feat(formats): Add MGH support

Author: thewtex

CMakeLists.txt

@@ -16,6 +16,7 @@ set(BridgeJavaScript_IOModules
   "ITKIOHDF5"
   "ITKIOMINC"
   "ITKIOLSM"
+  "MGHIO"
   "ITKIOBioRad"
   "ITKIOGIPL"
   "ITKIOGE"
@@ -30,6 +31,7 @@ set(imageios_ITKIOPNG itkPNGImageIO)
 set(imageios_ITKIOLSM itkLSMImageIO)
 set(imageios_ITKIOMeta itkMetaImageIO)
 set(imageios_ITKIOMINC itkMINCImageIO)
+set(imageios_MGHIO itkMGHImageIO)
 set(imageios_ITKIONIFTI itkNiftiImageIO)
 set(imageios_ITKIONRRD itkNrrdImageIO)
 set(imageios_ITKIOGDCM itkGDCMImageIO)

README.md

@@ -20,6 +20,7 @@ Supported file formats
 - [LSM](http://www.openwetware.org/wiki/Dissecting_LSM_files)
 - [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
 - [MINC 2.0](https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference)
+- [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat)
 - [NifTi](https://nifti.nimh.nih.gov/nifti-1)
 - [NRRD](http://teem.sourceforge.net/nrrd/format.html)
 - [Portable Network Graphics (PNG)](https://en.wikipedia.org/wiki/Portable_Network_Graphics)

src/extensionToIO.js

@@ -25,6 +25,10 @@ extensionToIO['MNC.GZ'] = 'itkMINCImageIOJSBinding'
 extensionToIO['mnc2'] = 'itkMINCImageIOJSBinding'
 extensionToIO['MNC2'] = 'itkMINCImageIOJSBinding'
 
+extensionToIO['mgh'] = 'itkMGHImageIOJSBinding'
+extensionToIO['mgz'] = 'itkMGHImageIOJSBinding'
+extensionToIO['mgh.gz'] = 'itkMGHImageIOJSBinding'
+
 extensionToIO['mha'] = 'itkMetaImageIOJSBinding'
 extensionToIO['mhd'] = 'itkMetaImageIOJSBinding'
 

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

test/CMakeLists.txt

@@ -36,4 +36,5 @@ ExternalData_Expand_Arguments(
   DATA{Input/ITKImage.hdf5}
   DATA{Input/cthead1.lsm}
   DATA{Input/t1_z+_short_cor.mnc}
+  DATA{Input/T1.mgz}
   )

test/Docker/Dockerfile

@@ -24,7 +24,7 @@ RUN git clone https://github.com/InsightSoftwareConsortium/ITK.git && \
     -DITK_BUILD_DEFAULT_MODULES:BOOL=OFF \
     -DITKGroup_IO:BOOL=ON \
     -DModule_ITKIOMINC:BOOL=ON \
-    -DModule_ITKIOMGH:BOOL=ON \
+    -DModule_MGHIO:BOOL=ON \
     -DModule_ITKImageFunction:BOOL=ON \
     ../ITK && \
   ninja -j7 && \

test/GETest.js

@@ -94,4 +94,3 @@ test('Test reading a GEAdw file', t => {
     t.is(image.buffer[10], 80, 'buffer[10]')
   })
 })
-

test/Input/T1.mgz.md5

@@ -0,0 +1 @@
+0409fb9d011d00b8a0d8f18997634017

test/MGHTest.js

@@ -0,0 +1,36 @@
+import test from 'ava'
+import path from 'path'
+
+const IntTypes = require(path.resolve(__dirname, '..', 'dist', 'IntTypes.js'))
+const PixelTypes = require(path.resolve(__dirname, '..', 'dist', 'PixelTypes.js'))
+const readImageLocalFile = require(path.resolve(__dirname, '..', 'dist', 'readImageLocalFile.js'))
+
+test('Test reading a MGH file', t => {
+  const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'T1.mgz')
+  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], -127.16149944067001, 'origin[0]')
+    t.is(image.origin[1], 148.39564514160156, 'origin[1]')
+    t.is(image.origin[2], 139.0726842880249, '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), 0.0, 'direction (1, 1)')
+    t.is(image.direction.getElement(1, 2), -1.0, 'direction (1, 2)')
+    t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
+    t.is(image.direction.getElement(2, 1), -1.0, 'direction (2, 1)')
+    t.is(image.direction.getElement(2, 2), 0.0, 'direction (2, 2)')
+    t.is(image.size[0], 256, 'size[0]')
+    t.is(image.size[1], 256, 'size[1]')
+    t.is(image.size[2], 256, 'size[2]')
+    t.is(image.buffer.length, 16777216, 'buffer.length')
+    t.is(image.buffer[1000], 0, 'buffer[1000]')
+  })
+})

test/PNGTest.js

@@ -25,4 +25,3 @@ test('Test reading a PNG file', t => {
     t.is(image.buffer.length, 196608, 'buffer.length')
   })
 })
-