diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000000000000000000000000000000000000..4fb662854f3175a3c793711a89b0c4942f3cdb6a
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,8 @@
+*.png filter=lfs diff=lfs merge=lfs -text
+*.jp2 filter=lfs diff=lfs merge=lfs -text
+*.tif filter=lfs diff=lfs merge=lfs -text
+*.data-* filter=lfs diff=lfs merge=lfs -text
+*.gpkg filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 271b1daf7274419b0577a9dc37a862c8b3eab5ab..fe0ab91251dabee7b08824aaf3e71be8f77e8daa 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,6 +3,9 @@ image: gitlab-registry.irstea.fr/remi.cresson/otbtf:2.4-cpu-basic-testing
variables:
OTB_BUILD: /src/otb/build/OTB/build # Local OTB build directory
OTBTF_SRC: /src/otbtf # Local OTBTF source directory
+ OTB_TEST_DIR: $OTB_BUILD/Testing/Temporary # OTB testing directory
+ ARTIFACT_TEST_DIR: $CI_PROJECT_DIR/testing
+ CRC_BOOK_TMP: /tmp/crc_book_tests_tmp
workflow:
rules:
@@ -13,13 +16,17 @@ stages:
- Build
- Static Analysis
- Test
+ - Applications Test
.update_otbtf_src: &update_otbtf_src
- sudo rm -rf $OTBTF_SRC && sudo ln -s $PWD $OTBTF_SRC # Replace local OTBTF source directory
.compile_otbtf: &compile_otbtf
- cd $OTB_BUILD && sudo make install -j$(nproc --all) # Rebuild OTB with new OTBTF sources
-
+
+.install_pytest: &install_pytest
+ - pip3 install pytest pytest-cov pytest-order # Install pytest stuff
+
before_script:
- *update_otbtf_src
@@ -60,21 +67,46 @@ ctest:
stage: Test
script:
- *compile_otbtf
- - sudo rm -rf $OTB_BUILD/Testing/Temporary/* # Empty testing temporary folder (old files here)
+ - sudo rm -rf $OTB_TEST_DIR/* # Empty testing temporary folder (old files here)
- cd $OTB_BUILD/ && sudo ctest -L OTBTensorflow # Run ctest
after_script:
- - cp -r $OTB_BUILD/Testing/Temporary $CI_PROJECT_DIR/testing # Copy artifacts (they must be in $CI_PROJECT_DIR)
+ - cp -r $OTB_TEST_DIR $ARTIFACT_TEST_DIR
artifacts:
paths:
- - testing/*.*
+ - $ARTIFACT_TEST_DIR/*.*
expire_in: 1 week
when: on_failure
+.applications_test_base:
+ stage: Applications Test
+ rules:
+ # Only for MR targeting 'develop' and 'master' branches because applications tests are slow
+ - if: $CI_MERGE_REQUEST_ID && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == 'develop'
+ - if: $CI_MERGE_REQUEST_ID && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == 'master'
+ artifacts:
+ when: on_failure
+ paths:
+ - $CI_PROJECT_DIR/report_*.xml
+ - $ARTIFACT_TEST_DIR/*.*
+ expire_in: 1 week
+
+crc_book:
+ extends: .applications_test_base
+ script:
+ - *compile_otbtf
+ - *install_pytest
+ - cd $CI_PROJECT_DIR
+ - mkdir -p $CRC_BOOK_TMP
+ - TMPDIR=$CRC_BOOK_TMP DATADIR=$CI_PROJECT_DIR/test/data python -m pytest --junitxml=$CI_PROJECT_DIR/report_tutorial.xml $OTBTF_SRC/test/tutorial_unittest.py
+ after_script:
+ - mkdir -p $ARTIFACT_TEST_DIR
+ - cp $CRC_BOOK_TMP/*.* $ARTIFACT_TEST_DIR/
+
sr4rs:
- stage: Test
+ extends: .applications_test_base
script:
- *compile_otbtf
- - pip3 install pytest pytest-cov
+ - *install_pytest
- cd $CI_PROJECT_DIR
- wget -O sr4rs_sentinel2_bands4328_france2020_savedmodel.zip
https://nextcloud.inrae.fr/s/boabW9yCjdpLPGX/download/sr4rs_sentinel2_bands4328_france2020_savedmodel.zip
@@ -85,8 +117,4 @@ sr4rs:
- git clone https://github.com/remicres/sr4rs.git
- export PYTHONPATH=$PYTHONPATH:$PWD/sr4rs
- python -m pytest --junitxml=$CI_PROJECT_DIR/report_sr4rs.xml $OTBTF_SRC/test/sr4rs_unittest.py
- artifacts:
- when: on_failure
- paths:
- - $CI_PROJECT_DIR/report_sr4rs.xml
- expire_in: 1 week
+
diff --git a/Dockerfile b/Dockerfile
index c9aa6e9fcb40cba228c9a4d2c0634eb055e38fdf..c2c5efa46dc17b7e81fa548e40a6e64cd29abae3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -74,6 +74,7 @@ RUN git clone --single-branch -b $TF https://github.com/tensorflow/tensorflow.gi
&& ln -s $(find /opt/otbtf -type d -wholename "*/site-packages/tensorflow/include") /opt/otbtf/include/tf \
# The only missing header in the wheel
&& cp tensorflow/cc/saved_model/tag_constants.h /opt/otbtf/include/tf/tensorflow/cc/saved_model/ \
+ && cp tensorflow/cc/saved_model/signature_constants.h /opt/otbtf/include/tf/tensorflow/cc/saved_model/ \
# Symlink external libs (required for MKL - libiomp5)
&& for f in $(find -L /opt/otbtf/include/tf -wholename "*/external/*/*.so"); do ln -s $f /opt/otbtf/lib/; done \
# Compress and save TF binaries
@@ -90,7 +91,10 @@ WORKDIR /src/otb
# SuperBuild OTB
COPY tools/docker/build-flags-otb.txt ./
-RUN git clone --single-branch -b $OTB https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git \
+RUN apt-get update -y \
+ && apt-get install --reinstall ca-certificates -y \
+ && update-ca-certificates \
+ && git clone --single-branch -b $OTB https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb.git \
&& mkdir -p build \
&& cd build \
# Set GL/Qt build flags
diff --git a/README.md b/README.md
index a18961b3038b680b4a52f86666bc2ef8005a18d9..9434ec96fd9a8bc8ffeeabd98bcc4e4200376761 100644
--- a/README.md
+++ b/README.md
@@ -18,21 +18,23 @@ Applications can be used to build OTB pipelines from Python or C++ APIs.
### Python
-This is a work in progress. For now, `tricks.py` provides a set of helpers to build deep nets, and `otbtf.py` provides datasets which can be used in Tensorflow pipelines to train networks from python.
+`otbtf.py` targets python developers that want to train their own model from python with TensorFlow or Keras.
+It provides various classes for datasets and iterators to handle the _patches images_ generated from the `PatchesExtraction` OTB application.
+For instance, the `otbtf.Dataset` class provides a method `get_tf_dataset()` which returns a `tf.dataset` that can be used in your favorite TensorFlow pipelines, or convert your patches into TFRecords.
-## Portfolio
+`tricks.py` is here for backward compatibility with codes based on OTBTF 1.x and 2.x.
-Below are some screen captures of deep learning applications performed at large scale with OTBTF.
- - Image to image translation (Spot-7 image --> Wikimedia Map using CGAN)
-<img src ="doc/images/pix2pix.png" />
+## Examples
+Below are some screen captures of deep learning applications performed at large scale with OTBTF.
- Landcover mapping (Spot-7 images --> Building map using semantic segmentation)
<img src ="doc/images/landcover.png" />
- - Image enhancement (Enhancement of Sentinel-2 images at 1.5m using SRGAN)
+ - Super resolution (Sentinel-2 images upsampled with the [SR4RS software](https://github.com/remicres/sr4rs), which is based on OTBTF)
<img src ="doc/images/supresol.png" />
-You can read more details about these applications on [this blog](https://mdl4eo.irstea.fr/2019/)
+ - Image to image translation (Spot-7 image --> Wikimedia Map using CGAN. So unnecessary but fun!)
+<img src ="doc/images/pix2pix.png" />
## How to install
@@ -42,8 +44,8 @@ For now you have two options: either use the existing **docker image**, or build
Use the latest image from dockerhub:
```
-docker pull mdl4eo/otbtf2.5:cpu
-docker run -u otbuser -v $(pwd):/home/otbuser mdl4eo/otbtf2.5:cpu otbcli_PatchesExtraction -help
+docker pull mdl4eo/otbtf3.0:cpu
+docker run -u otbuser -v $(pwd):/home/otbuser mdl4eo/otbtf3.0:cpu otbcli_PatchesExtraction -help
```
Read more in the [docker use documentation](doc/DOCKERUSE.md).
@@ -57,12 +59,13 @@ Read more in the [build from sources documentation](doc/HOWTOBUILD.md).
- Reading [the applications documentation](doc/APPLICATIONS.md) will help, of course 😉
- A small [tutorial](https://mdl4eo.irstea.fr/2019/01/04/an-introduction-to-deep-learning-on-remote-sensing-images-tutorial/) on MDL4EO's blog
- in the `python` folder are provided some [ready-to-use deep networks, with documentation and scientific references](doc/EXAMPLES.md).
-- A book: *Cresson, R. (2020). Deep Learning for Remote Sensing Images with Open Source Software. CRC Press.* Use QGIS, OTB and Tensorflow to perform various kind of deep learning sorcery on remote sensing images (patch-based classification for landcover mapping, semantic segmentation of buildings, optical image restoration from joint SAR/Optical time series).
+- A [book](https://doi.org/10.1201/9781003020851): *Cresson, R. (2020). Deep Learning for Remote Sensing Images with Open Source Software. CRC Press.* Use QGIS, OTB and Tensorflow to perform various kind of deep learning sorcery on remote sensing images (patch-based classification for landcover mapping, semantic segmentation of buildings, optical image restoration from joint SAR/Optical time series).
- Check [our repository](https://github.com/remicres/otbtf_tutorials_resources) containing stuff (data and models) to begin with with!
+- Finally, take a look in the `test` folder. You will find plenty of command lines for applications tests!
## Contribute
-Every one can **contribute** to OTBTF! Don't be shy.
+Every one can **contribute** to OTBTF. Just open a PR :)
## Cite
diff --git a/doc/DOCKERUSE.md b/doc/DOCKERUSE.md
index 0f1086015a59c46efd5a1ca3f93a61dd962fa75f..34e58cc3eab4a170e8e4abd445da8a826890b8bb 100644
--- a/doc/DOCKERUSE.md
+++ b/doc/DOCKERUSE.md
@@ -20,6 +20,10 @@ Here is the list of OTBTF docker images hosted on [dockerhub](https://hub.docker
| **mdl4eo/otbtf2.5:cpu** | Ubuntu Focal | r2.5 | 7.4.0 | CPU, few optimization | no | 5.2,6.1,7.0,7.5,8.6|
| **mdl4eo/otbtf2.5:gpu** | Ubuntu Focal | r2.5 | 7.4.0 | GPU | no | 5.2,6.1,7.0,7.5,8.6|
| **mdl4eo/otbtf2.5:gpu-dev** | Ubuntu Focal | r2.5 | 7.4.0 | GPU (dev) | yes | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf3.0:cpu-basic** | Ubuntu Focal | r2.5 | 7.4.0 | CPU, no optimization | no | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf3.0:cpu-basic-dev** | Ubuntu Focal | r2.5 | 7.4.0 | CPU, no optimization (dev) | yes | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf3.0:gpu** | Ubuntu Focal | r2.5 | 7.4.0 | GPU | yes | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf3.0:gpu-dev** | Ubuntu Focal | r2.5 | 7.4.0 | GPU (dev) | yes | 5.2,6.1,7.0,7.5,8.6|
- `cpu` tagged docker images are compiled without optimization.
- `gpu` tagged docker images are suited for **NVIDIA GPUs**. They use CUDA/CUDNN support.
diff --git a/doc/images/classif_map.png b/doc/images/classif_map.png
index bc2a10799b03752c6a720c1d6b0ecca2aa6ae15d..017118c778d6d553fd1499a2bef5848782bcfc9c 100644
Binary files a/doc/images/classif_map.png and b/doc/images/classif_map.png differ
diff --git a/doc/images/docker_desktop_1.jpeg b/doc/images/docker_desktop_1.jpeg
index 9a03bd58cae40dfb428de083531c687020572883..21902e77e6a2e77463ddc452b6359e0dc1b0ca3d 100644
Binary files a/doc/images/docker_desktop_1.jpeg and b/doc/images/docker_desktop_1.jpeg differ
diff --git a/doc/images/docker_desktop_2.jpeg b/doc/images/docker_desktop_2.jpeg
index e393cdb40d45c1fbcfd69c8983a47aef8731b899..ec9f5632ba49c2b3f642c777531802023882e4ea 100644
Binary files a/doc/images/docker_desktop_2.jpeg and b/doc/images/docker_desktop_2.jpeg differ
diff --git a/doc/images/landcover.png b/doc/images/landcover.png
index 913f3600614420a70adc1bfa8110cdc6e3c3f45a..0fecc763fd72bccb1aba68bf7a1cdc236980101e 100644
Binary files a/doc/images/landcover.png and b/doc/images/landcover.png differ
diff --git a/doc/images/logo.png b/doc/images/logo.png
index 13aeaffd1c9ba0c5836b4a06857084ee126cede6..13f91d5a4a91fc6f372996e6a72fd5de27167567 100644
Binary files a/doc/images/logo.png and b/doc/images/logo.png differ
diff --git a/doc/images/model_training.png b/doc/images/model_training.png
index d385dbb6c4c6d5fc8d5e95e210800165d388a0b4..3e7d168937add573723cc686b8b263dbaebe42f4 100644
Binary files a/doc/images/model_training.png and b/doc/images/model_training.png differ
diff --git a/doc/images/patches_extraction.png b/doc/images/patches_extraction.png
index 024beb692493896d450481ba54e6b7b2069d60e9..bd04ff592b0c11091763bc094f3f22dc8bb63303 100644
Binary files a/doc/images/patches_extraction.png and b/doc/images/patches_extraction.png differ
diff --git a/doc/images/pix2pix.png b/doc/images/pix2pix.png
index 1c79652ff0bae389cbee1c7cde40b2d46f20f089..5df6b349acb27a04419fb226c2085a757cb6fe40 100644
Binary files a/doc/images/pix2pix.png and b/doc/images/pix2pix.png differ
diff --git a/doc/images/savedmodel_simple_cnn.png b/doc/images/savedmodel_simple_cnn.png
index d494e99e824ec0c2852dd6d21686a5df33aaa4f5..7ebe28ee37d744c542ed66a4eb63bf3b95d2e8af 100644
Binary files a/doc/images/savedmodel_simple_cnn.png and b/doc/images/savedmodel_simple_cnn.png differ
diff --git a/doc/images/savedmodel_simple_fcnn.png b/doc/images/savedmodel_simple_fcnn.png
index bc9e7aab8246c02dec572df1daab3d3799e5f6d8..d2e13fc31d6adfd0c84feae0f836d1840411f8e9 100644
Binary files a/doc/images/savedmodel_simple_fcnn.png and b/doc/images/savedmodel_simple_fcnn.png differ
diff --git a/doc/images/savedmodel_simple_pxs_fcn.png b/doc/images/savedmodel_simple_pxs_fcn.png
index 169e9703faa25b3e934d888b637a0f7ecd182ed8..bfb72eab3b9d0de7488e386b2403adbd8eadb9e2 100644
Binary files a/doc/images/savedmodel_simple_pxs_fcn.png and b/doc/images/savedmodel_simple_pxs_fcn.png differ
diff --git a/doc/images/schema.png b/doc/images/schema.png
index df80fcc1cdbcc58e081e13a4918d3652e649c5ab..f5788e33078f20299e0275d1b8a950fcfda35882 100644
Binary files a/doc/images/schema.png and b/doc/images/schema.png differ
diff --git a/doc/images/supresol.png b/doc/images/supresol.png
index efff2fd23176e0fab501ced42aa24c56a2a77a9b..310d36abce642b6c3813c0c21f31c28e2904124a 100644
Binary files a/doc/images/supresol.png and b/doc/images/supresol.png differ
diff --git a/include/otbTensorflowCommon.cxx b/include/otbTensorflowCommon.cxx
index 662c9d3e979c5e67ccf9effc4564c9d9fd5c6d0e..b7a27c60c5ef49fbee42556ace70b54751f682f9 100644
--- a/include/otbTensorflowCommon.cxx
+++ b/include/otbTensorflowCommon.cxx
@@ -11,8 +11,10 @@
=========================================================================*/
#include "otbTensorflowCommon.h"
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
//
// Environment variable for the number of sources in "Multisource" applications
@@ -22,21 +24,21 @@ const std::string ENV_VAR_NAME_NSOURCES = "OTB_TF_NSOURCES";
//
// Get the environment variable as int
//
-int GetEnvironmentVariableAsInt(const std::string & variableName)
+int
+GetEnvironmentVariableAsInt(const std::string & variableName)
{
- int ret = -1;
- char const* tmp = getenv( variableName.c_str() );
- if ( tmp != NULL )
+ int ret = -1;
+ char const * tmp = getenv(variableName.c_str());
+ if (tmp != NULL)
{
- std::string s( tmp );
+ std::string s(tmp);
try
{
ret = std::stoi(s);
}
- catch(...)
+ catch (...)
{
- itkGenericExceptionMacro("Error parsing variable "
- << variableName << " as integer. Value is " << s);
+ itkGenericExceptionMacro("Error parsing variable " << variableName << " as integer. Value is " << s);
}
}
@@ -47,7 +49,8 @@ int GetEnvironmentVariableAsInt(const std::string & variableName)
// This function returns the numeric content of the ENV_VAR_NAME_NSOURCES
// environment variable
//
-int GetNumberOfSources()
+int
+GetNumberOfSources()
{
int ret = GetEnvironmentVariableAsInt(ENV_VAR_NAME_NSOURCES);
if (ret != -1)
@@ -60,15 +63,18 @@ int GetNumberOfSources()
//
// This function copy a patch from an input image to an output image
//
-template<class TImage>
-void CopyPatch(typename TImage::Pointer inputImg, typename TImage::IndexType & inputPatchIndex,
- typename TImage::Pointer outputImg, typename TImage::IndexType & outputPatchIndex,
- typename TImage::SizeType patchSize)
+template <class TImage>
+void
+CopyPatch(typename TImage::Pointer inputImg,
+ typename TImage::IndexType & inputPatchIndex,
+ typename TImage::Pointer outputImg,
+ typename TImage::IndexType & outputPatchIndex,
+ typename TImage::SizeType patchSize)
{
- typename TImage::RegionType inputPatchRegion(inputPatchIndex, patchSize);
- typename TImage::RegionType outputPatchRegion(outputPatchIndex, patchSize);
- typename itk::ImageRegionConstIterator<TImage> inIt (inputImg, inputPatchRegion);
- typename itk::ImageRegionIterator<TImage> outIt (outputImg, outputPatchRegion);
+ typename TImage::RegionType inputPatchRegion(inputPatchIndex, patchSize);
+ typename TImage::RegionType outputPatchRegion(outputPatchIndex, patchSize);
+ typename itk::ImageRegionConstIterator<TImage> inIt(inputImg, inputPatchRegion);
+ typename itk::ImageRegionIterator<TImage> outIt(outputImg, outputPatchRegion);
for (inIt.GoToBegin(), outIt.GoToBegin(); !inIt.IsAtEnd(); ++inIt, ++outIt)
{
outIt.Set(inIt.Get());
@@ -78,9 +84,9 @@ void CopyPatch(typename TImage::Pointer inputImg, typename TImage::IndexType & i
//
// Get image infos
//
-template<class TImage>
-void GetImageInfo(typename TImage::Pointer image,
- unsigned int & sizex, unsigned int & sizey, unsigned int & nBands)
+template <class TImage>
+void
+GetImageInfo(typename TImage::Pointer image, unsigned int & sizex, unsigned int & sizey, unsigned int & nBands)
{
nBands = image->GetNumberOfComponentsPerPixel();
sizex = image->GetLargestPossibleRegion().GetSize(0);
@@ -90,8 +96,9 @@ void GetImageInfo(typename TImage::Pointer image,
//
// Propagate the requested region in the image
//
-template<class TImage>
-void PropagateRequestedRegion(typename TImage::Pointer image, typename TImage::RegionType & region)
+template <class TImage>
+void
+PropagateRequestedRegion(typename TImage::Pointer image, typename TImage::RegionType & region)
{
image->SetRequestedRegion(region);
image->PropagateRequestedRegion();
@@ -101,13 +108,16 @@ void PropagateRequestedRegion(typename TImage::Pointer image, typename TImage::R
//
// Sample an input image at the specified location
//
-template<class TImage>
-bool SampleImage(const typename TImage::Pointer inPtr, typename TImage::Pointer outPtr,
- typename TImage::PointType point, unsigned int elemIdx,
- typename TImage::SizeType patchSize)
+template <class TImage>
+bool
+SampleImage(const typename TImage::Pointer inPtr,
+ typename TImage::Pointer outPtr,
+ typename TImage::PointType point,
+ unsigned int elemIdx,
+ typename TImage::SizeType patchSize)
{
typename TImage::IndexType index, outIndex;
- bool canTransform = inPtr->TransformPhysicalPointToIndex(point, index);
+ bool canTransform = inPtr->TransformPhysicalPointToIndex(point, index);
if (canTransform)
{
outIndex[0] = 0;
@@ -128,7 +138,6 @@ bool SampleImage(const typename TImage::Pointer inPtr, typename TImage::Pointer
}
}
return false;
-
}
} // end namespace tf
diff --git a/include/otbTensorflowCommon.h b/include/otbTensorflowCommon.h
index fbd7281035185c2acc3a56dac3850a23d76280df..a012173c66ec9c4a10ae0f5f7df9908f01dd4833 100644
--- a/include/otbTensorflowCommon.h
+++ b/include/otbTensorflowCommon.h
@@ -22,38 +22,49 @@
#include "itkImageRegionConstIterator.h"
#include "itkImageRegionIterator.h"
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
// Environment variable for the number of sources in "Multisource" applications
extern const std::string ENV_VAR_NAME_NSOURCES;
// Get the environment variable as int
-int GetEnvironmentVariableAsInt(const std::string & variableName);
+int
+GetEnvironmentVariableAsInt(const std::string & variableName);
// Get the value (as int) of the environment variable ENV_VAR_NAME_NSOURCES
-int GetNumberOfSources();
+int
+GetNumberOfSources();
// This function copy a patch from an input image to an output image
-template<class TImage>
-void CopyPatch(typename TImage::Pointer inputImg, typename TImage::IndexType & inputPatchIndex,
- typename TImage::Pointer outputImg, typename TImage::IndexType & outputPatchIndex,
- typename TImage::SizeType patchSize);
+template <class TImage>
+void
+CopyPatch(typename TImage::Pointer inputImg,
+ typename TImage::IndexType & inputPatchIndex,
+ typename TImage::Pointer outputImg,
+ typename TImage::IndexType & outputPatchIndex,
+ typename TImage::SizeType patchSize);
// Get image infos
-template<class TImage>
-void GetImageInfo(typename TImage::Pointer image,
- unsigned int & sizex, unsigned int & sizey, unsigned int & nBands);
+template <class TImage>
+void
+GetImageInfo(typename TImage::Pointer image, unsigned int & sizex, unsigned int & sizey, unsigned int & nBands);
// Propagate the requested region in the image
-template<class TImage>
-void PropagateRequestedRegion(typename TImage::Pointer image, typename TImage::RegionType & region);
+template <class TImage>
+void
+PropagateRequestedRegion(typename TImage::Pointer image, typename TImage::RegionType & region);
// Sample an input image at the specified location
-template<class TImage>
-bool SampleImage(const typename TImage::Pointer inPtr, typename TImage::Pointer outPtr,
- typename TImage::PointType point, unsigned int elemIdx,
- typename TImage::SizeType patchSize);
+template <class TImage>
+bool
+SampleImage(const typename TImage::Pointer inPtr,
+ typename TImage::Pointer outPtr,
+ typename TImage::PointType point,
+ unsigned int elemIdx,
+ typename TImage::SizeType patchSize);
} // end namespace tf
} // end namespace otb
diff --git a/include/otbTensorflowCopyUtils.cxx b/include/otbTensorflowCopyUtils.cxx
index e969051102c6babaaa2aa3433dd25bafb64af18e..3aa117691c96993574afc27a085cf64a0140524e 100644
--- a/include/otbTensorflowCopyUtils.cxx
+++ b/include/otbTensorflowCopyUtils.cxx
@@ -187,7 +187,13 @@ GetNumberOfChannelsFromShapeProto(const tensorflow::TensorShapeProto & proto)
return 1;
// any other dimension: we assume that the last dimension represent the
// number of channels in the output image.
