docs(transform): document Typescript interface types, supported file formats

Also add docker pull retry to hello-world. Apply linter to ploy-data.ts

Author: thewtex

.github/workflows/examples.yml

@@ -64,6 +64,12 @@ jobs:
         large-packages: false
         tool-cache: true
 
+    - uses: nick-fields/retry@v3
+      with:
+        max_attempts: 5
+        timeout_minutes: 10
+        command: ./src/docker/pull.sh --no-debug
+
     - name: Install
       uses: pnpm/action-setup@v4
       with:

docs/introduction/file_formats/images.md

@@ -1,6 +1,6 @@
 # Supported Image File Formats
 
-Read and write to and from [`Image`](/typescript/interface_types/Image.html) is supported. For visualization with [vtk.js](https://kitware.github.io/vtk-js/index.html), use [`convertItkToVtkImage`](https://kitware.github.io/vtk-js/api/Common_DataModel_ITKHelper.html).
+Read and write to and from an [`Image`](../../typescript/interface_types/Image).
 
 - [AIM,ISQ](https://www.scanco.ch/en/support/customer-login/faq-customers/faq-customers-import-export.html)
 - [BioRad](https://www.bio-rad.com/)
@@ -18,6 +18,4 @@ Read and write to and from [`Image`](/typescript/interface_types/Image.html) is
 - [NIfTI](https://nifti.nimh.nih.gov/nifti-1)
 - [NRRD](http://teem.sourceforge.net/nrrd/format.html)
 - [VTK legacy file format for images](https://www.vtk.org/VTK/img/file-formats.pdf)
-- [Varian FDF](https://github.com/InsightSoftwareConsortium/ITKIOFDF)
-
-For visualization with [vtk.js](https://kitware.github.io/vtk-js/index.html), use [`vtkITKHelper.convertItkToVtkImage`](https://kitware.github.io/vtk-js/api/Common_DataModel_ITKHelper.html) ([example](https://kitware.github.io/vtk-js/examples/ItkWasmVolume.html)).
+- [Varian FDF](https://github.com/InsightSoftwareConsortium/ITKIOFDF)

docs/introduction/file_formats/index.md

@@ -2,7 +2,7 @@
 
 Support for data serialized in file formats are a critical bridge that facilitate comprehensive analysis with a suite of diverse software tools.
 
-ITK-Wasm provides IO modules to work with a number of open standard [scientific image](./images) and [mesh](./meshes) file formats, These IO modules can be used to load data into language-native [interfaces types](/typescript/interface_types/index) in with bindings such as TypeScript and Python.
+ITK-Wasm provides IO modules to work with a number of open standard [scientific image](./images), [mesh](./meshes), and [transform](./transforms) file formats, These IO modules can be used to load data into language-native [interfaces types](/typescript/interface_types/index) in with bindings such as TypeScript and Python.
 
 ## ITK-Wasm file formats
 
@@ -17,6 +17,7 @@ ITK-Wasm file formats are available in ITK-Wasm IO functions but also in C++ via
 <dl>
   <dt><b>ITK-Wasm Image (.iwi, .iwi.cbor, .iwi.cbor.zst)</b><dt><dd>Serialization of an <a href="../../typescript/interface_types/Image.html"><code>Image</code></a>.</dd>
   <dt><b>ITK-Wasm Mesh (.iwm, .iwm.cbor, .iwm.cbor.zst)</b><dt><dd>Serialization of a <a href="../../typescript/interface_types/Mesh.html"><code>Mesh</code></a>, or <a href="../../typescript/interface_types/PolyData.html"><code>PolyData</code></a>.</dd>
+  <dt><b>ITK-Wasm Transform (.iwt, .iwt.cbor, .iwt.cbor.zst)</b><dt><dd>Serialization of an <a href="../../typescript/interface_types/TransformList.html"><code>TransformList</code></a>.</dd>
 </dl>
 
 
@@ -26,5 +27,6 @@ ITK-Wasm file formats are available in ITK-Wasm IO functions but also in C++ via
 
 images.md
 meshes.md
+transforms.md
 dicom.md
 ```

docs/introduction/file_formats/meshes.md

@@ -1,6 +1,6 @@
 # Supported Mesh and Point Set File Formats
 
-Read and write to and from [`Mesh`](/typescript/interface_types/Mesh.html) is supported.
+Read and write to and from [`Mesh`](../../typescript/interface_types/Mesh) is supported.
 
 - [BYU](http://www.eg-models.de/formats/Format_Byu.html)
 - [FreeSurfer surface, binary and ASCII](http://www.grahamwideman.com/gw/brain/fs/surfacefileformats.htm)
@@ -9,5 +9,3 @@ Read and write to and from [`Mesh`](/typescript/interface_types/Mesh.html) is su
 - [SWC Neuron Morphology](https://swc-specification.readthedocs.io/en/latest/)
 - [OBJ](https://en.wikipedia.org/wiki/Wavefront_.obj_file)
 - [VTK legacy file format for vtkPolyData](https://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf)
-
-For visualization with [vtk.js](https://kitware.github.io/vtk-js/index.html), use itk-wasm `meshToPolyData` and [`vtkITKHelper.convertItkToVtkPolyData`](https://kitware.github.io/vtk-js/api/Common_DataModel_ITKHelper.html) ([example](https://kitware.github.io/vtk-js/examples/ItkWasmGeometry.html)).

docs/introduction/file_formats/transforms.md

@@ -0,0 +1,8 @@
+# Supported Transform File Formats
+
+Read and write to and from a spatial [`TransformList`](../../typescript/interface_types/TransformList).
+
+- [ITK-HDF5](https://support.hdfgroup.org/HDF5/) - ITK HDF5 transform file format.
+- [ITK-TXT](https://docs.itk.org) - ITK Legacy text transform file format.
+- [MAT](https://www.mathworks.com/help/matlab/ref/matfile.html) - ITK MAT file format.
+- [XFM](https://github.com/BIC-MNI/minc-tools) - MNI XFM file format.

docs/typescript/interface_types/Image.md

@@ -1,6 +1,6 @@
 # Image
 
-An `Image` is the N-dimensional image data structure for *itk-wasm*.
+An `Image` is the N-dimensional image data structure for *ITK-Wasm*.
 
 `Image` is a JavaScript object with the following properties:
 
@@ -19,6 +19,4 @@ Note that the `origin`, `spacing`, `direction`, and `size` are indexed with an `
 
 ```
 const tensor = tf.tensor(image.data, image.size.reverse())
-```
-
-To visualize an `Image` with [vtk.js](https://kitware.github.io/vtk-js) use `convertItkToVtkImage` from [`vtk.js/Sources/Common/DataModel/ITKHelper`](https://kitware.github.io/vtk-js/api/Common_DataModel_ITKHelper.html).
+```

docs/typescript/interface_types/Transform.md

@@ -0,0 +1,12 @@
+# Transform
+
+A `Transform` specifies a spatial transformation that maps points from one coordinate system to another. The `Transform` interface is a JavaScript object with the following properties:
+
+- `transformType`: The [TransformType](./TransformType) for this transform.
+- `numberOfFixedParameters`: The number of fixed parameters for the transform. Fixed parameters are not optimized during registration.
+- `numberOfParameters`: The number of parameters for the transform.
+- `name`: An optional name string that describes this transform.
+- `inputSpaceName`: An optional name string that describes the input space.
+- `outputSpaceName`: An optional name string that describes the output space.
+- `parameters`: A [`TypedArray`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/TypedArray) containing the transform parameters.
+- `fixedParameters`: A [`TypedArray`](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/TypedArray) containing the fixed transform parameters.

docs/typescript/interface_types/TransformList.md

@@ -0,0 +1,5 @@
+# TransformList
+
+A `TransformList` is an ordered sequence of spatial [`Transform`](./Transform) objects.
+
+`TransformList` is a JavaScript array of `Transform` objects.

docs/typescript/interface_types/TransformParameterizations.md

@@ -0,0 +1,34 @@
+# TransformParameterizations
+
+The enumeration of transform parameterization values is:
+
+- `Composite`
+- `Identity`
+- `Translation`
+- `Euler2D`
+- `Euler3D`
+- `Rigid2D`
+- `Rigid3D`
+- `Rigid3DPerspective`
+- `Versor`
+- `VersorRigid3D`
+- `Scale`
+- `ScaleLogarithmic`
+- `ScaleSkewVersor3D`
+- `Similarity2D`
+- `Similarity3D`
+- `QuaternionRigid`
+- `Affine`
+- `ScalableAffine`
+- `AzimuthElevationToCartesian`
+- `BSpline`
+- `BSplineSmoothingOnUpdateDisplacementField`
+- `ConstantVelocityField`
+- `DisplacementField`
+- `GaussianSmoothingOnUpdateDisplacementField`
+- `GaussianExponentialDiffeomorphic`
+- `VelocityField`
+- `TimeVaryingVelocityField`
+- `GaussianSmoothingOnUpdateTimeVaryingVelocityField`
+
+The definition of these transform and the meaning of their parameters is described in detail in the [ITK Software Guide, Book 2, Section 3.9](https://github.com/InsightSoftwareConsortium/ITKSoftwareGuide/releases).

docs/typescript/interface_types/TransformType.md

@@ -0,0 +1,8 @@
+# TransformType
+
+An `TransformType` describes parameterization, parameter value type, and input and output dimensions of the transform. It is a JavaScript object with the following properties:
+
+- `transformParameterization`: The [TransformParameterization](./TransformParameterizations) for this transform.
+- `parametersValueType`: Whether the transform parameters are `float32` or `float64`.
+- `inputDimension`: The number of dimensions of the input space.
+- `outputDimension`: The number of dimensions of the output space.