feat(formats): add MetaImage support

CMakeLists.txt

@@ -3,12 +3,14 @@ project(BridgeJavaScript)
 
 set(BridgeJavaScript_IOModules
   "ITKIOGDCM"
+  "ITKIOMeta"
   "ITKIONRRD"
   "ITKIOPNG"
   "ITKIOVTK"
   CACHE STRING
   "String delimited list of ITK IO modules to support.")
 set(imageio_ITKIOPNG itkPNGImageIO)
+set(imageio_ITKIOMeta itkMetaImageIO)
 set(imageio_ITKIONRRD itkNrrdImageIO)
 set(imageio_ITKIOGDCM itkGDCMImageIO)
 set(imageio_ITKIOVTK itkVTKImageIO)

README.md

@@ -9,6 +9,7 @@ Provides general scientific image IO capability and bridges
 ## Supported file formats
 
 - [DICOM](http://dicom.nema.org/)
+- [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
 - [NRRD](http://teem.sourceforge.net/nrrd/format.html)
 - [Portable Network Graphics (PNG)](https://en.wikipedia.org/wiki/Portable_Network_Graphics)
 - [VTK legacy image file format](http://www.vtk.org/VTK/img/file-formats.pdf)

src/itkExtensionToIO.js

@@ -1,15 +1,20 @@
 let extensionToIO = {}
 
 extensionToIO['dcm'] = 'itkGDCMImageIOJSBinding'
+extensionToIO['DCM'] = 'itkGDCMImageIOJSBinding'
+
+extensionToIO['mha'] = 'itkMetaImageIOJSBinding'
+extensionToIO['mhd'] = 'itkMetaImageIOJSBinding'
 
 extensionToIO['nrrd'] = 'itkNrrdImageIOJSBinding'
 extensionToIO['NRRD'] = 'itkNrrdImageIOJSBinding'
-
 extensionToIO['nhdr'] = 'itkNrrdImageIOJSBinding'
 extensionToIO['NHDR'] = 'itkNrrdImageIOJSBinding'
+
 extensionToIO['png'] = 'itkPNGImageIOJSBinding'
 extensionToIO['PNG'] = 'itkPNGImageIOJSBinding'
 
 extensionToIO['vtk'] = 'itkVTKImageIOJSBinding'
+extensionToIO['VTK'] = 'itkVTKImageIOJSBinding'
 
 module.exports = extensionToIO

src/itkMetaImageIOJSBinding.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 "itkMetaImageIO.h"
+
+#include "itkImageIOBaseJSBinding.h"
+
+typedef itk::ImageIOBaseJSBinding< itk::MetaImageIO > MetaImageIOJSBindingType;
+
+EMSCRIPTEN_BINDINGS(itk_meta_image_io_js_binding) {
+  emscripten::register_vector<double>("AxisDirectionType");
+  emscripten::enum_<MetaImageIOJSBindingType::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_<MetaImageIOJSBindingType::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_<MetaImageIOJSBindingType>("ITKImageIO")
+  .constructor<>()
+  .function("SetNumberOfDimensions", &MetaImageIOJSBindingType::SetNumberOfDimensions)
+  .function("GetNumberOfDimensions", &MetaImageIOJSBindingType::GetNumberOfDimensions)
+  .function("SetFileName", &MetaImageIOJSBindingType::SetFileName)
+  .function("GetFileName", &MetaImageIOJSBindingType::GetFileName)
+  .function("CanReadFile", &MetaImageIOJSBindingType::CanReadFile)
+  .function("ReadImageInformation", &MetaImageIOJSBindingType::ReadImageInformation)
+  .function("SetDimensions", &MetaImageIOJSBindingType::SetDimensions)
+  .function("GetDimensions", &MetaImageIOJSBindingType::GetDimensions)
+  .function("SetOrigin", &MetaImageIOJSBindingType::SetOrigin)
+  .function("GetOrigin", &MetaImageIOJSBindingType::GetOrigin)
+  .function("SetSpacing", &MetaImageIOJSBindingType::SetSpacing)
+  .function("GetSpacing", &MetaImageIOJSBindingType::GetSpacing)
+  .function("SetDirection", &MetaImageIOJSBindingType::SetDirection)
+  .function("GetDirection", &MetaImageIOJSBindingType::GetDirection)
+  .function("GetDefaultDirection", &MetaImageIOJSBindingType::GetDefaultDirection)
+  .function("SetPixelType", &MetaImageIOJSBindingType::SetPixelType)
+  .function("GetPixelType", &MetaImageIOJSBindingType::GetPixelType)
+  .function("SetComponentType", &MetaImageIOJSBindingType::SetComponentType)
+  .function("GetComponentType", &MetaImageIOJSBindingType::GetComponentType)
+  .class_function("GetPixelTypeAsString", &MetaImageIOJSBindingType::GetPixelTypeAsString)
+  .class_function("GetComponentTypeAsString", &MetaImageIOJSBindingType::GetComponentTypeAsString)
+  .function("GetImageSizeInPixels", &MetaImageIOJSBindingType::GetImageSizeInPixels)
+  .function("GetImageSizeInBytes", &MetaImageIOJSBindingType::GetImageSizeInBytes)
+  .function("GetImageSizeInComponents", &MetaImageIOJSBindingType::GetImageSizeInComponents)
+  .function("SetNumberOfComponents", &MetaImageIOJSBindingType::SetNumberOfComponents)
+  .function("GetNumberOfComponents", &MetaImageIOJSBindingType::GetNumberOfComponents)
+  .function("Read", &MetaImageIOJSBindingType::Read)
+  ;
+}

test/CMakeLists.txt

@@ -20,6 +20,7 @@ itk_add_test(NAME itkPNGImageIOJSBindingTest
 ExternalData_Expand_Arguments(
   ITKData
   npm_test_inputs
+  DATA{Input/brainweb165a10f17.mha}
   DATA{Input/vol-raw-little.nrrd}
   DATA{Input/1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.100.0.dcm}
   DATA{Input/ironProt.vtk}

test/Input/brainweb165a10f17.mha.md5

@@ -0,0 +1 @@
+aa0a1e072e0c39fb8b26a769b5a54b68

test/formatsTest.js

@@ -118,3 +118,33 @@ test('Test reading a VTK legacy file', t => {
     t.is(image.buffer[1000], 0, 'buffer[1000]')
   })
 })
+
+test('Test reading a MetaImage file', t => {
+  const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'brainweb165a10f17.mha')
+  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], 0.0, 'origin[0]')
+    t.is(image.origin[1], 0.0, 'origin[1]')
+    t.is(image.origin[2], 0.0, 'origin[2]')
+    t.is(image.spacing[0], 1.0, 'spacing[0]')
+    t.is(image.spacing[1], 1.0, 'spacing[1]')
+    t.is(image.spacing[2], 1.0, 'spacing[2]')
+    t.is(image.direction.getElement(0, 0), 1.0, 'direction (0, 0)')
+    t.is(image.direction.getElement(0, 1), 0.0, 'direction (0, 1)')
+    t.is(image.direction.getElement(0, 2), 0.0, 'direction (0, 2)')
+    t.is(image.direction.getElement(1, 0), 0.0, 'direction (1, 0)')
+    t.is(image.direction.getElement(1, 1), 1.0, 'direction (1, 1)')
+    t.is(image.direction.getElement(1, 2), 0.0, '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], 181, 'size[0]')
+    t.is(image.size[1], 217, 'size[1]')
+    t.is(image.size[2], 180, 'size[2]')
+    t.is(image.buffer.length, 7069860, 'buffer.length')
+    t.is(image.buffer[1000], 0, 'buffer[1000]')
+  })
+})

test/itkExtensionToIOTest.js

@@ -8,6 +8,16 @@ test('png maps to itkPNGImageIOJSBinding', t => {
   t.is(io, 'itkPNGImageIOJSBinding')
 })
 
+test('mha maps to itkMetaImageIOJSBinding', t => {
+  let io = ExtensionToIO['mha']
+  t.is(io, 'itkMetaImageIOJSBinding')
+})
+
+test('mhd maps to itkMetaImageIOJSBinding', t => {
+  let io = ExtensionToIO['mhd']
+  t.is(io, 'itkMetaImageIOJSBinding')
+})
+
 test('nrrd maps to itkNrrdImageIOJSBinding', t => {
   let io = ExtensionToIO['nrrd']
   t.is(io, 'itkNrrdImageIOJSBinding')