- return proto.dim(nDims - 1).size();
+ tensorflow::int64 nbChannels = proto.dim(nDims - 1).size();
+ if (nbChannels < 1)
+ itkGenericExceptionMacro("Cannot determine the size of the last dimension of one output tensor. Dimension index is "
+ << (nDims - 1)
+ << ". Please rewrite your model with output tensors having a shape where the last "
+ "dimension is a constant value.");
+ return nbChannels;
}
//
@@ -218,9 +224,10 @@ CopyTensorToImageRegion(const tensorflow::Tensor & tensor,
const tensorflow::int64 nElmI = bufferRegion.GetNumberOfPixels() * outputDimSize_C;
if (nElmI != nElmT)
{
- itkGenericExceptionMacro("Number of elements in the tensor is " << nElmT
- << " but image outputRegion has " << nElmI << " values to fill.\n"
- << "Buffer region is: \n" << bufferRegion << "\n"
+ itkGenericExceptionMacro("Number of elements in the tensor is "
+ << nElmT << " but image outputRegion has " << nElmI << " values to fill.\n"
+ << "Buffer region is: \n"
+ << bufferRegion << "\n"
<< "Number of components in the output image: " << outputDimSize_C << "\n"
<< "Tensor shape: " << PrintTensorShape(tensor.shape()) << "\n"
<< "Please check the input(s) field of view (FOV), "
@@ -347,7 +354,7 @@ ValueToTensor(std::string value)
}
// Create tensor
- tensorflow::TensorShape shape({values.size()});
+ tensorflow::TensorShape shape({ values.size() });
tensorflow::Tensor out(tensorflow::DT_BOOL, shape);
if (is_digit)
{
@@ -409,7 +416,7 @@ ValueToTensor(std::string value)
}
idx++;
}
- otbLogMacro(Debug, << "Returning tensor: "<< out.DebugString());
+ otbLogMacro(Debug, << "Returning tensor: " << out.DebugString());
return out;
}
diff --git a/include/otbTensorflowCopyUtils.h b/include/otbTensorflowCopyUtils.h
index 174587913beb5a73f78cbffe614aef23c78c8147..59e1a7443ff78511b42d6d67c74023cd49864235 100644
--- a/include/otbTensorflowCopyUtils.h
+++ b/include/otbTensorflowCopyUtils.h
@@ -34,57 +34,94 @@
#include <string>
#include <regex>
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
// Generate a string with TensorShape infos
-std::string PrintTensorShape(const tensorflow::TensorShape & shp);
+std::string
+PrintTensorShape(const tensorflow::TensorShape & shp);
// Generate a string with tensor infos
-std::string PrintTensorInfos(const tensorflow::Tensor & tensor);
+std::string
+PrintTensorInfos(const tensorflow::Tensor & tensor);
// Create a tensor with the good datatype
-template<class TImage>
-tensorflow::Tensor CreateTensor(tensorflow::TensorShape & shape);
+template <class TImage>
+tensorflow::Tensor
+CreateTensor(tensorflow::TensorShape & shape);
// Populate a tensor with the buffered region of a vector image
-template<class TImage>
-void PopulateTensorFromBufferedVectorImage(const typename TImage::Pointer bufferedimagePtr, tensorflow::Tensor & out_tensor);
+template <class TImage>
+void
+PopulateTensorFromBufferedVectorImage(const typename TImage::Pointer bufferedimagePtr, tensorflow::Tensor & out_tensor);
// Populate the buffered region of a vector image with a given tensor's values
-template<class TImage>
-void TensorToImageBuffer(const tensorflow::Tensor & tensor, typename TImage::Pointer & image);
+template <class TImage>
+void
+TensorToImageBuffer(const tensorflow::Tensor & tensor, typename TImage::Pointer & image);
// Recopy an VectorImage region into a 4D-shaped tensorflow::Tensor ({-1, sz_y, sz_x, sz_bands})
-template<class TImage, class TValueType=typename TImage::InternalPixelType>
-void RecopyImageRegionToTensor(const typename TImage::Pointer inputPtr, const typename TImage::RegionType & region, tensorflow::Tensor & tensor, unsigned int elemIdx);
+template <class TImage, class TValueType = typename TImage::InternalPixelType>
+void
+RecopyImageRegionToTensor(const typename TImage::Pointer inputPtr,
+ const typename TImage::RegionType & region,
+ tensorflow::Tensor & tensor,
+ unsigned int elemIdx);
// Recopy an VectorImage region into a 4D-shaped tensorflow::Tensor (TValueType-agnostic function)
-template<class TImage>
-void RecopyImageRegionToTensorWithCast(const typename TImage::Pointer inputPtr, const typename TImage::RegionType & region, tensorflow::Tensor & tensor, unsigned int elemIdx);
+template <class TImage>
+void
+RecopyImageRegionToTensorWithCast(const typename TImage::Pointer inputPtr,
+ const typename TImage::RegionType & region,
+ tensorflow::Tensor & tensor,
+ unsigned int elemIdx);
// Sample a centered patch
-template<class TImage>
-void SampleCenteredPatch(const typename TImage::Pointer inputPtr, const typename TImage::IndexType & centerIndex, const typename TImage::SizeType & patchSize, tensorflow::Tensor & tensor, unsigned int elemIdx);
-template<class TImage>
-void SampleCenteredPatch(const typename TImage::Pointer inputPtr, const typename TImage::PointType & centerCoord, const typename TImage::SizeType & patchSize, tensorflow::Tensor & tensor, unsigned int elemIdx);
+template <class TImage>
+void
+SampleCenteredPatch(const typename TImage::Pointer inputPtr,
+ const typename TImage::IndexType & centerIndex,
+ const typename TImage::SizeType & patchSize,
+ tensorflow::Tensor & tensor,
+ unsigned int elemIdx);
+template <class TImage>
+void
+SampleCenteredPatch(const typename TImage::Pointer inputPtr,
+ const typename TImage::PointType & centerCoord,
+ const typename TImage::SizeType & patchSize,
+ tensorflow::Tensor & tensor,
+ unsigned int elemIdx);
// Return the number of channels from the TensorflowShapeProto
-tensorflow::int64 GetNumberOfChannelsFromShapeProto(const tensorflow::TensorShapeProto & proto);
+tensorflow::int64
+GetNumberOfChannelsFromShapeProto(const tensorflow::TensorShapeProto & proto);
// Copy a tensor into the image region
-template<class TImage, class TValueType>
-void CopyTensorToImageRegion(const tensorflow::Tensor & tensor, typename TImage::Pointer outputPtr, const typename TImage::RegionType & region, int & channelOffset);
+template <class TImage, class TValueType>
+void
+CopyTensorToImageRegion(const tensorflow::Tensor & tensor,
+ typename TImage::Pointer outputPtr,
+ const typename TImage::RegionType & region,
+ int & channelOffset);
// Copy a tensor into the image region (TValueType-agnostic version)
-template<class TImage>
-void CopyTensorToImageRegion(const tensorflow::Tensor & tensor, const typename TImage::RegionType & bufferRegion, typename TImage::Pointer outputPtr, const typename TImage::RegionType & outputRegion, int & channelOffset);
+template <class TImage>
+void
+CopyTensorToImageRegion(const tensorflow::Tensor & tensor,
+ const typename TImage::RegionType & bufferRegion,
+ typename TImage::Pointer outputPtr,
+ const typename TImage::RegionType & outputRegion,
+ int & channelOffset);
// Convert a value into a tensor
-tensorflow::Tensor ValueToTensor(std::string value);
+tensorflow::Tensor
+ValueToTensor(std::string value);
// Convert an expression into a dict
-std::pair<std::string, tensorflow::Tensor> ExpressionToTensor(std::string expression);
+std::pair<std::string, tensorflow::Tensor>
+ExpressionToTensor(std::string expression);
} // end namespace tf
} // end namespace otb
diff --git a/include/otbTensorflowDataTypeBridge.cxx b/include/otbTensorflowDataTypeBridge.cxx
index a510cb4ea5ecab0c1505e690d79922b2299ddc0d..71fcd8c6beca73f611aa919b237c9d719f6ec4a7 100644
--- a/include/otbTensorflowDataTypeBridge.cxx
+++ b/include/otbTensorflowDataTypeBridge.cxx
@@ -11,14 +11,17 @@
=========================================================================*/
#include "otbTensorflowDataTypeBridge.h"
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
//
// returns the datatype used by tensorflow
//
-template<class Type>
-tensorflow::DataType GetTensorflowDataType()
+template <class Type>
+tensorflow::DataType
+GetTensorflowDataType()
{
if (typeid(Type) == typeid(bool))
{
@@ -74,8 +77,9 @@ tensorflow::DataType GetTensorflowDataType()
//
// Return true if the tensor data type is correct
//
-template<class Type>
-bool HasSameDataType(const tensorflow::Tensor & tensor)
+template <class Type>
+bool
+HasSameDataType(const tensorflow::Tensor & tensor)
{
return GetTensorflowDataType<Type>() == tensor.dtype();
}
@@ -83,7 +87,8 @@ bool HasSameDataType(const tensorflow::Tensor & tensor)
//
// Return the datatype as string
//
-tensorflow::string GetDataTypeAsString(tensorflow::DataType dt)
+tensorflow::string
+GetDataTypeAsString(tensorflow::DataType dt)
{
return tensorflow::DataTypeString(dt);
}
diff --git a/include/otbTensorflowDataTypeBridge.h b/include/otbTensorflowDataTypeBridge.h
index af6be18d335761b7261e6b8c7288cf9b07122bc8..e815dafcba8bbb408a843e3ed63aa9a5a8b8dfe3 100644
--- a/include/otbTensorflowDataTypeBridge.h
+++ b/include/otbTensorflowDataTypeBridge.h
@@ -16,19 +16,24 @@
#include "tensorflow/core/framework/types.h"
#include "tensorflow/core/framework/tensor.h"
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
// returns the datatype used by tensorflow
-template<class Type>
-tensorflow::DataType GetTensorflowDataType();
+template <class Type>
+tensorflow::DataType
+GetTensorflowDataType();
// Return true if the tensor data type is correct
-template<class Type>
-bool HasSameDataType(const tensorflow::Tensor & tensor);
+template <class Type>
+bool
+HasSameDataType(const tensorflow::Tensor & tensor);
// Return datatype as string
-tensorflow::string GetDataTypeAsString(tensorflow::DataType dt);
+tensorflow::string
+GetDataTypeAsString(tensorflow::DataType dt);
} // end namespace tf
} // end namespace otb
diff --git a/include/otbTensorflowGraphOperations.cxx b/include/otbTensorflowGraphOperations.cxx
index d40c4da6a2f49a86cb28069094b4ab9f0cc5b231..b8e0920e0b04d6cb1dc30f5bf3e8fcbe30d29b1b 100644
--- a/include/otbTensorflowGraphOperations.cxx
+++ b/include/otbTensorflowGraphOperations.cxx
@@ -87,19 +87,39 @@ GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::Ten
std::vector<std::string> & tensorsNames,
std::vector<std::string> & layerNames,
std::vector<tensorflow::TensorShapeProto> & shapes,
- std::vector<tensorflow::DataType> & dataTypes)
+ std::vector<tensorflow::DataType> & dataTypes,
+ std::vector<std::string> blackList = {})
{
- // Allocation
+ // Clear shapes, datatypes, and layers names
shapes.clear();
dataTypes.clear();
layerNames.clear();
// Debug infos
- otbLogMacro(Debug, << "Nodes contained in the model: ");
+ otbLogMacro(Debug, << "Nodes contained in the model:");
for (auto const & layer : layers)
otbLogMacro(Debug, << "\t" << layer.first);
- // When the user doesn't specify output.names, m_OutputTensors defaults to an empty list that we can not iterate over.
+ // Sort nodes names alphabetically
+ std::size_t k = 0; // Keep track of the indices in the protobuf map
+ std::vector<std::pair<std::string, int>> sortedLayersNames; // vector of (name, index) pairs
+ for (auto const & layer : layers)
+ {
+ // We exclude names, if any in the blacklist. Useful to avoid confusion
+ // between user placeholders (aka constants) and input tensors.
+ // Not used for output tensors.
+ if (std::count(blackList.begin(), blackList.end(), layer.first) == 0)
+ {
+ sortedLayersNames.emplace_back(layer.first, k);
+ }
+ k++;
+ }
+ std::sort(sortedLayersNames.begin(), sortedLayersNames.end());
+ otbLogMacro(Debug, << "Sorted (alphabetically) nodes names:");
+ for (auto const & name : sortedLayersNames)
+ otbLogMacro(Debug, << "\t" << name.first << " (index: " << name.second << ")");
+
+ // When the user doesn't specify output.names, tensorsNames defaults to an empty list that we can not iterate over.
