Merge pull request #1284 from thewtex/mz3-mesh-io

mz3 mesh io
InsightSoftwareConsortium · Dec 11, 2024 · ff449f2 · ff449f2
2 parents b8ee114 + e257991
commit ff449f2
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diff --git a/itk_wasm_env.bash b/itk_wasm_env.bash
@@ -16,7 +16,7 @@ export ITK_WASM_DCMTK_REPOSITORY=${ITK_WASM_DCMTK_REPOSITORY:-"https://github.co
 export ITK_WASM_DCMTK_GIT_TAG=${ITK_WASM_DCMTK_GIT_TAG:-"93e6d1b20b476c388f0379245c8c6e96af7f16f4"}
 
 export ITK_WASM_ITK_REPOSITORY=${ITK_WASM_ITK_REPOSITORY:-"https://github.com/KitwareMedical/ITK"}
-export ITK_WASM_ITK_BRANCH=${ITK_WASM_ITK_BRANCH:-"itkwasm-2024-05-20-5db055d7ad3b-4"}
+export ITK_WASM_ITK_BRANCH=${ITK_WASM_ITK_BRANCH:-"itkwasm-2024-05-20-5db055d7ad3b-5"}
 
 export ITK_WASM_NATIVE_WORKSPACE=${ITK_WASM_NATIVE_WORKSPACE:-$(pwd)/native}
 

diff --git a/packages/compare-images/python/itkwasm-compare-images-emscripten/pyproject.toml b/packages/compare-images/python/itkwasm-compare-images-emscripten/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/compare-images/python/itkwasm-compare-images-wasi/pyproject.toml b/packages/compare-images/python/itkwasm-compare-images-wasi/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/compare-images/python/itkwasm-compare-images/pyproject.toml b/packages/compare-images/python/itkwasm-compare-images/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/compress-stringify/python/itkwasm-compress-stringify-emscripten/pyproject.toml b/packages/compress-stringify/python/itkwasm-compress-stringify-emscripten/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/compress-stringify/python/itkwasm-compress-stringify-wasi/pyproject.toml b/packages/compress-stringify/python/itkwasm-compress-stringify-wasi/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/compress-stringify/python/itkwasm-compress-stringify/pyproject.toml b/packages/compress-stringify/python/itkwasm-compress-stringify/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/core/python/itkwasm/pyproject.toml b/packages/core/python/itkwasm/pyproject.toml
@@ -11,7 +11,7 @@ license = {file = "LICENSE"}
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
     "Programming Language :: Python",
-    'Development Status :: 3 - Alpha',
+    'Development Status :: 4 - Beta',
     'Intended Audience :: Developers',
     'Intended Audience :: Science/Research',
     'Programming Language :: Python :: 3',

