Merge branch 'develop' into 'master'

Release 4.2.1

See merge request remi.cresson/otbtf!102

.gitlab-ci.yml

 variables:
-  OTBTF_VERSION: 4.2.0
+  OTBTF_VERSION: 4.2.1
   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
@@ -282,6 +282,7 @@ deploy_gpu:
     IMAGE_GPUOPTDEV: $CI_REGISTRY_PUBIMG-gpu-opt-dev
     DOCKERHUB_GPU: $DOCKERHUB_IMAGE_BASE-gpu
     DOCKERHUB_GPUDEV: $DOCKERHUB_IMAGE_BASE-gpu-dev
+    DOCKERHUB_GPULATEST: $DOCKERHUB_BASE:latest-gpu
   script:
     # gpu-opt
     - docker build --build-arg BZL_OPTIONS="--remote_cache=$BAZELCACHE" --tag $IMAGE_GPUOPT --build-arg BASE_IMG=$GPU_BASE_IMG .
@@ -301,5 +302,7 @@ deploy_gpu:
     - docker push $DOCKERHUB_GPU
     - docker tag $IMAGE_GPUDEV $DOCKERHUB_GPUDEV
     - docker push $DOCKERHUB_GPUDEV
-
+    # latest-gpu = gpu image
+    - docker tag $IMAGE_GPU $DOCKERHUB_GPULATEST
+    - docker push $DOCKERHUB_GPULATEST
 

Dockerfile

@@ -98,7 +98,7 @@ RUN cd tensorflow \
 ### OTB
 
 ARG GUI=false
-ARG OTB=5086d7601d80f2427f4d4d7f2398ec46e7efa300
+ARG OTB=8.1.2
 ARG OTBTESTS=false
 
 RUN mkdir /src/otb

README.md

@@ -33,8 +33,8 @@ The documentation is available on [otbtf.readthedocs.io](https://otbtf.readthedo
 You can use our latest GPU enabled docker images.
 
 ```bash
-docker run --runtime=nvidia -ti mdl4eo/otbtf:4.2.0-gpu otbcli_PatchesExtraction
-docker run --runtime=nvidia -ti mdl4eo/otbtf:4.2.0-gpu python -c "import otbtf"
+docker run --runtime=nvidia -ti mdl4eo/otbtf:latest-gpu otbcli_PatchesExtraction
+docker run --runtime=nvidia -ti mdl4eo/otbtf:latest-gpu python -c "import otbtf"
 ```
 
 You can also build OTBTF from sources (see the documentation)

RELEASE_NOTES.txt

+Version 4.2.1 (5 oct 2023)
+----------------------------------------------------------------
+* Fix a bug occuring when input images origins were not sharing the same pixel grid
+* CI to push "latest-gpu" tag on dockerhub
+* Move to OTB 8.2.1
+
 Version 4.2.0 (12 sep 2023)
 ----------------------------------------------------------------
 * Add new python modules: `otbtf.layers` (with new classes `DilatedMask`, `ApplyMask`, `ScalarsTile`, `ArgMax`, `Max`) and `otbtf.ops` (`one_hot()`)

doc/docker_use.md

@@ -5,13 +5,13 @@ We recommend to use OTBTF from official docker images.
 Latest CPU-only docker image:
 
 ```commandline
-docker pull mdl4eo/otbtf:4.2.0-cpu
+docker pull mdl4eo/otbtf:latest
 ```
 
 Latest GPU-ready docker image:
 
 ```commandline
-docker pull mdl4eo/otbtf:4.2.0-gpu
+docker pull mdl4eo/otbtf:latest-gpu
 ```
 