// We change it to a list containing an empty string [""]
if (tensorsNames.size() == 0)
{
@@ -108,8 +128,8 @@ GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::Ten
}
// Next, we fill layerNames
- int k = 0; // counter used for tensorsNames
- for (auto const & name: tensorsNames)
+ k = 0; // counter used for tensorsNames
+ for (auto const & name : tensorsNames)
{
bool found = false;
tensorflow::TensorInfo tensor_info;
@@ -118,18 +138,24 @@ GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::Ten
if (name.size() == 0)
{
found = true;
- // select the k-th element of `layers`
- auto it = layers.begin();
- std::advance(it, k);
+ // select the k-th element of `layers` names, alphabeticallly sorted
+ const std::string kthName = sortedLayersNames[k].first;
+ auto it = layers.begin();
+ const int kthIndex = sortedLayersNames[k].second;
+ std::advance(it, kthIndex);
layerNames.push_back(it->second.name());
tensor_info = it->second;
- otbLogMacro(Debug, << "Input " << k << " corresponds to " << it->first << " in the model");
+ if (sortedLayersNames.size() > 1)
+ otbLogMacro(Warning,
+ << "The provided tensor name is empty, and there are multiple available candidates in the graph. "
+ "Available tensors names from the graph have been sorted alphabetically, and the tensor #"
+ << kthIndex << " (aka \"" << it->first << "\") will be used. ");
}
// Else, if the user specified the placeholdername, find the corresponding layer inside the model
else
{
- otbLogMacro(Debug, << "Searching for corresponding node of: " << name << "... ");
+ otbLogMacro(Debug, << "Searching for corresponding node of \"" << name << "\"... ");
for (auto const & layer : layers)
{
// layer is a pair (name, tensor_info)
@@ -143,7 +169,7 @@ GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::Ten
otbLogMacro(Debug, << "Found: " << layer.second.name() << " in the model");
}
} // next layer
- } // end else
+ } // end else
k += 1;
@@ -178,7 +204,7 @@ PrintNodeAttributes(const tensorflow::GraphDef & graph, const std::vector<std::s
tensorflow::NodeDef node = graph.node(i);
std::cout << i << "\t" << node.name() << std::endl;
- for (auto const & name: nodesNames)
+ for (auto const & name : nodesNames)
{
if (node.name().compare(name) == 0)
{
diff --git a/include/otbTensorflowGraphOperations.h b/include/otbTensorflowGraphOperations.h
index 6ad4a4e29880e10a5f10cbc4f1e945db9ca3c6a6..dbfcaa8e57efe508850f0ef77e108ba7478c0538 100644
--- a/include/otbTensorflowGraphOperations.h
+++ b/include/otbTensorflowGraphOperations.h
@@ -27,27 +27,37 @@
// OTB log
#include "otbMacro.h"
-namespace otb {
-namespace tf {
+namespace otb
+{
+namespace tf
+{
// Load SavedModel variables
-void RestoreModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle);
+void
+RestoreModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle);
// Save SavedModel variables
-void SaveModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle);
+void
+SaveModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle);
// Load SavedModel
-void LoadModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle, std::vector<std::string> tagList);
+void
+LoadModel(const tensorflow::tstring path, tensorflow::SavedModelBundle & bundle, std::vector<std::string> tagList);
// Get the following attributes of the specified tensors (by name) of a graph:
// - shape
// - datatype
// Here we assume that the node's output is a tensor
-void GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::TensorInfo> layers, std::vector<std::string> & tensorsNames,
- std::vector<tensorflow::TensorShapeProto> & shapes, std::vector<tensorflow::DataType> & dataTypes);
+void
+GetTensorAttributes(const tensorflow::protobuf::Map<std::string, tensorflow::TensorInfo> layers,
+ std::vector<std::string> & tensorsNames,
+ std::vector<tensorflow::TensorShapeProto> & shapes,
+ std::vector<tensorflow::DataType> & dataTypes,
+ std::vector<std::string> blackList);
// Print a lot of stuff about the specified nodes of the graph
-void PrintNodeAttributes(const tensorflow::GraphDef & graph, const std::vector<std::string> & nodesNames);
+void
+PrintNodeAttributes(const tensorflow::GraphDef & graph, const std::vector<std::string> & nodesNames);
} // end namespace tf
} // end namespace otb
diff --git a/include/otbTensorflowMultisourceModelBase.h b/include/otbTensorflowMultisourceModelBase.h
index d10648ea00afc6fc624fc9ffac8e19bbdffdf4f2..6c943d1f1e777f8f7d26fc6be7f529b34535b5c7 100644
--- a/include/otbTensorflowMultisourceModelBase.h
+++ b/include/otbTensorflowMultisourceModelBase.h
@@ -65,34 +65,32 @@ namespace otb
*
* \ingroup OTBTensorflow
*/
-template <class TInputImage, class TOutputImage=TInputImage>
-class ITK_EXPORT TensorflowMultisourceModelBase :
-public itk::ImageToImageFilter<TInputImage, TOutputImage>
+template <class TInputImage, class TOutputImage = TInputImage>
+class ITK_EXPORT TensorflowMultisourceModelBase : public itk::ImageToImageFilter<TInputImage, TOutputImage>
{
public:
-
/** Standard class typedefs. */
- typedef TensorflowMultisourceModelBase Self;
+ typedef TensorflowMultisourceModelBase Self;
typedef itk::ImageToImageFilter<TInputImage, TOutputImage> Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
/** Run-time type information (and related methods). */
itkTypeMacro(TensorflowMultisourceModelBase, itk::ImageToImageFilter);
/** Images typedefs */
- typedef TInputImage ImageType;
- typedef typename TInputImage::Pointer ImagePointerType;
- typedef typename TInputImage::PixelType PixelType;
- typedef typename TInputImage::InternalPixelType InternalPixelType;
- typedef typename TInputImage::IndexType IndexType;
- typedef typename TInputImage::IndexValueType IndexValueType;
- typedef typename TInputImage::PointType PointType;
- typedef typename TInputImage::SizeType SizeType;
- typedef typename TInputImage::SizeValueType SizeValueType;
- typedef typename TInputImage::SpacingType SpacingType;
- typedef typename TInputImage::RegionType RegionType;
+ typedef TInputImage ImageType;
+ typedef typename TInputImage::Pointer ImagePointerType;
+ typedef typename TInputImage::PixelType PixelType;
+ typedef typename TInputImage::InternalPixelType InternalPixelType;
+ typedef typename TInputImage::IndexType IndexType;
+ typedef typename TInputImage::IndexValueType IndexValueType;
+ typedef typename TInputImage::PointType PointType;
+ typedef typename TInputImage::SizeType SizeType;
+ typedef typename TInputImage::SizeValueType SizeValueType;
+ typedef typename TInputImage::SpacingType SpacingType;
+ typedef typename TInputImage::RegionType RegionType;
/** Typedefs for parameters */
typedef std::pair<std::string, tensorflow::Tensor> DictElementType;
@@ -104,15 +102,26 @@ public:
typedef std::vector<tensorflow::Tensor> TensorListType;
/** Set and Get the Tensorflow session and graph */
- void SetSavedModel(tensorflow::SavedModelBundle * saved_model) {m_SavedModel = saved_model;}
- tensorflow::SavedModelBundle * GetSavedModel() {return m_SavedModel;}
+ void
+ SetSavedModel(tensorflow::SavedModelBundle * saved_model)
+ {
+ m_SavedModel = saved_model;
+ }
+ tensorflow::SavedModelBundle *
+ GetSavedModel()
+ {
+ return m_SavedModel;
+ }
/** Get the SignatureDef */
- tensorflow::SignatureDef GetSignatureDef();
+ tensorflow::SignatureDef
+ GetSignatureDef();
/** Model parameters */
- void PushBackInputTensorBundle(std::string name, SizeType receptiveField, ImagePointerType image);
- void PushBackOuputTensorBundle(std::string name, SizeType expressionField);
+ void
+ PushBackInputTensorBundle(std::string name, SizeType receptiveField, ImagePointerType image);
+ void
+ PushBackOuputTensorBundle(std::string name, SizeType expressionField);
/** Input placeholders names */
itkSetMacro(InputPlaceholders, StringList);
@@ -131,8 +140,16 @@ public:
itkGetMacro(OutputExpressionFields, SizeListType);
/** User placeholders */
- void SetUserPlaceholders(const DictType & dict) {m_UserPlaceholders = dict;}
- DictType GetUserPlaceholders() {return m_UserPlaceholders;}
+ void
+ SetUserPlaceholders(const DictType & dict)
+ {
+ m_UserPlaceholders = dict;
+ }
+ DictType
+ GetUserPlaceholders()
+ {
+ return m_UserPlaceholders;
+ }
/** Target nodes names */
itkSetMacro(TargetNodesNames, StringList);
@@ -144,40 +161,47 @@ public:
itkGetMacro(InputTensorsShapes, TensorShapeProtoList);
itkGetMacro(OutputTensorsShapes, TensorShapeProtoList);
- virtual void GenerateOutputInformation();
+ virtual void
+ GenerateOutputInformation();
protected:
TensorflowMultisourceModelBase();
- virtual ~TensorflowMultisourceModelBase() {};
+ virtual ~TensorflowMultisourceModelBase(){};
- virtual std::stringstream GenerateDebugReport(DictType & inputs);
+ virtual std::stringstream
+ GenerateDebugReport(DictType & inputs);
- virtual void RunSession(DictType & inputs, TensorListType & outputs);
+ virtual void
+ RunSession(DictType & inputs, TensorListType & outputs);
private:
- TensorflowMultisourceModelBase(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowMultisourceModelBase(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
// Tensorflow graph and session
- tensorflow::SavedModelBundle * m_SavedModel; // The TensorFlow model
+ tensorflow::SavedModelBundle * m_SavedModel; // The TensorFlow model
// Model parameters
- StringList m_InputPlaceholders; // Input placeholders names
- SizeListType m_InputReceptiveFields; // Input receptive fields
- StringList m_OutputTensors; // Output tensors names
- SizeListType m_OutputExpressionFields; // Output expression fields
- DictType m_UserPlaceholders; // User placeholders
- StringList m_TargetNodesNames; // User nodes target
+ StringList m_InputPlaceholders; // Input placeholders names
+ SizeListType m_InputReceptiveFields; // Input receptive fields
+ StringList m_OutputTensors; // Output tensors names
+ SizeListType m_OutputExpressionFields; // Output expression fields
+ DictType m_UserPlaceholders; // User placeholders
+ StringList m_TargetNodesNames; // User nodes target
// Internal, read-only
- DataTypeListType m_InputTensorsDataTypes; // Input tensors datatype
- DataTypeListType m_OutputTensorsDataTypes; // Output tensors datatype
- TensorShapeProtoList m_InputTensorsShapes; // Input tensors shapes
- TensorShapeProtoList m_OutputTensorsShapes; // Output tensors shapes
+ DataTypeListType m_InputConstantsDataTypes; // Input constants datatype
+ DataTypeListType m_InputTensorsDataTypes; // Input tensors datatype
+ DataTypeListType m_OutputTensorsDataTypes; // Output tensors datatype
+ TensorShapeProtoList m_InputConstantsShapes; // Input constants shapes
+ TensorShapeProtoList m_InputTensorsShapes; // Input tensors shapes
+ TensorShapeProtoList m_OutputTensorsShapes; // Output tensors shapes
// Layer names inside the model corresponding to inputs and outputs
- StringList m_InputLayers; // List of input names, as contained in the model
- StringList m_OutputLayers; // List of output names, as contained in the model
+ StringList m_InputConstants; // List of constants names, as contained in the model
+ StringList m_InputLayers; // List of input names, as contained in the model
+ StringList m_OutputLayers; // List of output names, as contained in the model
}; // end class
diff --git a/include/otbTensorflowMultisourceModelBase.hxx b/include/otbTensorflowMultisourceModelBase.hxx
index 752b7c9d61a861d260dc4dfac89efb66e772a42b..ba4612627381d01991dbd5c5d050e8c197c1f851 100644
--- a/include/otbTensorflowMultisourceModelBase.hxx
+++ b/include/otbTensorflowMultisourceModelBase.hxx
@@ -18,28 +18,26 @@ namespace otb
{
template <class TInputImage, class TOutputImage>
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::TensorflowMultisourceModelBase()
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::TensorflowMultisourceModelBase()
{
- Superclass::SetCoordinateTolerance(itk::NumericTraits<double>::max() );
- Superclass::SetDirectionTolerance(itk::NumericTraits<double>::max() );
-
+ Superclass::SetCoordinateTolerance(itk::NumericTraits<double>::max());
+ Superclass::SetDirectionTolerance(itk::NumericTraits<double>::max());
+
m_SavedModel = NULL;
}
template <class TInputImage, class TOutputImage>
tensorflow::SignatureDef
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::GetSignatureDef()
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::GetSignatureDef()
{
- auto signatures = this->GetSavedModel()->GetSignatures();
+ auto signatures = this->GetSavedModel()->GetSignatures();
tensorflow::SignatureDef signature_def;
if (signatures.size() == 0)
{
- itkExceptionMacro("There are no available signatures for this tag-set. \n" <<
- "Please check which tag-set to use by running "<<
- "`saved_model_cli show --dir your_model_dir --all`");
+ itkExceptionMacro("There are no available signatures for this tag-set. \n"
+ << "Please check which tag-set to use by running "
+ << "`saved_model_cli show --dir your_model_dir --all`");
}
// If serving_default key exists (which is the default for TF saved model), choose it as signature
@@ -57,8 +55,9 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::PushBackInputTensorBundle(std::string placeholder, SizeType receptiveField, ImagePointerType image)
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::PushBackInputTensorBundle(std::string placeholder,
+ SizeType receptiveField,
+ ImagePointerType image)
{
Superclass::PushBackInput(image);
m_InputReceptiveFields.push_back(receptiveField);
@@ -67,8 +66,7 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
template <class TInputImage, class TOutputImage>
std::stringstream
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::GenerateDebugReport(DictType & inputs)
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::GenerateDebugReport(DictType & inputs)
{
// Create a debug report
std::stringstream debugReport;
@@ -79,18 +77,18 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
debugReport << "Output image buffered region: " << outputReqRegion << "\n";
// Describe inputs
- for (unsigned int i = 0 ; i < this->GetNumberOfInputs() ; i++)
+ for (unsigned int i = 0; i < this->GetNumberOfInputs(); i++)
{
- const ImagePointerType inputPtr = const_cast<TInputImage*>(this->GetInput(i));
- const RegionType reqRegion = inputPtr->GetRequestedRegion();
+ const ImagePointerType inputPtr = const_cast<TInputImage *>(this->GetInput(i));
+ const RegionType reqRegion = inputPtr->GetRequestedRegion();
debugReport << "Input #" << i << ":\n";
debugReport << "Requested region: " << reqRegion << "\n";
debugReport << "Tensor \"" << inputs[i].first << "\": " << tf::PrintTensorInfos(inputs[i].second) << "\n";
}
// Show user placeholders
- debugReport << "User placeholders:\n" ;
- for (auto& dict: this->GetUserPlaceholders())
+ debugReport << "User placeholders:\n";
+ for (auto & dict : this->GetUserPlaceholders())
{
debugReport << "Tensor \"" << dict.first << "\": " << tf::PrintTensorInfos(dict.second) << "\n" << std::endl;
}
@@ -101,25 +99,31 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::RunSession(DictType & inputs, TensorListType & outputs)
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::RunSession(DictType & inputs, TensorListType & outputs)
{
- // Add the user's placeholders
- std::copy(this->GetUserPlaceholders().begin(), this->GetUserPlaceholders().end(), std::back_inserter(inputs));
-
// Run the TF session here
// The session will initialize the outputs
- // `inputs` corresponds to a mapping {name, tensor}, with the name being specified by the user when calling TensorFlowModelServe
- // we must adapt it to `inputs_new`, that corresponds to a mapping {layerName, tensor}, with the layerName being from the model
+ // `inputs` corresponds to a mapping {name, tensor}, with the name being specified by the user when calling
+ // TensorFlowModelServe we must adapt it to `inputs_new`, that corresponds to a mapping {layerName, tensor}, with the
+ // layerName being from the model
DictType inputs_new;
- int k = 0;
- for (auto& dict: inputs)
+
+ // Add the user's placeholders
+ std::size_t k = 0;
+ for (auto & dict : this->GetUserPlaceholders())
{
- DictElementType element = {m_InputLayers[k], dict.second};
- inputs_new.push_back(element);
- k+=1;
+ inputs_new.emplace_back(m_InputConstants[k], dict.second);
+ k++;
+ }
+
+ // Add input tensors
+ k = 0;
+ for (auto & dict : inputs)
+ {
+ inputs_new.emplace_back(m_InputLayers[k], dict.second);
+ k += 1;
}
// Run the session, evaluating our output tensors from the graph
@@ -132,16 +136,18 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
std::stringstream debugReport = GenerateDebugReport(inputs);
// Throw an exception with the report
- itkExceptionMacro("Can't run the tensorflow session !\n" <<
- "Tensorflow error message:\n" << status.ToString() << "\n"
- "OTB Filter debug message:\n" << debugReport.str() );
+ itkExceptionMacro("Can't run the tensorflow session !\n"
+ << "Tensorflow error message:\n"
+ << status.ToString()
+ << "\n"
+ "OTB Filter debug message:\n"
+ << debugReport.str());
}
}
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelBase<TInputImage, TOutputImage>
-::GenerateOutputInformation()
+TensorflowMultisourceModelBase<TInputImage, TOutputImage>::GenerateOutputInformation()
{
// Check that the number of the following is the same
@@ -151,9 +157,9 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
const unsigned int nbInputs = this->GetNumberOfInputs();
if (nbInputs != m_InputReceptiveFields.size() || nbInputs != m_InputPlaceholders.size())
{
- itkExceptionMacro("Number of input images is " << nbInputs <<
- " but the number of input patches size is " << m_InputReceptiveFields.size() <<
- " and the number of input tensors names is " << m_InputPlaceholders.size());
+ itkExceptionMacro("Number of input images is "
+ << nbInputs << " but the number of input patches size is " << m_InputReceptiveFields.size()
+ << " and the number of input tensors names is " << m_InputPlaceholders.size());
}
//////////////////////////////////////////////////////////////////////////////////////////
@@ -166,10 +172,30 @@ TensorflowMultisourceModelBase<TInputImage, TOutputImage>
// and other infos (shapes, dtypes)
// For example, for output names specified by the user m_OutputTensors = ['s2t', 's2t_pad'],
// this will return m_OutputLayers = ['PartitionedCall:0', 'PartitionedCall:1']
- // In case the user hasn't named the output, e.g. m_OutputTensors = [''],
+ // In case the user hasn't named the output, i.e. m_OutputTensors = [''],
// this will return the first output m_OutputLayers = ['PartitionedCall:0']
- tf::GetTensorAttributes(signaturedef.inputs(), m_InputPlaceholders, m_InputLayers, m_InputTensorsShapes, m_InputTensorsDataTypes);
- tf::GetTensorAttributes(signaturedef.outputs(), m_OutputTensors, m_OutputLayers, m_OutputTensorsShapes, m_OutputTensorsDataTypes);
+ StringList constantsNames;
+ std::transform(m_UserPlaceholders.begin(),
+ m_UserPlaceholders.end(),
+ std::back_inserter(constantsNames),
+ [](const DictElementType & p) { return p.first; });
+ if (m_UserPlaceholders.size() > 0)
+ {
+ // Avoid the unnecessary warning when no placeholder is fed
+ tf::GetTensorAttributes(signaturedef.inputs(),
+ constantsNames,
+ m_InputConstants,
+ m_InputConstantsShapes,
+ m_InputConstantsDataTypes);
+ }
+ tf::GetTensorAttributes(signaturedef.inputs(),
+ m_InputPlaceholders,
+ m_InputLayers,
+ m_InputTensorsShapes,
+ m_InputTensorsDataTypes,
+ constantsNames);
+ tf::GetTensorAttributes(
+ signaturedef.outputs(), m_OutputTensors, m_OutputLayers, m_OutputTensorsShapes, m_OutputTensorsDataTypes);
}
diff --git a/include/otbTensorflowMultisourceModelFilter.h b/include/otbTensorflowMultisourceModelFilter.h
index 36d781dd1519b964adce741a8adbcb1385b0c729..bdf9a02d0b00e9dbc228f3a0401ac8dab4c49e32 100644
--- a/include/otbTensorflowMultisourceModelFilter.h
+++ b/include/otbTensorflowMultisourceModelFilter.h
@@ -80,12 +80,10 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage, class TOutputImage>
-class ITK_EXPORT TensorflowMultisourceModelFilter :
-public TensorflowMultisourceModelBase<TInputImage, TOutputImage>
+class ITK_EXPORT TensorflowMultisourceModelFilter : public TensorflowMultisourceModelBase<TInputImage, TOutputImage>
{
public:
-
/** Standard class typedefs. */
typedef TensorflowMultisourceModelFilter Self;
typedef TensorflowMultisourceModelBase<TInputImage, TOutputImage> Superclass;
@@ -99,16 +97,16 @@ public:
itkTypeMacro(TensorflowMultisourceModelFilter, TensorflowMultisourceModelBase);
/** Images typedefs */
- typedef typename Superclass::ImageType ImageType;
- typedef typename Superclass::ImagePointerType ImagePointerType;
- typedef typename Superclass::PixelType PixelType;
- typedef typename Superclass::IndexType IndexType;
- typedef typename IndexType::IndexValueType IndexValueType;
- typedef typename Superclass::PointType PointType;
- typedef typename Superclass::SizeType SizeType;
- typedef typename SizeType::SizeValueType SizeValueType;
- typedef typename Superclass::SpacingType SpacingType;
- typedef typename Superclass::RegionType RegionType;
+ typedef typename Superclass::ImageType ImageType;
+ typedef typename Superclass::ImagePointerType ImagePointerType;
+ typedef typename Superclass::PixelType PixelType;
+ typedef typename Superclass::IndexType IndexType;
+ typedef typename IndexType::IndexValueType IndexValueType;
+ typedef typename Superclass::PointType PointType;
+ typedef typename Superclass::SizeType SizeType;
+ typedef typename SizeType::SizeValueType SizeValueType;
+ typedef typename Superclass::SpacingType SpacingType;
+ typedef typename Superclass::RegionType RegionType;
typedef TOutputImage OutputImageType;
typedef typename TOutputImage::PixelType OutputPixelType;
@@ -119,12 +117,12 @@ public:
typedef typename itk::ImageRegionConstIterator<TInputImage> InputConstIteratorType;
/* Typedefs for parameters */
- typedef typename Superclass::DictElementType DictElementType;
- typedef typename Superclass::DictType DictType;
- typedef typename Superclass::StringList StringList;
- typedef typename Superclass::SizeListType SizeListType;
- typedef typename Superclass::TensorListType TensorListType;
- typedef std::vector<float> ScaleListType;
+ typedef typename Superclass::DictElementType DictElementType;
+ typedef typename Superclass::DictType DictType;
+ typedef typename Superclass::StringList StringList;
+ typedef typename Superclass::SizeListType SizeListType;
+ typedef typename Superclass::TensorListType TensorListType;
+ typedef std::vector<float> ScaleListType;
itkSetMacro(OutputGridSize, SizeType);
itkGetMacro(OutputGridSize, SizeType);
@@ -137,34 +135,43 @@ public:
protected:
TensorflowMultisourceModelFilter();
- virtual ~TensorflowMultisourceModelFilter() {};
+ virtual ~TensorflowMultisourceModelFilter(){};
- virtual void SmartPad(RegionType& region, const SizeType &patchSize);
- virtual void SmartShrink(RegionType& region, const SizeType &patchSize);
- virtual void ImageToExtent(ImageType* image, PointType &extentInf, PointType &extentSup, SizeType &patchSize);
- virtual bool OutputRegionToInputRegion(const RegionType &outputRegion, RegionType &inputRegion, ImageType* &inputImage);
- virtual void EnlargeToAlignedRegion(RegionType& region);
+ virtual void
+ SmartPad(RegionType & region, const SizeType & patchSize);
+ virtual void
+ SmartShrink(RegionType & region, const SizeType & patchSize);
+ virtual void
+ ImageToExtent(ImageType * image, PointType & extentInf, PointType & extentSup, SizeType & patchSize);
+ virtual bool
+ OutputRegionToInputRegion(const RegionType & outputRegion, RegionType & inputRegion, ImageType *& inputImage);
+ virtual void
+ EnlargeToAlignedRegion(RegionType & region);
- virtual void GenerateOutputInformation(void);
+ virtual void
+ GenerateOutputInformation(void);
- virtual void GenerateInputRequestedRegion(void);
+ virtual void
+ GenerateInputRequestedRegion(void);
- virtual void GenerateData();
+ virtual void
+ GenerateData();
private:
- TensorflowMultisourceModelFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowMultisourceModelFilter(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- SizeType m_OutputGridSize; // Output grid size
- bool m_ForceOutputGridSize; // Force output grid size
- bool m_FullyConvolutional; // Convolution mode
- float m_OutputSpacingScale; // scaling of the output spacings
+ SizeType m_OutputGridSize; // Output grid size
+ bool m_ForceOutputGridSize; // Force output grid size
+ bool m_FullyConvolutional; // Convolution mode
+ float m_OutputSpacingScale; // scaling of the output spacings
// Internal
- SpacingType m_OutputSpacing; // Output image spacing
- PointType m_OutputOrigin; // Output image origin
- SizeType m_OutputSize; // Output image size
- PixelType m_NullPixel; // Pixel filled with zeros
+ SpacingType m_OutputSpacing; // Output image spacing
+ PointType m_OutputOrigin; // Output image origin
+ SizeType m_OutputSize; // Output image size
+ PixelType m_NullPixel; // Pixel filled with zeros
}; // end class
diff --git a/include/otbTensorflowMultisourceModelFilter.hxx b/include/otbTensorflowMultisourceModelFilter.hxx
index d208f01a8deb1834b98f64c1230423d44b2cfe7a..3cbb53d92857466d617e5547940c8e42a0ce971e 100644
--- a/include/otbTensorflowMultisourceModelFilter.hxx
+++ b/include/otbTensorflowMultisourceModelFilter.hxx
@@ -18,9 +18,8 @@ namespace otb
{
template <class TInputImage, class TOutputImage>
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::TensorflowMultisourceModelFilter()
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::TensorflowMultisourceModelFilter()
+{
m_OutputGridSize.Fill(0);
m_ForceOutputGridSize = false;
m_FullyConvolutional = false;
@@ -31,38 +30,37 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
m_OutputSpacingScale = 1.0f;
- Superclass::SetCoordinateTolerance(itk::NumericTraits<double>::max() );
- Superclass::SetDirectionTolerance(itk::NumericTraits<double>::max() );
- }
+ Superclass::SetCoordinateTolerance(itk::NumericTraits<double>::max());
+ Superclass::SetDirectionTolerance(itk::NumericTraits<double>::max());
+}
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::SmartPad(RegionType& region, const SizeType &patchSize)
- {
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::SmartPad(RegionType & region, const SizeType & patchSize)
+{
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
const SizeValueType psz = patchSize[dim];
const SizeValueType rval = 0.5 * psz;
const SizeValueType lval = psz - rval;
region.GetModifiableIndex()[dim] -= lval;
region.GetModifiableSize()[dim] += psz;
- }
- }
+ }
+}
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::SmartShrink(RegionType& region, const SizeType &patchSize)
- {
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::SmartShrink(RegionType & region,
+ const SizeType & patchSize)
+{
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
const SizeValueType psz = patchSize[dim];
const SizeValueType lval = 0.5 * psz;
region.GetModifiableIndex()[dim] += lval;
region.GetModifiableSize()[dim] -= psz - 1;
- }
- }
+ }
+}
/**
Compute the input image extent: corners inf and sup.
