Downsample register example #342

thewtex · 2025-05-16T16:59:00Z

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thewtex · 2025-05-16T16:59:34Z

@N-Dekker WIP for #341 but reviews welcome!

examples/downsample-register.mjs

thewtex · 2025-05-19T14:46:01Z

We still have the issue:

ENH: Add transformix wasm pipeline
Resamples the input with the transform.

The test fails with:

7: itk::ExceptionObject (0x5c4199ce1e70)
7: Location: "unknown"
7: File: /home/matt/bin/ITKElastix-GCC-Release/_deps/elx-src/Core/Main/itkTransformixFilter.hxx
7: Line: 377
7: Description: ITK ERROR: No entry Spacing found in transformParameterMap

Should we be adding the output spacing as a parameter?

N-Dekker · 2025-05-19T15:40:00Z

We still have the issue:

ENH: Add transformix wasm pipeline
Resamples the input with the transform.

The test fails with:

7: itk::ExceptionObject (0x5c4199ce1e70)
7: Location: "unknown"
7: File: /home/matt/bin/ITKElastix-GCC-Release/_deps/elx-src/Core/Main/itkTransformixFilter.hxx
7: Line: 377
7: Description: ITK ERROR: No entry Spacing found in transformParameterMap

Should we be adding the output spacing as a parameter?

Just checked: "Spacing" should indeed specify the spacing of the output image.

I think the idea is that it important that users explicitly specify the spacing, rather than leave it (1, 1, 1), for example, because for realistic images, it is very relevant. Right, Stefan and Marius (@stefanklein, @mstaring)?

wasm/itkElastixWasmParameterObject.h

thewtex · 2025-06-24T16:50:57Z

Should we be adding the output spacing as a parameter?

I ended up keeping maintaining the behavior of transformix by using the moving image parameters that elastix will output to a transform parameter file, by default. If the ParameterObject entries are not available, use reasonable default. And allow explicit overrides / specification by the caller.

thewtex · 2025-06-25T21:23:25Z

@N-Dekker this is ready for review! There are a number of related to Typescript, Javascript, artifacts, etc. that do not need much attention.

N-Dekker · 2025-07-04T10:19:48Z

@thewtex It appears that your last commit ENH: Base wasm on ITK-Wasm 1.0b192 is not on the branch of your fork! Looking at https://github.com/thewtex/ITKElastix/tree/downsample-register-example

Do you know how that is possible? I was reviewing based on your fork, but now your fork seems out of date!

N-Dekker · 2025-07-04T12:52:50Z

wasm/elastix-wasm.cxx

+    pipeline.add_option("-i,--initial-transform", initialTransform, "Initial transform to apply before registration")
+      ->type_name("INPUT_TRANSFORM");


Just wondering, the elastix.exe command-line interface has "-t0" for the initial transform of a registration, whereas elastix-wasm now has both "-i" and "-t" (but not "-t0"). Should these command-line flags still be brought in sync, one way or another? Or are they different for a fundamental reason?

Yes, we can/should bring them into sync! I will update this one -- please let me know if you see any others that should be updated.

thewtex · 2025-07-14T13:59:29Z

Do you know how that is possible? I was reviewing based on your fork, but now your fork seems out of date!

@N-Dekker GitHub has a hard time with PR's from my fork, so I have to push this up to this repository to make a PR. But I also updated the same branch on my fork 👍

N-Dekker · 2025-07-16T13:49:21Z

wasm/test/data/input/CT_3D_lung.json

@thewtex I think ITKElastix should still be adjusted to use TOML, instead of JSON, for parameter files. You know, we discussed JSON vs YAML vs TOML parameter files earlier this year. TOML appeared preferable to JSON, because unlike JSON, TOML allows users to add comments to their parameter files. (I think you suggested TOML to us 😃) So from February, elastix and transformix fully support TOML parameter files, both as input and output.

I think ITKElastix wasm executables (like "default-parameter-map.cxx") can output an elastix parameter map to stream as follows:

#include "Install/elxConversion.h" ... itk::wasm::OutputTextStream outputTextStream; outputTextStream.Get() << elastix::Conversion::ParameterMapToString(parameterMap, elastix::ParameterMapStringFormat::Toml);

Right?

@N-Dekker yes, for the pipelines like write-parameter-files, we should output the awesome new TOML support instead of the bespoke elastix parameter file format ✨ 🥇 .

For the elastix-wasm pipeline we want to output JSON from the wasm executable. This is for JavaScript / Python binding that transforms the JSON into JavaScript Objects and Python dict's for working with the data in JavaScript and Python. When the goal is to save or load the result to file, these are serialized / deserialized with read-parameter-file, write-parameter-file (soon in TOML!).

@thewtex Sorry, can you please clarify? Would it be OK to you to replace JSON parameter files like "wasm/test/data/input/CT_3D_lung.json" with the equivalent TOML parameter files?

@N-Dekker We will add wasm/test/data/input/CT_3D_lung.toml, and use this for the data format with read-parameter-files, write-parameter-files. I would like to also keep the wasm/test/data/input/CT_3D_lung.json file to help add tests with native binaries / in the CLI the same codepath used in the JavaScript and Python wrapping. This may be easier to understand after the toml support has been added.

Based on current sources.

For deployment, we also needed to add pip to the build environment.

Note: we support std::variant for the ValueVector to support, for example, the actual boolean or number types being specified in python or typescript.

Simple and fast.

More efficient and enables use in bindings.

More efficient, enables bindings, and improves wasm module size.

Resamples the input with the transform.

The `elastix` function's signature changed (returns transform outputs).

Required for transform interface type support.

Transforms are now outputs.

Easier to track changes.

Generated by VS Code.

To track changes.

Latest.

This is generated based on the javascript module contents.

Addresses: test/test_write_parameter_files_async.py:33: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E pyodide.ffi.JsException: DataCloneError: Failed to execute 'postMessage' on 'Worker': [object Map] could not be cloned. /lib/python3.12/site-packages/itkwasm_elastix_emscripten/write_parameter_files_async.py:36: JsException via: InsightSoftwareConsortium/ITK-Wasm@f805bf2

Shows how to: 1. Register with elastix 2. Apply the resulting transform with transformix 3. Downsample the input images. 4. Register the downsampled images. 5. Apply the resulting transform at the original resolution.

Improved Transform support.

Through: - Bump itk-wasm to 1.0.0-b.196 - Bump itkwasm python package dependency - Bump of supporting Docker images - Rebuild wasm packages

Python and Typescript/JavaScript and downsample register example.

thewtex requested a review from N-Dekker May 16, 2025 16:59

thewtex force-pushed the downsample-register-example branch 4 times, most recently from aee7c1e to f5f8aff Compare May 16, 2025 20:05

N-Dekker reviewed May 19, 2025

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N-Dekker reviewed May 20, 2025

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thewtex force-pushed the downsample-register-example branch from f5f8aff to 8410990 Compare May 27, 2025 21:38

N-Dekker reviewed Jun 2, 2025

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thewtex force-pushed the downsample-register-example branch from 8410990 to 6cb5d47 Compare June 2, 2025 14:02

thewtex force-pushed the downsample-register-example branch 3 times, most recently from e55ba4a to aec106b Compare June 24, 2025 16:45

thewtex marked this pull request as ready for review June 25, 2025 21:12

thewtex force-pushed the downsample-register-example branch from 8cb4a15 to 4370ecc Compare June 25, 2025 21:13

N-Dekker reviewed Jul 4, 2025

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N-Dekker reviewed Jul 16, 2025

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thewtex added 6 commits September 2, 2025 15:30

ENH: Update wasm module artifacts

e61116b

Based on current sources.

ENH: Bump wasm python package versions to 0.4.0

e7b0b95

For deployment, we also needed to add pip to the build environment.

ENH: Use glaze in wasm for parameter object parsing

d580450

Note: we support std::variant for the ValueVector to support, for example, the actual boolean or number types being specified in python or typescript.

ENH: Use glaze for parameter object parsing in elastix-wasm

26964be

Simple and fast.

ENH: Use itk::wasm::OutputTransform

ea8a069

More efficient and enables use in bindings.

ENH: Use itk::wasm::InputTransform in elastix-wasm

4c66514

More efficient, enables bindings, and improves wasm module size.

thewtex added 15 commits September 2, 2025 15:36

ENH: Add transformix wasm pipeline

5746516

Resamples the input with the transform.

COMP: Add full path for itkwasm docker images

f2db710

BUG: Update Node elastix-test for new tranform interface

6ce94f8

ENH: Bump wasm package version to 1.0.0 and update artifacts

771d239

The `elastix` function's signature changed (returns transform outputs).

BUG: Update itkwasm wasm Python dep to 1.0.b189

619ab8b

Required for transform interface type support.

BUG: Update test_elastix_wasm.py for API change

86574b2

Transforms are now outputs.

ENH: Add transformix generated typescript sources

61205eb

Easier to track changes.

STYLE: Add .vscode to .gitignore

4e0b8d4

Generated by VS Code.

ENH: Add transformix generated python interface artifacts

d26cf6f

To track changes.

ENH: Bump pnpm to 10.12.3

b74eadb

Latest.

ENH: Update js_package.py default_js_module

49c26f3

This is generated based on the javascript module contents.

STYLE: Apply clang-format to wasm files

bdd2ad3

DOC: downsample-register Node.js example

02f3e3f

Shows how to: 1. Register with elastix 2. Apply the resulting transform with transformix 3. Downsample the input images. 4. Register the downsampled images. 5. Apply the resulting transform at the original resolution.

ENH: Base wasm on ITK-Wasm 1.0b192

5cc7e7a

Improved Transform support.

thewtex force-pushed the downsample-register-example branch from 1f23b48 to 5cc7e7a Compare September 2, 2025 19:36

thewtex added 2 commits September 3, 2025 14:08

BUG: Add wasm CompositeTransform support in bindings

d906dc3

Through: - Bump itk-wasm to 1.0.0-b.196 - Bump itkwasm python package dependency - Bump of supporting Docker images - Rebuild wasm packages

ENH: Update wasm package versions to 1.0.2

2266e70

Python and Typescript/JavaScript and downsample register example.

		pipeline.add_option("-i,--initial-transform", initialTransform, "Initial transform to apply before registration")
		->type_name("INPUT_TRANSFORM");

Downsample register example #342

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Downsample register example #342

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thewtex commented May 16, 2025

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thewtex commented May 19, 2025

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thewtex commented Jun 24, 2025 •

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