Merge branch 'develop' into 1971-double-precision-parameters

.gitlab-ci.yml

@@ -136,9 +136,13 @@ legal-check:
 #------------------------- prepare & build jobs --------------------------------
 debian-build:
   extends: .common-build
-  image: $BUILD_IMAGE_REGISTRY/otb-debian-native:unstable
+  image: $BUILD_IMAGE_REGISTRY/otb-debian-native:testing
+  allow_failure: true
   script:
-    - xvfb-run -a -n 1 -s "-screen 0 1024x768x24 -dpi 96" ctest -V -S CI/main_ci.cmake -DIMAGE_NAME:string=debian-unstable-gcc
+    - xvfb-run -a -n 1 -s "-screen 0 1024x768x24 -dpi 96" ctest -V -S CI/main_ci.cmake -DIMAGE_NAME:string=debian-testing-gcc
+  after_script:
+    - export CI_ALLOW_FAILURE=ON
+    - python3 -u CI/cdash_handler.py
   dependencies: []
 
 ## Ubuntu superbuild

CI/cdash_handler.py

@@ -246,6 +246,9 @@ if __name__ == "__main__":
   if ( len(sys.argv) < 6 and len(sys.argv) > 1 ):
     print("Usage : "+sys.argv[0]+" commit_sha1 project_id project_directory token ref_name")
     sys.exit(1)
+
+  allow_failure = os.environ.get('CI_ALLOW_FAILURE', False)
+
   if ( len(sys.argv) >= 6):
     sha1 = sys.argv[1]
     proj = sys.argv[2]
@@ -286,6 +289,10 @@ if __name__ == "__main__":
     sys.exit(0)
   gitlab_url = "https://gitlab.orfeo-toolbox.org/api/v4/projects/"
   gitlab_url += proj + "/statuses/" + sha1
+
+  if allow_failure:
+    state = 'success'
+
   params = urllib.parse.urlencode({'name':'cdash:' + handler.site , 'state': state ,\
    'target_url' : cdash_url , 'description' : error , 'ref' : refn })
   gitlab_request = urllib.request.Request(gitlab_url)

CI/debian-unstable-gcc.cmake → CI/debian-testing-gcc.cmake

@@ -21,7 +21,7 @@
 # Configuration options for debian-unstable-gcc
 
 set(site_option
-"opencv_INCLUDE_DIR:PATH=/usr/include
+"OpenCV_DIR:PATH=/usr
 OTB_USE_MPI:BOOL=OFF
 OTB_USE_SHARK:BOOL=OFF
 ")

CMake/FindOpenCV.cmake

@@ -21,9 +21,9 @@
 set(OPENCV_SEARCH_PATH)
 
 if(OpenCV_DIR)
-  get_filename_component(OPENCV_SEARCH_PATH "${OpenCV_DIR}" PATH)
+  get_filename_component(OPENCV_SEARCH_PATH "${OpenCV_DIR}" REALPATH)
   if(OPENCV_SEARCH_PATH)
-    get_filename_component(OPENCV_SEARCH_PATH "${OPENCV_SEARCH_PATH}" PATH)
+    get_filename_component(OPENCV_SEARCH_PATH "${OPENCV_SEARCH_PATH}" REALPATH)
   endif()
   if(OPENCV_SEARCH_PATH)
     find_path(

Data/Baseline/OTB/Files/ioTvMultiResolutionReadingInfoOut.3.txt

+RESOLUTION: 0; DESC: Resolution: 0 (Image [w x h]: 2592x1944)
+RESOLUTION: 1; DESC: Resolution: 1 (Image [w x h]: 1296x972)
+RESOLUTION: 2; DESC: Resolution: 2 (Image [w x h]: 648x486)
+RESOLUTION: 3; DESC: Resolution: 3 (Image [w x h]: 324x243)
+RESOLUTION: 4; DESC: Resolution: 4 (Image [w x h]: 162x122)
+RESOLUTION: 5; DESC: Resolution: 5 (Image [w x h]: 81x61)

Documentation/Cookbook/rst/QGISInterface.rst

@@ -8,7 +8,7 @@ With QGIS < 3.8 you will need to manually install the plugin.
 You can follow the instruction here: https://gitlab.orfeo-toolbox.org/orfeotoolbox/qgis-otb-plugin#otb-provider-for-qgis-processing
 
 
-With QGIS > 3.8, the plugin is in the QGIS core. So you just need install OTB and set the plugin up.
+With QGIS > 3.8, the plugin is already in the QGIS core. So you just need to install OTB and activate the plugin: https://www.orfeo-toolbox.org/CookBook/QGISInterface.html#open-processing-settings
 
 Download and Install OTB
 ^^^^^^^^^^^^^^^^^^^^^^^^

Modules/Adapters/OSSIMAdapters/test/otbOssimElevManagerTest4.cxx

@@ -96,7 +96,7 @@ int otbOssimElevManagerTest4(int argc, char* argv[])
 
   std::ofstream file;
   std::cout << outfname << std::endl;
-  file.open(outfname, ios::binary | ios::out);
+  file.open(outfname, std::ios::binary | std::ios::out);
 
   file.write(reinterpret_cast<char*>(image), sizeof(double) * size[0] * size[1]);
   file.close();

Modules/Filtering/DimensionalityReduction/include/otbPCAImageFilter.hxx

@@ -325,36 +325,30 @@ void PCAImageFilter<TInputImage, TOutputImage, TDirectionOfTransformation>::Gene
   vnl_vector<double> vectValP;
   vnl_symmetric_eigensystem_compute(m_CovarianceMatrix.GetVnlMatrix(), transf, vectValP);
 
-  InternalMatrixType valP(vectValP.size(), vectValP.size(), vnl_matrix_null);
-  for (unsigned int i = 0; i < vectValP.size(); ++i)
-    valP(i, i) = vectValP[i];
 
   m_EigenValues.SetSize(m_NumberOfPrincipalComponentsRequired);
   for (unsigned int i                                            = 0; i < m_NumberOfPrincipalComponentsRequired; ++i)
     m_EigenValues[m_NumberOfPrincipalComponentsRequired - 1 - i] = static_cast<RealType>(vectValP[i]);
 
-  /* We used normalized PCA */
-  for (unsigned int i = 0; i < valP.rows(); ++i)
+  if (m_Whitening)
   {
-    if (valP(i, i) > 0.)
-    {
-      if (m_Whitening)
-        valP(i, i) = 1. / std::sqrt(valP(i, i));
-    }
-    else if (valP(i, i) < 0.)
+    InternalMatrixType valP(vectValP.size(), vectValP.size(), vnl_matrix_null);
+    for (unsigned int i = 0; i < vectValP.size(); ++i)
+    valP(i, i) = vectValP[i];
+
+    for (unsigned int i = 0; i < valP.rows(); ++i)
     {
-      otbMsgDebugMacro(<< "ValP(" << i << ") neg : " << valP(i, i) << " taking abs value");
-      if (m_Whitening)
-        valP(i, i) = 1. / std::sqrt(std::abs(valP(i, i)));
+      if (valP(i,i) != 0.0)
+        valP(i,i) = 1.0 / std::sqrt(std::abs(valP(i,i)));
       else
-        valP(i, i) = std::abs(valP(i, i));
-    }
-    else
-    {
-      throw itk::ExceptionObject(__FILE__, __LINE__, "Null Eigen value !!", ITK_LOCATION);
+        throw itk::ExceptionObject(__FILE__, __LINE__, "Null Eigen value !!", ITK_LOCATION);
     }
+    transf = valP * transf.transpose();
   }
-  transf = valP * transf.transpose();
+  else {
+      transf = transf.transpose();
+  }
+
   transf.flipud();
 
   if (m_NumberOfPrincipalComponentsRequired != this->GetInput()->GetNumberOfComponentsPerPixel())

Modules/Filtering/DimensionalityReduction/test/CMakeLists.txt

@@ -301,7 +301,8 @@ otb_add_test(NAME bfTvPCAImageFilter2 COMMAND otbDimensionalityReductionTestDriv
   ${TEMP}/bfTvPCAImageFilter2.tif
   ${TEMP}/bfTvPCAImageFilter2Inv.tif
   true
-  0)
+  0
+  true)
 
 otb_add_test(NAME bfTvPCAImageFilter4 COMMAND otbDimensionalityReductionTestDriver
   --compare-n-images ${EPSILON_7} 2
@@ -314,7 +315,8 @@ otb_add_test(NAME bfTvPCAImageFilter4 COMMAND otbDimensionalityReductionTestDriv
   ${TEMP}/bfTvPCAImageFilter4.tif
   ${TEMP}/bfTvPCAImageFilter4Inv.tif
   false
-  4)
+  4
+  true)
 
 otb_add_test(NAME bfTvPCAImageFilter4Norm COMMAND otbDimensionalityReductionTestDriver
   --compare-n-images ${EPSILON_7} 2
@@ -327,7 +329,8 @@ otb_add_test(NAME bfTvPCAImageFilter4Norm COMMAND otbDimensionalityReductionTest
   ${TEMP}/bfTvPCAImageFilter4Norm.tif
   ${TEMP}/bfTvPCAImageFilter4InvNorm.tif
   true
-  4)
+  4
+  true)
 
 otb_add_test(NAME bfTvPCAImageFilter3 COMMAND otbDimensionalityReductionTestDriver
   --compare-n-images ${EPSILON_7} 2
@@ -340,7 +343,22 @@ otb_add_test(NAME bfTvPCAImageFilter3 COMMAND otbDimensionalityReductionTestDriv
   ${TEMP}/bfTvPCAImageFilter3.tif
   ${TEMP}/bfTvPCAImageFilter3Inv.tif
   false
-  0)
+  0
+  true)
+
+otb_add_test(NAME bfTvPCAImageFilter5 COMMAND otbDimensionalityReductionTestDriver
+  --compare-n-images ${EPSILON_7} 2
+  ${BASELINE}/bfTvPCAImageFilter5.tif
+  ${TEMP}/bfTvPCAImageFilter5.tif
+  ${BASELINE}/bfTvPCAImageFilter5Inv.tif
+  ${TEMP}/bfTvPCAImageFilter5Inv.tif
+  otbPCAImageFilterTest
+  ${INPUTDATA}/cupriteSubHsi.tif
+  ${TEMP}/bfTvPCAImageFilter5.tif
+  ${TEMP}/bfTvPCAImageFilter5Inv.tif
+  false
+  0
+  false)
 
 otb_add_test(NAME bfTvPCAImageFilter1 COMMAND otbDimensionalityReductionTestDriver
   --compare-image ${EPSILON_7}
@@ -351,7 +369,8 @@ otb_add_test(NAME bfTvPCAImageFilter1 COMMAND otbDimensionalityReductionTestDriv
   ${TEMP}/bfTvPCAImageFilter1.tif
   ${TEMP}/bfTvPCAImageFilter1Inv.tif
   false
-  0)
+  0
+  true)
 
 
 otb_add_test(NAME bfTvPCAImageFilter3Norm COMMAND otbDimensionalityReductionTestDriver
@@ -365,7 +384,8 @@ otb_add_test(NAME bfTvPCAImageFilter3Norm COMMAND otbDimensionalityReductionTest
   ${TEMP}/bfTvPCAImageFilter3Norm.tif
   ${TEMP}/bfTvPCAImageFilter3InvNorm.tif
   true
-  0)
+  0
+  true)
 
 otb_add_test(NAME bfTvNAPCAImageFilter1 COMMAND otbDimensionalityReductionTestDriver
   --compare-image ${EPSILON_7}

Modules/Filtering/DimensionalityReduction/test/otbPCAImageFilter.cxx

@@ -33,6 +33,10 @@ int otbPCAImageFilterTest(int, char* argv[])
   bool normalization = false;
   if (std::string(argv[4]).compare("true") == 0)
     normalization = true;
+  
+  bool whitening = false;
+  if (std::string(argv[6]).compare("true") == 0)
+    whitening = true;
 
   // Main type definition
   const unsigned int Dimension = 2;
@@ -50,6 +54,7 @@ int otbPCAImageFilterTest(int, char* argv[])
   filter->SetInput(reader->GetOutput());
   filter->SetNumberOfPrincipalComponentsRequired(nbComponents);
   filter->SetUseNormalization(normalization);
+  filter->SetWhitening(whitening);
 
   typedef otb::CommandProgressUpdate<FilterType> CommandType;
   CommandType::Pointer                           observer = CommandType::New();