@@ -70,9 +68,11 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
*/
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::ImageToExtent(ImageType* image, PointType &extentInf, PointType &extentSup, SizeType &patchSize)
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::ImageToExtent(ImageType * image,
+ PointType & extentInf,
+ PointType & extentSup,
+ SizeType & patchSize)
+{
// Get largest possible region
RegionType largestPossibleRegion = image->GetLargestPossibleRegion();
@@ -89,13 +89,12 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
PointType imageEnd;
image->TransformIndexToPhysicalPoint(imageLastIndex, imageEnd);
image->TransformIndexToPhysicalPoint(imageFirstIndex, imageOrigin);
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
extentInf[dim] = vnl_math_min(imageOrigin[dim], imageEnd[dim]) - 0.5 * image->GetSpacing()[dim];
extentSup[dim] = vnl_math_max(imageOrigin[dim], imageEnd[dim]) + 0.5 * image->GetSpacing()[dim];
- }
-
- }
+ }
+}
/**
Compute the region of the input image which correspond to the given output requested region
@@ -104,9 +103,10 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
*/
template <class TInputImage, class TOutputImage>
bool
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::OutputRegionToInputRegion(const RegionType &outputRegion, RegionType &inputRegion, ImageType* &inputImage)
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::OutputRegionToInputRegion(const RegionType & outputRegion,
+ RegionType & inputRegion,
+ ImageType *& inputImage)
+{
// Mosaic Region Start & End (mosaic image index)
const IndexType outIndexStart = outputRegion.GetIndex();
@@ -115,45 +115,43 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Mosaic Region Start & End (geo)
PointType outPointStart, outPointEnd;
this->GetOutput()->TransformIndexToPhysicalPoint(outIndexStart, outPointStart);
- this->GetOutput()->TransformIndexToPhysicalPoint(outIndexEnd , outPointEnd );
+ this->GetOutput()->TransformIndexToPhysicalPoint(outIndexEnd, outPointEnd);
// Add the half-width pixel size of the input image
// and remove the half-width pixel size of the output image
// (coordinates = pixel center)
const SpacingType outputSpc = this->GetOutput()->GetSpacing();
const SpacingType inputSpc = inputImage->GetSpacing();
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
- const typename SpacingType::ValueType border =
- 0.5 * (inputSpc[dim] - outputSpc[dim]);
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
+ const typename SpacingType::ValueType border = 0.5 * (inputSpc[dim] - outputSpc[dim]);
if (outPointStart[dim] < outPointEnd[dim])
- {
+ {
outPointStart[dim] += border;
- outPointEnd [dim] -= border;
- }
+ outPointEnd[dim] -= border;
+ }
else
- {
+ {
outPointStart[dim] -= border;
- outPointEnd [dim] += border;
- }
+ outPointEnd[dim] += border;
}
+ }
// Mosaic Region Start & End (input image index)
IndexType defIndexStart, defIndexEnd;
inputImage->TransformPhysicalPointToIndex(outPointStart, defIndexStart);
- inputImage->TransformPhysicalPointToIndex(outPointEnd , defIndexEnd);
+ inputImage->TransformPhysicalPointToIndex(outPointEnd, defIndexEnd);
// Compute input image region
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
inputRegion.SetIndex(dim, vnl_math_min(defIndexStart[dim], defIndexEnd[dim]));
inputRegion.SetSize(dim, vnl_math_max(defIndexStart[dim], defIndexEnd[dim]) - inputRegion.GetIndex(dim) + 1);
- }
+ }
// crop the input requested region at the input's largest possible region
- return inputRegion.Crop( inputImage->GetLargestPossibleRegion() );
-
- }
+ return inputRegion.Crop(inputImage->GetLargestPossibleRegion());
+}
/*
* Enlarge the given region to the nearest aligned region.
@@ -161,11 +159,10 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
*/
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::EnlargeToAlignedRegion(RegionType& region)
- {
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::EnlargeToAlignedRegion(RegionType & region)
+{
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
// Get corners
IndexValueType lower = region.GetIndex(dim);
IndexValueType upper = lower + region.GetSize(dim);
@@ -177,22 +174,20 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Move corners to aligned positions
lower -= deltaLo;
if (deltaUp > 0)
- {
+ {
upper += m_OutputGridSize[dim] - deltaUp;
- }
+ }
// Update region
region.SetIndex(dim, lower);
region.SetSize(dim, upper - lower);
-
- }
- }
+ }
+}
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::GenerateOutputInformation()
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::GenerateOutputInformation()
+{
Superclass::GenerateOutputInformation();
@@ -204,8 +199,8 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// OTBTF assumes that the output image has the following geometric properties:
// (1) Image origin is the top-left pixel
// (2) Image pixel spacing has positive x-spacing and negative y-spacing
- m_OutputSpacing = this->GetInput(0)->GetSpacing(); // GetSpacing() returns abs. spacing
- m_OutputSpacing[1] *= -1.0; // Force negative y-spacing
+ m_OutputSpacing = this->GetInput(0)->GetSpacing(); // GetSpacing() returns abs. spacing
+ m_OutputSpacing[1] *= -1.0; // Force negative y-spacing
m_OutputSpacing[0] *= m_OutputSpacingScale;
m_OutputSpacing[1] *= m_OutputSpacingScale;
@@ -214,30 +209,32 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
PointType extentInf, extentSup;
extentSup.Fill(itk::NumericTraits<double>::max());
extentInf.Fill(itk::NumericTraits<double>::NonpositiveMin());
- for (unsigned int imageIndex = 0 ; imageIndex < this->GetNumberOfInputs() ; imageIndex++)
- {
- ImageType * currentImage = static_cast<ImageType *>(
- Superclass::ProcessObject::GetInput(imageIndex) );
+ for (unsigned int imageIndex = 0; imageIndex < this->GetNumberOfInputs(); imageIndex++)
+ {
+ ImageType * currentImage = static_cast<ImageType *>(Superclass::ProcessObject::GetInput(imageIndex));
// Update output image extent
PointType currentInputImageExtentInf, currentInputImageExtentSup;
- ImageToExtent(currentImage, currentInputImageExtentInf, currentInputImageExtentSup, this->GetInputReceptiveFields()[imageIndex]);
- for(unsigned int dim = 0; dim<ImageType::ImageDimension; ++dim)
- {
+ ImageToExtent(currentImage,
+ currentInputImageExtentInf,
+ currentInputImageExtentSup,
+ this->GetInputReceptiveFields()[imageIndex]);
+ for (unsigned int dim = 0; dim < ImageType::ImageDimension; ++dim)
+ {
extentInf[dim] = vnl_math_max(currentInputImageExtentInf[dim], extentInf[dim]);
extentSup[dim] = vnl_math_min(currentInputImageExtentSup[dim], extentSup[dim]);
- }
}
+ }
// Set final origin, aligned to the reference image grid.
// Here we simply get back to the center of the pixel (extents are pixels corners coordinates)
- m_OutputOrigin[0] = extentInf[0] + 0.5 * this->GetInput(0)->GetSpacing()[0];
- m_OutputOrigin[1] = extentSup[1] - 0.5 * this->GetInput(0)->GetSpacing()[1];
+ m_OutputOrigin[0] = extentInf[0] + 0.5 * this->GetInput(0)->GetSpacing()[0];
+ m_OutputOrigin[1] = extentSup[1] - 0.5 * this->GetInput(0)->GetSpacing()[1];
// Set final size
- m_OutputSize[0] = std::floor( (extentSup[0] - extentInf[0]) / std::abs(m_OutputSpacing[0]) );
- m_OutputSize[1] = std::floor( (extentSup[1] - extentInf[1]) / std::abs(m_OutputSpacing[1]) );
+ m_OutputSize[0] = std::floor((extentSup[0] - extentInf[0]) / std::abs(m_OutputSpacing[0]));
+ m_OutputSize[1] = std::floor((extentSup[1] - extentInf[1]) / std::abs(m_OutputSpacing[1]));
// We should take in account one more thing: the expression field. It enlarge slightly the output image extent.
m_OutputOrigin[0] -= m_OutputSpacing[0] * std::floor(0.5 * this->GetOutputExpressionFields().at(0)[0]);
@@ -247,18 +244,18 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Set output grid size
if (!m_ForceOutputGridSize)
- {
+ {
// Default is the output field of expression
m_OutputGridSize = this->GetOutputExpressionFields().at(0);
- }
+ }
// Resize the largestPossibleRegion to be a multiple of the grid size
- for(unsigned int dim = 0; dim<ImageType::ImageDimension; ++dim)
- {
+ for (unsigned int dim = 0; dim < ImageType::ImageDimension; ++dim)
+ {
if (m_OutputGridSize[dim] > m_OutputSize[dim])
itkGenericExceptionMacro("Output grid size is larger than output image size !");
m_OutputSize[dim] -= m_OutputSize[dim] % m_OutputGridSize[dim];
- }
+ }
// Set the largest possible region
RegionType largestPossibleRegion;
@@ -269,38 +266,39 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
//////////////////////////////////////////////////////////////////////////////////////////
unsigned int outputPixelSize = 0;
- for (auto& protoShape: this->GetOutputTensorsShapes())
- {
+ for (auto & protoShape : this->GetOutputTensorsShapes())
+ {
// Find the number of components
if (protoShape.dim_size() > 4)
- {
- itkExceptionMacro("dim_size=" << protoShape.dim_size() << " currently not supported. "
- "Keep in mind that output tensors must have 1, 2, 3 or 4 dimensions. "
- "In the case of 1-dimensional tensor, the first dimension is for the batch, "
- "and we assume that the output tensor has 1 channel. "
- "In the case of 2-dimensional tensor, the first dimension is for the batch, "
- "and the second is the number of components. "
- "In the case of 3-dimensional tensor, the first dimension is for the batch, "
- "and other dims are for (x, y). "
- "In the case of 4-dimensional tensor, the first dimension is for the batch, "
- "and the second and the third are for (x, y). The last is for the number of "
- "channels. ");
- }
+ {
+ itkExceptionMacro("dim_size=" << protoShape.dim_size()
+ << " currently not supported. "
+ "Keep in mind that output tensors must have 1, 2, 3 or 4 dimensions. "
+ "In the case of 1-dimensional tensor, the first dimension is for the batch, "
+ "and we assume that the output tensor has 1 channel. "
+ "In the case of 2-dimensional tensor, the first dimension is for the batch, "
+ "and the second is the number of components. "
+ "In the case of 3-dimensional tensor, the first dimension is for the batch, "
+ "and other dims are for (x, y). "
+ "In the case of 4-dimensional tensor, the first dimension is for the batch, "
+ "and the second and the third are for (x, y). The last is for the number of "
+ "channels. ");
+ }
unsigned int nComponents = tf::GetNumberOfChannelsFromShapeProto(protoShape);
outputPixelSize += nComponents;
- }
+ }
// Copy input image projection
- ImageType * inputImage = static_cast<ImageType * >( Superclass::ProcessObject::GetInput(0) );
+ ImageType * inputImage = static_cast<ImageType *>(Superclass::ProcessObject::GetInput(0));
const std::string projectionRef = inputImage->GetProjectionRef();
// Set output image origin/spacing/size/projection
ImageType * outputPtr = this->GetOutput();
outputPtr->SetNumberOfComponentsPerPixel(outputPixelSize);
- outputPtr->SetProjectionRef ( projectionRef );
- outputPtr->SetOrigin ( m_OutputOrigin );
- outputPtr->SetSignedSpacing ( m_OutputSpacing );
- outputPtr->SetLargestPossibleRegion( largestPossibleRegion );
+ outputPtr->SetProjectionRef(projectionRef);
+ outputPtr->SetOrigin(m_OutputOrigin);
+ outputPtr->SetSignedSpacing(m_OutputSpacing);
+ outputPtr->SetLargestPossibleRegion(largestPossibleRegion);
// Set null pixel
m_NullPixel.SetSize(outputPtr->GetNumberOfComponentsPerPixel());
@@ -312,14 +310,12 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
itk::EncapsulateMetaData(outputPtr->GetMetaDataDictionary(), MetaDataKey::TileHintX, m_OutputGridSize[0]);
itk::EncapsulateMetaData(outputPtr->GetMetaDataDictionary(), MetaDataKey::TileHintY, m_OutputGridSize[1]);
-
- }
+}
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::GenerateInputRequestedRegion()
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::GenerateInputRequestedRegion()
+{
Superclass::GenerateInputRequestedRegion();
// Output requested region
@@ -329,35 +325,37 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
EnlargeToAlignedRegion(requestedRegion);
// For each image, get the requested region
- for(unsigned int i = 0; i < this->GetNumberOfInputs(); ++i)
- {
- ImageType * inputImage = static_cast<ImageType * >( Superclass::ProcessObject::GetInput(i) );
+ for (unsigned int i = 0; i < this->GetNumberOfInputs(); ++i)
+ {
+ ImageType * inputImage = static_cast<ImageType *>(Superclass::ProcessObject::GetInput(i));
// Compute the requested region
RegionType inRegion;
- if (!OutputRegionToInputRegion(requestedRegion, inRegion, inputImage) )
- {
+ if (!OutputRegionToInputRegion(requestedRegion, inRegion, inputImage))
+ {
// Image does not overlap requested region: set requested region to null
- otbLogMacro(Debug, << "Image #" << i << " :\n" << inRegion << " is outside the requested region");
+ otbLogMacro(Debug, << "Image #" << i << " :\n" << inRegion << " is outside the requested region");
inRegion.GetModifiableIndex().Fill(0);
inRegion.GetModifiableSize().Fill(0);
- }
+ }
// Compute the FOV-scale*FOE radius to pad
SizeType toPad(this->GetInputReceptiveFields().at(i));
- for(unsigned int dim = 0; dim<ImageType::ImageDimension; ++dim)
- {
- int valToPad = 1 + (this->GetOutputExpressionFields().at(0)[dim] - 1) * m_OutputSpacingScale * this->GetInput(0)->GetSpacing()[dim] / this->GetInput(i)->GetSpacing()[dim] ;
+ for (unsigned int dim = 0; dim < ImageType::ImageDimension; ++dim)
+ {
+ int valToPad = 1 + (this->GetOutputExpressionFields().at(0)[dim] - 1) * m_OutputSpacingScale *
+ this->GetInput(0)->GetSpacing()[dim] / this->GetInput(i)->GetSpacing()[dim];
if (valToPad > toPad[dim])
- itkExceptionMacro("The input requested region of source #" << i << " is not consistent (dim "<< dim<< ")." <<
- "Please check RF, EF, SF vs physical spacing of your image!" <<
- "\nReceptive field: " << this->GetInputReceptiveFields().at(i)[dim] <<
- "\nExpression field: " << this->GetOutputExpressionFields().at(0)[dim] <<
- "\nScale factor: " << m_OutputSpacingScale <<
- "\nReference image spacing: " << this->GetInput(0)->GetSpacing()[dim] <<
- "\nImage " << i << " spacing: " << this->GetInput(i)->GetSpacing()[dim]);
+ itkExceptionMacro("The input requested region of source #"
+ << i << " is not consistent (dim " << dim << ")."
+ << "Please check RF, EF, SF vs physical spacing of your image!"
+ << "\nReceptive field: " << this->GetInputReceptiveFields().at(i)[dim]
+ << "\nExpression field: " << this->GetOutputExpressionFields().at(0)[dim]
+ << "\nScale factor: " << m_OutputSpacingScale
+ << "\nReference image spacing: " << this->GetInput(0)->GetSpacing()[dim] << "\nImage " << i
+ << " spacing: " << this->GetInput(i)->GetSpacing()[dim]);
toPad[dim] -= valToPad;
- }
+ }
// Pad with radius
SmartPad(inRegion, toPad);
@@ -368,30 +366,28 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// can be one pixel larger when the input image regions are not physically
// aligned.
if (!m_FullyConvolutional)
- {
+ {
inRegion.PadByRadius(1);
- }
+ }
inRegion.Crop(inputImage->GetLargestPossibleRegion());
// Update the requested region
inputImage->SetRequestedRegion(inRegion);
- } // next image
-
- }
+ } // next image
+}
/**
* Compute the output image
*/
template <class TInputImage, class TOutputImage>
void
-TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
-::GenerateData()
- {
+TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::GenerateData()
+{
// Output pointer and requested region
typename TOutputImage::Pointer outputPtr = this->GetOutput();
- const RegionType outputReqRegion = outputPtr->GetRequestedRegion();
+ const RegionType outputReqRegion = outputPtr->GetRequestedRegion();
// Get the aligned output requested region
RegionType outputAlignedReqRegion(outputReqRegion);
@@ -404,10 +400,10 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Populate input tensors
- for (unsigned int i = 0 ; i < nInputs ; i++)
- {
+ for (unsigned int i = 0; i < nInputs; i++)
+ {
// Input image pointer
- const ImagePointerType inputPtr = const_cast<TInputImage*>(this->GetInput(i));
+ const ImagePointerType inputPtr = const_cast<TInputImage *>(this->GetInput(i));
// Patch size of tensor #i
const SizeType inputPatchSize = this->GetInputReceptiveFields().at(i);
@@ -416,13 +412,13 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
const RegionType reqRegion = inputPtr->GetRequestedRegion();
if (m_FullyConvolutional)
- {
+ {
// Shape of input tensor #i
- tensorflow::int64 sz_n = 1;
- tensorflow::int64 sz_y = reqRegion.GetSize(1);
- tensorflow::int64 sz_x = reqRegion.GetSize(0);
- tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
- tensorflow::TensorShape inputTensorShape({sz_n, sz_y, sz_x, sz_c});
+ tensorflow::int64 sz_n = 1;
+ tensorflow::int64 sz_y = reqRegion.GetSize(1);
+ tensorflow::int64 sz_x = reqRegion.GetSize(0);
+ tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
+ tensorflow::TensorShape inputTensorShape({ sz_n, sz_y, sz_x, sz_c });
// Create the input tensor
tensorflow::Tensor inputTensor(this->GetInputTensorsDataTypes()[i], inputTensorShape);
@@ -433,16 +429,16 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Input is the tensor representing the subset of image
DictElementType input = { this->GetInputPlaceholders()[i], inputTensor };
inputs.push_back(input);
- }
+ }
else
- {
+ {
// Preparing patches
// Shape of input tensor #i
- tensorflow::int64 sz_n = outputReqRegion.GetNumberOfPixels();
- tensorflow::int64 sz_y = inputPatchSize[1];
- tensorflow::int64 sz_x = inputPatchSize[0];
- tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
- tensorflow::TensorShape inputTensorShape({sz_n, sz_y, sz_x, sz_c});
+ tensorflow::int64 sz_n = outputReqRegion.GetNumberOfPixels();
+ tensorflow::int64 sz_y = inputPatchSize[1];
+ tensorflow::int64 sz_x = inputPatchSize[0];
+ tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
+ tensorflow::TensorShape inputTensorShape({ sz_n, sz_y, sz_x, sz_c });
// Create the input tensor
tensorflow::Tensor inputTensor(this->GetInputTensorsDataTypes()[i], inputTensorShape);
@@ -450,10 +446,10 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Fill the input tensor.
