Merge pull request #130 from DerThorsten/models

2D / 3D UNet with flexible depth and side - out capabilities

CONTRIBUTING.rst

@@ -111,3 +111,22 @@ Tips
 To run a subset of tests::
 
     $ python -m unittest tests.test_inferno
+
+
+
+Sphinx Apidoc
+--------------
+before building the documentation
+one needs to generate the auto-generated
+sphinxs api documentation.
+These files need to be in the github repository.
+
+.. code:: bash
+  
+    cd docs
+    sphinx-apidoc -o inferno-apidoc ../inferno
+
+.. warning::
+
+    Do not make changes to `inferno/docs/inferno-apidoc` This folder is auto-generated
+    by the above mentioned command.

conda-recipe/meta.yaml

@@ -27,11 +27,13 @@ requirements:
         - pyyaml
         - scipy
         - scikit-image
+        - scikit-learn
         - h5py
         - dill
         - networkx 1.11
         - tensorboardx
 
+
 test:
     imports:
         - inferno

docs/conf.py

@@ -62,6 +62,9 @@ def __getattr__(cls, name):
 
 import inferno
 import inferno.extensions
+import inferno.extensions.layers
+from inferno.extensions.layers import *
+from inferno.extensions.layers.reshape import *
 
 # -- General configuration ---------------------------------------------
 
@@ -98,7 +101,7 @@ def __getattr__(cls, name):
     'scan_used_functions':
         True,
     'doc_module' :
-        ('inferno'),
+        ('inferno','inferno.extensions','inferno.extensions.layers','inferno.extensions.layers.convolutional'),
 
     'docs_resolv': True,
 

docs/index.rst

@@ -10,7 +10,6 @@ Contents:
    installation
    usage
    examples
-   modules
    contributing
    inferno-apidoc/modules
    authors

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

@@ -1,19 +1,19 @@
-inferno\.extensions\.containers package
-=======================================
+inferno.extensions.containers package
+=====================================
 
 Submodules
 ----------
 
-inferno\.extensions\.containers\.graph module
----------------------------------------------
+inferno.extensions.containers.graph module
+------------------------------------------
 
 .. automodule:: inferno.extensions.containers.graph
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.containers\.sequential module
---------------------------------------------------
+inferno.extensions.containers.sequential module
+-----------------------------------------------
 
 .. automodule:: inferno.extensions.containers.sequential
     :members:

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

@@ -1,19 +1,35 @@
-inferno\.extensions\.criteria package
-=====================================
+inferno.extensions.criteria package
+===================================
 
 Submodules
 ----------
 
-inferno\.extensions\.criteria\.core module
-------------------------------------------
+inferno.extensions.criteria.core module
+---------------------------------------
 
 .. automodule:: inferno.extensions.criteria.core
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.criteria\.set\_similarity\_measures module
----------------------------------------------------------------
+inferno.extensions.criteria.elementwise\_measures module
+--------------------------------------------------------
+
+.. automodule:: inferno.extensions.criteria.elementwise_measures
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.criteria.regularized module
+----------------------------------------------
+
+.. automodule:: inferno.extensions.criteria.regularized
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.criteria.set\_similarity\_measures module
+------------------------------------------------------------
 
 .. automodule:: inferno.extensions.criteria.set_similarity_measures
     :members:

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

@@ -1,19 +1,19 @@
-inferno\.extensions\.initializers package
-=========================================
+inferno.extensions.initializers package
+=======================================
 
 Submodules
 ----------
 
-inferno\.extensions\.initializers\.base module
-----------------------------------------------
+inferno.extensions.initializers.base module
+-------------------------------------------
 
 .. automodule:: inferno.extensions.initializers.base
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.initializers\.presets module
--------------------------------------------------
+inferno.extensions.initializers.presets module
+----------------------------------------------
 
 .. automodule:: inferno.extensions.initializers.presets
     :members:

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

@@ -1,41 +1,73 @@
-inferno\.extensions\.layers package
-===================================
+inferno.extensions.layers package
+=================================
 
 Submodules
 ----------
 
-inferno\.extensions\.layers\.activations module
------------------------------------------------
+inferno.extensions.layers.activations module
+--------------------------------------------
 
 .. automodule:: inferno.extensions.layers.activations
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.convolutional module
+inferno.extensions.layers.building\_blocks module
 -------------------------------------------------
 
+.. automodule:: inferno.extensions.layers.building_blocks
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.convolutional module
+----------------------------------------------
+
 .. automodule:: inferno.extensions.layers.convolutional
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.device module
-------------------------------------------
+inferno.extensions.layers.device module
+---------------------------------------
 
 .. automodule:: inferno.extensions.layers.device
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.layers\.reshape module
--------------------------------------------
+inferno.extensions.layers.prefab module
+---------------------------------------
+
+.. automodule:: inferno.extensions.layers.prefab
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.reshape module
+----------------------------------------
 
 .. automodule:: inferno.extensions.layers.reshape
     :members:
     :undoc-members:
     :show-inheritance:
 
+inferno.extensions.layers.sampling module
+-----------------------------------------
+
+.. automodule:: inferno.extensions.layers.sampling
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.layers.unet module
+-------------------------------------
+
+.. automodule:: inferno.extensions.layers.unet
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

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

@@ -1,33 +1,49 @@
-inferno\.extensions\.metrics package
-====================================
+inferno.extensions.metrics package
+==================================
 
 Submodules
 ----------
 
-inferno\.extensions\.metrics\.arand module
-------------------------------------------
+inferno.extensions.metrics.arand module
+---------------------------------------
 
 .. automodule:: inferno.extensions.metrics.arand
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.metrics\.base module
------------------------------------------
+inferno.extensions.metrics.base module
+--------------------------------------
 
 .. automodule:: inferno.extensions.metrics.base
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.metrics\.categorical module
-------------------------------------------------
+inferno.extensions.metrics.categorical module
+---------------------------------------------
 
 .. automodule:: inferno.extensions.metrics.categorical
     :members:
     :undoc-members:
     :show-inheritance:
 
+inferno.extensions.metrics.cremi\_score module
+----------------------------------------------
+
+.. automodule:: inferno.extensions.metrics.cremi_score
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.extensions.metrics.voi module
+-------------------------------------
+
+.. automodule:: inferno.extensions.metrics.voi
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

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

@@ -1,19 +1,19 @@
-inferno\.extensions\.optimizers package
-=======================================
+inferno.extensions.optimizers package
+=====================================
 
 Submodules
 ----------
 
-inferno\.extensions\.optimizers\.adam module
---------------------------------------------
+inferno.extensions.optimizers.adam module
+-----------------------------------------
 
 .. automodule:: inferno.extensions.optimizers.adam
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.extensions\.optimizers\.annealed\_adam module
-------------------------------------------------------
+inferno.extensions.optimizers.annealed\_adam module
+---------------------------------------------------
 
 .. automodule:: inferno.extensions.optimizers.annealed_adam
     :members:

docs/inferno-apidoc/inferno.extensions.rst

@@ -1,5 +1,5 @@
-inferno\.extensions package
-===========================
+inferno.extensions package
+==========================
 
 Subpackages
 -----------

docs/inferno-apidoc/inferno.io.box.rst

@@ -1,27 +1,35 @@
-inferno\.io\.box package
-========================
+inferno.io.box package
+======================
 
 Submodules
 ----------
 
-inferno\.io\.box\.camvid module
--------------------------------
+inferno.io.box.binary\_blobs module
+-----------------------------------
+
+.. automodule:: inferno.io.box.binary_blobs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+inferno.io.box.camvid module
+----------------------------
 
 .. automodule:: inferno.io.box.camvid
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.io\.box\.cifar module
-------------------------------
+inferno.io.box.cifar module
+---------------------------
 
 .. automodule:: inferno.io.box.cifar
     :members:
     :undoc-members:
     :show-inheritance:
 
-inferno\.io\.box\.cityscapes module
------------------------------------
+inferno.io.box.cityscapes module
+--------------------------------
 
 .. automodule:: inferno.io.box.cityscapes
     :members: