Merge pull request #141 from DerThorsten/master

docs and examples update

CONTRIBUTING.rst

@@ -129,4 +129,11 @@ These files need to be in the github repository.
 .. warning::
 
     Do not make changes to `inferno/docs/inferno-apidoc` This folder is auto-generated
-    by the above mentioned command.
+    by the above mentioned command.
+
+The following combines all the commands necessary to build the html documentation:
+
+.. code:: bash
+  
+    ./build_docs.sh
+

HISTORY.rst

@@ -45,3 +45,9 @@ History
 ------------------
 
 * setup.py critical bugix in install procedure
+
+
+
+CURRENT CHANGES
+-----------------
+* Flexible Unet

README.rst

@@ -53,7 +53,7 @@ Current features include:
   *   `various utility layers <https://github.com/nasimrahaman/inferno/tree/master/inferno/extensions/layers>`_ with more underway,
   *   `a submodule <https://github.com/nasimrahaman/inferno/blob/master/inferno/io/volumetric>`_ for volumetric datasets, and more!
 
-
+  
 
 
 
@@ -152,10 +152,9 @@ Planned features include:
 Credits
 ---------
 All contributors are listed here_. 
+.. _here: https://inferno-pytorch.github.io/inferno/html/authors.html
 
-.. _here: https://pytorch-inferno.readthedocs.io/en/latest/authors.html
-
-This packag was partially generated with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template + lots of work by Thorsten. 
+This package was partially generated with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template + lots of work by Thorsten. 
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

build_docs.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+cd docs
+rm -r -f inferno-apidoc
+sphinx-apidoc -o inferno-apidoc ../inferno
+make html
+cd ..

conda-recipe/meta.yaml

@@ -32,6 +32,7 @@ requirements:
         - dill
         - networkx 1.11
         - tensorboardx
+        - sphinx_rtd_theme
 
 
 test:

docs/conf.py

@@ -152,7 +152,7 @@ def __getattr__(cls, name):
 
 # General information about the project.
 project = u'inferno'
-copyright = u"2017, Nasim Rahaman"
+copyright = u"2018, f"
 
 # The version info for the project you're documenting, acts as replacement
 # for |version| and |release|, also used in various other places throughout
@@ -207,7 +207,7 @@ def __getattr__(cls, name):
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -306,7 +306,7 @@ def __getattr__(cls, name):
 latex_documents = [
     ('index', 'inferno.tex',
      u'inferno Documentation',
-     u'Nasim Rahaman', 'manual'),
+     u'Inferno Team', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at
@@ -337,7 +337,7 @@ def __getattr__(cls, name):
 man_pages = [
     ('index', 'inferno',
      u'inferno Documentation',
-     [u'Nasim Rahaman'], 1)
+     [u'Inferno Team'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -352,7 +352,7 @@ def __getattr__(cls, name):
 texinfo_documents = [
     ('index', 'inferno',
      u'inferno Documentation',
-     u'Nasim Rahaman',
+     u'Inferno Team',
      'inferno',
      'One line description of project.',
      'Miscellaneous'),

docs/inferno-apidoc/inferno.extensions.layers.rst

@@ -36,6 +36,14 @@ inferno.extensions.layers.device module
     :undoc-members:
     :show-inheritance:
 
+inferno.extensions.layers.identity module
+-----------------------------------------
+
+.. automodule:: inferno.extensions.layers.identity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 inferno.extensions.layers.prefab module
 ---------------------------------------
 
@@ -44,6 +52,14 @@ inferno.extensions.layers.prefab module
     :undoc-members:
     :show-inheritance:
 
+inferno.extensions.layers.res\_unet module
+------------------------------------------
+
+.. automodule:: inferno.extensions.layers.res_unet
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 inferno.extensions.layers.reshape module
 ----------------------------------------
 
@@ -60,10 +76,10 @@ inferno.extensions.layers.sampling module
     :undoc-members:
     :show-inheritance:
 
-inferno.extensions.layers.unet module
--------------------------------------
+inferno.extensions.layers.unet\_base module
+-------------------------------------------
 
-.. automodule:: inferno.extensions.layers.unet
+.. automodule:: inferno.extensions.layers.unet_base
     :members:
     :undoc-members:
     :show-inheritance:

examples/train_side_loss_unet.py → examples/plot_train_side_loss_unet.py

@@ -151,13 +151,13 @@ def forward(self, predictions, target):
 )
 
 # Build trainer
-trainer = Trainer(model) \
-.build_criterion(MySideLoss()) \
-.build_optimizer('Adam') \
-.validate_every((10, 'epochs')) \
-.save_every((10, 'epochs')) \
-.save_to_directory(SAVE_DIRECTORY) \
-.set_max_num_epochs(40) \
+trainer = Trainer(model)
+trainer.build_criterion(MySideLoss())
+trainer.build_optimizer('Adam')
+trainer.validate_every((10, 'epochs'))
+#trainer.save_every((10, 'epochs'))
+#trainer.save_to_directory(SAVE_DIRECTORY)
+trainer.set_max_num_epochs(40)
 
 # Bind loaders
 trainer \
@@ -176,7 +176,7 @@ def forward(self, predictions, target):
 # and visualize the results
 
 # predict:
-trainer.load(best=True)
+#trainer.load(best=True)
 trainer.bind_loader('train', train_loader)
 trainer.bind_loader('validate', validate_loader)
 trainer.eval_mode()

examples/plot_unet_tutorial.py

@@ -68,7 +68,7 @@ def label_transform(x):
 # With :code:`activated=False` we make sure that the last layer
 # is not activated since we chain the UNet with a sigmoid
 # activation function.
-from inferno.extensions.layers.unet import ResBlockUNet
+from inferno.extensions.layers import ResBlockUNet
 from inferno.extensions.layers import RemoveSingletonDimension
 
 model = torch.nn.Sequential(