WIP bmp reading

CGAL_ImageIO/include/CGAL/IO/read_vtk_image_data.h

@@ -69,26 +69,55 @@ read_vtk_image_data(vtkImageData* vtk_image, Image_3::Own owning = Image_3::OWN_
   image->ty = static_cast<float>(offset[1]);
   image->tz = static_cast<float>(offset[2]);
   image->endianness = ::_getEndianness();
+
   int vtk_type = vtk_image->GetScalarType();
   if(vtk_type == VTK_SIGNED_CHAR) vtk_type = VTK_CHAR;
-  if(vtk_type < 0 || vtk_type > VTK_DOUBLE)
-    vtk_type = VTK_DOUBLE;
-  const VTK_to_ImageIO_type_mapper& imageio_type =
-    VTK_to_ImageIO_type[vtk_type];
+  if(vtk_type < 0 || vtk_type > VTK_DOUBLE) vtk_type = VTK_DOUBLE;
+  const VTK_to_ImageIO_type_mapper& imageio_type = VTK_to_ImageIO_type[vtk_type];
   image->wdim = imageio_type.wdim;
   image->wordKind = imageio_type.wordKind;
   image->sign = imageio_type.sign;
+
+  const int cn = vtk_image->GetNumberOfScalarComponents();
+
   if (!vtk_image->GetPointData() || !vtk_image->GetPointData()->GetScalars()) {
     ::_freeImage(image);
     return Image_3();
   }
+
+  // If there is more than a scalar per point, vtk_image->data is not immediately
+  // interpretable in Image_3->data
+  CGAL_assertion(owning == Image_3::OWN_THE_DATA || cn == 1);
+
   CGAL_assertion(vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() == dims[0]*dims[1]*dims[2]);
+
   if(owning == Image_3::OWN_THE_DATA) {
-    image->data = ::ImageIO_alloc(dims[0]*dims[1]*dims[2]*image->wdim);
-     std::cerr << "GetNumberOfTuples()=" << vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples()
-               << "\nimage->size()=" << dims[0]*dims[1]*dims[2]
-               << "\nwdim=" << image->wdim << '\n';
-    vtk_image->GetPointData()->GetScalars()->ExportToVoidPointer(image->data);
+    int dims_n = dims[0]*dims[1]*dims[2];
+    image->data = ::ImageIO_alloc(dims_n * image->wdim);
+    std::cerr << "GetNumberOfTuples() = " << vtk_image->GetPointData()->GetScalars()->GetNumberOfTuples() << "\n"
+              << "components = " << cn << "\n"
+              << "wdim = " << image->wdim << "\n"
+              << "image->size() = " << dims_n << std::endl;
+
+    if(cn == 1) {
+      vtk_image->GetPointData()->GetScalars()->ExportToVoidPointer(image->data);
+    } else {
+      std::cerr << "Warning: input has " << cn << " components; only the value of the first component will be used." << std::endl;
+
+      // cast the data void pointers to make it possible to do pointer arithmetic
+      char* src = static_cast<char*>(vtk_image->GetPointData()->GetScalars()->GetVoidPointer(0));
+      char* dest = static_cast<char*>(image->data);
+
+      for(int i=0; i<dims_n; ++i)
+      {
+        // multiply by image->wdim because we casted to char* and not the actual data type
+        memcpy(dest + image->wdim*i, src + cn*image->wdim*i, image->wdim * sizeof(char));
+
+        // Check that we are not discarding useful data
+        CGAL_assertion(*(src + cn*image->wdim*i) == *(src + cn*image->wdim*i + 1));
+        CGAL_assertion(*(src + cn*image->wdim*i) == *(src + cn*image->wdim*i + 2));
+      }
+    }
   } else {
     image->data = vtk_image->GetPointData()->GetScalars()->GetVoidPointer(0);
   }

CGAL_ImageIO/include/CGAL/Image_3.h

@@ -87,7 +87,7 @@ public:
 protected:
   Image_shared_ptr image_ptr;
 
-   // implementation in src/CGAL_ImageIO/Image_3.cpp
+   // implementation in Image_3_impl.h
   bool private_read(_image* im, Own own_the_data = OWN_THE_DATA);
 
 public:

Mesh_3/doc/Mesh_3/CGAL/Image_3.h

@@ -14,7 +14,7 @@ public:
   /// The default-constructor. The object is invalid until a call to `read()`.
   Image_3();
 
-  /// Open an 3D image file.
+  /// Open a 3D image file.
   ///
   /// Returns `true` if the file was sucessfully loaded.
   bool read(const char* file);

Polyhedron/demo/Polyhedron/Plugins/Mesh_3/Io_image_plugin.cpp

@@ -1321,14 +1321,23 @@ Image* Io_image_plugin::createDCMImage(QString dirname)
   bool is_dcm = false;
   bool is_bmp = false;
 
+  std::vector<boost::filesystem::path> paths;
   vtkStringArray* files = vtkStringArray::New();
   boost::filesystem::path p(dirname.toUtf8().data());
   for(boost::filesystem::directory_entry& x : boost::filesystem::directory_iterator(p)){
     std::string s(x.path().extension().string());
-    if(s == std::string(".dcm") || (s == std::string(".DCM"))){ is_dcm = true;}
-    if(s == std::string(".bmp") || (s == std::string(".BMP"))){ is_bmp = true;}
-    std::cout << x.path().string() << std::endl;
-    files->InsertNextValue(x.path().string());
+    if(s == std::string(".dcm") || (s == std::string(".DCM"))){ is_dcm = true; CGAL_assertion(!is_bmp); }
+    if(s == std::string(".bmp") || (s == std::string(".BMP"))){ is_bmp = true; CGAL_assertion(!is_dcm); }
+    paths.push_back(x.path());
+  }
+
+  // directory_iterator does not guarantee a sorted order
+  std::sort(std::begin(paths), std::end(paths));
+
+  for(const boost::filesystem::path& p : paths)
+  {
+    std::cout << p.string() << std::endl;
+    files->InsertNextValue(p.string());
   }
 
   if(is_dcm){
@@ -1369,17 +1378,14 @@ Image* Io_image_plugin::createDCMImage(QString dirname)
     smoother->Update();
     auto vtk_image = smoother->GetOutput();
     vtk_image->Print(std::cerr);
-    image = new Image;
 
-    std::cout << "A" << std::endl;
+    image = new Image;
     *image = CGAL::IO::read_vtk_image_data(vtk_image); // copy the
                                                        // image data
-
-    std::cout << "B" << std::endl;
   }
 
 #else
-  CGAL::Three::Three::warning("You need VTK to read a DCM file");
+  CGAL::Three::Three::warning("You need VTK to read DCM/BMP files");
   CGAL_USE(dirname);
 #endif
   return image;