4 -docutils==0.14 -entrypoints==0.3 -Flask==1.0.2 -future==0.17.1 -graphviz==0.10.1 -h5py==2.9.0 -hyperopt==0.1.1 -hyppopy==0.0.1 -idna==2.8 -imagesize==1.1.0 -ipykernel==5.1.0 -ipython==7.2.0 -ipython-genutils==0.2.0 -itsdangerous==1.1.0 -jedi==0.13.2 -Jinja2==2.10 -jsonschema==3.0.0a3 -jupyter-client==5.2.4 -jupyter-core==4.4.0 -kiwisolver==1.0.1 -linecache2==1.0.0 -llvmlite==0.27.0 -MarkupSafe==1.1.0 -matplotlib==3.0.2 -MedPy==0.3.0 -mistune==0.8.4 -more-itertools==5.0.0 -nbconvert==5.3.1 -nbformat==4.4.0 -networkx==2.2 -nibabel==2.3.3 -notebook==5.7.4 -numba==0.42.0 -numpy==1.16.0 -optunity==1.1.1 -packaging==19.0 -pandas==0.24.1 -pandocfilters==1.4.2 -parso==0.3.4 -pickleshare==0.7.5 -pillow==5.4.1 -plotly==3.6.1 -pluggy==0.8.1 -portalocker==1.4.0 -prometheus-client==0.5.0 -prompt-toolkit==2.0.8 -py==1.7.0 -pydicom==1.2.2 -Pygments==2.3.1 -pymongo==3.7.2 -pyparsing==2.3.1 -pypiwin32==223 -pyrsistent==0.14.10 -pytest==4.1.1 -python-dateutil==2.8.0 -python-telegram-bot==10.1.0 -pytz==2018.9 -pywavelets==1.0.1 -pywin32==224 -pywinpty==0.5.5 -pyzmq==17.1.2 -requests==2.21.0 -retrying==1.3.3 -scikit-image==0.14.2 -scikit-learn==0.20.2 -scipy==1.2.0 -seaborn==0.9.0 -Send2Trash==1.5.0 -six==1.12.0 -sklearn==0.0 -snowballstemmer==1.2.1 -Sphinx==1.8.3 -sphinxcontrib-websupport==1.1.0 -terminado==0.8.1 -testpath==0.4.2 -toolz==0.9.0 -torch==1.0.0 -torchfile==0.1.0 -torchvision==0.2.1 -tornado==5.1.1 -traceback2==1.4.0 -traitlets==4.3.2 -trixi==0.1.1.6 -umap-learn==0.3.7 -unittest2==1.1.0 -urllib3==1.24.1 -visdom==0.1.8.8 -wcwidth==0.1.7 -webencodings==0.5.1 -websocket-client==0.54.0 -Werkzeug==0.14.1 -wincertstore==0.2 -xmlrunner==1.7.7 -xmltodict==0.11.0 -Yapsy==1.11.223