Merge branch 'dev' into 'master'

Merge dev to master before tagging v0.2.0

See merge request !64

.gitlab-ci.yml

@@ -8,8 +8,9 @@ pylintjob:
  stage: pylint_test
  except:
  - 139-correct-toynet-demo-instructions
+ - 148-publish-niftynet-v0-2-0-on-python-package-index-pypi
  script:
- - pylint --rcfile=pylintrc niftynet/engine
+ - pylint --rcfile=tests/pylintrc niftynet/engine
 
 testjob:
  stage: dev_test
@@ -154,6 +155,7 @@ quicktest:
  - 147-revise-contribution-guidelines-to-include-github
  - 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
  script:
  # print system info
  - which nvidia-smi

README.md

@@ -66,12 +66,25 @@ The API reference is available on [Read the Docs][rtd-niftynet].
 
 [rtd-niftynet]: http:https://niftynet.rtfd.io/
 
+#### Contributing
 
-### Contributing
+Please see the [contribution guidelines](./CONTRIBUTING.md).
 
-Feature requests and bug reports are collected on [Issues](https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet/issues).
+#### Useful links
+
+[NiftyNet website][niftynet-io]
+
+[NiftyNet source code on CmicLab][niftynet-cmiclab]
+
+[NiftyNet source code mirror on GitHub][niftynet-github]
+
+NiftyNet mailing list: [[email protected]][ml-niftynet]
+
+[niftynet-io]: http:https://niftynet.io/
+[niftynet-cmiclab]: https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet
+[niftynet-github]: https://github.com/NifTK/NiftyNet
+[ml-niftynet]: mailto:[email protected]
 
-Contributors are encouraged to take a look at [CONTRIBUTING.md](./CONTRIBUTING.md).
 
 ### Citing NiftyNet
 

doc/source/index.rst

@@ -53,6 +53,8 @@ Useful links
 
 `NiftyNet source code mirror on GitHub`_
 
+NiftyNet mailing list: [email protected]
+
 
 .. _`NiftyNet website`: http:https://niftynet.io/
 .. _`NiftyNet source code on CmicLab`: https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet

niftynet/engine/sampler_resize.py

@@ -25,6 +25,7 @@ def __init__(self,
  reader,
  data_param,
  batch_size,
+ spatial_window_size=(),
  windows_per_image=1,
  shuffle_buffer=True,
  queue_length=10):
@@ -44,6 +45,12 @@ def __init__(self,
  self.reader.shapes,
  self.reader.tf_dtypes,
  data_param)
+ if spatial_window_size:
+ # override all spatial window defined in input
+ # modalities sections
+ # this is useful when do inference with a spatial window
+ # which is different from the training specifications
+ self.window.set_spatial_shape(spatial_window_size)
  tf.logging.info('initialised window instance')
  self._create_queue_and_ops(self.window,
  enqueue_size=1,

niftynet/engine/windows_aggregator_resize.py

@@ -69,6 +69,12 @@ def _save_current_image(self, image_out, resize_to):
  window_shape = resize_to
  while image_out.ndim < 5:
  image_out = image_out[..., np.newaxis, :]
+ if self.window_border and any([b > 0 for b in self.window_border]):
+ np_border = self.window_border
+ while len(np_border) < 5:
+ np_border = np_border + (0,)
+ np_border = [(b,) for b in np_border]
+ image_out = np.pad(image_out, np_border, mode='edge')
  image_shape = image_out.shape
  zoom_ratio = \
  [float(p) / float(d) for p, d in zip(window_shape, image_shape)]

pip/long_description.rst

@@ -78,6 +78,8 @@ Useful links
 
 `NiftyNet source code mirror on GitHub`_
 
+NiftyNet mailing list: [email protected]
+
 
 .. _`NiftyNet website`: http:https://niftynet.io/
 .. _`NiftyNet source code on CmicLab`: https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet