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tbirdsotbirdso
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Merge pull request #54 from tbirdso/bump-workflows
ENH: Bump ITK CI Reusable Workflow
2 parents 0f69d0a + f963101 commit d962330

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‎.github/workflows/build-test-package.yml‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,9 +4,11 @@ on: [push,pull_request]
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jobs:
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cxx-build-workflow:
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uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.3.0
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uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@03626a23c22246e89e36c7e918a158c440f9b099
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python-build-workflow:
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uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/[email protected]
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uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@03626a23c22246e89e36c7e918a158c440f9b099
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with:
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test-notebooks: true
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secrets:
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pypi_password: ${{ secrets.pypi_password }}

‎examples/itkPolyDataToMeshFilter.ipynb‎

Lines changed: 61 additions & 91 deletions
Original file line numberDiff line numberDiff line change
@@ -35,46 +35,68 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"MESH_FILE = 'Input/cow.vtk'\n",
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"MESH_FILE = \"Input/cow.vtk\"\n",
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"\n",
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"# Download mesh\n",
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"os.makedirs('Input', exist_ok=True)\n",
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"os.makedirs(\"Input\", exist_ok=True)\n",
4242
"if not os.path.exists(MESH_FILE):\n",
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" url = 'https://data.kitware.com/api/v1/file/5c43feba8d777f072b0cd3da/download'\n",
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" url = \"https://data.kitware.com/api/v1/file/5c43feba8d777f072b0cd3da/download\"\n",
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" urlretrieve(url, MESH_FILE)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"mesh_input = itk.meshread(MESH_FILE, itk.D)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"2903\n",
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"3263\n"
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"Mesh (0000026EE123F310)\n",
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" RTTI typeinfo: class itk::Mesh<double,3,class itk::DefaultStaticMeshTraits<double,3,3,float,float,double> >\n",
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" Reference Count: 1\n",
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" Modified Time: 28464\n",
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" Debug: Off\n",
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" Object Name: \n",
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" Observers: \n",
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" none\n",
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" Source: (none)\n",
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" Source output name: (none)\n",
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" Release Data: Off\n",
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" Data Released: False\n",
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" Global Release Data: Off\n",
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" PipelineMTime: 19016\n",
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" UpdateMTime: 28463\n",
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" RealTimeStamp: 0 seconds \n",
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" Number Of Points: 2903\n",
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" Requested Number Of Regions: 1\n",
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" Requested Region: 0\n",
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" Buffered Region: 0\n",
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" Maximum Number Of Regions: 1\n",
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" Point Data Container pointer: 0000000000000000\n",
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" Size of Point Data Container: 0\n",
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" Number Of Points: 2903\n",
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" Number Of Cell Links: 0\n",
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" Number Of Cells: 3263\n",
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" Cell Data Container pointer: 0000000000000000\n",
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" Size of Cell Data Container: 0\n",
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" Number of explicit cell boundary assignments: 3\n",
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" CellsAllocationMethod: itk::MeshEnums::MeshClassCellsAllocationMethod::CellsAllocatedDynamicallyCellByCell\n",
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"\n"
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]
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}
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],
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"source": [
71-
"print(mesh_input.GetNumberOfPoints())\n",
72-
"print(mesh_input.GetNumberOfCells())"
91+
"mesh_input = itk.meshread(MESH_FILE, itk.D)\n",
92+
"\n",
93+
"assert type(mesh_input) == itk.Mesh[itk.D, 3]\n",
94+
"print(mesh_input)"
7395
]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
@@ -90,20 +112,20 @@
90112
}
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],
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"source": [
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"# Visualize points\n",
94-