 Read more in the following sections.
@@ -25,12 +25,12 @@ Since OTBTF >= 3.2.1 you can find the latest docker images on
 
 | Name                                                                               | Os            | TF    | OTB   | Description            | Dev files | Compute capability |
 |------------------------------------------------------------------------------------| ------------- |-------|-------| ---------------------- | --------- | ------------------ |
-| **mdl4eo/otbtf:4.2.0-cpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.0 | CPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
-| **mdl4eo/otbtf:4.2.0-cpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.0 | CPU, no optimization (dev) |  yes  | 5.2,6.1,7.0,7.5,8.6|
-| **mdl4eo/otbtf:4.2.0-gpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
-| **mdl4eo/otbtf:4.2.0-gpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU, no optimization (dev) | yes   | 5.2,6.1,7.0,7.5,8.6|
-| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.0-gpu-opt**     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt.          | no        | 5.2,6.1,7.0,7.5,8.6|
-| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.0-gpu-opt-dev** | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt. (dev)    | yes       | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.1-cpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.2 | CPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.1-cpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.2 | CPU, no optimization (dev) |  yes  | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.1-gpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.2 | GPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.1-gpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.2 | GPU, no optimization (dev) | yes   | 5.2,6.1,7.0,7.5,8.6|
+| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.1-gpu-opt**     | Ubuntu Jammy  | r2.12 | 8.1.2 | GPU with opt.          | no        | 5.2,6.1,7.0,7.5,8.6|
+| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.1-gpu-opt-dev** | Ubuntu Jammy  | r2.12 | 8.1.2 | GPU with opt. (dev)    | yes       | 5.2,6.1,7.0,7.5,8.6|
 
 The list of older releases is available [here](#older-images).
 
@@ -51,13 +51,13 @@ You can then use the OTBTF `gpu` tagged docker images with the **NVIDIA runtime*
 With Docker version earlier than 19.03 :
 
 ```bash
-docker run --runtime=nvidia -ti mdl4eo/otbtf:4.2.0-gpu bash
+docker run --runtime=nvidia -ti mdl4eo/otbtf:latest-gpu bash
 ```
 
 With Docker version including and after 19.03 :
 
 ```bash
-docker run --gpus all -ti mdl4eo/otbtf:4.2.0-gpu bash
+docker run --gpus all -ti mdl4eo/otbtf:latest-gpu bash
 ```
 
 You can find some details on the **GPU docker image** and some **docker tips 
@@ -80,7 +80,7 @@ See here how to install docker on Ubuntu
 1. Install [WSL2](https://docs.microsoft.com/en-us/windows/wsl/install-win10#manual-installation-steps) (Windows Subsystem for Linux)
 2. Install [docker desktop](https://www.docker.com/products/docker-desktop)
 3. Start **docker desktop** and **enable WSL2** from *Settings* > *General* then tick the box *Use the WSL2 based engine*
-3. Open a **cmd.exe** or **PowerShell** terminal, and type `docker create --name otbtf-cpu --interactive --tty mdl4eo/otbtf:4.2.0-cpu`
+3. Open a **cmd.exe** or **PowerShell** terminal, and type `docker create --name otbtf-cpu --interactive --tty mdl4eo/otbtf:latest`
 4. Open **docker desktop**, and check that the docker is running in the **Container/Apps** menu
 ![Docker desktop, after the docker image is downloaded and ready to use](images/docker_desktop_1.jpeg)
 5. From **docker desktop**, click on the icon highlighted as shown below, and use the bash terminal that should pop up!
@@ -172,4 +172,10 @@ Here you can find the list of older releases of OTBTF:
 | **mdl4eo/otbtf:4.1.0-gpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU, no optimization (dev) | yes   | 5.2,6.1,7.0,7.5,8.6|
 | **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.1.0-gpu-opt**     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt.          | no        | 5.2,6.1,7.0,7.5,8.6|
 | **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.1.0-gpu-opt-dev** | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt. (dev)    | yes       | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.0-cpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.0 | CPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.0-cpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.0 | CPU, no optimization (dev) |  yes  | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.0-gpu**                                                         | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU, no optimization   | no        | 5.2,6.1,7.0,7.5,8.6|
+| **mdl4eo/otbtf:4.2.0-gpu-dev**                                                     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU, no optimization (dev) | yes   | 5.2,6.1,7.0,7.5,8.6|
+| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.0-gpu-opt**     | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt.          | no        | 5.2,6.1,7.0,7.5,8.6|
+| **gitlab.irstea.fr/remi.cresson/otbtf/container_registry/otbtf:4.2.0-gpu-opt-dev** | Ubuntu Jammy  | r2.12 | 8.1.0 | GPU with opt. (dev)    | yes       | 5.2,6.1,7.0,7.5,8.6|
 

include/otbTensorflowMultisourceModelFilter.hxx

@@ -204,6 +204,24 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::GenerateOutputInfor
   m_OutputSpacing[0] *= m_OutputSpacingScale;
   m_OutputSpacing[1] *= m_OutputSpacingScale;
 
+  // Check that inputs are aligned
+  if (m_FullyConvolutional)
+  {
+    for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+    {
+      const float ref_spc = this->GetInput(0)->GetSpacing()[dim];
+      const float ref = this->GetInput(0)->GetOrigin()[dim] - 0.5 * ref_spc;
+      for (unsigned int imageIndex = 1; imageIndex < this->GetNumberOfInputs(); imageIndex++)
+      {
+        const float orig = this->GetInput(imageIndex)->GetOrigin()[dim] - 0.5 * this->GetInput(imageIndex)->GetSpacing()[dim];
+        if (ref != orig)
+          otbLogMacro(Warning, << "Input #" << imageIndex << " origin does not match reference (first) input");
+        if (std::fmod(ref - orig, ref_spc) != 0.0)
+          otbLogMacro(Warning, << "Input #" << imageIndex << " pixels are not aligned with reference (first) input");
+      } // next input
+    } // next dim
+  }
+
   // Compute the extent of each input images and update the extent or the output image.
   // The extent of the output image is the intersection of all input images extents.
   PointType extentInf, extentSup;
@@ -226,6 +244,28 @@ TensorflowMultisourceModelFilter<TInputImage, TOutputImage>::GenerateOutputInfor
     }
   }
 
+  if (m_FullyConvolutional)
+  {
+    // Align extent over inputs pixel grid, so that the extent lies on the
+    // common pixel grid of all inputs.
+    // When this can't be done (i.e. shifted origins), a bug is likely to occur.
+    // However the warning issued previously should give a hint about the issue.
+    PointType alignedExtentInf, alignedExtentSup;
+    alignedExtentSup.Fill(itk::NumericTraits<double>::max());
+    alignedExtentInf.Fill(itk::NumericTraits<double>::NonpositiveMin());
+    for (unsigned int imageIndex = 0; imageIndex < this->GetNumberOfInputs(); imageIndex++)
+      for (unsigned int dim = 0; dim < OutputImageType::ImageDimension; ++dim)
+      {
+        const double spc = this->GetInput(imageIndex)->GetSpacing()[dim];
+        const double ref = this->GetInput(imageIndex)->GetOrigin()[dim] - 0.5 * spc;
+        const double alignedInf = std::ceil((extentInf[dim] - ref) / spc) * spc + ref;
+        const double alignedSup = std::floor((extentSup[dim] - ref) / spc) * spc + ref;
+        alignedExtentInf[dim] = vnl_math_max(alignedInf, alignedExtentInf[dim]);
+        alignedExtentSup[dim] = vnl_math_min(alignedSup, alignedExtentSup[dim]);
+      }
+    extentInf = alignedExtentInf;
+    extentSup = alignedExtentSup;
+  }
 
   // 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)

setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
 
 setuptools.setup(
     name="otbtf",
-    version="4.2.0",
+    version="4.2.1",
     author="Remi Cresson",
     author_email="remi.cresson@inrae.fr",
     description="OTBTF: Orfeo ToolBox meets TensorFlow",

tools/docker/build-flags-otb.txt

@@ -17,3 +17,12 @@
 -DUSE_SYSTEM_TINYXML=ON
 -DUSE_SYSTEM_ZLIB=ON
 -DUSE_SYSTEM_SWIG=ON
+
+-DOTB_USE_QT=OFF
+-DOTB_USE_OPENGL=OFF
+-DOTB_USE_GLUT=OFF
+-DOTB_USE_GLEW=OFF
+-DOTB_USE_GLFW=OFF
+
+-DGDAL_SB_EXTRA_OPTIONS=--with-geos
+