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thewtexthewtex
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feat(formats): add initial DICOM format support
Reads a single DICOM file. Eventually we will also move to a DCMTK backend (see #10) and support multi-file series.
1 parent ddaf302 commit dc4efb4

8 files changed

Lines changed: 181 additions & 34 deletions

‎CMakeLists.txt‎

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@@ -2,12 +2,14 @@ cmake_minimum_required(VERSION 2.8.9)
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project(BridgeJavaScript)
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set(BridgeJavaScript_IOModules
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"ITKIOPNG"
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"ITKIOGDCM"
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"ITKIONRRD"
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"ITKIOPNG"
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CACHE STRING
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"String delimited list of ITK IO modules to support.")
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set(imageio_ITKIOPNG itkPNGImageIO)
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set(imageio_ITKIONRRD itkNrrdImageIO)
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set(imageio_ITKIOGDCM itkGDCMImageIO)
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if(NOT ITK_SOURCE_DIR)

‎README.md‎

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@@ -2,8 +2,13 @@
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[![CircleCI](https://circleci.com/gh/InsightSoftwareConsortium/ITKBridgeJavaScript.svg?style=svg)](https://circleci.com/gh/InsightSoftwareConsortium/ITKBridgeJavaScript)
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5+
Provides general scientific image IO capability and bridges
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[ITK](https://itk.org) code running in the
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[Emscripten](http://emscripten.org/) runtime environment.
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## Supported file formats
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- [DICOM](http://dicom.nema.org/)
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- [NRRD](http://teem.sourceforge.net/nrrd/format.html)
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- [Portable Network Graphics (PNG)](https://en.wikipedia.org/wiki/Portable_Network_Graphics)
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@@ -30,8 +35,8 @@ npm test
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### Contributing
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We use semantic-release for handling change log and version.
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Therefore we recommend using the following command line when
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We use semantic-release for handling change log and version.
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Therefore we recommend using the following command line when
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creating a commit:
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```sh

‎src/itkExtensionToIO.js‎

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@@ -1,10 +1,13 @@
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let extensionToIO = {}
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3-
extensionToIO['png'] = 'itkPNGImageIOJSBinding'
4-
extensionToIO['PNG'] = 'itkPNGImageIOJSBinding'
3+
extensionToIO['dcm'] = 'itkGDCMImageIOJSBinding'
4+
55
extensionToIO['nrrd'] = 'itkNrrdImageIOJSBinding'
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extensionToIO['NRRD'] = 'itkNrrdImageIOJSBinding'
7+
78
extensionToIO['nhdr'] = 'itkNrrdImageIOJSBinding'
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extensionToIO['NHDR'] = 'itkNrrdImageIOJSBinding'
10+
extensionToIO['png'] = 'itkPNGImageIOJSBinding'
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extensionToIO['PNG'] = 'itkPNGImageIOJSBinding'
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module.exports = extensionToIO

‎src/itkGDCMImageIOJSBinding.cxx‎

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@@ -0,0 +1,91 @@
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/*=========================================================================
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*
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* Copyright Insight Software Consortium
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#include <emscripten.h>
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#include <emscripten/bind.h>
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22+
#include "itkGDCMImageIO.h"
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24+
#include "itkImageIOBaseJSBinding.h"
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typedef itk::ImageIOBaseJSBinding< itk::GDCMImageIO > GDCMImageIOJSBindingType;
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EMSCRIPTEN_BINDINGS(itk_gdcm_image_io_js_binding) {
29+
emscripten::register_vector<double>("AxisDirectionType");
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emscripten::enum_<GDCMImageIOJSBindingType::IOPixelType>("IOPixelType")
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.value("UNKNOWNPIXELTYPE", itk::ImageIOBase::UNKNOWNPIXELTYPE)
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.value("SCALAR", itk::ImageIOBase::SCALAR)
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.value("RGB", itk::ImageIOBase::RGB)
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.value("RGBA", itk::ImageIOBase::RGBA)
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.value("OFFSET", itk::ImageIOBase::OFFSET)
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.value("VECTOR", itk::ImageIOBase::VECTOR)
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.value("POINT", itk::ImageIOBase::POINT)
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.value("COVARIANTVECTOR", itk::ImageIOBase::COVARIANTVECTOR)
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.value("SYMMETRICSECONDRANKTENSOR", itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR)
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.value("POINT", itk::ImageIOBase::POINT)
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.value("COVARIANTVECTOR", itk::ImageIOBase::COVARIANTVECTOR)
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.value("SYMMETRICSECONDRANKTENSOR", itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR)
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.value("DIFFUSIONTENSOR3D", itk::ImageIOBase::DIFFUSIONTENSOR3D)
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.value("COMPLEX", itk::ImageIOBase::COMPLEX)
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.value("FIXEDARRAY", itk::ImageIOBase::FIXEDARRAY)
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.value("MATRIX", itk::ImageIOBase::MATRIX)
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;
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emscripten::enum_<GDCMImageIOJSBindingType::IOComponentType>("IOComponentType")
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.value("UNKNOWNCOMPONENTTYPE", itk::ImageIOBase::UNKNOWNCOMPONENTTYPE)
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.value("UCHAR", itk::ImageIOBase::UCHAR)
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.value("CHAR", itk::ImageIOBase::CHAR)
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.value("USHORT", itk::ImageIOBase::USHORT)
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.value("SHORT", itk::ImageIOBase::SHORT)
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.value("UINT", itk::ImageIOBase::UINT)
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.value("INT", itk::ImageIOBase::INT)
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.value("ULONG", itk::ImageIOBase::ULONG)
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.value("LONG", itk::ImageIOBase::LONG)
58+
.value("FLOAT", itk::ImageIOBase::FLOAT)
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.value("DOUBLE", itk::ImageIOBase::DOUBLE)
60+
;
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emscripten::class_<GDCMImageIOJSBindingType>("ITKImageIO")
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.constructor<>()
63+
.function("SetNumberOfDimensions", &GDCMImageIOJSBindingType::SetNumberOfDimensions)
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.function("GetNumberOfDimensions", &GDCMImageIOJSBindingType::GetNumberOfDimensions)
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.function("SetFileName", &GDCMImageIOJSBindingType::SetFileName)
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.function("GetFileName", &GDCMImageIOJSBindingType::GetFileName)
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.function("CanReadFile", &GDCMImageIOJSBindingType::CanReadFile)
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.function("ReadImageInformation", &GDCMImageIOJSBindingType::ReadImageInformation)
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.function("SetDimensions", &GDCMImageIOJSBindingType::SetDimensions)
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.function("GetDimensions", &GDCMImageIOJSBindingType::GetDimensions)
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.function("SetOrigin", &GDCMImageIOJSBindingType::SetOrigin)
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.function("GetOrigin", &GDCMImageIOJSBindingType::GetOrigin)
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.function("SetSpacing", &GDCMImageIOJSBindingType::SetSpacing)
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.function("GetSpacing", &GDCMImageIOJSBindingType::GetSpacing)
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.function("SetDirection", &GDCMImageIOJSBindingType::SetDirection)
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.function("GetDirection", &GDCMImageIOJSBindingType::GetDirection)
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.function("GetDefaultDirection", &GDCMImageIOJSBindingType::GetDefaultDirection)
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.function("SetPixelType", &GDCMImageIOJSBindingType::SetPixelType)
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.function("GetPixelType", &GDCMImageIOJSBindingType::GetPixelType)
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.function("SetComponentType", &GDCMImageIOJSBindingType::SetComponentType)
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.function("GetComponentType", &GDCMImageIOJSBindingType::GetComponentType)
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.class_function("GetPixelTypeAsString", &GDCMImageIOJSBindingType::GetPixelTypeAsString)
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.class_function("GetComponentTypeAsString", &GDCMImageIOJSBindingType::GetComponentTypeAsString)
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.function("GetImageSizeInPixels", &GDCMImageIOJSBindingType::GetImageSizeInPixels)
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.function("GetImageSizeInBytes", &GDCMImageIOJSBindingType::GetImageSizeInBytes)
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.function("GetImageSizeInComponents", &GDCMImageIOJSBindingType::GetImageSizeInComponents)
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.function("SetNumberOfComponents", &GDCMImageIOJSBindingType::SetNumberOfComponents)
88+
.function("GetNumberOfComponents", &GDCMImageIOJSBindingType::GetNumberOfComponents)
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.function("Read", &GDCMImageIOJSBindingType::Read)
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;
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}

‎src/itkMimeToIO.js‎

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@@ -1,5 +1,6 @@
11
let mimeToIO = {}
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mimeToIO['image/png'] = 'itkPNGImageIOJSBinding'
4+
mimeToIO['application/dicom'] = 'itkGDCMImageIOJSBinding'
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module.exports = mimeToIO

‎test/formatsTest.js‎

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@@ -11,45 +11,80 @@ itkConfig.imageIOsPath = path.resolve(__dirname, '..', 'dist', 'itkImageIOs')
1111
test('Test reading a PNG file', t => {
1212
const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'cthead1.png')
1313
return readImageLocalFile(testFilePath).then(function (image) {
14-
t.is(image.imageType.dimension, 2)
15-
t.is(image.imageType.componentType, IntTypes.UInt8)
16-
t.is(image.imageType.pixelType, PixelTypes.RGB)
17-
t.is(image.imageType.components, 3)
18-
t.is(image.origin[0], 0.0)
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t.is(image.origin[1], 0.0)
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t.is(image.spacing[0], 1.0)
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t.is(image.spacing[1], 1.0)
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t.is(image.direction.getElement(0, 0), 1.0)
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t.is(image.direction.getElement(0, 1), 0.0)
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t.is(image.direction.getElement(1, 0), 0.0)
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t.is(image.direction.getElement(1, 1), 1.0)
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t.is(image.size[0], 256)
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t.is(image.size[1], 256)
28-
t.is(image.buffer.length, 196608)
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t.is(image.imageType.dimension, 2, 'dimension')
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t.is(image.imageType.componentType, IntTypes.UInt8, 'componentType')
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t.is(image.imageType.pixelType, PixelTypes.RGB, 'pixelType')
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t.is(image.imageType.components, 3, 'components')
18+
t.is(image.origin[0], 0.0, 'origin[0]')
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t.is(image.origin[1], 0.0, 'origin[1]')
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t.is(image.spacing[0], 1.0, 'spacing[0]')
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t.is(image.spacing[1], 1.0, 'spacing[1]')
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t.is(image.direction.getElement(0, 0), 1.0, 'direction (0, 0)')
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t.is(image.direction.getElement(0, 1), 0.0, 'direction (0, 1)')
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t.is(image.direction.getElement(1, 0), 0.0, 'direction (1, 0)')
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t.is(image.direction.getElement(1, 1), 1.0, 'direction (1, 1)')
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t.is(image.size[0], 256, 'size[0]')
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t.is(image.size[1], 256, 'size[1]')
28+
t.is(image.buffer.length, 196608, 'buffer.length')
2929
})
3030
})
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3232
test('Test reading a NRRD file', t => {
3333
const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'vol-raw-little.nrrd')
3434
return readImageLocalFile(testFilePath).then(function (image) {
35-
t.is(image.imageType.dimension, 3)
36-
t.is(image.imageType.componentType, FloatTypes.Float64)
35+
t.is(image.imageType.dimension, 3, 'dimension')
36+
t.is(image.imageType.componentType, FloatTypes.Float64, 'componentType')
37+
t.is(image.imageType.pixelType, PixelTypes.Scalar, 'pixelType')
38+
t.is(image.imageType.components, 1, 'components')
39+
t.is(image.origin[0], 0.0, 'origin[0]')
40+
t.is(image.origin[1], 0.0, 'origin[1]')
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t.is(image.origin[2], 0.0, 'origin[2]')
42+
t.is(image.spacing[0], 1.0, 'spacing[0]')
43+
t.is(image.spacing[1], 1.0, 'spacing[1]')
44+
t.is(image.spacing[2], 1.0, 'spacing[2]')
45+
t.is(image.direction.getElement(0, 0), 1.0, 'direction (0, 0)')
46+
t.is(image.direction.getElement(0, 1), 0.0, 'direction (0, 1)')
47+
t.is(image.direction.getElement(0, 2), 0.0, 'direction (0, 2)')
48+
t.is(image.direction.getElement(1, 0), 0.0, 'direction (1, 0)')
49+
t.is(image.direction.getElement(1, 1), 1.0, 'direction (1, 1)')
50+
t.is(image.direction.getElement(1, 2), 0.0, 'direction (1, 2)')
51+
t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
52+
t.is(image.direction.getElement(2, 1), 0.0, 'direction (2, 1)')
53+
t.is(image.direction.getElement(2, 2), 1.0, 'direction (2, 2)')
54+
t.is(image.size[0], 5, 'size[0]')
55+
t.is(image.size[1], 6, 'size[1]')
56+
t.is(image.size[2], 7, 'size[2]')
57+
t.is(image.buffer.length, 210, 'buffer.length')
58+
t.is(image.buffer[2], 5.0, 'buffer[2]')
59+
})
60+
})
61+
62+
test('Test reading a DICOM file', t => {
63+
const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', '1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.100.0.dcm')
64+
return readImageLocalFile(testFilePath).then(function (image) {
65+
t.is(image.imageType.dimension, 3, 'dimension')
66+
t.is(image.imageType.componentType, IntTypes.Int16)
3767
t.is(image.imageType.pixelType, PixelTypes.Scalar)
3868
t.is(image.imageType.components, 1)
39-
t.is(image.origin[0], 0.0)
40-
t.is(image.origin[1], 0.0)
41-
t.is(image.origin[2], 0.0)
69+
t.is(image.origin[0], -32.9551)
70+
t.is(image.origin[1], -133.9286)
71+
t.is(image.origin[2], 116.7857)
4272
t.is(image.spacing[0], 1.0)
4373
t.is(image.spacing[1], 1.0)
4474
t.is(image.spacing[2], 1.0)
45-
t.is(image.direction.getElement(0, 0), 1.0)
46-
t.is(image.direction.getElement(0, 1), 0.0)
47-
t.is(image.direction.getElement(1, 0), 0.0)
48-
t.is(image.direction.getElement(1, 1), 1.0)
49-
t.is(image.size[0], 5)
50-
t.is(image.size[1], 6)
51-
t.is(image.size[2], 7)
52-
t.is(image.buffer.length, 210)
53-
t.is(image.buffer[2], 5.0)
75+
t.is(image.direction.getElement(0, 0), 0.0, 'direction (0, 0)')
76+
t.is(image.direction.getElement(0, 1), 0.0, 'direction (0, 1)')
77+
t.is(image.direction.getElement(0, 2), -1.0, 'direction (0, 2)')
78+
t.is(image.direction.getElement(1, 0), 1.0, 'direction (1, 0)')
79+
t.is(image.direction.getElement(1, 1), 0.0, 'direction (1, 1)')
80+
t.is(image.direction.getElement(1, 2), 0.0, 'direction (1, 2)')
81+
t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
82+
t.is(image.direction.getElement(2, 1), -1.0, 'direction (2, 1)')
83+
t.is(image.direction.getElement(2, 2), 0.0, 'direction (2, 2)')
84+
t.is(image.size[0], 256, 'size[0]')
85+
t.is(image.size[1], 256, 'size[1]')
86+
t.is(image.size[2], 1, 'size[2]')
87+
t.is(image.buffer.length, 65536, 'buffer.length')
88+
t.is(image.buffer[1000], 3, 'buffer[1000]')
5489
})
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})

‎test/itkExtensionToIOTest.js‎

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@@ -17,3 +17,8 @@ test('nhdr maps to itkNrrdImageIOJSBinding', t => {
1717
let io = ExtensionToIO['nhdr']
1818
t.is(io, 'itkNrrdImageIOJSBinding')
1919
})
20+
21+
test('dcm maps to itkGDCMImageIOJSBinding', t => {
22+
let io = ExtensionToIO['dcm']
23+
t.is(io, 'itkGDCMImageIOJSBinding')
24+
})

‎test/itkMimeToIOTest.js‎

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@@ -7,3 +7,8 @@ test('image/png maps to itkPNGImageIOJSBinding', t => {
77
let io = MimeToIO['image/png']
88
t.is(io, 'itkPNGImageIOJSBinding')
99
})
10+
11+
test('application/dicom maps to itkGDCMImageIOJSBinding', t => {
12+
let io = MimeToIO['application/dicom']
13+
t.is(io, 'itkGDCMImageIOJSBinding')
14+
})

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