"for i in range(0,5):\n",
115+
"# Inspect a few points\n",
116+
"for i in range(0, 5):\n",
95117
" print(mesh_input.GetPoints().GetElement(i))"
96118
]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 7,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "9a86a686b49a44bb982404601090aa47",
128+
"model_id": "dd14dc2d3e1942c48e154f89573a872d",
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"version_major": 2,
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"version_minor": 0
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},
@@ -119,64 +141,28 @@
119141
"view(geometries=[mesh_input])"
120142
]
121143
},
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{
123-
"cell_type": "code",
124-
"execution_count": 7,
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"metadata": {},
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"outputs": [],
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"source": [
128-
"# Test preservation of point data\n",
129-
"mesh_input.GetPointData().Reserve(1)\n",
130-
"mesh_input.GetPointData().SetElement(0,500) #FIXME remove"
131-
]
132-
},
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{
134145
"cell_type": "markdown",
135146
"metadata": {},
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"source": [
137148
"### Convert to `itk.PolyData`"
138149
]
139150
},
140-
{
141-
"cell_type": "code",
142-
"execution_count": 8,
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"metadata": {},
144-
"outputs": [],
145-
"source": [
146-
"filter = itk.MeshToPolyDataFilter[type(mesh_input)].New(Input=mesh_input)"
147-
]
148-
},
149151
{
150152
"cell_type": "code",
151153
"execution_count": 9,
152154
"metadata": {},
153155
"outputs": [],
154156
"source": [
155-
"filter.Update()"
157+
"poly_data = itk.mesh_to_poly_data_filter(mesh_input)\n",
158+
"\n",
159+
"assert type(poly_data) == itk.PolyData[itk.D]"
156160
]
157161
},
158162
{
159163
"cell_type": "code",
160164
"execution_count": 10,
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"metadata": {},
162-
"outputs": [],
163-
"source": [
164-
"poly_data = filter.GetOutput()"
165-
]
166-
},
167-
{
168-
"cell_type": "code",
169-
"execution_count": 11,
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"metadata": {},
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"outputs": [],
172-
"source": [
173-
"assert(type(poly_data) == itk.PolyData[itk.D])"
174-
]
175-
},
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{
177-
"cell_type": "code",
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"execution_count": 12,
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"metadata": {},
180166
"outputs": [
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{
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"name": "stdout",
@@ -407,7 +393,7 @@
407393
"polygons = poly_data.GetPolygons()\n",
408394
"while i < 1000:\n",
409395
" x = list()\n",
410-
" for j in range(0,polygons.ElementAt(i)):\n",
396+
" for j in range(0, polygons.ElementAt(i)):\n",
411397
" x.append(polygons.ElementAt(i + 1 + j))\n",
412398
" print(x)\n",
413399
" i += polygons.ElementAt(i) + 1"
@@ -422,54 +408,38 @@
422408
},
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{
424410
"cell_type": "code",
425-
"execution_count": 13,
426-
"metadata": {},
427-
"outputs": [],
428-
"source": [
429-
"filter = itk.PolyDataToMeshFilter[type(poly_data)].New(Input=poly_data)"
430-
]
431-
},
432-
{
433-
"cell_type": "code",
434-
"execution_count": 14,
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"metadata": {},
436-
"outputs": [],
437-
"source": [
438-
"filter.Update()"
439-
]
440-
},
441-
{
442-
"cell_type": "code",
443-
"execution_count": 15,
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"execution_count": 12,
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"metadata": {},
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"outputs": [],
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"source": [
447-
"mesh_output = filter.GetOutput()"
415+
"mesh_output = itk.poly_data_to_mesh_filter(poly_data)\n",
416+
"\n",
417+
"assert type(mesh_output) == itk.Mesh[itk.D, 3]"
448418
]
449419
},
450420
{
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"cell_type": "code",
452-
"execution_count": 16,
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"execution_count": 13,
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"metadata": {
454424
"scrolled": true
455425
},
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"outputs": [],
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"source": [
458-
"assert(mesh_output.GetNumberOfPoints() == mesh_input.GetNumberOfPoints())\n",
459-
"assert(mesh_output.GetNumberOfCells() == mesh_input.GetNumberOfCells())\n",
460-
"for i in range(0,mesh_output.GetNumberOfPoints()):\n",
461-
" assert(mesh_output.GetPoint(i) == mesh_input.GetPoint(i))"
428+
"assert mesh_output.GetNumberOfPoints() == mesh_input.GetNumberOfPoints()\n",
429+
"assert mesh_output.GetNumberOfCells() == mesh_input.GetNumberOfCells()\n",
430+
"for i in range(0, mesh_output.GetNumberOfPoints()):\n",
431+
" assert mesh_output.GetPoint(i) == mesh_input.GetPoint(i)"
462432
]
463433
},
464434
{
465435
"cell_type": "code",
466-
"execution_count": 17,
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"execution_count": 14,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
472-
"model_id": "de7f8f07558e443392b3dbd6859b2ef0",
442+
"model_id": "71ab9ed224294f46a4ecc1711b479cea",
473443
"version_major": 2,
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"version_minor": 0
475445
},
@@ -488,9 +458,9 @@
488458
],
489459
"metadata": {
490460
"kernelspec": {
491-
"display_name": "venv-itk4",
461+
"display_name": "Python 3",
492462
"language": "python",
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"name": "venv-itk4"
463+
"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {

‎requirements.txt‎

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Original file line numberDiff line numberDiff line change
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1+
itk>=v5.3.0
2+
itk-meshtopolydata>=0.10.0
3+
traitlets<5.7.0
4+
ipywidgets>=7.1.2
5+
itkwidgets

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