FIX: for openslide v3.4.0-1 in ubuntu

Domains/Microscopy/CMakeLists.txt

@@ -7,7 +7,9 @@ mark_as_advanced(OPENSLIDE_INCLUDE_DIR OPENSLIDE_LIBRARY)
 set(OPENSLIDE_SRCS vtkOpenSlideReader.cxx)
 
 include_directories(${OPENSLIDE_INCLUDE_DIRS})
-set_source_files_properties(vtkOPENSLIDE WRAP_EXCLUDE)
+
+set(${vtk-module}_SYSTEM_INCLUDE_DIRS
+    ${OPENSLIDE_INCLUDE_DIRS})
 
 vtk_module_library(vtkDomainsMicroscopy ${OPENSLIDE_SRCS})
 

Domains/Microscopy/Testing/Cxx/CMakeLists.txt

@@ -7,8 +7,8 @@ vtk_add_test_cxx(${vtk-module}CxxTests tests
   )
 
 vtk_add_test_cxx(${vtk-module}CxxTests  tests
-  TestOpenSlideReaderPartial.cxx
-  "DATA{${VTK_TEST_INPUT_DIR}/Microscopy/small2.ndpi}"
+    TestOpenSlideReaderPartialTIF,TestOpenSlideReaderPartial.cxx
+  "DATA{${VTK_TEST_INPUT_DIR}/Microscopy/pathology.tif}"
   )
 
 vtk_test_cxx_executable(${vtk-module}CxxTests tests RENDERING_FACTORY)

Domains/Microscopy/Testing/Cxx/TestOpenSlideReader.cxx

@@ -30,6 +30,9 @@
 // Main program
 int TestOpenSlideReader(int argc, char** argv)
 {
+  // This test is known to fail with openslide library libopenslide-dev shipped
+  // with ubuntu 14.04 as of March 31'2016. It does pass on fedora23, or if the
+  // openslide library is built from source
   const char* rasterFileName = vtkTestUtilities::ExpandDataFileName(argc, argv,
                                  "Data/Microscopy/small2.ndpi");
 

Domains/Microscopy/Testing/Cxx/TestOpenSlideReaderPartial.cxx

@@ -30,19 +30,20 @@
 // Main program
 int TestOpenSlideReaderPartial(int argc, char** argv)
 {
-  const char* rasterFileName = vtkTestUtilities::ExpandDataFileName(argc, argv,
-                                 "Data/Microscopy/small2.ndpi");
+  if ( argc <= 1 )
+    {
+    std::cout << "Usage: " << argv[0] << " <image file>" << endl;
+    return EXIT_FAILURE;
+    }
 
-  //std::cout << "Got Filename: " << rasterFileName << std::endl;
+  std::cout << "Got Filename: " << argv[1] << std::endl;
 
   // Create reader to read shape file.
   vtkNew<vtkOpenSlideReader> reader;
-  reader->SetFileName(rasterFileName);
+  reader->SetFileName(argv[1]);
   reader->UpdateInformation();
-  // reader->Print(cout);
-  delete [] rasterFileName;
 
-  int extent[6] = {200,499,200,499,0,0};
+  int extent[6] = {100,299,100,299,0,0};
 
   reader->UpdateExtent(extent);
 

Domains/Microscopy/Testing/Data/Baseline/TestOpenSlideReaderPartialTIF.png.md5

+2513faaa18fd17a568b47e0bf0c10531

Domains/Microscopy/vtkOpenSlideReader.cxx

@@ -67,18 +67,17 @@ void vtkOpenSlideReader::ExecuteDataWithInformation(vtkDataObject *output,
       outInfo,
       inExtent);
 
-  // cout << "OpenSlideReaderDataInf: " << inExtent[0] << ", " << inExtent[1] << ", " << inExtent[2] << ", " << inExtent[3] << endl;
-
   vtkImageData *data = this->AllocateOutputData(output, outInfo);
-  //data->GetExtent(this->OutputExtent);
-  //data->GetIncrements(this->OutputIncrements);
 
   if(this->openslide_handle == NULL)
     {
-    std::cout << "In the data info update, file is not updated" << std::endl;
+    vtkErrorWithObjectMacro(this,
+                            "File could not be read by openslide"
+                           );
+    return;
     }
 
-  //std::cout << "Extents: " << data->GetExtent() << std::endl;
+  //std::cout << "OpenSlideReader Extents: " << data->GetExtent() << std::endl;
 
   this->ComputeDataIncrements();
 

Testing/Data/Microscopy/pathology.tif.md5

+6a89389966723771bc54d12bbcba1a0b