// We iterate over points which are located from the index iterator
// moving through the output image requested region
- unsigned int elemIndex = 0;
+ unsigned int elemIndex = 0;
IndexIteratorType idxIt(outputPtr, outputReqRegion);
for (idxIt.GoToBegin(); !idxIt.IsAtEnd(); ++idxIt)
- {
+ {
// Get the coordinates of the current output pixel
PointType point;
outputPtr->TransformIndexToPhysicalPoint(idxIt.GetIndex(), point);
@@ -461,15 +457,15 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Sample the i-th input patch centered on the point
tf::SampleCenteredPatch<TInputImage>(inputPtr, point, inputPatchSize, inputTensor, elemIndex);
elemIndex++;
- }
+ }
// Input is the tensor of patches (aka the batch)
DictElementType input = { this->GetInputPlaceholders()[i], inputTensor };
inputs.push_back(input);
- } // mode is not full convolutional
+ } // mode is not full convolutional
- } // next input tensor
+ } // next input tensor
// Run session
// TODO: see if we print some info about inputs/outputs of the model e.g. m_OutputTensors
@@ -483,26 +479,25 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>
// Get output tensors
int bandOffset = 0;
- for (unsigned int i = 0 ; i < outputs.size() ; i++)
- {
+ for (unsigned int i = 0; i < outputs.size(); i++)
+ {
// The offset (i.e. the starting index of the channel for the output tensor) is updated
// during this call
- // TODO: implement a generic strategy enabling expression field copy in patch-based mode (see tf::CopyTensorToImageRegion)
+ // TODO: implement a generic strategy enabling expression field copy in patch-based mode (see
+ // tf::CopyTensorToImageRegion)
try
- {
- tf::CopyTensorToImageRegion<TOutputImage> (outputs[i],
- outputAlignedReqRegion, outputPtr, outputReqRegion, bandOffset);
- }
- catch( itk::ExceptionObject & err )
- {
+ {
+ tf::CopyTensorToImageRegion<TOutputImage>(
+ outputs[i], outputAlignedReqRegion, outputPtr, outputReqRegion, bandOffset);
+ }
+ catch (itk::ExceptionObject & err)
+ {
std::stringstream debugMsg = this->GenerateDebugReport(inputs);
itkExceptionMacro("Error occurred during tensor to image conversion.\n"
- << "Context: " << debugMsg.str()
- << "Error:" << err);
- }
+ << "Context: " << debugMsg.str() << "Error:" << err);
}
-
- }
+ }
+}
} // end namespace otb
diff --git a/include/otbTensorflowMultisourceModelLearningBase.h b/include/otbTensorflowMultisourceModelLearningBase.h
index 0663f17a3f6367d5f5fe0ebbc76b1ca71d64957d..6e01317db89d235e7ddae6740136d28f6470cc59 100644
--- a/include/otbTensorflowMultisourceModelLearningBase.h
+++ b/include/otbTensorflowMultisourceModelLearningBase.h
@@ -53,37 +53,35 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage>
-class ITK_EXPORT TensorflowMultisourceModelLearningBase :
-public TensorflowMultisourceModelBase<TInputImage>
+class ITK_EXPORT TensorflowMultisourceModelLearningBase : public TensorflowMultisourceModelBase<TInputImage>
{
public:
-
/** Standard class typedefs. */
- typedef TensorflowMultisourceModelLearningBase Self;
- typedef TensorflowMultisourceModelBase<TInputImage> Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef TensorflowMultisourceModelLearningBase Self;
+ typedef TensorflowMultisourceModelBase<TInputImage> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
/** Run-time type information (and related methods). */
itkTypeMacro(TensorflowMultisourceModelLearningBase, TensorflowMultisourceModelBase);
/** Images typedefs */
- typedef typename Superclass::ImageType ImageType;
- typedef typename Superclass::ImagePointerType ImagePointerType;
- typedef typename Superclass::RegionType RegionType;
- typedef typename Superclass::SizeType SizeType;
- typedef typename Superclass::IndexType IndexType;
+ typedef typename Superclass::ImageType ImageType;
+ typedef typename Superclass::ImagePointerType ImagePointerType;
+ typedef typename Superclass::RegionType RegionType;
+ typedef typename Superclass::SizeType SizeType;
+ typedef typename Superclass::IndexType IndexType;
/* Typedefs for parameters */
- typedef typename Superclass::DictType DictType;
- typedef typename Superclass::DictElementType DictElementType;
- typedef typename Superclass::StringList StringList;
- typedef typename Superclass::SizeListType SizeListType;
- typedef typename Superclass::TensorListType TensorListType;
+ typedef typename Superclass::DictType DictType;
+ typedef typename Superclass::DictElementType DictElementType;
+ typedef typename Superclass::StringList StringList;
+ typedef typename Superclass::SizeListType SizeListType;
+ typedef typename Superclass::TensorListType TensorListType;
/* Typedefs for index */
- typedef typename ImageType::IndexValueType IndexValueType;
- typedef std::vector<IndexValueType> IndexListType;
+ typedef typename ImageType::IndexValueType IndexValueType;
+ typedef std::vector<IndexValueType> IndexListType;
// Batch size
itkSetMacro(BatchSize, IndexValueType);
@@ -98,29 +96,36 @@ public:
protected:
TensorflowMultisourceModelLearningBase();
- virtual ~TensorflowMultisourceModelLearningBase() {};
+ virtual ~TensorflowMultisourceModelLearningBase(){};
- virtual void GenerateOutputInformation(void) override;
+ virtual void
+ GenerateOutputInformation(void) override;
- virtual void GenerateInputRequestedRegion();
+ virtual void
+ GenerateInputRequestedRegion();
- virtual void GenerateData();
+ virtual void
+ GenerateData();
- virtual void PopulateInputTensors(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize, const IndexListType & order);
+ virtual void
+ PopulateInputTensors(DictType & inputs,
+ const IndexValueType & sampleStart,
+ const IndexValueType & batchSize,
+ const IndexListType & order);
- virtual void ProcessBatch(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize) = 0;
+ virtual void
+ ProcessBatch(DictType & inputs, const IndexValueType & sampleStart, const IndexValueType & batchSize) = 0;
private:
- TensorflowMultisourceModelLearningBase(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowMultisourceModelLearningBase(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- unsigned int m_BatchSize; // Batch size
- bool m_UseStreaming; // Use streaming on/off
+ unsigned int m_BatchSize; // Batch size
+ bool m_UseStreaming; // Use streaming on/off
// Read only
- IndexValueType m_NumberOfSamples; // Number of samples
+ IndexValueType m_NumberOfSamples; // Number of samples
}; // end class
diff --git a/include/otbTensorflowMultisourceModelLearningBase.hxx b/include/otbTensorflowMultisourceModelLearningBase.hxx
index 28b2328b8b82c49896ed40a1edd18fba5cebd7a7..bfa26d4dc3789a18879891fc9df9581a03fb4d1a 100644
--- a/include/otbTensorflowMultisourceModelLearningBase.hxx
+++ b/include/otbTensorflowMultisourceModelLearningBase.hxx
@@ -18,39 +18,38 @@ namespace otb
{
template <class TInputImage>
-TensorflowMultisourceModelLearningBase<TInputImage>
-::TensorflowMultisourceModelLearningBase(): m_BatchSize(100),
-m_UseStreaming(false), m_NumberOfSamples(0)
- {
- }
+TensorflowMultisourceModelLearningBase<TInputImage>::TensorflowMultisourceModelLearningBase()
+ : m_BatchSize(100)
+ , m_UseStreaming(false)
+ , m_NumberOfSamples(0)
+{}
template <class TInputImage>
void
-TensorflowMultisourceModelLearningBase<TInputImage>
-::GenerateOutputInformation()
- {
+TensorflowMultisourceModelLearningBase<TInputImage>::GenerateOutputInformation()
+{
Superclass::GenerateOutputInformation();
// Set an empty output buffered region
ImageType * outputPtr = this->GetOutput();
- RegionType nullRegion;
+ RegionType nullRegion;
nullRegion.GetModifiableSize().Fill(1);
outputPtr->SetNumberOfComponentsPerPixel(1);
- outputPtr->SetLargestPossibleRegion( nullRegion );
+ outputPtr->SetLargestPossibleRegion(nullRegion);
// Count the number of samples
m_NumberOfSamples = 0;
- for (unsigned int i = 0 ; i < this->GetNumberOfInputs() ; i++)
- {
+ for (unsigned int i = 0; i < this->GetNumberOfInputs(); i++)
+ {
// Input image pointer
- ImagePointerType inputPtr = const_cast<ImageType*>(this->GetInput(i));
+ ImagePointerType inputPtr = const_cast<ImageType *>(this->GetInput(i));
// Make sure input is available
- if ( inputPtr.IsNull() )
- {
+ if (inputPtr.IsNull())
+ {
itkExceptionMacro(<< "Input " << i << " is null!");
- }
+ }
// Update input information
inputPtr->UpdateOutputInformation();
@@ -63,67 +62,62 @@ TensorflowMultisourceModelLearningBase<TInputImage>
// Check size X
if (inputPatchSize[0] != reqRegion.GetSize(0))
- itkExceptionMacro("Patch size for input " << i
- << " is " << inputPatchSize
- << " but input patches image size is " << reqRegion.GetSize());
+ itkExceptionMacro("Patch size for input " << i << " is " << inputPatchSize << " but input patches image size is "
+ << reqRegion.GetSize());
// Check size Y
if (reqRegion.GetSize(1) % inputPatchSize[1] != 0)
itkExceptionMacro("Input patches image must have a number of rows which is "
- << "a multiple of the patch size Y! Patches image has " << reqRegion.GetSize(1)
- << " rows but patch size Y is " << inputPatchSize[1] << " for input " << i);
+ << "a multiple of the patch size Y! Patches image has " << reqRegion.GetSize(1)
+ << " rows but patch size Y is " << inputPatchSize[1] << " for input " << i);
// Get the batch size
const IndexValueType currNumberOfSamples = reqRegion.GetSize(1) / inputPatchSize[1];
// Check the consistency with other inputs
if (m_NumberOfSamples == 0)
- {
+ {
m_NumberOfSamples = currNumberOfSamples;
- }
+ }
else if (m_NumberOfSamples != currNumberOfSamples)
- {
- itkGenericExceptionMacro("Batch size of input " << (i-1)
- << " was " << m_NumberOfSamples
- << " but input " << i
- << " has a batch size of " << currNumberOfSamples );
- }
- } // next input
- }
+ {
+ itkGenericExceptionMacro("Batch size of input " << (i - 1) << " was " << m_NumberOfSamples << " but input " << i
+ << " has a batch size of " << currNumberOfSamples);
+ }
+ } // next input
+}
template <class TInputImage>
void
-TensorflowMultisourceModelLearningBase<TInputImage>
-::GenerateInputRequestedRegion()
- {
+TensorflowMultisourceModelLearningBase<TInputImage>::GenerateInputRequestedRegion()
+{
Superclass::GenerateInputRequestedRegion();
// For each image, set the requested region
RegionType nullRegion;
- for(unsigned int i = 0; i < this->GetNumberOfInputs(); ++i)
- {
- ImageType * inputImage = static_cast<ImageType * >( Superclass::ProcessObject::GetInput(i) );
+ for (unsigned int i = 0; i < this->GetNumberOfInputs(); ++i)
+ {
+ ImageType * inputImage = static_cast<ImageType *>(Superclass::ProcessObject::GetInput(i));
// If the streaming is enabled, we don't read the full image
if (m_UseStreaming)
- {
+ {
inputImage->SetRequestedRegion(nullRegion);
- }
+ }
else
- {
+ {
inputImage->SetRequestedRegion(inputImage->GetLargestPossibleRegion());
- }
- } // next image
- }
+ }
+ } // next image
+}
/**
*
*/
template <class TInputImage>
void
-TensorflowMultisourceModelLearningBase<TInputImage>
-::GenerateData()
- {
+TensorflowMultisourceModelLearningBase<TInputImage>::GenerateData()
+{
// Batches loop
const IndexValueType nBatches = std::ceil(m_NumberOfSamples / m_BatchSize);
@@ -131,15 +125,15 @@ TensorflowMultisourceModelLearningBase<TInputImage>
itk::ProgressReporter progress(this, 0, nBatches);
- for (IndexValueType batch = 0 ; batch < nBatches ; batch++)
- {
+ for (IndexValueType batch = 0; batch < nBatches; batch++)
+ {
// Feed dict
DictType inputs;
// Batch start and size
const IndexValueType sampleStart = batch * m_BatchSize;
- IndexValueType batchSize = m_BatchSize;
+ IndexValueType batchSize = m_BatchSize;
if (rest != 0 && batch == nBatches - 1)
{
batchSize = rest;
@@ -149,40 +143,40 @@ TensorflowMultisourceModelLearningBase<TInputImage>
this->ProcessBatch(inputs, sampleStart, batchSize);
progress.CompletedPixel();
- } // Next batch
-
- }
+ } // Next batch
+}
template <class TInputImage>
void
-TensorflowMultisourceModelLearningBase<TInputImage>
-::PopulateInputTensors(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize, const IndexListType & order)
- {
+TensorflowMultisourceModelLearningBase<TInputImage>::PopulateInputTensors(DictType & inputs,
+ const IndexValueType & sampleStart,
+ const IndexValueType & batchSize,
+ const IndexListType & order)
+{
const bool reorder = order.size();
// Populate input tensors
- for (unsigned int i = 0 ; i < this->GetNumberOfInputs() ; i++)
- {
+ for (unsigned int i = 0; i < this->GetNumberOfInputs(); i++)
+ {
// Input image pointer
- ImagePointerType inputPtr = const_cast<ImageType*>(this->GetInput(i));
+ ImagePointerType inputPtr = const_cast<ImageType *>(this->GetInput(i));
// Patch size of tensor #i
const SizeType inputPatchSize = this->GetInputReceptiveFields().at(i);
// Create the tensor for the batch
- const tensorflow::int64 sz_n = batchSize;
- const tensorflow::int64 sz_y = inputPatchSize[1];
- const tensorflow::int64 sz_x = inputPatchSize[0];
- const tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
- const tensorflow::TensorShape inputTensorShape({sz_n, sz_y, sz_x, sz_c});
- tensorflow::Tensor inputTensor(this->GetInputTensorsDataTypes()[i], inputTensorShape);
+ const tensorflow::int64 sz_n = batchSize;
+ const tensorflow::int64 sz_y = inputPatchSize[1];
+ const tensorflow::int64 sz_x = inputPatchSize[0];
+ const tensorflow::int64 sz_c = inputPtr->GetNumberOfComponentsPerPixel();
+ const tensorflow::TensorShape inputTensorShape({ sz_n, sz_y, sz_x, sz_c });
+ tensorflow::Tensor inputTensor(this->GetInputTensorsDataTypes()[i], inputTensorShape);
// Populate the tensor
- for (IndexValueType elem = 0 ; elem < batchSize ; elem++)
- {
+ for (IndexValueType elem = 0; elem < batchSize; elem++)
+ {
const tensorflow::uint64 samplePos = sampleStart + elem;
- IndexType start;
+ IndexType start;
start[0] = 0;
if (reorder)
{
@@ -190,7 +184,8 @@ TensorflowMultisourceModelLearningBase<TInputImage>
}
else
{
- start[1] = samplePos * sz_y;;
+ start[1] = samplePos * sz_y;
+ ;
}
RegionType patchRegion(start, inputPatchSize);
if (m_UseStreaming)
@@ -198,14 +193,14 @@ TensorflowMultisourceModelLearningBase<TInputImage>
// If streaming is enabled, we need to explicitly propagate requested region
tf::PropagateRequestedRegion<TInputImage>(inputPtr, patchRegion);
}
- tf::RecopyImageRegionToTensorWithCast<TInputImage>(inputPtr, patchRegion, inputTensor, elem );
- }
+ tf::RecopyImageRegionToTensorWithCast<TInputImage>(inputPtr, patchRegion, inputTensor, elem);
+ }
// Input #i : the tensor of patches (aka the batch)
DictElementType input = { this->GetInputPlaceholders()[i], inputTensor };
inputs.push_back(input);
- } // next input tensor
- }
+ } // next input tensor
+}
} // end namespace otb
diff --git a/include/otbTensorflowMultisourceModelTrain.h b/include/otbTensorflowMultisourceModelTrain.h
index 8ec4c38c369d532a706746c9674197ad766f657b..694f09e0b0ebfdd65305432a602e9f3908c8eadf 100644
--- a/include/otbTensorflowMultisourceModelTrain.h
+++ b/include/otbTensorflowMultisourceModelTrain.h
@@ -34,11 +34,9 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage>
-class ITK_EXPORT TensorflowMultisourceModelTrain :
-public TensorflowMultisourceModelLearningBase<TInputImage>
+class ITK_EXPORT TensorflowMultisourceModelTrain : public TensorflowMultisourceModelLearningBase<TInputImage>
{
public:
-
/** Standard class typedefs. */
typedef TensorflowMultisourceModelTrain Self;
typedef TensorflowMultisourceModelLearningBase<TInputImage> Superclass;
@@ -52,25 +50,27 @@ public:
itkTypeMacro(TensorflowMultisourceModelTrain, TensorflowMultisourceModelLearningBase);
/** Superclass typedefs */
- typedef typename Superclass::DictType DictType;
- typedef typename Superclass::TensorListType TensorListType;
- typedef typename Superclass::IndexValueType IndexValueType;
- typedef typename Superclass::IndexListType IndexListType;
+ typedef typename Superclass::DictType DictType;
+ typedef typename Superclass::TensorListType TensorListType;
+ typedef typename Superclass::IndexValueType IndexValueType;
+ typedef typename Superclass::IndexListType IndexListType;
protected:
TensorflowMultisourceModelTrain();
- virtual ~TensorflowMultisourceModelTrain() {};
+ virtual ~TensorflowMultisourceModelTrain(){};
- virtual void GenerateData();
- virtual void ProcessBatch(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize);
+ virtual void
+ GenerateData();
+ virtual void
+ ProcessBatch(DictType & inputs, const IndexValueType & sampleStart, const IndexValueType & batchSize);
private:
- TensorflowMultisourceModelTrain(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowMultisourceModelTrain(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- IndexListType m_RandomIndices; // Reordered indices
+ IndexListType m_RandomIndices; // Reordered indices
}; // end class
diff --git a/include/otbTensorflowMultisourceModelTrain.hxx b/include/otbTensorflowMultisourceModelTrain.hxx
index 272dd6390668bd233c5ec41b99ff2b088ef313c3..46bc2d7bd22cab4a90a40131436bd428dc77aff9 100644
--- a/include/otbTensorflowMultisourceModelTrain.hxx
+++ b/include/otbTensorflowMultisourceModelTrain.hxx
@@ -18,37 +18,33 @@ namespace otb
{
template <class TInputImage>
-TensorflowMultisourceModelTrain<TInputImage>
-::TensorflowMultisourceModelTrain()
- {
- }
+TensorflowMultisourceModelTrain<TInputImage>::TensorflowMultisourceModelTrain()
+{}
template <class TInputImage>
void
-TensorflowMultisourceModelTrain<TInputImage>
-::GenerateData()
- {
+TensorflowMultisourceModelTrain<TInputImage>::GenerateData()
+{
// Initial sequence 1...N
m_RandomIndices.resize(this->GetNumberOfSamples());
- std::iota (std::begin(m_RandomIndices), std::end(m_RandomIndices), 0);
+ std::iota(std::begin(m_RandomIndices), std::end(m_RandomIndices), 0);
// Shuffle the sequence
std::random_device rd;
- std::mt19937 g(rd());
+ std::mt19937 g(rd());
std::shuffle(m_RandomIndices.begin(), m_RandomIndices.end(), g);
// Call the generic method
Superclass::GenerateData();
-
- }
+}
template <class TInputImage>
void
-TensorflowMultisourceModelTrain<TInputImage>
-::ProcessBatch(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize)
- {
+TensorflowMultisourceModelTrain<TInputImage>::ProcessBatch(DictType & inputs,
+ const IndexValueType & sampleStart,
+ const IndexValueType & batchSize)
+{
// Populate input tensors
this->PopulateInputTensors(inputs, sampleStart, batchSize, m_RandomIndices);
@@ -57,12 +53,11 @@ TensorflowMultisourceModelTrain<TInputImage>
this->RunSession(inputs, outputs);
// Display outputs tensors
- for (auto& o: outputs)
+ for (auto & o : outputs)
{
tf::PrintTensorInfos(o);
}
-
- }
+}
} // end namespace otb
diff --git a/include/otbTensorflowMultisourceModelValidate.h b/include/otbTensorflowMultisourceModelValidate.h
index 322f6a24e288db9d9acf202e72ffe04ff8d8a8d4..54691747a7128d625c4a637972da67d02f11e1e1 100644
--- a/include/otbTensorflowMultisourceModelValidate.h
+++ b/include/otbTensorflowMultisourceModelValidate.h
@@ -42,11 +42,9 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage>
-class ITK_EXPORT TensorflowMultisourceModelValidate :
-public TensorflowMultisourceModelLearningBase<TInputImage>
+class ITK_EXPORT TensorflowMultisourceModelValidate : public TensorflowMultisourceModelLearningBase<TInputImage>
{
public:
-
/** Standard class typedefs. */
typedef TensorflowMultisourceModelValidate Self;
typedef TensorflowMultisourceModelLearningBase<TInputImage> Superclass;
@@ -60,20 +58,20 @@ public:
itkTypeMacro(TensorflowMultisourceModelValidate, TensorflowMultisourceModelLearningBase);
/** Images typedefs */
- typedef typename Superclass::ImageType ImageType;
- typedef typename Superclass::ImagePointerType ImagePointerType;
- typedef typename Superclass::RegionType RegionType;
- typedef typename Superclass::SizeType SizeType;
- typedef typename Superclass::IndexType IndexType;
- typedef std::vector<ImagePointerType> ImageListType;
+ typedef typename Superclass::ImageType ImageType;
+ typedef typename Superclass::ImagePointerType ImagePointerType;
+ typedef typename Superclass::RegionType RegionType;
+ typedef typename Superclass::SizeType SizeType;
+ typedef typename Superclass::IndexType IndexType;
+ typedef std::vector<ImagePointerType> ImageListType;
/* Typedefs for parameters */
- typedef typename Superclass::DictType DictType;
- typedef typename Superclass::StringList StringList;
- typedef typename Superclass::SizeListType SizeListType;
- typedef typename Superclass::TensorListType TensorListType;
- typedef typename Superclass::IndexValueType IndexValueType;
- typedef typename Superclass::IndexListType IndexListType;
+ typedef typename Superclass::DictType DictType;
+ typedef typename Superclass::StringList StringList;
+ typedef typename Superclass::SizeListType SizeListType;
+ typedef typename Superclass::TensorListType TensorListType;
+ typedef typename Superclass::IndexValueType IndexValueType;
+ typedef typename Superclass::IndexListType IndexListType;
/* Typedefs for validation */
typedef unsigned long CountValueType;
@@ -87,36 +85,43 @@ public:
typedef itk::ImageRegionConstIterator<ImageType> IteratorType;
/** Set and Get the input references */
- virtual void SetInputReferences(ImageListType input);
- ImagePointerType GetInputReference(unsigned int index);
+ virtual void
+ SetInputReferences(ImageListType input);
+ ImagePointerType
+ GetInputReference(unsigned int index);
/** Get the confusion matrix */
- const ConfMatType GetConfusionMatrix(unsigned int target);
+ const ConfMatType
+ GetConfusionMatrix(unsigned int target);
/** Get the map of classes matrix */
- const MapOfClassesType GetMapOfClasses(unsigned int target);
+ const MapOfClassesType
+ GetMapOfClasses(unsigned int target);
protected:
TensorflowMultisourceModelValidate();
- virtual ~TensorflowMultisourceModelValidate() {};
+ virtual ~TensorflowMultisourceModelValidate(){};
- void GenerateOutputInformation(void);
- void GenerateData();
- void ProcessBatch(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize);
+ void
+ GenerateOutputInformation(void);
+ void
+ GenerateData();
+ void
+ ProcessBatch(DictType & inputs, const IndexValueType & sampleStart, const IndexValueType & batchSize);
private:
- TensorflowMultisourceModelValidate(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowMultisourceModelValidate(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- ImageListType m_References; // The references images
+ ImageListType m_References; // The references images
// Read only
- ConfMatListType m_ConfusionMatrices; // Confusion matrix
- MapOfClassesListType m_MapsOfClasses; // Maps of classes
+ ConfMatListType m_ConfusionMatrices; // Confusion matrix
+ MapOfClassesListType m_MapsOfClasses; // Maps of classes
// Internal
- std::vector<MatMapType> m_ConfMatMaps; // Accumulators
+ std::vector<MatMapType> m_ConfMatMaps; // Accumulators
}; // end class
diff --git a/include/otbTensorflowMultisourceModelValidate.hxx b/include/otbTensorflowMultisourceModelValidate.hxx
index 8ec685ba81c1ae51111a077e8170dd227be7241e..a929aa884ea97ff3f80af968b275dc1029fb0de4 100644
--- a/include/otbTensorflowMultisourceModelValidate.hxx
+++ b/include/otbTensorflowMultisourceModelValidate.hxx
@@ -18,82 +18,77 @@ namespace otb
{
template <class TInputImage>
-TensorflowMultisourceModelValidate<TInputImage>
-::TensorflowMultisourceModelValidate()
- {
- }
+TensorflowMultisourceModelValidate<TInputImage>::TensorflowMultisourceModelValidate()
+{}
template <class TInputImage>
void
-TensorflowMultisourceModelValidate<TInputImage>
-::GenerateOutputInformation()
- {
+TensorflowMultisourceModelValidate<TInputImage>::GenerateOutputInformation()
+{
Superclass::GenerateOutputInformation();
// Check that there is some reference
const unsigned int nbOfRefs = m_References.size();
if (nbOfRefs == 0)
- {
+ {
itkExceptionMacro("No reference is set");
- }
+ }
// Check the number of references
SizeListType outputPatchSizes = this->GetOutputExpressionFields();
if (nbOfRefs != outputPatchSizes.size())
- {
- itkExceptionMacro("There is " << nbOfRefs << " references but only " <<
- outputPatchSizes.size() << " output patch sizes");
- }
+ {
+ itkExceptionMacro("There is " << nbOfRefs << " references but only " << outputPatchSizes.size()
+ << " output patch sizes");
+ }
// Check reference image infos
- for (unsigned int i = 0 ; i < nbOfRefs ; i++)
- {
- const SizeType outputPatchSize = outputPatchSizes[i];
+ for (unsigned int i = 0; i < nbOfRefs; i++)
+ {
+ const SizeType outputPatchSize = outputPatchSizes[i];
const RegionType refRegion = m_References[i]->GetLargestPossibleRegion();
if (refRegion.GetSize(0) != outputPatchSize[0])
- {
- itkExceptionMacro("Reference image " << i << " width is " << refRegion.GetSize(0) <<
- " but patch size (x) is " << outputPatchSize[0]);
- }
+ {
+ itkExceptionMacro("Reference image " << i << " width is " << refRegion.GetSize(0) << " but patch size (x) is "
+ << outputPatchSize[0]);
+ }
if (refRegion.GetSize(1) != this->GetNumberOfSamples() * outputPatchSize[1])
- {
- itkExceptionMacro("Reference image " << i << " height is " << refRegion.GetSize(1) <<
- " but patch size (y) is " << outputPatchSize[1] <<
- " which is not consistent with the number of samples (" << this->GetNumberOfSamples() << ")");
- }
+ {
+ itkExceptionMacro("Reference image "
+ << i << " height is " << refRegion.GetSize(1) << " but patch size (y) is " << outputPatchSize[1]
+ << " which is not consistent with the number of samples (" << this->GetNumberOfSamples()
+ << ")");
}
-
- }
+ }
+}
/*
* Set the references images
*/
-template<class TInputImage>
+template <class TInputImage>
void
-TensorflowMultisourceModelValidate<TInputImage>
-::SetInputReferences(ImageListType input)
- {
+TensorflowMultisourceModelValidate<TInputImage>::SetInputReferences(ImageListType input)
+{
m_References = input;
- }
+}
/*
* Retrieve the i-th reference image
* An exception is thrown if it doesn't exist.
*/
-template<class TInputImage>
+template <class TInputImage>
typename TensorflowMultisourceModelValidate<TInputImage>::ImagePointerType
-TensorflowMultisourceModelValidate<TInputImage>
-::GetInputReference(unsigned int index)
- {
+TensorflowMultisourceModelValidate<TInputImage>::GetInputReference(unsigned int index)
+{
if (m_References.size <= index || !m_References[index])
- {
+ {
itkExceptionMacro("There is no input reference #" << index);
- }
+ }
return m_References[index];
- }
+}
/**
* Perform the validation
@@ -103,73 +98,70 @@ TensorflowMultisourceModelValidate<TInputImage>
*/
template <class TInputImage>
void
-TensorflowMultisourceModelValidate<TInputImage>
-::GenerateData()
- {
+TensorflowMultisourceModelValidate<TInputImage>::GenerateData()
+{
// Temporary images for outputs
m_ConfusionMatrices.clear();
m_MapsOfClasses.clear();
m_ConfMatMaps.clear();
- for (auto const& ref: m_References)
- {
- (void) ref;
+ for (auto const & ref : m_References)
+ {
+ (void)ref;
// New confusion matrix
MatMapType mat;
m_ConfMatMaps.push_back(mat);
- }
+ }
// Run all the batches
Superclass::GenerateData();
// Compute confusion matrices
- for (unsigned int i = 0 ; i < m_ConfMatMaps.size() ; i++)
- {
+ for (unsigned int i = 0; i < m_ConfMatMaps.size(); i++)
+ {
// Confusion matrix (map) for current target
MatMapType mat = m_ConfMatMaps[i];
// List all values
MapOfClassesType values;
- LabelValueType curVal = 0;
- for (auto const& ref: mat)
- {
+ LabelValueType curVal = 0;
+ for (auto const & ref : mat)
+ {
if (values.count(ref.first) == 0)
- {
+ {
values[ref.first] = curVal;
curVal++;
- }
- for (auto const& in: ref.second)
+ }
+ for (auto const & in : ref.second)
if (values.count(in.first) == 0)
- {
+ {
values[in.first] = curVal;
curVal++;
- }
- }
+ }
+ }
// Build the confusion matrix
const LabelValueType nValues = values.size();
- ConfMatType matrix(nValues, nValues);
+ ConfMatType matrix(nValues, nValues);
matrix.Fill(0);
- for (auto const& ref: mat)
- for (auto const& in: ref.second)
+ for (auto const & ref : mat)
+ for (auto const & in : ref.second)
matrix[values[ref.first]][values[in.first]] = in.second;
// Add the confusion matrix
m_ConfusionMatrices.push_back(matrix);
m_MapsOfClasses.push_back(values);
-
- }
-
- }
+ }
+}
template <class TInputImage>
void
-TensorflowMultisourceModelValidate<TInputImage>
-::ProcessBatch(DictType & inputs, const IndexValueType & sampleStart,
- const IndexValueType & batchSize)
- {
+TensorflowMultisourceModelValidate<TInputImage>::ProcessBatch(DictType & inputs,
+ const IndexValueType & sampleStart,
+ const IndexValueType & batchSize)
+{
// Populate input tensors
IndexListType empty;
this->PopulateInputTensors(inputs, sampleStart, batchSize, empty);
@@ -180,16 +172,16 @@ TensorflowMultisourceModelValidate<TInputImage>
// Perform the validation
if (outputs.size() != m_References.size())
- {
- itkWarningMacro("There is " << outputs.size() << " outputs returned after session run, " <<
- "but only " << m_References.size() << " reference(s) set");
- }
+ {
+ itkWarningMacro("There is " << outputs.size() << " outputs returned after session run, "
+ << "but only " << m_References.size() << " reference(s) set");
+ }
SizeListType outputEFSizes = this->GetOutputExpressionFields();
- for (unsigned int refIdx = 0 ; refIdx < outputs.size() ; refIdx++)
- {
+ for (unsigned int refIdx = 0; refIdx < outputs.size(); refIdx++)
+ {
// Recopy the chunk
const SizeType outputFOESize = outputEFSizes[refIdx];
- IndexType cpyStart;
+ IndexType cpyStart;
cpyStart.Fill(0);
IndexType refRegStart;
refRegStart.Fill(0);
@@ -216,31 +208,30 @@ TensorflowMultisourceModelValidate<TInputImage>
IteratorType inIt(img, cpyRegion);
IteratorType refIt(m_References[refIdx], refRegion);
for (inIt.GoToBegin(), refIt.GoToBegin(); !inIt.IsAtEnd(); ++inIt, ++refIt)
- {
+ {
const int classIn = static_cast<LabelValueType>(inIt.Get()[0]);
const int classRef = static_cast<LabelValueType>(refIt.Get()[0]);
if (m_ConfMatMaps[refIdx].count(classRef) == 0)
- {
+ {
MapType newMap;
newMap[classIn] = 1;
m_ConfMatMaps[refIdx][classRef] = newMap;
- }
+ }
else
- {
+ {
if (m_ConfMatMaps[refIdx][classRef].count(classIn) == 0)
- {
+ {
m_ConfMatMaps[refIdx][classRef][classIn] = 1;
- }
+ }
else
- {
+ {
m_ConfMatMaps[refIdx][classRef][classIn]++;
- }
}
}
}
-
- }
+ }
+}
/*
* Get the confusion matrix
@@ -248,17 +239,17 @@ TensorflowMultisourceModelValidate<TInputImage>
*/
template <class TInputImage>
const typename TensorflowMultisourceModelValidate<TInputImage>::ConfMatType
-TensorflowMultisourceModelValidate<TInputImage>
-::GetConfusionMatrix(unsigned int target)
- {
+TensorflowMultisourceModelValidate<TInputImage>::GetConfusionMatrix(unsigned int target)
+{
if (target >= m_ConfusionMatrices.size())
- {
- itkExceptionMacro("Unable to get confusion matrix #" << target << ". " <<
- "There is only " << m_ConfusionMatrices.size() << " available.");
- }
+ {
+ itkExceptionMacro("Unable to get confusion matrix #" << target << ". "
+ << "There is only " << m_ConfusionMatrices.size()
+ << " available.");
+ }
return m_ConfusionMatrices[target];
- }
+}
/*
* Get the map of classes
@@ -266,17 +257,17 @@ TensorflowMultisourceModelValidate<TInputImage>
*/
template <class TInputImage>
const typename TensorflowMultisourceModelValidate<TInputImage>::MapOfClassesType
-TensorflowMultisourceModelValidate<TInputImage>
-::GetMapOfClasses(unsigned int target)
- {
+TensorflowMultisourceModelValidate<TInputImage>::GetMapOfClasses(unsigned int target)
+{
if (target >= m_MapsOfClasses.size())
- {
- itkExceptionMacro("Unable to get confusion matrix #" << target << ". " <<
- "There is only " << m_MapsOfClasses.size() << " available.");
- }
+ {
+ itkExceptionMacro("Unable to get confusion matrix #" << target << ". "
+ << "There is only " << m_MapsOfClasses.size()
+ << " available.");
+ }
return m_MapsOfClasses[target];
- }
+}
} // end namespace otb
diff --git a/include/otbTensorflowSampler.h b/include/otbTensorflowSampler.h
index bd363bc8ee191ce7506ca012b68171f6d8bdc828..4fae38e75245ca417c638105379ec7ff7dddf6dd 100644
--- a/include/otbTensorflowSampler.h
+++ b/include/otbTensorflowSampler.h
@@ -52,16 +52,14 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage, class TVectorData>
-class ITK_EXPORT TensorflowSampler :
-public itk::ProcessObject
+class ITK_EXPORT TensorflowSampler : public itk::ProcessObject
{
public:
-
/** Standard class typedefs. */
- typedef TensorflowSampler Self;
- typedef itk::ProcessObject Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
+ typedef TensorflowSampler Self;
+ typedef itk::ProcessObject Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
@@ -70,33 +68,28 @@ public:
itkTypeMacro(TensorflowSampler, itk::ProcessObject);
/** Images typedefs */
- typedef TInputImage ImageType;
- typedef typename TInputImage::Pointer ImagePointerType;
- typedef typename TInputImage::InternalPixelType InternalPixelType;
- typedef typename TInputImage::PixelType PixelType;
- typedef typename TInputImage::RegionType RegionType;
- typedef typename TInputImage::PointType PointType;
- typedef typename TInputImage::SizeType SizeType;
- typedef typename TInputImage::IndexType IndexType;
- typedef typename otb::MultiChannelExtractROI<InternalPixelType,
- InternalPixelType> ExtractROIMultiFilterType;
- typedef typename ExtractROIMultiFilterType::Pointer
- ExtractROIMultiFilterPointerType;
- typedef typename std::vector<ImagePointerType> ImagePointerListType;
- typedef typename std::vector<SizeType> SizeListType;
- typedef typename itk::ImageRegionConstIterator<ImageType>
- IteratorType;
+ typedef TInputImage ImageType;
+ typedef typename TInputImage::Pointer ImagePointerType;
+ typedef typename TInputImage::InternalPixelType InternalPixelType;
+ typedef typename TInputImage::PixelType PixelType;
+ typedef typename TInputImage::RegionType RegionType;
+ typedef typename TInputImage::PointType PointType;
+ typedef typename TInputImage::SizeType SizeType;
+ typedef typename TInputImage::IndexType IndexType;
+ typedef typename otb::MultiChannelExtractROI<InternalPixelType, InternalPixelType> ExtractROIMultiFilterType;
+ typedef typename ExtractROIMultiFilterType::Pointer ExtractROIMultiFilterPointerType;
+ typedef typename std::vector<ImagePointerType> ImagePointerListType;
+ typedef typename std::vector<SizeType> SizeListType;
+ typedef typename itk::ImageRegionConstIterator<ImageType> IteratorType;
/** Vector data typedefs */
- typedef TVectorData VectorDataType;
- typedef typename VectorDataType::Pointer VectorDataPointer;
- typedef typename VectorDataType::DataTreeType DataTreeType;
- typedef typename itk::PreOrderTreeIterator<DataTreeType>
- TreeIteratorType;
- typedef typename VectorDataType::DataNodeType DataNodeType;
- typedef typename DataNodeType::Pointer DataNodePointer;
- typedef typename DataNodeType::PolygonListPointerType
- PolygonListPointerType;
+ typedef TVectorData VectorDataType;
+ typedef typename VectorDataType::Pointer VectorDataPointer;
+ typedef typename VectorDataType::DataTreeType DataTreeType;
+ typedef typename itk::PreOrderTreeIterator<DataTreeType> TreeIteratorType;
+ typedef typename VectorDataType::DataNodeType DataNodeType;
+ typedef typename DataNodeType::Pointer DataNodePointer;
+ typedef typename DataNodeType::PolygonListPointerType PolygonListPointerType;
/** Set / get parameters */
itkSetMacro(Field, std::string);
@@ -107,15 +100,18 @@ public:
itkGetConstMacro(InputVectorData, VectorDataPointer);
/** Set / get image */
- virtual void PushBackInputWithPatchSize(const ImageType *input, SizeType & patchSize, InternalPixelType nodataval);
- const ImageType* GetInput(unsigned int index);
+ virtual void
+ PushBackInputWithPatchSize(const ImageType * input, SizeType & patchSize, InternalPixelType nodataval);
+ const ImageType *
+ GetInput(unsigned int index);
/** Set / get no-data related parameters */
itkSetMacro(RejectPatchesWithNodata, bool);
itkGetMacro(RejectPatchesWithNodata, bool);
/** Do the real work */
- virtual void Update();
+ virtual void
+ Update();
/** Get outputs */
itkGetMacro(OutputPatchImages, ImagePointerListType);
@@ -125,18 +121,21 @@ public:
protected:
TensorflowSampler();
- virtual ~TensorflowSampler() {};
+ virtual ~TensorflowSampler(){};
- virtual void ResizeImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples);
- virtual void AllocateImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples, unsigned int nbComponents);
+ virtual void
+ ResizeImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples);
+ virtual void
+ AllocateImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples, unsigned int nbComponents);
private:
- TensorflowSampler(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowSampler(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- std::string m_Field;
- SizeListType m_PatchSizes;
- VectorDataPointer m_InputVectorData;
+ std::string m_Field;
+ SizeListType m_PatchSizes;
+ VectorDataPointer m_InputVectorData;
// Read only
ImagePointerListType m_OutputPatchImages;
@@ -146,7 +145,7 @@ private:
// No data stuff
std::vector<InternalPixelType> m_NoDataValues;
- bool m_RejectPatchesWithNodata;
+ bool m_RejectPatchesWithNodata;
}; // end class
diff --git a/include/otbTensorflowSampler.hxx b/include/otbTensorflowSampler.hxx
index 8c0ea7459ad5e1ac0060438e3c6a73b760fc535a..77558c7ba08c6dc75ce8ced1d389a537150a68f7 100644
--- a/include/otbTensorflowSampler.hxx
+++ b/include/otbTensorflowSampler.hxx
@@ -18,36 +18,35 @@ namespace otb
{
template <class TInputImage, class TVectorData>
-TensorflowSampler<TInputImage, TVectorData>
-::TensorflowSampler()
- {
+TensorflowSampler<TInputImage, TVectorData>::TensorflowSampler()
+{
m_NumberOfAcceptedSamples = 0;
m_NumberOfRejectedSamples = 0;
m_RejectPatchesWithNodata = false;
- }
+}
template <class TInputImage, class TVectorData>
void
-TensorflowSampler<TInputImage, TVectorData>
-::PushBackInputWithPatchSize(const ImageType *input, SizeType & patchSize, InternalPixelType nodataval)
- {
- this->ProcessObject::PushBackInput(const_cast<ImageType*>(input));
+TensorflowSampler<TInputImage, TVectorData>::PushBackInputWithPatchSize(const ImageType * input,
+ SizeType & patchSize,
+ InternalPixelType nodataval)
+{
+ this->ProcessObject::PushBackInput(const_cast<ImageType *>(input));
m_PatchSizes.push_back(patchSize);
m_NoDataValues.push_back(nodataval);
- }
+}
template <class TInputImage, class TVectorData>
-const TInputImage*
-TensorflowSampler<TInputImage, TVectorData>
-::GetInput(unsigned int index)
- {
+const TInputImage *
+TensorflowSampler<TInputImage, TVectorData>::GetInput(unsigned int index)
+{
if (this->GetNumberOfInputs() < 1)
{
itkExceptionMacro("Input not set");
}
- return static_cast<const ImageType*>(this->ProcessObject::GetInput(index));
- }
+ return static_cast<const ImageType *>(this->ProcessObject::GetInput(index));
+}
/**
@@ -55,9 +54,10 @@ TensorflowSampler<TInputImage, TVectorData>
*/
template <class TInputImage, class TVectorData>
void
-TensorflowSampler<TInputImage, TVectorData>
-::ResizeImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples)
- {
+TensorflowSampler<TInputImage, TVectorData>::ResizeImage(ImagePointerType & image,
+ SizeType & patchSize,
+ unsigned int nbSamples)
+{
// New image region
RegionType region;
region.SetSize(0, patchSize[0]);
@@ -71,16 +71,18 @@ TensorflowSampler<TInputImage, TVectorData>
// Assign
image = resizer->GetOutput();
- }
+}
/**
* Allocate an image given a patch size and a number of samples
*/
template <class TInputImage, class TVectorData>
void
-TensorflowSampler<TInputImage, TVectorData>
-::AllocateImage(ImagePointerType & image, SizeType & patchSize, unsigned int nbSamples, unsigned int nbComponents)
- {
+TensorflowSampler<TInputImage, TVectorData>::AllocateImage(ImagePointerType & image,
+ SizeType & patchSize,
+ unsigned int nbSamples,
+ unsigned int nbComponents)
+{
// Image region
RegionType region;
region.SetSize(0, patchSize[0]);
@@ -91,16 +93,15 @@ TensorflowSampler<TInputImage, TVectorData>
image->SetNumberOfComponentsPerPixel(nbComponents);
image->SetRegions(region);
image->Allocate();
- }
+}
/**
* Do the work
*/
template <class TInputImage, class TVectorData>
void
-TensorflowSampler<TInputImage, TVectorData>
-::Update()
- {
+TensorflowSampler<TInputImage, TVectorData>::Update()
+{
// Check number of inputs
if (this->GetNumberOfInputs() != m_PatchSizes.size())
@@ -109,8 +110,8 @@ TensorflowSampler<TInputImage, TVectorData>
}
// Count points
- unsigned int nTotal = 0;
- unsigned int geomId = 0;
+ unsigned int nTotal = 0;
+ unsigned int geomId = 0;
TreeIteratorType itVector(m_InputVectorData->GetDataTree());
itVector.GoToBegin();
while (!itVector.IsAtEnd())
@@ -146,7 +147,7 @@ TensorflowSampler<TInputImage, TVectorData>
const unsigned int nbInputs = this->GetNumberOfInputs();
m_OutputPatchImages.clear();
m_OutputPatchImages.reserve(nbInputs);
- for (unsigned int i = 0 ; i < nbInputs ; i++)
+ for (unsigned int i = 0; i < nbInputs; i++)
{
ImagePointerType newImage;
AllocateImage(newImage, m_PatchSizes[i], nTotal, GetInput(i)->GetNumberOfComponentsPerPixel());
@@ -160,7 +161,7 @@ TensorflowSampler<TInputImage, TVectorData>
itVector.GoToBegin();
unsigned long count = 0;
unsigned long rejected = 0;
- IndexType labelIndex;
+ IndexType labelIndex;
labelIndex[0] = 0;
PixelType labelPix;
labelPix.SetSize(1);
@@ -169,13 +170,13 @@ TensorflowSampler<TInputImage, TVectorData>
if (!itVector.Get()->IsRoot() && !itVector.Get()->IsDocument() && !itVector.Get()->IsFolder())
{
DataNodePointer currentGeometry = itVector.Get();
- PointType point = currentGeometry->GetPoint();
+ PointType point = currentGeometry->GetPoint();
// Get the label value
labelPix[0] = static_cast<InternalPixelType>(currentGeometry->GetFieldAsInt(m_Field));
bool hasBeenSampled = true;
- for (unsigned int i = 0 ; i < nbInputs ; i++)
+ for (unsigned int i = 0; i < nbInputs; i++)
{
// Get input
ImagePointerType inputPtr = const_cast<ImageType *>(this->GetInput(i));
@@ -188,7 +189,7 @@ TensorflowSampler<TInputImage, TVectorData>
}
// Check if the sampled patch contains a no-data value
if (m_RejectPatchesWithNodata && hasBeenSampled)
- {
+ {
IndexType outIndex;
outIndex[0] = 0;
outIndex[1] = count * m_PatchSizes[i][1];
@@ -196,13 +197,13 @@ TensorflowSampler<TInputImage, TVectorData>
IteratorType it(m_OutputPatchImages[i], region);
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
- {
+ {
PixelType pix = it.Get();
- for (unsigned int band = 0 ; band < pix.Size() ; band++)
+ for (unsigned int band = 0; band < pix.Size(); band++)
if (pix[band] == m_NoDataValues[i])
hasBeenSampled = false;
- }
}
+ }
} // Next input
if (hasBeenSampled)
{
@@ -220,7 +221,6 @@ TensorflowSampler<TInputImage, TVectorData>
// Update progress
progress.CompletedPixel();
-
}
++itVector;
@@ -228,7 +228,7 @@ TensorflowSampler<TInputImage, TVectorData>
// Resize output images
ResizeImage(m_OutputLabelImage, labelPatchSize, count);
- for (unsigned int i = 0 ; i < nbInputs ; i++)
+ for (unsigned int i = 0; i < nbInputs; i++)
{
ResizeImage(m_OutputPatchImages[i], m_PatchSizes[i], count);
}
@@ -236,8 +236,7 @@ TensorflowSampler<TInputImage, TVectorData>
// Update number of samples produced
m_NumberOfAcceptedSamples = count;
m_NumberOfRejectedSamples = rejected;
-
- }
+}
} // end namespace otb
diff --git a/include/otbTensorflowSamplingUtils.cxx b/include/otbTensorflowSamplingUtils.cxx
index 5cf88f6b171b61c9576b4ca68d855a0d6059d42f..db4d9ea01d718c5957a9080486dcb18b83097995 100644
--- a/include/otbTensorflowSamplingUtils.cxx
+++ b/include/otbTensorflowSamplingUtils.cxx
@@ -19,13 +19,15 @@ namespace tf
//
// Update the distribution of the patch located at the specified location
//
-template<class TImage, class TDistribution>
-bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
- typename TImage::PointType point, typename TImage::SizeType patchSize,
- TDistribution & dist)
+template <class TImage, class TDistribution>
+bool
+UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
+ typename TImage::PointType point,
+ typename TImage::SizeType patchSize,
+ TDistribution & dist)
{
typename TImage::IndexType index;
- bool canTransform = inPtr->TransformPhysicalPointToIndex(point, index);
+ bool canTransform = inPtr->TransformPhysicalPointToIndex(point, index);
if (canTransform)
{
index[0] -= patchSize[0] / 2;
@@ -38,7 +40,7 @@ bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
// Fill patch
PropagateRequestedRegion<TImage>(inPtr, inPatchRegion);
- typename itk::ImageRegionConstIterator<TImage> inIt (inPtr, inPatchRegion);
+ typename itk::ImageRegionConstIterator<TImage> inIt(inPtr, inPatchRegion);
for (inIt.GoToBegin(); !inIt.IsAtEnd(); ++inIt)
{
dist.Update(inIt.Get());
@@ -47,7 +49,6 @@ bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
}
}
return false;
-
}
diff --git a/include/otbTensorflowSamplingUtils.h b/include/otbTensorflowSamplingUtils.h
index 585f90132ea71509fe2a08ff8f56aa1eac2abb3f..846b71318e57e2f64b7b5d582c4a85223bd809b3 100644
--- a/include/otbTensorflowSamplingUtils.h
+++ b/include/otbTensorflowSamplingUtils.h
@@ -20,77 +20,89 @@ namespace otb
namespace tf
{
-template<class TImage>
+template <class TImage>
class Distribution
{
public:
typedef typename TImage::PixelType ValueType;
- typedef vnl_vector<float> CountsType;
-
- explicit Distribution(unsigned int nClasses): m_NbOfClasses(nClasses), m_Dist(CountsType(nClasses, 0))
- {
- }
- Distribution(unsigned int nClasses, float fillValue): m_NbOfClasses(nClasses), m_Dist(CountsType(nClasses, fillValue))
- {
- }
- Distribution(): m_NbOfClasses(2), m_Dist(CountsType(m_NbOfClasses, 0))
- {
- }
- Distribution(const Distribution & other): m_Dist(other.Get()), m_NbOfClasses(m_Dist.size())
- {
- }
- ~Distribution(){}
-
- void Update(const typename TImage::PixelType & pixel)
+ typedef vnl_vector<float> CountsType;
+
+ explicit Distribution(unsigned int nClasses)
+ : m_NbOfClasses(nClasses)
+ , m_Dist(CountsType(nClasses, 0))
+ {}
+ Distribution(unsigned int nClasses, float fillValue)
+ : m_NbOfClasses(nClasses)
+ , m_Dist(CountsType(nClasses, fillValue))
+ {}
+ Distribution()
+ : m_NbOfClasses(2)
+ , m_Dist(CountsType(m_NbOfClasses, 0))
+ {}
+ Distribution(const Distribution & other)
+ : m_Dist(other.Get())
+ , m_NbOfClasses(m_Dist.size())
+ {}
+ ~Distribution() {}
+
+ void
+ Update(const typename TImage::PixelType & pixel)
{
m_Dist[pixel]++;
}
- void Update(const Distribution & other)
+ void
+ Update(const Distribution & other)
{
const CountsType otherDist = other.Get();
- for (unsigned int c = 0 ; c < m_NbOfClasses ; c++)
+ for (unsigned int c = 0; c < m_NbOfClasses; c++)
m_Dist[c] += otherDist[c];
}
- CountsType Get() const
+ CountsType
+ Get() const
{
return m_Dist;
}
- CountsType GetNormalized() const
+ CountsType
+ GetNormalized() const
{
- const float invNorm = 1.0 / std::sqrt(dot_product(m_Dist, m_Dist));
+ const float invNorm = 1.0 / std::sqrt(dot_product(m_Dist, m_Dist));
const CountsType normalizedDist = invNorm * m_Dist;
return normalizedDist;
}
- float Cosinus(const Distribution & other) const
+ float
+ Cosinus(const Distribution & other) const
{
return dot_product(other.GetNormalized(), GetNormalized());
}
- std::string ToString()
+ std::string
+ ToString()
{
std::stringstream ss;
ss << "\n";
- for (unsigned int c = 0 ; c < m_NbOfClasses ; c++)
+ for (unsigned int c = 0; c < m_NbOfClasses; c++)
ss << "\tClass #" << c << " : " << m_Dist[c] << "\n";
return ss.str();
}
private:
unsigned int m_NbOfClasses;
- CountsType m_Dist;
+ CountsType m_Dist;
};
// Update the distribution of the patch located at the specified location
-template<class TImage, class TDistribution>
-bool UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
- typename TImage::PointType point, typename TImage::SizeType patchSize,
- TDistribution & dist);
-
-} // namesapce tf
+template <class TImage, class TDistribution>
+bool
+UpdateDistributionFromPatch(const typename TImage::Pointer inPtr,
+ typename TImage::PointType point,
+ typename TImage::SizeType patchSize,
+ TDistribution & dist);
+
+} // namespace tf
} // namespace otb
#include "otbTensorflowSamplingUtils.cxx"
diff --git a/include/otbTensorflowSource.h b/include/otbTensorflowSource.h
index 1556997f9a20c02c1f5f9fd80f92c0fc38270657..9bbeed12fbe07820c1a59d125d0af5343dfd3492 100644
--- a/include/otbTensorflowSource.h
+++ b/include/otbTensorflowSource.h
@@ -29,45 +29,43 @@ namespace otb
* Images must have the same size.
* This is the common input type used in every OTB-TF applications.
*/
-template<class TImage>
+template <class TImage>
class TensorflowSource
{
public:
/** Typedefs for images */
- typedef TImage FloatVectorImageType;
- typedef typename FloatVectorImageType::Pointer FloatVectorImagePointerType;
- typedef typename FloatVectorImageType::InternalPixelType InternalPixelType;
- typedef otb::Image<InternalPixelType> FloatImageType;
- typedef typename FloatImageType::SizeType SizeType;
+ typedef TImage FloatVectorImageType;
+ typedef typename FloatVectorImageType::Pointer FloatVectorImagePointerType;
+ typedef typename FloatVectorImageType::InternalPixelType InternalPixelType;
+ typedef otb::Image<InternalPixelType> FloatImageType;
+ typedef typename FloatImageType::SizeType SizeType;
/** Typedefs for image concatenation */
- typedef otb::ImageList<FloatImageType> ImageListType;
- typedef typename ImageListType::Pointer ImageListPointer;
- typedef ImageListToVectorImageFilter<ImageListType,
- FloatVectorImageType> ListConcatenerFilterType;
- typedef typename ListConcatenerFilterType::Pointer ListConcatenerFilterPointer;
- typedef MultiToMonoChannelExtractROI<InternalPixelType,
- InternalPixelType> MultiToMonoChannelFilterType;
- typedef ObjectList<MultiToMonoChannelFilterType> ExtractROIFilterListType;
- typedef typename ExtractROIFilterListType::Pointer ExtractROIFilterListPointer;
- typedef otb::MultiChannelExtractROI<InternalPixelType,
- InternalPixelType> ExtractFilterType;
- typedef otb::ObjectList<FloatVectorImageType> FloatVectorImageListType;
+ typedef otb::ImageList<FloatImageType> ImageListType;
+ typedef typename ImageListType::Pointer ImageListPointer;
+ typedef ImageListToVectorImageFilter<ImageListType, FloatVectorImageType> ListConcatenerFilterType;
+ typedef typename ListConcatenerFilterType::Pointer ListConcatenerFilterPointer;
+ typedef MultiToMonoChannelExtractROI<InternalPixelType, InternalPixelType> MultiToMonoChannelFilterType;
+ typedef ObjectList<MultiToMonoChannelFilterType> ExtractROIFilterListType;
+ typedef typename ExtractROIFilterListType::Pointer ExtractROIFilterListPointer;
+ typedef otb::MultiChannelExtractROI<InternalPixelType, InternalPixelType> ExtractFilterType;
+ typedef otb::ObjectList<FloatVectorImageType> FloatVectorImageListType;
// Initialize the source
- void Set(FloatVectorImageListType * inputList);
+ void
+ Set(FloatVectorImageListType * inputList);
// Get the source output
- FloatVectorImagePointerType Get();
+ FloatVectorImagePointerType
+ Get();
TensorflowSource();
- virtual ~TensorflowSource (){};
+ virtual ~TensorflowSource(){};
private:
ListConcatenerFilterPointer m_Concatener; // Mono-images stacker
ImageListPointer m_List; // List of mono-images
ExtractROIFilterListPointer m_ExtractorList; // Mono-images extractors
-
};
} // end namespace otb
diff --git a/include/otbTensorflowSource.hxx b/include/otbTensorflowSource.hxx
index 2ad575866fda4ba7baa9dc494c44bcc38b79f0cd..2e41253c69c70e328e9d6827ee1a5f5971c716cb 100644
--- a/include/otbTensorflowSource.hxx
+++ b/include/otbTensorflowSource.hxx
@@ -21,8 +21,7 @@ namespace otb
// Constructor
//
template <class TImage>
-TensorflowSource<TImage>
-::TensorflowSource()
+TensorflowSource<TImage>::TensorflowSource()
{}
//
@@ -30,40 +29,38 @@ TensorflowSource<TImage>
//
template <class TImage>
void
-TensorflowSource<TImage>
-::Set(FloatVectorImageListType * inputList)
+TensorflowSource<TImage>::Set(FloatVectorImageListType * inputList)
{
// Create one stack for input images list
- m_Concatener = ListConcatenerFilterType::New();
- m_List = ImageListType::New();
+ m_Concatener = ListConcatenerFilterType::New();
+ m_List = ImageListType::New();
m_ExtractorList = ExtractROIFilterListType::New();
// Split each input vector image into image
// and generate an mono channel image list
inputList->GetNthElement(0)->UpdateOutputInformation();
SizeType size = inputList->GetNthElement(0)->GetLargestPossibleRegion().GetSize();
- for( unsigned int i = 0; i < inputList->Size(); i++ )
+ for (unsigned int i = 0; i < inputList->Size(); i++)
{
FloatVectorImagePointerType vectIm = inputList->GetNthElement(i);
vectIm->UpdateOutputInformation();
- if( size != vectIm->GetLargestPossibleRegion().GetSize() )
+ if (size != vectIm->GetLargestPossibleRegion().GetSize())
{
itkGenericExceptionMacro("Input image size number " << i << " mismatch");
}
- for( unsigned int j = 0; j < vectIm->GetNumberOfComponentsPerPixel(); j++)
+ for (unsigned int j = 0; j < vectIm->GetNumberOfComponentsPerPixel(); j++)
{
typename MultiToMonoChannelFilterType::Pointer extractor = MultiToMonoChannelFilterType::New();
- extractor->SetInput( vectIm );
- extractor->SetChannel( j+1 );
+ extractor->SetInput(vectIm);
+ extractor->SetChannel(j + 1);
extractor->UpdateOutputInformation();
- m_ExtractorList->PushBack( extractor );
- m_List->PushBack( extractor->GetOutput() );
+ m_ExtractorList->PushBack(extractor);
+ m_List->PushBack(extractor->GetOutput());
}
}
- m_Concatener->SetInput( m_List );
+ m_Concatener->SetInput(m_List);
m_Concatener->UpdateOutputInformation();
-
}
//
diff --git a/include/otbTensorflowStreamerFilter.h b/include/otbTensorflowStreamerFilter.h
index 4730d3691cd3bd64954091c3bfdbb5bb7422d870..fa985d007a1040bc5325d3831724c4108316da5e 100644
--- a/include/otbTensorflowStreamerFilter.h
+++ b/include/otbTensorflowStreamerFilter.h
@@ -26,12 +26,10 @@ namespace otb
* \ingroup OTBTensorflow
*/
template <class TInputImage, class TOutputImage>
-class ITK_EXPORT TensorflowStreamerFilter :
-public itk::ImageToImageFilter<TInputImage, TOutputImage>
+class ITK_EXPORT TensorflowStreamerFilter : public itk::ImageToImageFilter<TInputImage, TOutputImage>
{
public:
-
/** Standard class typedefs. */
typedef TensorflowStreamerFilter Self;
typedef itk::ImageToImageFilter<TInputImage, TOutputImage> Superclass;
@@ -51,24 +49,31 @@ public:
typedef typename ImageType::SizeType SizeType;
typedef typename Superclass::InputImageRegionType RegionType;
- typedef TOutputImage OutputImageType;
+ typedef TOutputImage OutputImageType;
itkSetMacro(OutputGridSize, SizeType);
itkGetMacro(OutputGridSize, SizeType);
protected:
TensorflowStreamerFilter();
- virtual ~TensorflowStreamerFilter() {};
+ virtual ~TensorflowStreamerFilter(){};
- virtual void UpdateOutputData(itk::DataObject *output){(void) output; this->GenerateData();}
+ virtual void
+ UpdateOutputData(itk::DataObject * output)
+ {
+ (void)output;
+ this->GenerateData();
+ }
- virtual void GenerateData();
+ virtual void
+ GenerateData();
private:
- TensorflowStreamerFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
+ TensorflowStreamerFilter(const Self &); // purposely not implemented
+ void
+ operator=(const Self &); // purposely not implemented
- SizeType m_OutputGridSize; // Output grid size
+ SizeType m_OutputGridSize; // Output grid size
}; // end class
diff --git a/include/otbTensorflowStreamerFilter.hxx b/include/otbTensorflowStreamerFilter.hxx
index 59904a54f3df99048dfa383e22dad0ee7bef9784..3aa1afca538841126700484f34f9261731b75d1e 100644
--- a/include/otbTensorflowStreamerFilter.hxx
+++ b/include/otbTensorflowStreamerFilter.hxx
@@ -19,30 +19,28 @@ namespace otb
{
template <class TInputImage, class TOutputImage>
-TensorflowStreamerFilter<TInputImage, TOutputImage>
-::TensorflowStreamerFilter()
- {
+TensorflowStreamerFilter<TInputImage, TOutputImage>::TensorflowStreamerFilter()
+{
m_OutputGridSize.Fill(1);
- }
+}
/**
* Compute the output image
*/
template <class TInputImage, class TOutputImage>
void
-TensorflowStreamerFilter<TInputImage, TOutputImage>
-::GenerateData()
- {
+TensorflowStreamerFilter<TInputImage, TOutputImage>::GenerateData()
+{
// Output pointer and requested region
OutputImageType * outputPtr = this->GetOutput();
- const RegionType outputReqRegion = outputPtr->GetRequestedRegion();
+ const RegionType outputReqRegion = outputPtr->GetRequestedRegion();
outputPtr->SetBufferedRegion(outputReqRegion);
outputPtr->Allocate();
// Compute the aligned region
RegionType region;
- for(unsigned int dim = 0; dim<OutputImageType::ImageDimension; ++dim)
- {
+ for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+ {
// Get corners
IndexValueType lower = outputReqRegion.GetIndex(dim);
IndexValueType upper = lower + outputReqRegion.GetSize(dim);
@@ -54,35 +52,34 @@ TensorflowStreamerFilter<TInputImage, TOutputImage>
// Move corners to aligned positions
lower -= deltaLo;
if (deltaUp > 0)
- {
+ {
upper += m_OutputGridSize[dim] - deltaUp;
- }
+ }
// Update region
region.SetIndex(dim, lower);
region.SetSize(dim, upper - lower);
-
- }
+ }
// Compute the number of subregions to process
const unsigned int nbTilesX = region.GetSize(0) / m_OutputGridSize[0];
const unsigned int nbTilesY = region.GetSize(1) / m_OutputGridSize[1];
// Progress
- itk::ProgressReporter progress(this, 0, nbTilesX*nbTilesY);
+ itk::ProgressReporter progress(this, 0, nbTilesX * nbTilesY);
// For each tile, propagate the input region and recopy the output
- ImageType * inputImage = static_cast<ImageType * >( Superclass::ProcessObject::GetInput(0) );
+ ImageType * inputImage = static_cast<ImageType *>(Superclass::ProcessObject::GetInput(0));
unsigned int tx, ty;
- RegionType subRegion;
+ RegionType subRegion;
subRegion.SetSize(m_OutputGridSize);
for (ty = 0; ty < nbTilesY; ty++)
{
- subRegion.SetIndex(1, ty*m_OutputGridSize[1] + region.GetIndex(1));
+ subRegion.SetIndex(1, ty * m_OutputGridSize[1] + region.GetIndex(1));
for (tx = 0; tx < nbTilesX; tx++)
{
// Update the input subregion
- subRegion.SetIndex(0, tx*m_OutputGridSize[0] + region.GetIndex(0));
+ subRegion.SetIndex(0, tx * m_OutputGridSize[0] + region.GetIndex(0));
// The actual region to copy
RegionType cpyRegion(subRegion);
@@ -94,12 +91,12 @@ TensorflowStreamerFilter<TInputImage, TOutputImage>
inputImage->UpdateOutputData();
// Copy the subregion to output
- itk::ImageAlgorithm::Copy( inputImage, outputPtr, cpyRegion, cpyRegion );
+ itk::ImageAlgorithm::Copy(inputImage, outputPtr, cpyRegion, cpyRegion);
progress.CompletedPixel();
}
}
- }
+}
} // end namespace otb
diff --git a/test/data/RF_model_from_deep_features_map.tif b/test/data/RF_model_from_deep_features_map.tif
new file mode 100644
index 0000000000000000000000000000000000000000..8d01ec195605327cb613eed99b3bebc5bb2c5583
--- /dev/null
+++ b/test/data/RF_model_from_deep_features_map.tif
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:7c603c85a80e6d59d18fe686a827e77066dbedb76c53fb6c35c7ed291d20cf34
+size 1316
diff --git a/test/data/Sentinel-2_B4328_10m_labels_A.tif b/test/data/Sentinel-2_B4328_10m_labels_A.tif
index fe3f31127413c33b44dc6522d628111ebc7ddc24..63fa4e2e8209aabd881087754c97fc615553e283 100644
Binary files a/test/data/Sentinel-2_B4328_10m_labels_A.tif and b/test/data/Sentinel-2_B4328_10m_labels_A.tif differ
diff --git a/test/data/Sentinel-2_B4328_10m_labels_B.tif b/test/data/Sentinel-2_B4328_10m_labels_B.tif
index 501f44affb72fa1d4eed1c9f8607ac5284aab87a..0b0edfa08641a1ecb142105db6b80411dbfd838b 100644
Binary files a/test/data/Sentinel-2_B4328_10m_labels_B.tif and b/test/data/Sentinel-2_B4328_10m_labels_B.tif differ
diff --git a/test/data/Sentinel-2_B4328_10m_patches_A.jp2 b/test/data/Sentinel-2_B4328_10m_patches_A.jp2
index b3e3d058a2d0c948c1d0e88732e6378945a13a79..fb686f59c9f168e902a7201d03b3859e155f49ec 100644
Binary files a/test/data/Sentinel-2_B4328_10m_patches_A.jp2 and b/test/data/Sentinel-2_B4328_10m_patches_A.jp2 differ
diff --git a/test/data/Sentinel-2_B4328_10m_patches_B.jp2 b/test/data/Sentinel-2_B4328_10m_patches_B.jp2
index 795af2ecd5908737b62574810b1701ca78eb3bd6..e34e865f8c0321d77ab95dc3831e6b66da56f65b 100644
Binary files a/test/data/Sentinel-2_B4328_10m_patches_B.jp2 and b/test/data/Sentinel-2_B4328_10m_patches_B.jp2 differ
diff --git a/test/data/amsterdam_labels_A.tif b/test/data/amsterdam_labels_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..a7b0dbcf01de410b0e5f8303ede2e5cdefda9db2
--- /dev/null
+++ b/test/data/amsterdam_labels_A.tif
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bdd9ecd2e54992d712ee44fc05a91bc38f25bfa6c6cbcdc11874fe9070a4fc0f
+size 11411
diff --git a/test/data/amsterdam_labels_B.tif b/test/data/amsterdam_labels_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..fff31bcfd6b0c4f0d498cf79ce626de9937a6100
--- /dev/null
+++ b/test/data/amsterdam_labels_B.tif
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5ce48d4d57f46ca39d940ead160d7968f9b6c2a62b4f6b49132372d1a8916622
+size 11362
diff --git a/test/data/amsterdam_patches_A.tif b/test/data/amsterdam_patches_A.tif
new file mode 100644
index 0000000000000000000000000000000000000000..41323cf2dd8645e28952fdcd9db7bb8cd2542d8d
--- /dev/null
+++ b/test/data/amsterdam_patches_A.tif
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b8d606712ba9b1493ffd02c08135c5d1072d2bc1e64228d00425f17cc62280c9
+size 3840365
diff --git a/test/data/amsterdam_patches_B.tif b/test/data/amsterdam_patches_B.tif
new file mode 100644
index 0000000000000000000000000000000000000000..ace9beebf09fd5066ded88bdbf3fec05f752456e
--- /dev/null
+++ b/test/data/amsterdam_patches_B.tif
@@ -0,0 +1,3 @@
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
+++ b/test/data/terrain_truth_epsg32654_A.tif
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new file mode 100644
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diff --git a/test/models/model5/saved_model.pb b/test/models/model5/saved_model.pb
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diff --git a/test/models/model5/variables/variables.data-00000-of-00001 b/test/models/model5/variables/variables.data-00000-of-00001
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diff --git a/test/sr4rs_unittest.py b/test/sr4rs_unittest.py
index fbb921f8451cc83b3fd7b9e9e90bf61755511eca..89c3945f153304d04d35c23ef34513cf668120bc 100644
--- a/test/sr4rs_unittest.py
+++ b/test/sr4rs_unittest.py
@@ -4,8 +4,7 @@
import unittest
import os
from pathlib import Path
-import gdal
-import otbApplication as otb
+import test_utils
def command_train_succeed(extra_opts=""):
@@ -54,21 +53,7 @@ class SR4RSv1Test(unittest.TestCase):
command += "--output '{}?&box=256:256:512:512'".format(out_img)
os.system(command)
- nbchannels_reconstruct = gdal.Open(out_img).RasterCount
- nbchannels_baseline = gdal.Open(baseline).RasterCount
-
- self.assertTrue(nbchannels_reconstruct == nbchannels_baseline)
-
- for i in range(1, 1 + nbchannels_baseline):
- comp = otb.Registry.CreateApplication('CompareImages')
- comp.SetParameterString('ref.in', baseline)
- comp.SetParameterInt('ref.channel', i)
- comp.SetParameterString('meas.in', out_img)
- comp.SetParameterInt('meas.channel', i)
- comp.Execute()
- mae = comp.GetParameterFloat('mae')
-
- self.assertTrue(mae < 0.01)
+ self.assertTrue(test_utils.compare(baseline, out_img))
if __name__ == '__main__':
diff --git a/test/test_utils.py b/test/test_utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..c07301e91bb2eab4a808d53beaa46396c3ea82fc
--- /dev/null
+++ b/test/test_utils.py
@@ -0,0 +1,56 @@
+import otbApplication
+import os
+
+
+def get_nb_of_channels(raster):
+ """
+ Return the number of channels in the input raster
+ :param raster: raster filename (str)
+ :return the number of channels in the image (int)
+ """
+ info = otbApplication.Registry.CreateApplication("ReadImageInfo")
+ info.SetParameterString("in", raster)
+ info.ExecuteAndWriteOutput()
+ return info.GetParameterInt('numberbands')
+
+
+def compare(raster1, raster2, tol=0.01):
+ """
+ Return True if the two rasters have the same contents in each bands
+ :param raster1: raster 1 filename (str)
+ :param raster2: raster 2 filename (str)
+ :param tol: tolerance (float)
+ """
+ n_bands1 = get_nb_of_channels(raster1)
+ n_bands2 = get_nb_of_channels(raster2)
+ if n_bands1 != n_bands2:
+ print("The images have not the same number of channels")
+ return False
+
+ for i in range(1, 1 + n_bands1):
+ comp = otbApplication.Registry.CreateApplication('CompareImages')
+ comp.SetParameterString('ref.in', raster1)
+ comp.SetParameterInt('ref.channel', i)
+ comp.SetParameterString('meas.in', raster2)
+ comp.SetParameterInt('meas.channel', i)
+ comp.Execute()
+ mae = comp.GetParameterFloat('mae')
+ if mae > tol:
+ print("The images have not the same content in channel {} "
+ "(Mean average error: {})".format(i, mae))
+ return False
+ return True
+
+
+def resolve_paths(filename, var_list):
+ """
+ Retrieve environment variables in paths
+ :param filename: file name
+ :params var_list: variable list
+ :return filename with retrieved environment variables
+ """
+ new_filename = filename
+ for var in var_list:
+ new_filename = new_filename.replace("${}".format(var), os.environ[var])
+ print("Resolve filename...\n\tfilename: {}, \n\tnew filename: {}".format(filename, new_filename))
+ return new_filename
diff --git a/test/tutorial_unittest.py b/test/tutorial_unittest.py
new file mode 100644
index 0000000000000000000000000000000000000000..7934862f348326de13a11eef4c81a4fe6512cec6
--- /dev/null
+++ b/test/tutorial_unittest.py
@@ -0,0 +1,513 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+import pytest
+import unittest
+import os
+from pathlib import Path
+import test_utils
+
+INFERENCE_MAE_TOL = 10.0 # Dummy value: we don't really care of the mae value but rather the image size etc
+
+
+def resolve_paths(path):
+ """
+ Resolve a path with the environment variables
+ """
+ return test_utils.resolve_paths(path, var_list=["TMPDIR", "DATADIR"])
+
+
+def run_command(command):
+ """
+ Run a command
+ :param command: the command to run
+ """
+ full_command = resolve_paths(command)
+ print("Running command: \n\t {}".format(full_command))
+ os.system(full_command)
+
+
+def run_command_and_test_exist(command, file_list):
+ """
+ :param command: the command to run (str)
+ :param file_list: list of files to check
+ :return True or False
+ """
+ run_command(command)
+ print("Checking if files exist...")
+ for file in file_list:
+ print("\t{}".format(file))
+ path = Path(resolve_paths(file))
+ if not path.is_file():
+ print("File {} does not exist!".format(file))
+ return False
+ print("\tOk")
+ return True
+
+
+def run_command_and_compare(command, to_compare_dict, tol=0.01):
+ """
+ :param command: the command to run (str)
+ :param to_compare_dict: a dict of {baseline1: output1, ..., baselineN: outputN}
+ :param tol: tolerance (float)
+ :return True or False
+ """
+
+ run_command(command)
+ for baseline, output in to_compare_dict.items():
+ if not test_utils.compare(resolve_paths(baseline), resolve_paths(output), tol):
+ print("Baseline {} and output {} differ.".format(baseline, output))
+ return False
+ return True
+
+
+class TutorialTest(unittest.TestCase):
+
+ @pytest.mark.order(1)
+ def test_sample_selection(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_LabelImageSampleSelection "
+ "-inref $DATADIR/terrain_truth_epsg32654_A.tif "
+ "-nodata 255 "
+ "-outvec $TMPDIR/outvec_A.gpkg",
+ file_list=["$TMPDIR/outvec_A.gpkg"]))
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_LabelImageSampleSelection "
+ "-inref $DATADIR/terrain_truth_epsg32654_B.tif "
+ "-nodata 255 "
+ "-outvec $TMPDIR/outvec_B.gpkg",
+ file_list=["$TMPDIR/outvec_B.gpkg"]))
+
+ @pytest.mark.order(2)
+ def test_patches_extraction(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.out $TMPDIR/s2_patches_A.tif "
+ "-source1.patchsizex 16 "
+ "-source1.patchsizey 16 "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_labels_A.tif",
+ to_compare_dict={"$DATADIR/s2_patches_A.tif": "$TMPDIR/s2_patches_A.tif",
+ "$DATADIR/s2_labels_A.tif": "$TMPDIR/s2_labels_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.out $TMPDIR/s2_patches_B.tif "
+ "-source1.patchsizex 16 "
+ "-source1.patchsizey 16 "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_labels_B.tif",
+ to_compare_dict={"$DATADIR/s2_patches_B.tif": "$TMPDIR/s2_patches_B.tif",
+ "$DATADIR/s2_labels_B.tif": "$TMPDIR/s2_labels_B.tif"}))
+
+ @pytest.mark.order(3)
+ def test_generate_model1(self):
+ run_command("git clone https://github.com/remicres/otbtf_tutorials_resources.git "
+ "$TMPDIR/otbtf_tuto_repo")
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model1.py "
+ "$TMPDIR/model1",
+ file_list=["$TMPDIR/model1/saved_model.pb"]))
+
+ @pytest.mark.order(4)
+ def test_model1_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_patches_A.tif "
+ "-training.source1.patchsizex 16 "
+ "-training.source1.patchsizey 16 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/s2_labels_A.tif "
+ "-training.source2.patchsizex 1 "
+ "-training.source2.patchsizey 1 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model1 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/s2_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model1/variables/variables",
+ file_list=["$TMPDIR/model1/variables/variables.index"]
+ )
+ )
+
+ @pytest.mark.order(5)
+ def test_model1_inference_pb(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model1 "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model1.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={"$DATADIR/classif_model1.tif": "$TMPDIR/classif_model1.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(6)
+ def test_model1_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model1 "
+ "-output.names prediction "
+ "-model.fullyconv on "
+ "-output.spcscale 4 "
+ "-out \"$TMPDIR/classif_model1.tif?&box=1000:1000:256:256\" uint8",
+ to_compare_dict={"$DATADIR/classif_model1.tif": "$TMPDIR/classif_model1.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(7)
+ def test_rf_sampling(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_SampleExtraction "
+ "-in $DATADIR/s2_stack.jp2 "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-out $TMPDIR/pixelvalues_A.gpkg",
+ file_list=["$TMPDIR/pixelvalues_A.gpkg"]))
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_SampleExtraction "
+ "-in $DATADIR/s2_stack.jp2 "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-out $TMPDIR/pixelvalues_B.gpkg",
+ file_list=["$TMPDIR/pixelvalues_B.gpkg"]))
+
+ @pytest.mark.order(8)
+ def test_rf_training(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TrainVectorClassifier "
+ "-io.vd $TMPDIR/pixelvalues_A.gpkg "
+ "-valid.vd $TMPDIR/pixelvalues_B.gpkg "
+ "-feat value_0 value_1 value_2 value_3 "
+ "-cfield class "
+ "-classifier rf "
+ "-io.out $TMPDIR/randomforest_model.yaml ",
+ file_list=["$TMPDIR/randomforest_model.yaml"]))
+
+ @pytest.mark.order(9)
+ def test_generate_model2(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model2.py "
+ "$TMPDIR/model2",
+ file_list=["$TMPDIR/model2/saved_model.pb"]))
+
+ @pytest.mark.order(10)
+ def test_model2_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_patches_A.tif "
+ "-training.source1.patchsizex 16 "
+ "-training.source1.patchsizey 16 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/s2_labels_A.tif "
+ "-training.source2.patchsizex 1 "
+ "-training.source2.patchsizey 1 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model2 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/s2_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model2/variables/variables",
+ file_list=["$TMPDIR/model2/variables/variables.index"]))
+
+ @pytest.mark.order(11)
+ def test_model2_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(command="otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model2 "
+ "-model.fullyconv on "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model2.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={"$DATADIR/classif_model2.tif": "$TMPDIR/classif_model2.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(12)
+ def test_model2rf_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_TrainClassifierFromDeepFeatures "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model2 "
+ "-model.fullyconv on "
+ "-optim.tilesizex 999999 "
+ "-optim.tilesizey 128 "
+ "-output.names features "
+ "-vd $TMPDIR/outvec_A.gpkg "
+ "-valid $TMPDIR/outvec_B.gpkg "
+ "-sample.vfn class "
+ "-sample.bm 0 "
+ "-classifier rf "
+ "-out $TMPDIR/RF_model_from_deep_features.yaml",
+ file_list=["$TMPDIR/RF_model_from_deep_features.yaml"]))
+
+ @pytest.mark.order(13)
+ def test_model2rf_inference(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="otbcli_ImageClassifierFromDeepFeatures "
+ "-source1.il $DATADIR/s2_stack.jp2 "
+ "-source1.rfieldx 16 "
+ "-source1.rfieldy 16 "
+ "-source1.placeholder x "
+ "-deepmodel.dir $TMPDIR/model2 "
+ "-deepmodel.fullyconv on "
+ "-output.names features "
+ "-model $TMPDIR/RF_model_from_deep_features.yaml "
+ "-out \"$TMPDIR/RF_model_from_deep_features_map.tif?&box=4000:4000:1000:1000\" uint8",
+ to_compare_dict={
+ "$DATADIR/RF_model_from_deep_features_map.tif": "$TMPDIR/RF_model_from_deep_features_map.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(14)
+ def test_patch_extraction_20m(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.patchsizex 8 "
+ "-source1.patchsizey 8 "
+ "-source1.out $TMPDIR/s2_20m_patches_A.tif "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.patchsizex 16 "
+ "-source2.patchsizey 16 "
+ "-source2.out $TMPDIR/s2_10m_patches_A.tif "
+ "-vec $TMPDIR/outvec_A.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_10m_labels_A.tif uint8",
+ to_compare_dict={"$DATADIR/s2_10m_labels_A.tif": "$TMPDIR/s2_10m_labels_A.tif",
+ "$DATADIR/s2_10m_patches_A.tif": "$TMPDIR/s2_10m_patches_A.tif",
+ "$DATADIR/s2_20m_patches_A.tif": "$TMPDIR/s2_20m_patches_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.patchsizex 8 "
+ "-source1.patchsizey 8 "
+ "-source1.out $TMPDIR/s2_20m_patches_B.tif "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.patchsizex 16 "
+ "-source2.patchsizey 16 "
+ "-source2.out $TMPDIR/s2_10m_patches_B.tif "
+ "-vec $TMPDIR/outvec_B.gpkg "
+ "-field class "
+ "-outlabels $TMPDIR/s2_10m_labels_B.tif uint8",
+ to_compare_dict={"$DATADIR/s2_10m_labels_B.tif": "$TMPDIR/s2_10m_labels_B.tif",
+ "$DATADIR/s2_10m_patches_B.tif": "$TMPDIR/s2_10m_patches_B.tif",
+ "$DATADIR/s2_20m_patches_B.tif": "$TMPDIR/s2_20m_patches_B.tif"}))
+
+ @pytest.mark.order(15)
+ def test_generate_model3(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/01_patch_based_classification/models/create_model3.py "
+ "$TMPDIR/model3",
+ file_list=["$TMPDIR/model3/saved_model.pb"]))
+
+ @pytest.mark.order(16)
+ def test_model3_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="OTB_TF_NSOURCES=2 otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/s2_20m_patches_A.tif "
+ "-training.source1.patchsizex 8 "
+ "-training.source1.patchsizey 8 "
+ "-training.source1.placeholder x1 "
+ "-training.source2.il $DATADIR/s2_10m_patches_A.tif "
+ "-training.source2.patchsizex 16 "
+ "-training.source2.patchsizey 16 "
+ "-training.source2.placeholder x2 "
+ "-training.source3.il $DATADIR/s2_10m_labels_A.tif "
+ "-training.source3.patchsizex 1 "
+ "-training.source3.patchsizey 1 "
+ "-training.source3.placeholder y "
+ "-model.dir $TMPDIR/model3 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/s2_20m_patches_B.tif "
+ "-validation.source1.name x1 "
+ "-validation.source2.il $DATADIR/s2_10m_patches_B.tif "
+ "-validation.source2.name x2 "
+ "-validation.source3.il $DATADIR/s2_10m_labels_B.tif "
+ "-validation.source3.name prediction "
+ "-model.saveto $TMPDIR/model3/variables/variables",
+ file_list=["$TMPDIR/model3/variables/variables.index"]))
+
+ @pytest.mark.order(17)
+ def test_model3_inference_pb(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "OTB_TF_NSOURCES=2 otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.rfieldx 8 "
+ "-source1.rfieldy 8 "
+ "-source1.placeholder x1 "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.rfieldx 16 "
+ "-source2.rfieldy 16 "
+ "-source2.placeholder x2 "
+ "-model.dir $TMPDIR/model3 "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model3_pb.tif?&box=2000:2000:500:500&gdal:co:compress=deflate\"",
+ to_compare_dict={"$DATADIR/classif_model3_pb.tif": "$TMPDIR/classif_model3_pb.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(18)
+ def test_model3_inference_fcn(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "OTB_TF_NSOURCES=2 otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/s2_20m_stack.jp2 "
+ "-source1.rfieldx 8 "
+ "-source1.rfieldy 8 "
+ "-source1.placeholder x1 "
+ "-source2.il $DATADIR/s2_stack.jp2 "
+ "-source2.rfieldx 16 "
+ "-source2.rfieldy 16 "
+ "-source2.placeholder x2 "
+ "-model.dir $TMPDIR/model3 "
+ "-model.fullyconv on "
+ "-output.names prediction "
+ "-out \"$TMPDIR/classif_model3_fcn.tif?&box=2000:2000:500:500&gdal:co:compress=deflate\"",
+ to_compare_dict={"$DATADIR/classif_model3_fcn.tif": "$TMPDIR/classif_model3_fcn.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+ @pytest.mark.order(19)
+ def test_generate_model4(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="python $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/models/create_model4.py "
+ "$TMPDIR/model4",
+ file_list=["$TMPDIR/model4/saved_model.pb"]))
+
+ @pytest.mark.order(20)
+ def test_patches_selection_semseg(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="otbcli_PatchesSelection "
+ "-in $DATADIR/fake_spot6.jp2 "
+ "-grid.step 64 "
+ "-grid.psize 64 "
+ "-outtrain $TMPDIR/outvec_A_semseg.gpkg "
+ "-outvalid $TMPDIR/outvec_B_semseg.gpkg",
+ file_list=["$TMPDIR/outvec_A_semseg.gpkg",
+ "$TMPDIR/outvec_B_semseg.gpkg"]))
+
+ @pytest.mark.order(21)
+ def test_patch_extraction_semseg(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.patchsizex 64 "
+ "-source1.patchsizey 64 "
+ "-source1.out \"$TMPDIR/amsterdam_patches_A.tif?&gdal:co:compress=deflate\" "
+ "-source2.il $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/"
+ "amsterdam_dataset/terrain_truth/amsterdam_labelimage.tif "
+ "-source2.patchsizex 64 "
+ "-source2.patchsizey 64 "
+ "-source2.out \"$TMPDIR/amsterdam_labels_A.tif?&gdal:co:compress=deflate\" "
+ "-vec $TMPDIR/outvec_A_semseg.gpkg "
+ "-field id ",
+ to_compare_dict={"$DATADIR/amsterdam_labels_A.tif": "$TMPDIR/amsterdam_labels_A.tif",
+ "$DATADIR/amsterdam_patches_A.tif": "$TMPDIR/amsterdam_patches_A.tif"}))
+ self.assertTrue(
+ run_command_and_compare(
+ command="OTB_TF_NSOURCES=2 otbcli_PatchesExtraction "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.patchsizex 64 "
+ "-source1.patchsizey 64 "
+ "-source1.out \"$TMPDIR/amsterdam_patches_B.tif?&gdal:co:compress=deflate\" "
+ "-source2.il $TMPDIR/otbtf_tuto_repo/02_semantic_segmentation/"
+ "amsterdam_dataset/terrain_truth/amsterdam_labelimage.tif "
+ "-source2.patchsizex 64 "
+ "-source2.patchsizey 64 "
+ "-source2.out \"$TMPDIR/amsterdam_labels_B.tif?&gdal:co:compress=deflate\" "
+ "-vec $TMPDIR/outvec_B_semseg.gpkg "
+ "-field id ",
+ to_compare_dict={"$DATADIR/amsterdam_labels_B.tif": "$TMPDIR/amsterdam_labels_B.tif",
+ "$DATADIR/amsterdam_patches_B.tif": "$TMPDIR/amsterdam_patches_B.tif"}))
+
+ @pytest.mark.order(22)
+ def test_model4_train(self):
+ self.assertTrue(
+ run_command_and_test_exist(
+ command="OTB_TF_NSOURCES=1 otbcli_TensorflowModelTrain "
+ "-training.source1.il $DATADIR/amsterdam_patches_A.tif "
+ "-training.source1.patchsizex 64 "
+ "-training.source1.patchsizey 64 "
+ "-training.source1.placeholder x "
+ "-training.source2.il $DATADIR/amsterdam_labels_A.tif "
+ "-training.source2.patchsizex 64 "
+ "-training.source2.patchsizey 64 "
+ "-training.source2.placeholder y "
+ "-model.dir $TMPDIR/model4 "
+ "-training.targetnodes optimizer "
+ "-training.epochs 10 "
+ "-validation.mode class "
+ "-validation.source1.il $DATADIR/amsterdam_patches_B.tif "
+ "-validation.source1.name x "
+ "-validation.source2.il $DATADIR/amsterdam_labels_B.tif "
+ "-validation.source2.name prediction "
+ "-model.saveto $TMPDIR/model4/variables/variables",
+ file_list=["$TMPDIR/model4/variables/variables.index"]))
+
+ @pytest.mark.order(23)
+ def test_model4_inference(self):
+ self.assertTrue(
+ run_command_and_compare(
+ command=
+ "otbcli_TensorflowModelServe "
+ "-source1.il $DATADIR/fake_spot6.jp2 "
+ "-source1.rfieldx 64 "
+ "-source1.rfieldy 64 "
+ "-source1.placeholder x "
+ "-model.dir $TMPDIR/model4 "
+ "-model.fullyconv on "
+ "-output.names prediction_fcn "
+ "-output.efieldx 32 "
+ "-output.efieldy 32 "
+ "-out \"$TMPDIR/classif_model4.tif?&gdal:co:compress=deflate\" uint8",
+ to_compare_dict={"$DATADIR/classif_model4.tif": "$TMPDIR/classif_model4.tif"},
+ tol=INFERENCE_MAE_TOL))
+
+
+if __name__ == '__main__':
+ unittest.main()