Merge pull request #280 from deephealthproject/develop

EDDL v1.0a

.gitignore

@@ -8,6 +8,7 @@
 .vscode
 *~
 *.tar.gz
+*.swp
 
 # Build
 /[Bb]uild*
@@ -28,6 +29,11 @@ docs/sphinx/source/_build
 old_build/example_*
 old_build/test_*
 
+# ONNX tests
+scripts/tests/py_onnx/**/data/
+scripts/tests/py_onnx/**/.data/
+scripts/tests/py_onnx/**/onnx_models/
+
 # Files generated by CLion
 cmake-build-*
 

docs/markdown/eddl_progress_documentation.md

@@ -25,9 +25,9 @@
 | :------ | :---------: | :----------: | :------- |
 | External dependencies | ✔️ |    ✔️     |          |
 | Build and optimization |
-|       Build | ✔️ | ✔️ |    |
-|       Backend support | ✔️ | ✔️ | FPGA support note: not yet implemented |
-|       Additional flags | ✔️ |  ✔️ |   |
+| Build | ✔️ | ✔️ |    |
+| Backend support | ✔️ | ✔️ | FPGA support note: not yet implemented |
+| Additional flags | ✔️ |  ✔️ |   |
 
 
 ## Troubleshoot
@@ -104,8 +104,11 @@
 | Input   |     ✔️       |      ✔️       |          |
 | Droput  |     ✔️       |      ✔️       |          |
 | Select  |     ✔️       |      ✔️       |          |
+| Slice  |     ✔️       |      ✔️       |          |
 | Permute |     ✔️       |      ✔️       |          |
-| Transpose  |  ✔️       |      ✔️       |          |
+| Expand  |     ✔️       |      ✔️       |          |
+| Split  |     ✔️       |      ✔️       |          |
+| Transpose |  ✔️       |      ✔️       |          |
 
 ## Activations
 

docs/sphinx/source/index.rst

@@ -43,6 +43,7 @@ The code is open source, and `available on github`_.
     :caption: Layers
 
     layers/core.rst
+    layers/auxiliar.rst
     layers/activations.rst
     layers/data_augmentation.rst
     layers/data_transformation.rst
@@ -98,6 +99,13 @@ The code is open source, and `available on github`_.
     bundle/computing_service.rst
 
 
+.. toctree::
+    :maxdepth: 1
+    :caption: Model Zoo
+
+    models_zoo/classification.rst
+
+
 .. toctree::
     :maxdepth: 1
     :caption: Datasets
@@ -129,4 +137,4 @@ Indices and tables
 
 
 .. _available on github: https://github.com/deephealthproject/eddl
-
+

docs/sphinx/source/layers/auxiliar.rst

@@ -0,0 +1,26 @@
+Auxiliar Layers
+================
+
+Constant Of Tensor
+-------------------
+
+.. doxygenfunction:: ConstOfTensor
+
+Example:
+
+.. code-block:: c++
+
+    t = Tensor::ones({16, 16, 16}};
+    l = ConstOfTensor(t);
+
+
+Where
+------------------
+
+.. doxygenfunction:: Where
+
+Example:
+
+.. code-block:: c++
+
+    l = Where(parent1, parent2, condition);

docs/sphinx/source/layers/convolutional.rst

@@ -31,9 +31,9 @@ Conv3D
 
 .. doxygenfunction:: eddl::Conv3D
 
-.. note::
+.. code-block:: c++
 
-    **Work in progress**. Not yet implemented.
+    l = Conv3D(l, 32, {3, 3, 3}, {1, 1, 1}, "same");
 
 
 Pointwise Convolution 2D
@@ -48,27 +48,49 @@ Example:
     l = PointwiseConv2D(l, 32, {3,3}, {1,1});
 
 
-2D Upsampling 
+2D UpSampling
 --------------
 
+Soon to be deprecated. We recommend the use of the Resize layer.
+
 .. doxygenfunction:: eddl::UpSampling2D
 
-.. note::
+Example:
+
+.. code-block:: c++
+
+    l = UpSampling2D(l, {2, 2});
+
+
+3D UpSampling
+--------------
+
+UpSampling for 3D images
 
-    In future versions this function will call ``scale`` instead of ``repeat``
+.. doxygenfunction:: eddl::UpSampling3D
 
 Example:
 
 .. code-block:: c++
 
-    l = UpSampling2D(l, {2, 2});
-
+   l = UpSampling3D(l, {32, 32});
 
-Convolutional Transpose
-------------------------
+
+2D Convolutional Transpose
+----------------------------
 
 .. doxygenfunction:: eddl::ConvT2D
 
-.. note::
+.. code-block:: c++
+
+    l = ConvT2D(l, 32, {3, 3}, {1, 1}, "same");
+
+
+3D Convolutional Transpose
+----------------------------
+
+.. doxygenfunction:: eddl::ConvT3D
+
+.. code-block:: c++
 
-    **Work in progress**. Not yet implemented.
+    l = ConvT3D(l, 32, {3, 3, 3}, {1, 1, 1}, "same");

docs/sphinx/source/layers/core.rst

@@ -130,6 +130,54 @@ Example:
    l = Select(l, {"-1", "20:100", "50:-10", ":"});
 
 
+Slice
+---------------
+
+Alias for Select
+Selects a subset of the output tensor using indices (similar to Numpy; the batch is ignored)
+
+.. doxygenfunction:: eddl::Slice
+
+
+Example:
+
+.. code-block:: c++
+
+   l = Slice(l, {"-1", "20:100", "50:-10", ":"});
+
+
+Expand
+---------------
+
+Returns a layer with singleton dimensions expanded to a larger size.
+
+.. doxygenfunction:: eddl::Expand(layer l, int size, string name="")
+
+
+Example:
+
+.. code-block:: c++
+
+    // {3, 1, 5, 1, 5} and size=100 => {3, 100, 5, 100, 5}
+   l = Expand(l, 100);
+
+Split
+---------------
+
+
+Split a tensor (layer) into a list of tensors (layers). (The batch is ignored).
+The indexes mark the split points.
+
+.. doxygenfunction:: eddl::Split
+
+
+Example:
+
+.. code-block:: c++
+
+    // e.g.: l=> Output shape: {B, 3, 32, 32}
+    // vl: {l1, l2, l3}; l1= {B, :1, 32, 32}, l2= {B, 1:2, 32, 32}, l3= {B, 2:, 32, 32}
+   vector<layer> vl = Split(l, {1,2}, 0);
 
 Permute
 ---------------
@@ -158,3 +206,17 @@ Example:
 .. code-block:: c++
 
    l = Transpose(l);
+
+
+Resize
+-------
+
+Same as Scale but with support for backward operation.
+
+.. doxygenfunction:: Resize
+
+Example:
+
+.. code-block:: c++
+
+   l = Resize(l, {35, 35});

docs/sphinx/source/layers/data_augmentation.rst

@@ -2,32 +2,6 @@ Data augmentation
 =================
 
 These layers perform random transformations over the previous layer.
-Ranges are defined using relative coordinates between 0 and 1.
-
-.. note::
-
-    **Work in progress**. Not all transformation modes are implemented.
-
-    Currently implemented:
-
-    - ``constant``: The input is extended by filling all values beyond the edge with the same constant value, defined by the cval parameter.
-    - ``original`` (for rotation): The input is extended by filling all values beyond the edge with the original values
-
-
-
-
-RandomAffine
--------------
-
-.. doxygenfunction:: RandomAffine
-
-.. note::
-
-    **Not implemented yet**
-
-    Check development progress in https://github.com/deephealthproject/eddl/blob/master/docs/markdown/eddl_progress.md#data-augmentations
-
-
 
 
 RandomCrop
@@ -87,20 +61,6 @@ Example:
 
 
 
-RandomGrayscale
-----------------
-
-.. doxygenfunction:: RandomGrayscale
-
-.. note::
-
-    **Not implemented yet**
-
-    Check development progress in https://github.com/deephealthproject/eddl/blob/master/docs/markdown/eddl_progress.md#data-augmentations
-
-
-
-
 RandomHorizontalFlip
 ---------------------
 
@@ -132,7 +92,7 @@ Example:
 RandomScale
 --------------
 
-.. doxygenfunction:: RandomScale
+.. doxygenfunction::  RandomScale(layer parent, vector<float> factor, string da_mode = "nearest", float constant = 0.0f, string name = "")
 
 Example: