Add netcdf support (#2335)

- Integrated `vtkNetCDFReader` into the HDF plugin for `.nc`, `.cdf`, `.ncdf` 
- Updated `f3d-hdf-formats.xml` with the mime-types
- Added tests
- Updated `SUPPORTED_FORMATS.md` to list NetCDF and include a usage example and other docs

Author: vk1cd314

.github/actions/vtk-install-dep/action.yml

@@ -29,7 +29,7 @@ runs:
       uses: actions/cache/restore@v4
       with:
         path: dependencies/vtk_install
-        key: vtk-${{ inputs.vtk_version }}${{ inputs.openvdb_version != '' && format('-openvdb-{0}', inputs.openvdb_version) || '' }}-${{runner.os}}-${{inputs.raytracing_label}}-${{inputs.cpu}}-0
+        key: vtk-${{ inputs.vtk_version }}${{ inputs.openvdb_version != '' && format('-openvdb-{0}', inputs.openvdb_version) || '' }}-${{runner.os}}-${{inputs.raytracing_label}}-${{inputs.cpu}}-1
 
     - name: Setup VTK
       if: steps.cache-vtk.outputs.cache-hit != 'true'
@@ -93,6 +93,7 @@ runs:
         -DVTK_MODULE_ENABLE_VTK_IOHDF=YES
         -DVTK_MODULE_ENABLE_VTK_IOImage=YES
         -DVTK_MODULE_ENABLE_VTK_IOImport=YES
+        -DVTK_MODULE_ENABLE_VTK_IONetCDF=YES
         -DVTK_MODULE_ENABLE_VTK_IOOpenVDB=${{ inputs.openvdb_version != '' && 'YES' || 'DEFAULT' }}
         -DVTK_MODULE_ENABLE_VTK_IOPLY=YES
         -DVTK_MODULE_ENABLE_VTK_IOParallel=YES

CMakeLists.txt

@@ -109,6 +109,7 @@ find_package(VTK 9.2.6 REQUIRED
     opengl
     IOExodus
     IOHDF
+    IONetCDF
     IOOpenVDB
     RenderingRayTracing)
 message(STATUS "VTK ${VTK_VERSION} found")

application/testing/CMakeLists.txt

@@ -833,6 +833,14 @@ if(F3D_PLUGIN_BUILD_HDF)
     f3d_test(NAME TestPluginFullPath DATA disk_out_ref.ex2 ARGS --verbose --load-plugins "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_SHARED_MODULE_PREFIX}f3d-plugin-hdf${CMAKE_SHARED_MODULE_SUFFIX}" NO_BASELINE REGEXP "Loaded plugin hdf from")
   endif()
 
+  # NetCDF tests
+  # Basic rendering test with scalar coloring
+  f3d_test(NAME TestNetCDF DATA temperature_grid.nc ARGS --load-plugins=hdf -s)
+
+  if(NOT F3D_MACOS_BUNDLE)
+    f3d_test(NAME TestDefaultConfigFileNetCDF DATA temperature_grid.nc CONFIG config_build LONG_TIMEOUT TONE_MAPPING UI)
+    f3d_test(NAME TestThumbnailConfigFileNetCDF DATA temperature_grid.nc CONFIG thumbnail_build LONG_TIMEOUT TONE_MAPPING)
+  endif()
 endif()
 
 if(F3D_PLUGIN_BUILD_OCCT)

doc/dev/BUILD.md

@@ -24,7 +24,7 @@ F3D is tested continuously against versions recommended by the [VFX reference pl
 
 ## VTK compatibility
 
-As stated in the dependencies, F3D is compatible with VTK >= 9.2.6, however, some features may not be available. We suggest using VTK 9.5.0 with RenderingRayTracing, IOExodus, IOHDF and IOOpenVDB modules enabled in order to get as many features as possible in F3D.
+As stated in the dependencies, F3D is compatible with VTK >= 9.2.6, however, some features may not be available. We suggest using VTK 9.5.0 with RenderingRayTracing, IOExodus, IOHDF, IONetCDF and IOOpenVDB modules enabled in order to get as many features as possible in F3D.
 
 ## Configuration and building
 
@@ -46,7 +46,7 @@ Some modules, plugins and language bindings depending on external libraries can
 - `F3D_MODULE_RAYTRACING`: Support for raytracing rendering. Requires that VTK has been built with `OSPRay` and `VTK_MODULE_ENABLE_VTK_RenderingRayTracing` turned on. Disabled by default.
 - `F3D_MODULE_EXR`: Support for OpenEXR images. Requires `OpenEXR`. Disabled by default.
 - `F3D_MODULE_UI`: Support for ImGui widgets. Uses provided ImGui. Enabled by default.
-- `F3D_PLUGIN_BUILD_HDF`: Support for VTKHDF (.vtkhdf) and ExodusII (.ex2) file formats. Requires that VTK has been built with `IOHDF` and `IOExodus` modules (and `hdf5`). Enabled by default.
+- `F3D_PLUGIN_BUILD_HDF`: Support for VTKHDF (.vtkhdf), ExodusII (.ex2), and NetCDF (.nc) file formats. Requires that VTK has been built with `IOHDF`, `IOExodus`, and `IONetCDF` modules (and `hdf5`). Enabled by default.
 - `F3D_PLUGIN_BUILD_OCCT`: Support for STEP, IGES, BREP, and XBF file formats. Requires `OpenCASCADE`. Disabled by default.
 - `F3D_PLUGIN_BUILD_ASSIMP`: Support for FBX, DAE, OFF, DXF, X and 3MF file formats. Requires `Assimp`. Disabled by default.
 - `F3D_PLUGIN_BUILD_ALEMBIC`: Support for ABC file format. Requires `Alembic`. Disabled by default.

doc/user/SUPPORTED_FORMATS.md

@@ -8,6 +8,7 @@ F3D supports the following file formats:
 | VTK XML                                   | `.vtp`, `.vtu`, `.vtr`, `.vti`, `.vts`, `.vtm` | No         | No                   | `native`  | `VTKXMLVT<P,U,R,I,S,M>` |
 | VTKHDF                                    | `.vtkhdf`                                      | No         | Yes                  | `hdf`     | `VTKHDF`                |
 | EXODUS II                                 | `.e`, `.ex2`, `.exo`, `.g`                     | No         | Yes                  | `hdf`     | `ExodusII`              |
+| NetCDF                                    | `.nc`, `.cdf`, `.ncdf`                         | No         | No                   | `hdf`     | `NetCDF`                |
 | Polygon File Format                       | `.ply`                                         | No         | No                   | `native`  | `PLYReader`             |
 | Standard Triangle Language                | `.stl`                                         | No         | No                   | `native`  | `STL`                   |
 | DICOM                                     | `.dcm`                                         | No         | No                   | `native`  | `DICOM`                 |

plugins/hdf/CMakeLists.txt

@@ -31,11 +31,20 @@ f3d_plugin_declare_reader(
   CUSTOM_CODE "${CMAKE_CURRENT_SOURCE_DIR}/exodus.inl"
 )
 
+f3d_plugin_declare_reader(
+  NAME NetCDF
+  EXTENSIONS nc cdf ncdf
+  MIMETYPES application/netcdf application/x-netcdf
+  VTK_READER vtkNetCDFReader
+  FORMAT_DESCRIPTION "NetCDF"
+  CUSTOM_CODE "${CMAKE_CURRENT_SOURCE_DIR}/netcdf.inl"
+)
+
 f3d_plugin_build(
   NAME hdf
   VERSION 1.0
   DESCRIPTION "VTK HDF formats support"
-  VTK_MODULES IOHDF IOExodus
+  VTK_MODULES IOHDF IOExodus IONetCDF
   MIMETYPE_XML_FILES "${CMAKE_CURRENT_SOURCE_DIR}/f3d-hdf-formats.xml"
   CONFIGURATION_DIRS "${CMAKE_CURRENT_SOURCE_DIR}/configs/config.d" "${CMAKE_CURRENT_SOURCE_DIR}/configs/thumbnail.d"
   FREEDESKTOP

plugins/hdf/configs/config.d/10_hdf.json

@@ -1,7 +1,7 @@
 [
   {
     "match-type": "glob",
-    "match": "*.{exo,ex2,e,g,vtkhdf}",
+    "match": "*.{exo,ex2,e,g,vtkhdf,nc,cdf,ncdf}",
     "options": {
       "scalar-coloring": true,
       "load-plugins": "hdf",

plugins/hdf/configs/thumbnail.d/10_hdf.json

@@ -1,7 +1,7 @@
 [
   {
     "match-type": "glob",
-    "match": "*.{exo,ex2,e,g,vtkhdf}",
+    "match": "*.{exo,ex2,e,g,vtkhdf,nc,cdf,ncdf}",
     "options": {
       "scalar-coloring": true,
       "load-plugins": "hdf"

plugins/hdf/f3d-hdf-formats.xml

@@ -11,4 +11,10 @@
     <comment>VTKHDF file</comment>
     <glob pattern="*.vtkhdf"/>
   </mime-type>
+  <mime-type type="application/netcdf">
+    <comment>NetCDF file</comment>
+    <glob pattern="*.nc"/>
+    <glob pattern="*.cdf"/>
+    <glob pattern="*.ncdf"/>
+  </mime-type>
 </mime-info>

plugins/hdf/netcdf.inl

@@ -0,0 +1,15 @@
+void applyCustomReader(vtkAlgorithm* algo, const std::string&) const override
+{
+  vtkNetCDFReader* ncReader = vtkNetCDFReader::SafeDownCast(algo);
+  ncReader->UpdateInformation();
+  
+  int numArrays = ncReader->GetNumberOfVariableArrays();
+  for (int i = 0; i < numArrays; i++)
+  {
+    const char* arrayName = ncReader->GetVariableArrayName(i);
+    if (arrayName)
+    {
+      ncReader->SetVariableArrayStatus(arrayName, 1);
+    }
+  }
+}