Merge branch 'dev' into 'master'

Merge dev to master before tagging v0.2.0.post1

See merge request !66

.gitlab-ci.yml

@@ -156,6 +156,9 @@ quicktest:
  - 150-properly-format-the-bibtex-entry-to-the-ipmi-2017-paper-on-the-main-readme
  - 139-correct-toynet-demo-instructions
  - 148-publish-niftynet-v0-2-0-on-python-package-index-pypi
+ - 159-add-net_run-command-line-entry-to-pip-installer
+ - 160-add-net_gan-command-line-entry-to-pip-installer
+ - 161-add-net_autoencode-command-line-entry-to-pip-installer
  script:
  # print system info
  - which nvidia-smi
@@ -196,6 +199,9 @@ pip-installer:
  - dev-staging
  - tags
  - supports-axbxc-patch
+ - 159-add-net_run-command-line-entry-to-pip-installer
+ - 160-add-net_gan-command-line-entry-to-pip-installer
+ - 161-add-net_autoencode-command-line-entry-to-pip-installer
  script:
  # source utils
  - source ci/utils.sh
@@ -245,6 +251,20 @@ pip-installer:
  - ln -s /home/gitlab-runner/environments/niftynet/data/example_volumes ./example_volumes
  - net_segment train -c $niftynet_dir/config/default_segmentation.ini --name toynet --batch_size 3 --max_iter 5
  - net_segment inference -c $niftynet_dir/config/default_segmentation.ini --name toynet --spatial_window_size 80,80,80 --batch_size 8
+ - net_run train --app net_segment -c $niftynet_dir/config/default_segmentation.ini --name toynet --batch_size 3 --max_iter 5
+ - net_run inference --app net_segment -c $niftynet_dir/config/default_segmentation.ini --name toynet --spatial_window_size 80,80,80 --batch_size 8
+ - net_gan train -c $niftynet_dir/config/GAN_demo_train_config.ini --max_iter 5
+ - net_gan inference -c $niftynet_dir/config/GAN_demo_train_config.ini
+ - net_run train --app net_gan -c $niftynet_dir/config/GAN_demo_train_config.ini --max_iter 5
+ - net_run inference --app net_gan -c $niftynet_dir/config/GAN_demo_train_config.ini
+ - net_autoencoder train -c $niftynet_dir/config/vae_config.ini --max_iter 5
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type sample
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type encode --save_seg_dir output/vae_demo_features
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type encode-decode
+ - net_run train --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --max_iter 5
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type sample
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type encode --save_seg_dir output/vae_demo_features
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type encode-decode
  # deactivate virtual environment
  - deactivate
  - cd $niftynet_dir
@@ -279,6 +299,21 @@ pip-installer:
  - ln -s /home/gitlab-runner/environments/niftynet/data/example_volumes ./example_volumes
  - net_segment train -c $niftynet_dir/config/default_segmentation.ini --name toynet --batch_size 3 --max_iter 5
  - net_segment inference -c $niftynet_dir/config/default_segmentation.ini --name toynet --spatial_window_size 80,80,80 --batch_size 8
+ - net_run train --app net_segment -c $niftynet_dir/config/default_segmentation.ini --name toynet --batch_size 3 --max_iter 5
+ - net_run inference --app net_segment -c $niftynet_dir/config/default_segmentation.ini --name toynet --spatial_window_size 80,80,80 --batch_size 8
+ - net_gan train -c $niftynet_dir/config/GAN_demo_train_config.ini --max_iter 5
+ - net_gan inference -c $niftynet_dir/config/GAN_demo_train_config.ini
+ - net_run train --app net_gan -c $niftynet_dir/config/GAN_demo_train_config.ini --max_iter 5
+ - net_run inference --app net_gan -c $niftynet_dir/config/GAN_demo_train_config.ini
+ - net_autoencoder train -c $niftynet_dir/config/vae_config.ini --max_iter 5
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type sample
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type encode --save_seg_dir output/vae_demo_features
+ - net_autoencoder inference -c $niftynet_dir/config/vae_config.ini --inference_type encode-decode
+ - net_run train --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --max_iter 5
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type sample
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type encode --save_seg_dir output/vae_demo_features
+ - net_run inference --app net_autoencoder -c $niftynet_dir/config/vae_config.ini --inference_type encode-decode
+
  # deactivate virtual environment
  - deactivate
  - cd $niftynet_dir

niftynet/utilities/util_csv.py

@@ -244,7 +244,8 @@ def load_and_merge_csv_files(data_param):
  except AttributeError:
  tf.logging.fatal('unrecognised parameter format')
  raise
- if hasattr(data_param[modality_name], 'path_to_search'):
+ if hasattr(data_param[modality_name], 'path_to_search') and \
+ len(data_param[modality_name].path_to_search):
  tf.logging.info(
  '[%s] search file folders, writing csv file %s',
  modality_name, csv_file)

setup.py

@@ -104,6 +104,9 @@
  'console_scripts': [
  'net_segment=niftynet:main',
  'net_download=niftynet.utilities.download:main',
+ 'net_run=niftynet:main',
+ 'net_gan=niftynet:main',
+ 'net_autoencoder=niftynet:main',
  ],
  },
 )