FIX: Image streaming

- Release openslide handle correctly
- Also tests partial updates
- OpenSlideReader extent orientation
- Also uses new UpdateExtent to set reqeuested extents

Domains/Microscopy/Testing/Cxx/CMakeLists.txt

+
+# OpenSlideReader Tests
+
 vtk_add_test_cxx(${vtk-module}CxxTests tests
   TestOpenSlideReader.cxx
   "DATA{${VTK_TEST_INPUT_DIR}/Microscopy/small2.ndpi}"
   )
 
+vtk_add_test_cxx(${vtk-module}CxxTests  tests
+  TestOpenSlideReaderPartial.cxx
+  "DATA{${VTK_TEST_INPUT_DIR}/Microscopy/small2.ndpi}"
+  )
+
 vtk_test_cxx_executable(${vtk-module}CxxTests tests RENDERING_FACTORY)

Domains/Microscopy/Testing/Cxx/TestOpenSlideReader.cxx

@@ -41,15 +41,14 @@ int TestOpenSlideReader(int argc, char** argv)
   reader->UpdateInformation();
   delete [] rasterFileName;
 
-  int extent[6] = {20,120,20,120,0,0};
-
-  reader->SetUpdateExtent(extent);
-  vtkNew<vtkPNGWriter> writer;
-  writer->SetInputConnection(reader->GetOutputPort());
-  writer->SetFileName("this.png");
-  writer->SetUpdateExtent(extent);
-  writer->Update();
-  writer->Write();
+  // For debug
+  // reader->SetUpdateExtent(extent);
+  // vtkNew<vtkPNGWriter> writer;
+  // writer->SetInputConnection(reader->GetOutputPort());
+  // writer->SetFileName("this.png");
+  // writer->SetUpdateExtent(extent);
+  // writer->Update();
+  // writer->Write();
 
   // Visualize
   vtkNew<vtkRenderer> renderer;

Domains/Microscopy/Testing/Cxx/TestOpenSlideReaderPartial.cxx

+/*=========================================================================
+
+  Program:   Visualization Toolkit
+  Module:    TestOpenSlideReader.cxx
+
+  Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
+  All rights reserved.
+  See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
+
+     This software is distributed WITHOUT ANY WARRANTY; without even
+     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+     PURPOSE.  See the above copyright notice for more information.
+
+=========================================================================*/
+#include <vtkNew.h>
+#include <vtkOpenSlideReader.h>
+#include <vtkRenderer.h>
+#include <vtkRenderWindow.h>
+#include <vtkRenderWindowInteractor.h>
+#include <vtkImageViewer2.h>
+#include <vtkImageData.h>
+#include <vtkPNGWriter.h>
+
+// VTK includes
+#include <vtkTestUtilities.h>
+
+// C++ includes
+#include <sstream>
+
+// Main program
+int TestOpenSlideReaderPartial(int argc, char** argv)
+{
+  const char* rasterFileName = vtkTestUtilities::ExpandDataFileName(argc, argv,
+                                 "Data/Microscopy/small2.ndpi");
+
+  //std::cout << "Got Filename: " << rasterFileName << std::endl;
+
+  // Create reader to read shape file.
+  vtkNew<vtkOpenSlideReader> reader;
+  reader->SetFileName(rasterFileName);
+  reader->UpdateInformation();
+  // reader->Print(cout);
+  delete [] rasterFileName;
+
+  int extent[6] = {200,499,200,499,0,0};
+
+  reader->UpdateExtent(extent);
+
+  vtkNew<vtkImageData> data;
+  data->ShallowCopy(reader->GetOutput());
+
+  // // For debug
+  // vtkNew<vtkPNGWriter> writer;
+  // writer->SetInputData(data.GetPointer());
+  // writer->SetFileName("this.png");
+  // writer->SetUpdateExtent(extent);
+  // writer->Update();
+  // writer->Write();
+
+  // Visualize
+  vtkNew<vtkRenderer> renderer;
+  vtkNew<vtkRenderWindow> window;
+  window->AddRenderer(renderer.GetPointer());
+
+  vtkNew<vtkRenderWindowInteractor> renderWindowInteractor;
+  renderWindowInteractor->SetRenderWindow(window.GetPointer());
+
+  vtkNew<vtkImageViewer2> imageViewer;
+  imageViewer->SetInputData(data.GetPointer());
+  //imageViewer->SetExtent(1000,1500,1000,1500,0,0);
+  imageViewer->SetupInteractor(renderWindowInteractor.GetPointer());
+  //imageViewer->SetSlice(0);
+  imageViewer->Render();
+  imageViewer->GetRenderer()->ResetCamera();
+  renderWindowInteractor->Initialize();
+  imageViewer->Render();
+  renderWindowInteractor->Start();
+
+  return EXIT_SUCCESS;
+}

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

+4b2972c7011281baa9a0fb3c883ffb7a

Domains/Microscopy/vtkOpenSlideReader.cxx

@@ -85,10 +85,8 @@ void vtkOpenSlideReader::ExecuteDataWithInformation(vtkDataObject *output,
   data->GetPointData()->GetScalars()->SetName("OpenSlideImage");
   //// Leverage openslide to read the region
 
-  // int inExtent[6];
-  // data->GetExtent(inExtent);
-  // cout << inExtent[0] << ", " << inExtent[1] << endl;
-  // cout << inExtent[2] << ", " << inExtent[3] << endl;
+  // VTK extents have origin at top left and y axis looking downwards
+  // openslide needs to convert
 
   int w = inExtent[1] - inExtent[0] + 1;
   int h = inExtent[3]- inExtent[2] + 1;
@@ -96,7 +94,7 @@ void vtkOpenSlideReader::ExecuteDataWithInformation(vtkDataObject *output,
 
   openslide_read_region(this->openslide_handle, (unsigned int *) buffer,
     inExtent[0],
-    inExtent[2],
+    this->DataExtent[3]-inExtent[3],
     0,  // level
     w,
     h
@@ -104,7 +102,8 @@ void vtkOpenSlideReader::ExecuteDataWithInformation(vtkDataObject *output,
 
   if(openslide_get_error(this->openslide_handle) != NULL)
     {
-    delete[] buffer;
+    // Buffer is deleted by the openslide in case the error occurs
+    // delete[] buffer;
     vtkErrorWithObjectMacro(this,
                             "File could not be read by openslide"
                            );
@@ -129,7 +128,7 @@ void vtkOpenSlideReader::ExecuteDataWithInformation(vtkDataObject *output,
     }
 
   delete[] buffer;
-  openslide_close(this->openslide_handle);
+  // openslide_close(this->openslide_handle);
 }
 
 
@@ -150,10 +149,23 @@ int vtkOpenSlideReader::CanReadFile(const char* fname)
   else
   {
     // Pretty sure
+    if(this->openslide_handle != NULL)
+      {
+      openslide_close(this->openslide_handle);
+      this->openslide_handle = NULL;
+      }
     return 2;
   }
 }
 
+vtkOpenSlideReader::~vtkOpenSlideReader()
+  {
+  // Release openslide_handle if being used
+  if(this->openslide_handle != NULL)
+    {
+    openslide_close(this->openslide_handle);
+    }
+  }
 
 //----------------------------------------------------------------------------
 void vtkOpenSlideReader::PrintSelf(ostream& os, vtkIndent indent)

Domains/Microscopy/vtkOpenSlideReader.h

@@ -60,7 +60,7 @@ public:
     }
 protected:
   vtkOpenSlideReader() {}
-  ~vtkOpenSlideReader() {}
+  ~vtkOpenSlideReader();
 
   virtual void ExecuteInformation();
   virtual void ExecuteDataWithInformation(vtkDataObject *out, vtkInformation *outInfo);