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thewtexthewtex
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Merge pull request #34 from thewtex/tiff
feat(formats): add TIFF support
2 parents d0610ba + deebabf commit 02b55b6

10 files changed

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‎CMakeLists.txt‎

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@@ -6,13 +6,15 @@ set(BridgeJavaScript_IOModules
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"ITKIOMeta"
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"ITKIONRRD"
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"ITKIOPNG"
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"ITKIOTIFF"
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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_ITKIOPNG itkPNGImageIO)
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set(imageio_ITKIOMeta itkMetaImageIO)
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set(imageio_ITKIONRRD itkNrrdImageIO)
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set(imageio_ITKIOGDCM itkGDCMImageIO)
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set(imageio_ITKIOTIFF itkTIFFImageIO)
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set(imageio_ITKIOVTK itkVTKImageIO)
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‎README.md‎

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@@ -12,6 +12,7 @@ Provides general scientific image IO capability and bridges
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- [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
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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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- [Tagged Image File Format (TIFF)](https://en.wikipedia.org/wiki/TIFF)
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- [VTK legacy image file format](http://www.vtk.org/VTK/img/file-formats.pdf)
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## Hacking ITKBridgeJavaScript

‎src/itkExtensionToIO.js‎

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@@ -14,6 +14,11 @@ extensionToIO['NHDR'] = 'itkNrrdImageIOJSBinding'
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extensionToIO['png'] = 'itkPNGImageIOJSBinding'
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extensionToIO['PNG'] = 'itkPNGImageIOJSBinding'
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extensionToIO['tif'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['TIF'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['tiff'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['TIFF'] = 'itkTIFFImageIOJSBinding'
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extensionToIO['vtk'] = 'itkVTKImageIOJSBinding'
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extensionToIO['VTK'] = 'itkVTKImageIOJSBinding'
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‎src/itkMimeToIO.js‎

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let mimeToIO = {}
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mimeToIO['image/png'] = 'itkPNGImageIOJSBinding'
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mimeToIO['image/tiff'] = 'itkTIFFImageIOJSBinding'
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mimeToIO['application/dicom'] = 'itkGDCMImageIOJSBinding'
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module.exports = mimeToIO

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

‎test/CMakeLists.txt‎

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@@ -24,4 +24,5 @@ ExternalData_Expand_Arguments(
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DATA{Input/vol-raw-little.nrrd}
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DATA{Input/1.3.6.1.4.1.5962.99.1.3814087073.479799962.1489872804257.100.0.dcm}
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DATA{Input/ironProt.vtk}
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DATA{Input/ShortTestImage.tiff}
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)

‎test/Input/ShortTestImage.tiff.md5‎

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11aa67285ef4d1e2106abbdbb2a87a4f

‎test/formatsTest.js‎

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@@ -29,6 +29,28 @@ test('Test reading a PNG file', t => {
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})
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})
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test('Test reading a TIFF file', t => {
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const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'ShortTestImage.tiff')
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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.Int16, '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], 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], 20, 'size[0]')
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t.is(image.size[1], 20, 'size[1]')
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t.is(image.buffer.length, 400, 'buffer.length')
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t.is(image.buffer[100], -9, 'buffer[100]')
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})
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})
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test('Test reading a NRRD file', t => {
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const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'vol-raw-little.nrrd')
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return readImageLocalFile(testFilePath).then(function (image) {

‎test/itkExtensionToIOTest.js‎

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@@ -33,7 +33,32 @@ test('dcm maps to itkGDCMImageIOJSBinding', t => {
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t.is(io, 'itkGDCMImageIOJSBinding')
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})
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test('tif maps to itkTIFFImageIOJSBinding', t => {
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let io = ExtensionToIO['tif']
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t.is(io, 'itkTIFFImageIOJSBinding')
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})
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test('TIF maps to itkTIFFImageIOJSBinding', t => {
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let io = ExtensionToIO['TIF']
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t.is(io, 'itkTIFFImageIOJSBinding')
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})
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test('tiff maps to itkTIFFImageIOJSBinding', t => {
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let io = ExtensionToIO['tiff']
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t.is(io, 'itkTIFFImageIOJSBinding')
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})
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test('TIFF maps to itkTIFFImageIOJSBinding', t => {
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let io = ExtensionToIO['TIFF']
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t.is(io, 'itkTIFFImageIOJSBinding')
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})
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test('vtk maps to itkVTKImageIOJSBinding', t => {
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let io = ExtensionToIO['vtk']
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t.is(io, 'itkVTKImageIOJSBinding')
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})
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test('VTK maps to itkVTKImageIOJSBinding', t => {
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let io = ExtensionToIO['VTK']
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t.is(io, 'itkVTKImageIOJSBinding')
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})

‎test/itkMimeToIOTest.js‎

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t.is(io, 'itkPNGImageIOJSBinding')
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})
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test('image/tiff maps to itkTIFFImageIOJSBinding', t => {
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let io = MimeToIO['image/tiff']
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t.is(io, 'itkTIFFImageIOJSBinding')
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})
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test('application/dicom maps to itkGDCMImageIOJSBinding', t => {
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let io = MimeToIO['application/dicom']
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t.is(io, 'itkGDCMImageIOJSBinding')

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