feat(formats): Add GIPL support

Also, .gz extension identification is removed in favor of .CanReadFile detection.

Author: thewtex

CMakeLists.txt

@@ -14,12 +14,14 @@ set(BridgeJavaScript_IOModules
   "ITKIOVTK"
   "ITKIOBMP"
   "ITKIOBioRad"
+  "ITKIOGIPL"
   "ITKIOGE"
   CACHE STRING
   "String delimited list of ITK IO modules to support.")
 set(imageios_ITKIOBioRad itkBioRadImageIO)
 set(imageios_ITKIOBMP itkBMPImageIO)
 set(imageios_ITKIOGE itkGEAdwImageIO itkGE4ImageIO itkGE5ImageIO)
+set(imageios_ITKIOGIPL itkGiplImageIO)
 set(imageios_ITKIOPNG itkPNGImageIO)
 set(imageios_ITKIOMeta itkMetaImageIO)
 set(imageios_ITKIONIFTI itkNiftiImageIO)

README.md

@@ -15,6 +15,7 @@ Supported file formats
 - [DICOM](http://dicom.nema.org/)
 - [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format)
 - [GE4,GE5,GEAdw](http://www3.gehealthcare.com)
+- [Gipl (Guys Image Processing Lab)](https://www.ncbi.nlm.nih.gov/pubmed/12956259)
 - [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
 - [NifTi](https://nifti.nimh.nih.gov/nifti-1)
 - [NRRD](http://teem.sourceforge.net/nrrd/format.html)

src/extensionToIO.js

@@ -6,6 +6,9 @@ extensionToIO['BMP'] = 'itkBMPImageIOJSBinding'
 extensionToIO['dcm'] = 'itkGDCMImageIOJSBinding'
 extensionToIO['DCM'] = 'itkGDCMImageIOJSBinding'
 
+extensionToIO['gipl'] = 'itkGiplImageIOJSBinding'
+extensionToIO['gipl.gz'] = 'itkGiplImageIOJSBinding'
+
 extensionToIO['jpg'] = 'itkJPEGImageIOJSBinding'
 extensionToIO['JPG'] = 'itkJPEGImageIOJSBinding'
 extensionToIO['jpeg'] = 'itkJPEGImageIOJSBinding'
@@ -16,8 +19,7 @@ extensionToIO['mhd'] = 'itkMetaImageIOJSBinding'
 
 extensionToIO['nia'] = 'itkNiftiImageIOJSBinding'
 extensionToIO['nii'] = 'itkNiftiImageIOJSBinding'
-// todo: properly support .nii.gz
-extensionToIO['gz'] = 'itkNiftiImageIOJSBinding'
+extensionToIO['nii.gz'] = 'itkNiftiImageIOJSBinding'
 extensionToIO['hdr'] = 'itkNiftiImageIOJSBinding'
 
 extensionToIO['nrrd'] = 'itkNrrdImageIOJSBinding'

src/getFileExtension.js

@@ -1,5 +1,10 @@
 const getFileExtension = (filePath) => {
-  return filePath.slice((filePath.lastIndexOf('.') - 1 >>> 0) + 2)
+  let extension = filePath.slice((filePath.lastIndexOf('.') - 1 >>> 0) + 2)
+  if (extension === 'gz') {
+    const index = filePath.slice(0, -3).lastIndexOf('.')
+    extension = filePath.slice((index - 1 >>> 0) + 2)
+  }
+  return extension
 }
 
 module.exports = getFileExtension

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

test/CMakeLists.txt

@@ -32,4 +32,5 @@ ExternalData_Expand_Arguments(
   DATA{Input/19771.002.001}
   DATA{Input/113766.003.001}
   DATA{Input/I.001}
+  DATA{Input/ramp.gipl}
   )

test/Input/ramp.gipl.md5

@@ -0,0 +1 @@
+77411a7f9359b867e69dd5fa75100982

test/extensionToIOTest.js

@@ -48,11 +48,6 @@ test('nii maps to itkNiftiImageIOJSBinding', t => {
   t.is(io, 'itkNiftiImageIOJSBinding')
 })
 
-test('gz maps to itkNiftiImageIOJSBinding', t => {
-  let io = ExtensionToIO['gz']
-  t.is(io, 'itkNiftiImageIOJSBinding')
-})
-
 test('hdr maps to itkNiftiImageIOJSBinding', t => {
   let io = ExtensionToIO['hdr']
   t.is(io, 'itkNiftiImageIOJSBinding')
@@ -68,6 +63,11 @@ test('nhdr maps to itkNrrdImageIOJSBinding', t => {
   t.is(io, 'itkNrrdImageIOJSBinding')
 })
 
+test('gipl maps to itkGiplImageIOJSBinding', t => {
+  let io = ExtensionToIO['gipl']
+  t.is(io, 'itkGiplImageIOJSBinding')
+})
+
 test('dcm maps to itkGDCMImageIOJSBinding', t => {
   let io = ExtensionToIO['dcm']
   t.is(io, 'itkGDCMImageIOJSBinding')

test/formatsTest.js

@@ -93,6 +93,36 @@ test('Test reading a JPEG file', t => {
   })
 })
 
+test('Test reading a GIPL file', t => {
+  const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'ramp.gipl')
+  return readImageLocalFile(testFilePath).then(function (image) {
+    t.is(image.imageType.dimension, 3, 'dimension')
+    t.is(image.imageType.componentType, IntTypes.Int16, 'componentType')
+    t.is(image.imageType.pixelType, PixelTypes.Scalar, 'pixelType')
+    t.is(image.imageType.components, 1, 'components')
+    t.is(image.origin[0], 0.0, 'origin[0]')
+    t.is(image.origin[1], 0.0, 'origin[1]')
+    t.is(image.origin[2], 0.0, '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), 1.0, 'direction (1, 1)')
+    t.is(image.direction.getElement(1, 2), 0.0, 'direction (1, 2)')
+    t.is(image.direction.getElement(2, 0), 0.0, 'direction (2, 0)')
+    t.is(image.direction.getElement(2, 1), 0.0, 'direction (2, 1)')
+    t.is(image.direction.getElement(2, 2), 1.0, 'direction (2, 2)')
+    t.is(image.size[0], 30, 'size[0]')
+    t.is(image.size[1], 30, 'size[1]')
+    t.is(image.size[2], 30, 'size[2]')
+    t.is(image.buffer.length, 27000, 'buffer.length')
+    t.is(image.buffer[2], 2, 'buffer[2]')
+  })
+})
+
 test('Test reading a TIFF file', t => {
   const testFilePath = path.resolve(__dirname, '..', 'build', 'ExternalData', 'test', 'Input', 'ShortTestImage.tiff')
   return readImageLocalFile(testFilePath).then(function (image) {