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thewtexthewtex
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Merge pull request #43 from thewtex/biorad
feat(formats): add BioRad support.
2 parents 505efb8 + e96e733 commit 6c706a3

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‎CMakeLists.txt‎

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@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 2.8.9)
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project(BridgeJavaScript)
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set(BridgeJavaScript_IOModules
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"ITKIOBioRad"
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"ITKIOBMP"
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"ITKIOGDCM"
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"ITKIOJPEG"
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"ITKIOVTK"
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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_ITKIOBioRad itkBioRadImageIO)
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set(imageio_ITKIOBMP itkBMPImageIO)
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set(imageio_ITKIOPNG itkPNGImageIO)
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set(imageio_ITKIOMeta itkMetaImageIO)

‎README.md‎

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@@ -8,6 +8,7 @@ Provides general scientific image IO capability and bridges
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## Supported file formats
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- [BioRad](http://www.bio-rad.com/)
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- [BMP](https://en.wikipedia.org/wiki/BMP_file_format)
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- [DICOM](http://dicom.nema.org/)
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- [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format)

‎src/extensionToIO.js‎

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@@ -28,6 +28,9 @@ extensionToIO['NHDR'] = 'itkNrrdImageIOJSBinding'
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extensionToIO['png'] = 'itkPNGImageIOJSBinding'
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extensionToIO['PNG'] = 'itkPNGImageIOJSBinding'
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extensionToIO['pic'] = 'itkBioRadImageIOJSBinding'
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extensionToIO['PIC'] = 'itkBioRadImageIOJSBinding'
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extensionToIO['tif'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['TIF'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['tiff'] = 'itkTIFFImageIOJSBinding'

‎src/itkBioRadImageIOJSBinding.cxx‎

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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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#include "itkBioRadImageIO.h"
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#include "itkImageIOBaseJSBinding.h"
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typedef itk::ImageIOBaseJSBinding< itk::BioRadImageIO > BioRadImageIOJSBindingType;
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EMSCRIPTEN_BINDINGS(itk_biorad_image_io_js_binding) {
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emscripten::register_vector<double>("AxisDirectionType");
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emscripten::enum_<BioRadImageIOJSBindingType::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_<BioRadImageIOJSBindingType::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)
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.value("FLOAT", itk::ImageIOBase::FLOAT)
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.value("DOUBLE", itk::ImageIOBase::DOUBLE)
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;
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emscripten::class_<BioRadImageIOJSBindingType>("ITKImageIO")
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.constructor<>()
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.function("SetNumberOfDimensions", &BioRadImageIOJSBindingType::SetNumberOfDimensions)
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.function("GetNumberOfDimensions", &BioRadImageIOJSBindingType::GetNumberOfDimensions)
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.function("SetFileName", &BioRadImageIOJSBindingType::SetFileName)
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.function("GetFileName", &BioRadImageIOJSBindingType::GetFileName)
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.function("CanReadFile", &BioRadImageIOJSBindingType::CanReadFile)
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.function("ReadImageInformation", &BioRadImageIOJSBindingType::ReadImageInformation)
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.function("SetDimensions", &BioRadImageIOJSBindingType::SetDimensions)
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.function("GetDimensions", &BioRadImageIOJSBindingType::GetDimensions)
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.function("SetOrigin", &BioRadImageIOJSBindingType::SetOrigin)
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.function("GetOrigin", &BioRadImageIOJSBindingType::GetOrigin)
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.function("SetSpacing", &BioRadImageIOJSBindingType::SetSpacing)
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.function("GetSpacing", &BioRadImageIOJSBindingType::GetSpacing)
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.function("SetDirection", &BioRadImageIOJSBindingType::SetDirection)
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.function("GetDirection", &BioRadImageIOJSBindingType::GetDirection)
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.function("GetDefaultDirection", &BioRadImageIOJSBindingType::GetDefaultDirection)
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.function("SetPixelType", &BioRadImageIOJSBindingType::SetPixelType)
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.function("GetPixelType", &BioRadImageIOJSBindingType::GetPixelType)
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.function("SetComponentType", &BioRadImageIOJSBindingType::SetComponentType)
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.function("GetComponentType", &BioRadImageIOJSBindingType::GetComponentType)
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.class_function("GetPixelTypeAsString", &BioRadImageIOJSBindingType::GetPixelTypeAsString)
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.class_function("GetComponentTypeAsString", &BioRadImageIOJSBindingType::GetComponentTypeAsString)
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.function("GetImageSizeInPixels", &BioRadImageIOJSBindingType::GetImageSizeInPixels)
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.function("GetImageSizeInBytes", &BioRadImageIOJSBindingType::GetImageSizeInBytes)
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.function("GetImageSizeInComponents", &BioRadImageIOJSBindingType::GetImageSizeInComponents)
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.function("SetNumberOfComponents", &BioRadImageIOJSBindingType::SetNumberOfComponents)
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.function("GetNumberOfComponents", &BioRadImageIOJSBindingType::GetNumberOfComponents)
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.function("Read", &BioRadImageIOJSBindingType::Read)
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;
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}

‎test/CMakeLists.txt‎

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@@ -28,4 +28,5 @@ ExternalData_Expand_Arguments(
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DATA{Input/r16slice.nii.gz}
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DATA{Input/image_color.bmp}
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DATA{Input/apple.jpg}
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DATA{Input/biorad.pic}
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)

‎test/Input/biorad.pic.md5‎

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d174069b573416012e21b1af66b774c3

‎test/extensionToIOTest.js‎

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@@ -23,6 +23,11 @@ test('png maps to itkPNGImageIOJSBinding', t => {
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t.is(io, 'itkPNGImageIOJSBinding')
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})
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test('pic maps to itkBioRadImageIOJSBinding', t => {
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let io = ExtensionToIO['pic']
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t.is(io, 'itkBioRadImageIOJSBinding')
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})
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test('mha maps to itkMetaImageIOJSBinding', t => {
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let io = ExtensionToIO['mha']
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t.is(io, 'itkMetaImageIOJSBinding')

‎test/formatsTest.js‎

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@@ -27,6 +27,28 @@ test('Test reading a PNG file', t => {
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})
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})
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test('Test reading a BioRad file', t => {
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const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'biorad.pic')
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return readImageLocalFile(testFilePath).then(function (image) {
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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.Scalar, 'pixelType')
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t.is(image.imageType.components, 1, 'components')
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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], 0.06000000238418579, 'spacing[0]')
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t.is(image.spacing[1], 0.06000000238418579, '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], 768, 'size[0]')
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t.is(image.size[1], 512, 'size[1]')
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t.is(image.buffer.length, 393216, 'buffer.length')
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t.is(image.buffer[1000], 27, 'buffer[1000]')
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})
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})
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test('Test reading a BMP file', t => {
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const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'image_color.bmp')
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return readImageLocalFile(testFilePath).then(function (image) {

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