feat(formats): Add ITK HDF5 format support

Author: thewtex

CMakeLists.txt

@@ -13,13 +13,15 @@ set(BridgeJavaScript_IOModules
   "ITKIONRRD"
   "ITKIOVTK"
   "ITKIOBMP"
+  "ITKIOHDF5"
   "ITKIOBioRad"
   "ITKIOGIPL"
   "ITKIOGE"
   CACHE STRING
   "String delimited list of ITK IO modules to support.")
 set(imageios_ITKIOBioRad itkBioRadImageIO)
 set(imageios_ITKIOBMP itkBMPImageIO)
+set(imageios_ITKIOHDF5 itkHDF5ImageIO)
 set(imageios_ITKIOGE itkGEAdwImageIO itkGE4ImageIO itkGE5ImageIO)
 set(imageios_ITKIOGIPL itkGiplImageIO)
 set(imageios_ITKIOPNG itkPNGImageIO)

README.md

@@ -13,6 +13,7 @@ Supported file formats
 - [BioRad](http://www.bio-rad.com/)
 - [BMP](https://en.wikipedia.org/wiki/BMP_file_format)
 - [DICOM](http://dicom.nema.org/)
+- [ITK HDF5](https://support.hdfgroup.org/HDF5/)
 - [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format)
 - [GE4,GE5,GEAdw](http://www3.gehealthcare.com)
 - [Gipl (Guys Image Processing Lab)](https://www.ncbi.nlm.nih.gov/pubmed/12956259)

src/extensionToIO.js

@@ -9,6 +9,8 @@ extensionToIO['DCM'] = 'itkGDCMImageIOJSBinding'
 extensionToIO['gipl'] = 'itkGiplImageIOJSBinding'
 extensionToIO['gipl.gz'] = 'itkGiplImageIOJSBinding'
 
+extensionToIO['hdf5'] = 'itkHDF5ImageIOJSBinding'
+
 extensionToIO['jpg'] = 'itkJPEGImageIOJSBinding'
 extensionToIO['JPG'] = 'itkJPEGImageIOJSBinding'
 extensionToIO['jpeg'] = 'itkJPEGImageIOJSBinding'

src/itkHDF5ImageIOJSBinding.cxx

@@ -0,0 +1,91 @@
+/*=========================================================================
+ *
+ *  Copyright Insight Software Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+
+#include <emscripten.h>
+#include <emscripten/bind.h>
+
+#include "itkHDF5ImageIO.h"
+
+#include "itkImageIOBaseJSBinding.h"
+
+typedef itk::ImageIOBaseJSBinding< itk::HDF5ImageIO > HDF5ImageIOJSBindingType;
+
+EMSCRIPTEN_BINDINGS(itk_biorad_image_io_js_binding) {
+  emscripten::register_vector<double>("AxisDirectionType");
+  emscripten::enum_<HDF5ImageIOJSBindingType::IOPixelType>("IOPixelType")
+    .value("UNKNOWNPIXELTYPE", itk::ImageIOBase::UNKNOWNPIXELTYPE)
+    .value("SCALAR", itk::ImageIOBase::SCALAR)
+    .value("RGB", itk::ImageIOBase::RGB)
+    .value("RGBA", itk::ImageIOBase::RGBA)
+    .value("OFFSET", itk::ImageIOBase::OFFSET)
+    .value("VECTOR", itk::ImageIOBase::VECTOR)
+    .value("POINT", itk::ImageIOBase::POINT)
+    .value("COVARIANTVECTOR", itk::ImageIOBase::COVARIANTVECTOR)
+    .value("SYMMETRICSECONDRANKTENSOR", itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR)
+    .value("POINT", itk::ImageIOBase::POINT)
+    .value("COVARIANTVECTOR", itk::ImageIOBase::COVARIANTVECTOR)
+    .value("SYMMETRICSECONDRANKTENSOR", itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR)
+    .value("DIFFUSIONTENSOR3D", itk::ImageIOBase::DIFFUSIONTENSOR3D)
+    .value("COMPLEX", itk::ImageIOBase::COMPLEX)
+    .value("FIXEDARRAY", itk::ImageIOBase::FIXEDARRAY)
+    .value("MATRIX", itk::ImageIOBase::MATRIX)
+    ;
+  emscripten::enum_<HDF5ImageIOJSBindingType::IOComponentType>("IOComponentType")
+    .value("UNKNOWNCOMPONENTTYPE", itk::ImageIOBase::UNKNOWNCOMPONENTTYPE)
+    .value("UCHAR", itk::ImageIOBase::UCHAR)
+    .value("CHAR", itk::ImageIOBase::CHAR)
+    .value("USHORT", itk::ImageIOBase::USHORT)
+    .value("SHORT", itk::ImageIOBase::SHORT)
+    .value("UINT", itk::ImageIOBase::UINT)
+    .value("INT", itk::ImageIOBase::INT)
+    .value("ULONG", itk::ImageIOBase::ULONG)
+    .value("LONG", itk::ImageIOBase::LONG)
+    .value("FLOAT", itk::ImageIOBase::FLOAT)
+    .value("DOUBLE", itk::ImageIOBase::DOUBLE)
+    ;
+  emscripten::class_<HDF5ImageIOJSBindingType>("ITKImageIO")
+  .constructor<>()
+  .function("SetNumberOfDimensions", &HDF5ImageIOJSBindingType::SetNumberOfDimensions)
+  .function("GetNumberOfDimensions", &HDF5ImageIOJSBindingType::GetNumberOfDimensions)
+  .function("SetFileName", &HDF5ImageIOJSBindingType::SetFileName)
+  .function("GetFileName", &HDF5ImageIOJSBindingType::GetFileName)
+  .function("CanReadFile", &HDF5ImageIOJSBindingType::CanReadFile)
+  .function("ReadImageInformation", &HDF5ImageIOJSBindingType::ReadImageInformation)
+  .function("SetDimensions", &HDF5ImageIOJSBindingType::SetDimensions)
+  .function("GetDimensions", &HDF5ImageIOJSBindingType::GetDimensions)
+  .function("SetOrigin", &HDF5ImageIOJSBindingType::SetOrigin)
+  .function("GetOrigin", &HDF5ImageIOJSBindingType::GetOrigin)
+  .function("SetSpacing", &HDF5ImageIOJSBindingType::SetSpacing)
+  .function("GetSpacing", &HDF5ImageIOJSBindingType::GetSpacing)
+  .function("SetDirection", &HDF5ImageIOJSBindingType::SetDirection)
+  .function("GetDirection", &HDF5ImageIOJSBindingType::GetDirection)
+  .function("GetDefaultDirection", &HDF5ImageIOJSBindingType::GetDefaultDirection)
+  .function("SetPixelType", &HDF5ImageIOJSBindingType::SetPixelType)
+  .function("GetPixelType", &HDF5ImageIOJSBindingType::GetPixelType)
+  .function("SetComponentType", &HDF5ImageIOJSBindingType::SetComponentType)
+  .function("GetComponentType", &HDF5ImageIOJSBindingType::GetComponentType)
+  .class_function("GetPixelTypeAsString", &HDF5ImageIOJSBindingType::GetPixelTypeAsString)
+  .class_function("GetComponentTypeAsString", &HDF5ImageIOJSBindingType::GetComponentTypeAsString)
+  .function("GetImageSizeInPixels", &HDF5ImageIOJSBindingType::GetImageSizeInPixels)
+  .function("GetImageSizeInBytes", &HDF5ImageIOJSBindingType::GetImageSizeInBytes)
+  .function("GetImageSizeInComponents", &HDF5ImageIOJSBindingType::GetImageSizeInComponents)
+  .function("SetNumberOfComponents", &HDF5ImageIOJSBindingType::SetNumberOfComponents)
+  .function("GetNumberOfComponents", &HDF5ImageIOJSBindingType::GetNumberOfComponents)
+  .function("Read", &HDF5ImageIOJSBindingType::Read)
+  ;
+}

test/CMakeLists.txt

@@ -33,4 +33,5 @@ ExternalData_Expand_Arguments(
   DATA{Input/113766.003.001}
   DATA{Input/I.001}
   DATA{Input/ramp.gipl}
+  DATA{Input/ITKImage.hdf5}
   )

test/Input/ITKImage.hdf5.sha512

@@ -0,0 +1 @@
+51b046bc538849eaffd0707dc88a1d24456fc266cf3a2aca495740b37339f9ac4e82ad4a4fa3979b0edfbe1f4a64447859731087a053c9a3ab962624834d6e06

test/extensionToIOTest.js

@@ -53,6 +53,11 @@ test('hdr maps to itkNiftiImageIOJSBinding', t => {
   t.is(io, 'itkNiftiImageIOJSBinding')
 })
 
+test('hdf5 maps to itkHDF5ImageIOJSBinding', t => {
+  let io = ExtensionToIO['hdf5']
+  t.is(io, 'itkHDF5ImageIOJSBinding')
+})
+
 test('nrrd maps to itkNrrdImageIOJSBinding', t => {
   let io = ExtensionToIO['nrrd']
   t.is(io, 'itkNrrdImageIOJSBinding')

test/formatsTest.js

@@ -375,3 +375,33 @@ test('Test reading a GEAdw file', t => {
     t.is(image.buffer[10], 80, 'buffer[10]')
   })
 })
+
+test('Test reading an ITK HDF5 file', t => {
+  const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'ITKImage.hdf5')
+  return readImageLocalFile(testFilePath).then(function (image) {
+    t.is(image.imageType.dimension, 3, 'dimension')
+    t.is(image.imageType.componentType, IntTypes.UInt8, 'componentType')
+    t.is(image.imageType.pixelType, PixelTypes.Scalar, 'pixelType')
+    t.is(image.imageType.components, 1, 'components')
+    t.is(image.origin[0], 0, 'origin[0]')
+    t.is(image.origin[1], 5, 'origin[1]')
+    t.is(image.origin[2], 10, 'origin[2]')
+    t.is(image.spacing[0], 1, 'spacing[0]')
+    t.is(image.spacing[1], 2, 'spacing[1]')
+    t.is(image.spacing[2], 3, 'spacing[2]')
+    t.is(image.direction.getElement(0, 0), 0.866025403784439, 'direction (0, 0)')
+    t.is(image.direction.getElement(0, 1), -0.5, 'direction (0, 1)')
+    t.is(image.direction.getElement(0, 2), 0.0, 'direction (0, 2)')
+    t.is(image.direction.getElement(1, 0), 0.5, 'direction (1, 0)')
+    t.is(image.direction.getElement(1, 1), 0.866025403784439, 'direction (1, 1)')
+    t.is(image.direction.getElement(1, 2), 0, 'direction (1, 2)')
+    t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
+    t.is(image.direction.getElement(2, 1), 0.0, 'direction (2, 1)')
+    t.is(image.direction.getElement(2, 2), 1.0, 'direction (2, 2)')
+    t.is(image.size[0], 5, 'size[0]')
+    t.is(image.size[1], 5, 'size[1]')
+    t.is(image.size[2], 5, 'size[2]')
+    t.is(image.buffer.length, 125, 'buffer.length')
+    t.is(image.buffer[10], 90, 'buffer[10]')
+  })
+})