Merge pull request #1246 from thewtex/point-set-io

point set io
InsightSoftwareConsortium · Oct 17, 2024 · 2bbfc74 · 2bbfc74
2 parents 007e79a + c41eea9
commit 2bbfc74
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diff --git a/include/itkWasmMeshIO.h b/include/itkWasmMeshIO.h
@@ -23,6 +23,7 @@
 #include <fstream>
 
 #include "itkMeshJSON.h"
+#include "itkPointSetJSON.h"
 #include "cbor.h"
 
 namespace itk
@@ -72,6 +73,9 @@ class WebAssemblyInterface_EXPORT WasmMeshIO: public MeshIOBase
   /** Set the JSON representation of the image information. */
   void SetJSON(const MeshJSON & json);
 
+  /** Set the JSON representation of the image information. */
+  void SetJSON(const PointSetJSON & json);
+
   /*-------- This part of the interfaces deals with writing data ----- */
 
   /** Writes the data to disk from the memory buffer provided. Make sure
@@ -93,6 +97,9 @@ class WebAssemblyInterface_EXPORT WasmMeshIO: public MeshIOBase
 #if !defined(ITK_WRAPPING_PARSER)
   /** Get the JSON representation of the mesh information. */
   auto GetJSON() -> MeshJSON;
+
+  /** Get the JSON representation of the point set information. */
+  auto GetPointSetJSON() -> PointSetJSON;
 #endif
 
 protected:

diff --git a/.../python/itkwasm-compare-images-emscripten/itkwasm_compare_images_emscripten/js_package.py b/.../python/itkwasm-compare-images-emscripten/itkwasm_compare_images_emscripten/js_package.py
diff --git a/...itkwasm-compress-stringify-emscripten/itkwasm_compress_stringify_emscripten/js_package.py b/...itkwasm-compress-stringify-emscripten/itkwasm_compress_stringify_emscripten/js_package.py
diff --git a/packages/core/python/itkwasm/itkwasm/__init__.py b/packages/core/python/itkwasm/itkwasm/__init__.py
@@ -1,10 +1,10 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b178"
+__version__ = "1.0b179"
 
 from .interface_types import InterfaceTypes
 from .image import Image, ImageType, ImageRegion
-from .pointset import PointSet, PointSetType
+from .point_set import PointSet, PointSetType
 from .mesh import Mesh, MeshType
 from .transform import Transform, TransformType, TransformParameterizations
 from .polydata import PolyData, PolyDataType

diff --git a/packages/core/python/itkwasm/itkwasm/interface_types.py b/packages/core/python/itkwasm/itkwasm/interface_types.py
@@ -7,6 +7,7 @@ class InterfaceTypes(str, Enum):
     BinaryStream = "BinaryStream"
     Image = "Image"
     Mesh = "Mesh"
+    PointSet = "PointSet"
     PolyData = "PolyData"
     Transform = "Transform"
     JsonCompatible = "JsonCompatible"
diff --git a/packages/core/python/itkwasm/itkwasm/pipeline.py b/packages/core/python/itkwasm/itkwasm/pipeline.py
@@ -22,6 +22,7 @@
 from .binary_file import BinaryFile
 from .image import Image
 from .mesh import Mesh
+from .point_set import PointSet
 from .polydata import PolyData
 from .json_compatible import JsonCompatible
 from .int_types import IntTypes
@@ -277,6 +278,27 @@ def run(
                     "cellData": f"data:application/vnd.itk.address,0:{cell_data_ptr}",
                 }
                 ri.set_input_json(mesh_json, index)
+            elif input_.type == InterfaceTypes.PointSet:
+                point_set = input_.data
+                if point_set.numberOfPoints:
+                    pv = array_like_to_bytes(point_set.points)
+                else:
+                    pv = bytes([])
+                points_ptr = ri.set_input_array(pv, index, 0)
+                if point_set.numberOfPointPixels:
+                    pdv = array_like_to_bytes(point_set.pointData)
+                else:
+                    pdv = bytes([])
+                point_data_ptr = ri.set_input_array(pdv, index, 1)
+                point_set_json = {
+                    "pointSetType": asdict(point_set.pointSetType),
+                    "name": point_set.name,
+                    "numberOfPoints": point_set.numberOfPoints,
+                    "points": f"data:application/vnd.itk.address,0:{points_ptr}",
+                    "numberOfPointPixels": point_set.numberOfPointPixels,
+                    "pointData": f"data:application/vnd.itk.address,0:{point_data_ptr}",
+                }
+                ri.set_input_json(point_set_json, index)
             elif input_.type == InterfaceTypes.PolyData:
                 polydata = input_.data
                 if polydata.numberOfPoints:
@@ -442,6 +464,31 @@ def run(
                         mesh.cellData = buffer_to_numpy_array(mesh.meshType.cellPixelComponentType, bytes([]))
 
                     output_data = PipelineOutput(InterfaceTypes.Mesh, mesh)
+                elif output.type == InterfaceTypes.PointSet:
+                    point_set_json = ri.get_output_json(index)
+                    point_set = PointSet(**point_set_json)
+
+                    if point_set.numberOfPoints > 0:
+                        data_ptr = ri.get_output_array_address(0, index, 0)
+                        data_size = ri.get_output_array_size(0, index, 0)
+                        point_set.points = buffer_to_numpy_array(
+                            point_set.pointSetType.pointComponentType,
+                            ri.wasmtime_lift(data_ptr, data_size),
+                        )
+                    else:
+                        point_set.points = buffer_to_numpy_array(point_set.pointSetType.pointComponentType, bytes([]))
+
+                    if point_set.numberOfPointPixels > 0:
+                        data_ptr = ri.get_output_array_address(0, index, 1)
+                        data_size = ri.get_output_array_size(0, index, 1)
+                        point_set.pointData = buffer_to_numpy_array(
+                            point_set.pointSetType.pointPixelComponentType,
+                            ri.wasmtime_lift(data_ptr, data_size),
+                        )
+                    else:
+                        point_set.pointData = buffer_to_numpy_array(point_set.pointSetType.pointPixelComponentType, bytes([]))
+
+                    output_data = PipelineOutput(InterfaceTypes.PointSet, point_set)
                 elif output.type == InterfaceTypes.PolyData:
                     polydata_json = ri.get_output_json(index)
                     polydata = PolyData(**polydata_json)

diff --git a/...s/core/python/itkwasm/itkwasm/pointset.py → .../core/python/itkwasm/itkwasm/point_set.py b/...s/core/python/itkwasm/itkwasm/pointset.py → .../core/python/itkwasm/itkwasm/point_set.py
diff --git a/packages/core/python/itkwasm/itkwasm/pyodide.py b/packages/core/python/itkwasm/itkwasm/pyodide.py
@@ -2,7 +2,7 @@
 from typing import Optional
 
 from .image import Image, ImageType
-from .pointset import PointSet, PointSetType
+from .point_set import PointSet, PointSetType
 from .mesh import Mesh, MeshType
 from .polydata import PolyData, PolyDataType
 from .binary_file import BinaryFile

diff --git a/packages/core/python/itkwasm/pyproject.toml b/packages/core/python/itkwasm/pyproject.toml
@@ -47,6 +47,7 @@ dependencies = [
     "itk>=5.4.0",
     "pytest >=2.7.3",
     "pytest-pyodide",
+    "pyodide-py",
     "dask[array]",
     "test_accelerator @ {root:uri}/test/test-accelerator",
 ]
@@ -57,7 +58,7 @@ test = [
     "pytest --dist-dir=./dist --rt=chrome",
 ]
 download-pyodide = [
-  "curl -L https://github.com/pyodide/pyodide/releases/download/0.25.1/pyodide-0.25.1.tar.bz2 -o pyodide.tar.bz2",
+  "curl -L https://github.com/pyodide/pyodide/releases/download/0.26.2/pyodide-0.26.2.tar.bz2 -o pyodide.tar.bz2",
   "tar xjf pyodide.tar.bz2",
   "rm -rf dist pyodide.tar.bz2",
   "mv pyodide dist",

diff --git a/packages/core/typescript/itk-wasm/package.json b/packages/core/typescript/itk-wasm/package.json
@@ -1,6 +1,6 @@
 {
   "name": "itk-wasm",
-  "version": "1.0.0-b.178",
+  "version": "1.0.0-b.179",
   "packageManager": "[email protected]",
   "description": "High-performance spatial analysis in a web browser, Node.js, and reproducible execution across programming languages and hardware architectures.",
   "type": "module",

diff --git a/packages/core/typescript/itk-wasm/src/bindgen/interface-json-type-to-interface-type.js b/packages/core/typescript/itk-wasm/src/bindgen/interface-json-type-to-interface-type.js
@@ -15,6 +15,8 @@ const interfaceJsonTypeToInterfaceType = new Map([
   ['OUTPUT_IMAGE', 'Image'],
   ['INPUT_MESH', 'Mesh'],
   ['OUTPUT_MESH', 'Mesh'],
+  ['INPUT_POINT_SET', 'PointSet'],
+  ['OUTPUT_POINT_SET', 'PointSet'],
   ['INPUT_POLYDATA', 'PolyData'],
   ['OUTPUT_POLYDATA', 'PolyData'],
   ['INPUT_TRANSFORM', 'Transform'],

diff --git a/packages/core/typescript/itk-wasm/src/bindgen/python/interface-json-type-to-python-type.js b/packages/core/typescript/itk-wasm/src/bindgen/python/interface-json-type-to-python-type.js
@@ -15,6 +15,8 @@ const interfaceJsonTypeToPythonType = new Map([
   ['OUTPUT_IMAGE', 'Image'],
   ['INPUT_MESH', 'Mesh'],
   ['OUTPUT_MESH', 'Mesh'],
+  ['INPUT_POINT_SET', 'PointSet'],
+  ['OUTPUT_POINT_SET', 'PointSet'],
   ['INPUT_POLYDATA', 'PolyData'],
   ['OUTPUT_POLYDATA', 'PolyData'],
   ['INPUT_TRANSFORM', 'Transform'],

diff --git a/packages/core/typescript/itk-wasm/src/bindgen/typescript/demo/all-demo-types-supported.js b/packages/core/typescript/itk-wasm/src/bindgen/typescript/demo/all-demo-types-supported.js
@@ -11,7 +11,8 @@ const demoSupportedInputTypes = new Set([
   'BOOL',
   'INPUT_JSON',
   'INPUT_IMAGE',
-  'INPUT_MESH'
+  'INPUT_MESH',
+  'INPUT_POINT_SET'
 ])
 const demoSupportedOutputTypes = new Set([
   'OUTPUT_TEXT_FILE',
@@ -20,7 +21,8 @@ const demoSupportedOutputTypes = new Set([
   'OUTPUT_BINARY_STREAM',
   'OUTPUT_JSON',
   'OUTPUT_IMAGE',
-  'OUTPUT_MESH'
+  'OUTPUT_MESH',
+  'OUTPUT_POINT_SET'
 ])
 
 function allDemoTypesSupported(interfaceJson) {

diff --git a/packages/core/typescript/itk-wasm/src/bindgen/typescript/demo/input-parameters-demo-html.js b/packages/core/typescript/itk-wasm/src/bindgen/typescript/demo/input-parameters-demo-html.js
@@ -1,29 +1,40 @@
 import camelCase from '../../camel-case.js'
 import snakeCase from '../../snake-case.js'
 
-function inputParametersDemoHtml (functionName, prefix, indent, parameter, required, useCamelCase) {
+function inputParametersDemoHtml(
+  functionName,
+  prefix,
+  indent,
+  parameter,
+  required,
+  useCamelCase
+) {
   let result = ''
   const description = parameter.description.replaceAll('"', '&quot;')
   const requiredAttr = required ? 'required ' : ''
-  const label = useCamelCase ? camelCase(parameter.name) : snakeCase(parameter.name)
+  const label = useCamelCase
+    ? camelCase(parameter.name)
+    : snakeCase(parameter.name)
   const tooltipContent = `content="Use the Upload button to provide the ${label}"`
   const parameterType = parameter.type.split(' ')[0].split(':')[0]
   switch (parameterType) {
     case 'INPUT_TEXT_FILE':
-    case 'INPUT_TEXT_STREAM': {
-      result += `${prefix}${indent}<sl-tooltip ${tooltipContent}><sl-details id="${functionName}-${parameter.name}-details"  summary="${label}: ${description}" disabled></sl-details></sl-tooltip>\n`
-      const multiple = parameter.itemsExpectedMax > 1 ? 'multiple ' : ''
-      result += `${prefix}${indent}<label for="${parameter.name}-file"><sl-button name="${parameter.name}-file-button" variant="primary" outline onclick="this.parentElement.nextElementSibling.click()">Upload</sp-button></label><input type="file" ${multiple} name="${parameter.name}-file" style="display: none"/>\n`
-      result += '<br /><br />\n'
-    }
+    case 'INPUT_TEXT_STREAM':
+      {
+        result += `${prefix}${indent}<sl-tooltip ${tooltipContent}><sl-details id="${functionName}-${parameter.name}-details"  summary="${label}: ${description}" disabled></sl-details></sl-tooltip>\n`
+        const multiple = parameter.itemsExpectedMax > 1 ? 'multiple ' : ''
+        result += `${prefix}${indent}<label for="${parameter.name}-file"><sl-button name="${parameter.name}-file-button" variant="primary" outline onclick="this.parentElement.nextElementSibling.click()">Upload</sp-button></label><input type="file" ${multiple} name="${parameter.name}-file" style="display: none"/>\n`
+        result += '<br /><br />\n'
+      }
       break
     case 'INPUT_BINARY_FILE':
-    case 'INPUT_BINARY_STREAM': {
-      result += `${prefix}${indent}<sl-tooltip ${tooltipContent}><sl-details id="${functionName}-${parameter.name}-details" summary="${label}: ${description}" disabled></sl-details></sl-tooltip>\n`
-      const multiple = parameter.itemsExpectedMax > 1 ? 'multiple ' : ''
-      result += `${prefix}${indent}<label for="${parameter.name}-file"><sl-button name="${parameter.name}-file-button" ${requiredAttr}variant="primary" outline onclick="this.parentElement.nextElementSibling.click()">Upload</sl-button></label><input type="file" ${multiple} name="${parameter.name}-file" style="display: none"/>\n`
-      result += '<br /><br />\n'
-    }
+    case 'INPUT_BINARY_STREAM':
+      {
+        result += `${prefix}${indent}<sl-tooltip ${tooltipContent}><sl-details id="${functionName}-${parameter.name}-details" summary="${label}: ${description}" disabled></sl-details></sl-tooltip>\n`
+        const multiple = parameter.itemsExpectedMax > 1 ? 'multiple ' : ''
+        result += `${prefix}${indent}<label for="${parameter.name}-file"><sl-button name="${parameter.name}-file-button" ${requiredAttr}variant="primary" outline onclick="this.parentElement.nextElementSibling.click()">Upload</sl-button></label><input type="file" ${multiple} name="${parameter.name}-file" style="display: none"/>\n`
+        result += '<br /><br />\n'
+      }
       break
     case 'TEXT':
     case 'OUTPUT_TEXT_FILE':
@@ -32,28 +43,30 @@ function inputParametersDemoHtml (functionName, prefix, indent, parameter, requi
       break
     case 'INT':
     case 'UINT':
-    case 'FLOAT': {
-      const typeName = parameter.itemsExpectedMax > 1 ? "text" : "number"
-      let constraints = ''
-      if (parameter.itemsExpected !== 1) {
-        constraints = ''
-      } else if (parameterType === 'INT') {
-        constraints = 'step="1" '
-      } else if (parameterType === 'UINT') {
-        constraints = 'min="0" step="1" '
-      } else if (parameterType === 'FLOAT') {
-        constraints = 'step="any" '
+    case 'FLOAT':
+      {
+        const typeName = parameter.itemsExpectedMax > 1 ? 'text' : 'number'
+        let constraints = ''
+        if (parameter.itemsExpected !== 1) {
+          constraints = ''
+        } else if (parameterType === 'INT') {
+          constraints = 'step="1" '
+        } else if (parameterType === 'UINT') {
+          constraints = 'min="0" step="1" '
+        } else if (parameterType === 'FLOAT') {
+          constraints = 'step="any" '
+        }
+        result += `${prefix}${indent}<sl-input ${requiredAttr}name="${parameter.name}" type="${typeName}" value="${parameter.default}" ${constraints}label="${label}" help-text="${description}"></sl-input>\n`
+        result += '<br />\n'
       }
-      result += `${prefix}${indent}<sl-input ${requiredAttr}name="${parameter.name}" type="${typeName}" value="${parameter.default}" ${constraints}label="${label}" help-text="${description}"></sl-input>\n`
-      result += '<br />\n'
-    }
       break
     case 'BOOL':
       result += `${prefix}${indent}<sl-checkbox name="${parameter.name}">${label} - <i>${description}</i></sl-checkbox>\n`
       result += '<br /><br />\n'
       break
     case 'INPUT_JSON':
     case 'INPUT_MESH':
+    case 'INPUT_POINT_SET':
       result += `${prefix}${indent}<label for="${parameter.name}-file"><sl-button name="${parameter.name}-file-button" variant="primary" outline onclick="this.parentElement.nextElementSibling.click()">Upload</sp-button></label><input type="file" name="${parameter.name}-file" style="display: none"/>\n`
       result += `${prefix}${indent}<sl-tooltip ${tooltipContent}><sl-details id="${functionName}-${parameter.name}-details" summary="${label}: ${description}" disabled></sl-details></sl-tooltip>\n`
       result += '<br /><br />\n'