diff --git a/packages/core/typescript/itk-wasm/src/bindgen/python/resources/template.pyproject.toml b/packages/core/typescript/itk-wasm/src/bindgen/python/resources/template.pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/core/typescript/itk-wasm/src/cli/default-image-tag.js b/packages/core/typescript/itk-wasm/src/cli/default-image-tag.js
@@ -1,2 +1,2 @@
-const defaultImageTag = '20241111-d4fcf16c'
+const defaultImageTag = '20241205-b5c57616'
 export default defaultImageTag
diff --git a/...-interface-types-pipeline/python/itkwasm-bindgen-interface-types-test-wasi/pyproject.toml b/...-interface-types-pipeline/python/itkwasm-bindgen-interface-types-test-wasi/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/...ndgen-interface-types-pipeline/python/itkwasm-bindgen-interface-types-test/pyproject.toml b/...ndgen-interface-types-pipeline/python/itkwasm-bindgen-interface-types-test/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/dicom/python/itkwasm-dicom-emscripten/pyproject.toml b/packages/dicom/python/itkwasm-dicom-emscripten/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/dicom/python/itkwasm-dicom-wasi/pyproject.toml b/packages/dicom/python/itkwasm-dicom-wasi/pyproject.toml
@@ -14,7 +14,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/dicom/python/itkwasm-dicom/pyproject.toml b/packages/dicom/python/itkwasm-dicom/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/downsample/python/itkwasm-downsample-cucim/pyproject.toml b/packages/downsample/python/itkwasm-downsample-cucim/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/downsample/python/itkwasm-downsample-emscripten/pyproject.toml b/packages/downsample/python/itkwasm-downsample-emscripten/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/downsample/python/itkwasm-downsample-wasi/pyproject.toml b/packages/downsample/python/itkwasm-downsample-wasi/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/downsample/python/itkwasm-downsample/pyproject.toml b/packages/downsample/python/itkwasm-downsample/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/image-io/python/itkwasm-image-io-emscripten/pyproject.toml b/packages/image-io/python/itkwasm-image-io-emscripten/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/image-io/python/itkwasm-image-io-wasi/pyproject.toml b/packages/image-io/python/itkwasm-image-io-wasi/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/image-io/python/itkwasm-image-io/pyproject.toml b/packages/image-io/python/itkwasm-image-io/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
   "Environment :: WebAssembly",
   "Environment :: WebAssembly :: Emscripten",
   "Environment :: WebAssembly :: WASI",
-  "Development Status :: 3 - Alpha",
+  "Development Status :: 4 - Beta",
   "Intended Audience :: Developers",
   "Intended Audience :: Science/Research",
   "Programming Language :: Python :: 3",

diff --git a/packages/mesh-io/CMakeLists.txt b/packages/mesh-io/CMakeLists.txt
@@ -19,6 +19,7 @@ set(WebAssemblyInterface_MeshIOModules
   "IOMeshSWC"
   "ITKIOMeshBYU"
   "ITKIOMeshFreeSurfer"
+  "IOMeshMZ3"
   CACHE STRING
   "String delimited list of ITK mesh IO modules to support.")
 
@@ -58,6 +59,10 @@ set(meshio_kebab_itkWasmMeshIO "wasm")
 set(meshio_id_itkWasmZstdMeshIO 9)
 set(meshio_kebab_itkWasmZstdMeshIO "wasm-zstd")
 
+set(meshios_IOMeshMZ3 itkMZ3MeshIO)
+set(meshio_id_itkMZ3MeshIO 10)
+set(meshio_kebab_itkMZ3MeshIO "mz3")
+
 set(ITK_NO_MESHIO_FACTORY_REGISTER_MANAGER 1)
 set(MeshIOIndex_ARRAY "")
 foreach(io_module ${WebAssemblyInterface_MeshIOModules} WebAssemblyInterface)
@@ -132,13 +137,25 @@ add_test(NAME byu-write-mesh-test
   ${output_dir}/byu-write-mesh-test.could-write.json
   ${output_dir}/byu-write-mesh-test.byu)
 
+add_test(NAME mz3-read-mesh-test
+  COMMAND mz3-read-mesh
+  ${input_dir}/11ScalarMesh.mz3
+  ${output_dir}/mz3-read-mesh-test.could-read.json
+  ${output_dir}/mz3-read-mesh-test.iwm.cbor)
+
+add_test(NAME mz3-write-mesh-test
+  COMMAND mz3-write-mesh
+  ${baseline_dir}/mz3-read-mesh-test.iwm.cbor
+  ${output_dir}/mz3-write-mesh-test.could-write.json
+  ${output_dir}/mz3-write-mesh-test.mz3)
 
 # This list should be ordered from approximately most commonly to least
 # commonly used modules.
 set(WebAssemblyInterface_PointSetIOModules
   "ITKIOMeshVTK"
   "ITKIOMeshOBJ"
   "ITKIOMeshOFF"
+  "IOMeshMZ3"
   CACHE STRING
   "String delimited list of ITK point set IO modules to support.")
 
@@ -160,6 +177,10 @@ set(pointsetio_kebab_itkWasmMeshIO "wasm")
 set(pointsetio_id_itkWasmZstdMeshIO 4)
 set(pointsetio_kebab_itkWasmZstdMeshIO "wasm-zstd")
 
+set(pointsetios_IOMeshMZ3 itkMZ3MeshIO)
+set(pointsetio_id_itkMZ3MeshIO 5)
+set(pointsetio_kebab_itkMZ3MeshIO "mz3")
+
 set(ITK_NO_MESHIO_FACTORY_REGISTER_MANAGER 1)
 set(PointSetIOIndex_ARRAY "")
 foreach(io_module ${WebAssemblyInterface_PointSetIOModules} WebAssemblyInterface)
@@ -227,3 +248,15 @@ add_test(NAME obj-write-point-set-test
   ${baseline_dir}/obj-read-point-set-test.iwm.cbor
   ${output_dir}/obj-write-point-set-test.could-write.json
   ${output_dir}/obj-write-point-set-test.obj)
+
+add_test(NAME mz3-read-point-set-test
+  COMMAND mz3-read-point-set
+  ${input_dir}/11ScalarMesh.mz3
+  ${output_dir}/mz3-read-point-set-test.could-read.json
+  ${output_dir}/mz3-read-point-set-test.iwm.cbor)
+
+add_test(NAME mz3-write-point-set-test
+  COMMAND mz3-write-point-set
+  ${baseline_dir}/mz3-read-point-set-test.iwm.cbor
+  ${output_dir}/mz3-write-point-set-test.could-write.json
+  ${output_dir}/mz3-write-point-set-test.mz3)
diff --git a/packages/mesh-io/package.json b/packages/mesh-io/package.json
@@ -1,13 +1,13 @@
 {
   "name": "@itk-wasm/mesh-io-build",
-  "version": "1.4.2",
+  "version": "1.5.0",
   "private": true,
   "description": "scripts to generate @itk-wasm/compare-stringify itk-wasm artifacts.",
   "type": "module",
   "itk-wasm": {
-    "test-data-hash": "bafkreiahocrgb3p4xrjozr7cg5wdpdt6wp77kolnqyupae6awkplb5p4he",
+    "test-data-hash": "bafkreiey5fjpunmy6lkmfa5a4mc4ghyfxogfuwcixm7jdtf65pjxmwhaim",
     "test-data-urls": [
-      "https://bafybeian677gvnngces3pbcv6zpzauf3yn5bedxdis4smwzwh5xeewazuq.ipfs.w3s.link/ipfs/bafybeian677gvnngces3pbcv6zpzauf3yn5bedxdis4smwzwh5xeewazuq/data.tar.gz"
+      "https://bafybeibc5xkdxpu2vwpcmbmu34jfdnr4grnpcrhnnjoeq546zovvfeuixu.ipfs.w3s.link/ipfs/bafybeibc5xkdxpu2vwpcmbmu34jfdnr4grnpcrhnnjoeq546zovvfeuixu/data.tar.gz"
     ],
     "emscripten-docker-image": "quay.io/itkwasm/emscripten:latest",
     "wasi-docker-image": "quay.io/itkwasm/wasi:latest",
@@ -28,7 +28,7 @@
     "build:gen:typescript": "itk-wasm pnpm-script build:gen:typescript",
     "build:gen:python": "pnpm build:wasi && pnpm bindgen:python",
     "test": "pnpm test:data:download && pnpm build:gen:python && pnpm test:python",
-    "test:data:download": "dam download test/data test/data.tar.gz bafkreiahocrgb3p4xrjozr7cg5wdpdt6wp77kolnqyupae6awkplb5p4he https://bafybeian677gvnngces3pbcv6zpzauf3yn5bedxdis4smwzwh5xeewazuq.ipfs.w3s.link/ipfs/bafybeian677gvnngces3pbcv6zpzauf3yn5bedxdis4smwzwh5xeewazuq/data.tar.gz",
+    "test:data:download": "dam download test/data test/data.tar.gz bafkreiey5fjpunmy6lkmfa5a4mc4ghyfxogfuwcixm7jdtf65pjxmwhaim https://bafybeibc5xkdxpu2vwpcmbmu34jfdnr4grnpcrhnnjoeq546zovvfeuixu.ipfs.w3s.link/ipfs/bafybeibc5xkdxpu2vwpcmbmu34jfdnr4grnpcrhnnjoeq546zovvfeuixu/data.tar.gz",
     "test:data:pack": "dam pack test/data test/data.tar.gz",
     "test:python:wasi": "pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-wasi",
     "test:python:emscripten": "pnpm test:data:download && pixi run --manifest-path=./pixi.toml test-emscripten",

diff --git a/packages/mesh-io/pixi.toml b/packages/mesh-io/pixi.toml
@@ -74,7 +74,7 @@ cwd = "python/itkwasm-mesh-io"
 
 [tasks.publish]
 depends-on = ["publish-typescript", "publish-python-wasi", "publish-python-emscripten", "publish-python-dispatch"]
-description = "Synchronize package versions"
+description = "Publish packages"
 
 [feature.python.dependencies]
 pytest = ">=8.3.3,<9"

diff --git a/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/__init__.py b/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/__init__.py
@@ -12,6 +12,8 @@
 from .free_surfer_ascii_write_mesh_async import free_surfer_ascii_write_mesh_async
 from .free_surfer_binary_read_mesh_async import free_surfer_binary_read_mesh_async
 from .free_surfer_binary_write_mesh_async import free_surfer_binary_write_mesh_async
+from .mz3_read_mesh_async import mz3_read_mesh_async
+from .mz3_write_mesh_async import mz3_write_mesh_async
 from .obj_read_mesh_async import obj_read_mesh_async
 from .obj_write_mesh_async import obj_write_mesh_async
 from .off_read_mesh_async import off_read_mesh_async
@@ -27,6 +29,8 @@
 from .wasm_zstd_read_mesh_async import wasm_zstd_read_mesh_async
 from .wasm_zstd_write_mesh_async import wasm_zstd_write_mesh_async
 
+from .mz3_read_point_set_async import mz3_read_point_set_async
+from .mz3_write_point_set_async import mz3_write_point_set_async
 from .obj_read_point_set_async import obj_read_point_set_async
 from .obj_write_point_set_async import obj_write_point_set_async
 from .off_read_point_set_async import off_read_point_set_async

diff --git a/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/_version.py b/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/_version.py
@@ -1 +1 @@
-__version__ = "1.4.2"
+__version__ = "1.5.0"
diff --git a/...h-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/extension_to_mesh_io.py b/...h-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/extension_to_mesh_io.py
@@ -5,6 +5,7 @@
     ('.byu', 'byu'),
     ('.fsa', 'freeSurferAscii'),
     ('.fsb', 'freeSurferBinary'),
+    ('.mz3', 'mz3'),
     ('.obj', 'obj'),
     ('.off', 'off'),
     ('.stl', 'stl'),

diff --git a/...python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/extension_to_point_set_io.py b/...python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/extension_to_point_set_io.py
@@ -2,6 +2,7 @@
 
 extension_to_point_set_io = OrderedDict([
     ('.vtk', 'vtkPolyData'),
+    ('.mz3', 'mz3'),
     ('.obj', 'obj'),
     ('.off', 'off'),
     ('.iwm', 'wasm'),

diff --git a/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/js_package.py b/packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/js_package.py
diff --git a/...ges/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/mesh_io_index.py b/...ges/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/mesh_io_index.py
@@ -3,6 +3,7 @@
     'byu',
     'free_surfer_ascii',
     'free_surfer_binary',
+    'mz3',
     'obj',
     'off',
     'stl',
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,6 +3,7 @@ @@
         'byu',
         'free_surfer_ascii',
         'free_surfer_binary',
+        'mz3',
         'obj',
         'off',
         'stl',
@@ Expand Down @@