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://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://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://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://niftynet.io/
 .. _`NiftyNet source code on CmicLab`: https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyNet