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feat(formats): Add MRC support
1 parent d6edbd8 commit 7d6bc89

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‎CMakeLists.txt‎

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@@ -15,6 +15,7 @@ set(BridgeJavaScript_IOModules
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"ITKIOBMP"
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"ITKIOHDF5"
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"ITKIOMINC"
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"ITKIOMRC"
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"ITKIOLSM"
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"MGHIO"
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"ITKIOBioRad"
@@ -32,6 +33,7 @@ set(imageios_ITKIOLSM itkLSMImageIO)
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set(imageios_ITKIOMeta itkMetaImageIO)
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set(imageios_ITKIOMINC itkMINCImageIO)
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set(imageios_MGHIO itkMGHImageIO)
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set(imageios_ITKIOMRC itkMRCImageIO)
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set(imageios_ITKIONIFTI itkNiftiImageIO)
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set(imageios_ITKIONRRD itkNrrdImageIO)
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set(imageios_ITKIOGDCM itkGDCMImageIO)

‎README.md‎

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@@ -21,6 +21,7 @@ Supported file formats
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- [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
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- [MINC 2.0](https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference)
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- [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat)
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- [MRC](https://en.wikipedia.org/wiki/MRC_(file_format))
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- [NifTi](https://nifti.nimh.nih.gov/nifti-1)
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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)

‎src/extensionToIO.js‎

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@@ -32,6 +32,8 @@ extensionToIO['mgh.gz'] = 'itkMGHImageIOJSBinding'
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extensionToIO['mha'] = 'itkMetaImageIOJSBinding'
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extensionToIO['mhd'] = 'itkMetaImageIOJSBinding'
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extensionToIO['mrc'] = 'itkMRCImageIOJSBinding'
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extensionToIO['nia'] = 'itkNiftiImageIOJSBinding'
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extensionToIO['nii'] = 'itkNiftiImageIOJSBinding'
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extensionToIO['nii.gz'] = 'itkNiftiImageIOJSBinding'

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

‎test/CMakeLists.txt‎

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@@ -37,4 +37,5 @@ ExternalData_Expand_Arguments(
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DATA{Input/cthead1.lsm}
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DATA{Input/t1_z+_short_cor.mnc}
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DATA{Input/T1.mgz}
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DATA{Input/tilt_series_little.mrc}
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)

‎test/Input/tilt_series_little.mrc.md5‎

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@@ -0,0 +1 @@
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d80a4ac201f5b9933d3c87a3dbcb16bb

‎test/MRCTest.js‎

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import test from 'ava'
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import path from 'path'
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const IntTypes = require(path.resolve(__dirname, '..', 'dist', 'IntTypes.js'))
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const PixelTypes = require(path.resolve(__dirname, '..', 'dist', 'PixelTypes.js'))
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const readImageLocalFile = require(path.resolve(__dirname, '..', 'dist', 'readImageLocalFile.js'))
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test('Test reading a MRC file', t => {
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const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'tilt_series_little.mrc')
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return readImageLocalFile(testFilePath).then(function (image) {
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t.is(image.imageType.dimension, 3, '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], 30, 'origin[0]')
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t.is(image.origin[1], 30, 'origin[1]')
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t.is(image.origin[2], 0, 'origin[2]')
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t.is(image.spacing[0], 62.0, 'spacing[0]')
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t.is(image.spacing[1], 62.0, 'spacing[1]')
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t.is(image.spacing[2], 1.0, 'spacing[2]')
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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(0, 2), 0.0, 'direction (0, 2)')
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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.direction.getElement(1, 2), 0.0, 'direction (1, 2)')
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t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
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t.is(image.direction.getElement(2, 1), 0.0, 'direction (2, 1)')
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t.is(image.direction.getElement(2, 2), 1.0, 'direction (2, 2)')
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t.is(image.size[0], 34, 'size[0]')
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t.is(image.size[1], 34, 'size[1]')
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t.is(image.size[2], 141, 'size[2]')
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t.is(image.buffer.length, 162996, 'buffer.length')
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t.is(image.buffer[1000], 0, 'buffer[1000]')
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})
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})

‎test/extensionToIOTest.js‎

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@@ -88,6 +88,11 @@ test('mhd maps to itkMetaImageIOJSBinding', t => {
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t.is(io, 'itkMetaImageIOJSBinding')
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})
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test('mrc maps to itkMRCImageIOJSBinding', t => {
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let io = ExtensionToIO['mrc']
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t.is(io, 'itkMRCImageIOJSBinding')
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})
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test('nia maps to itkNiftiImageIOJSBinding', t => {
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let io = ExtensionToIO['nia']
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t.is(io, 'itkNiftiImageIOJSBinding')

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