109 layer descriptor shape parameters

.github/workflows/testmatrix.yml

@@ -9,6 +9,7 @@ on:
       - '*.md'
       - '*.svg'
       - '*.png'
+      - .github/workflows/testreporting.yml
       - .github/workflows/testwindows.yml
     branches: [ "master" ]
   pull_request:
@@ -19,6 +20,7 @@ on:
       - '*.md'
       - '*.svg'
       - '*.png'
+      - .github/workflows/testreporting.yml
       - .github/workflows/testwindows.yml
     branches: [ "master" ]
 
@@ -32,16 +34,22 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
-        os: [ubuntu-20.04]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-22.04]
     # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
     # You can convert this to a matrix build if you need cross-platform coverage.
     # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
     runs-on: ${{matrix.os}}
 
     steps:
     - name: Checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
+
+    - name: Setup Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
 
     - name: Install dependencies
       run: |
@@ -68,7 +76,7 @@ jobs:
       run: |
         sudo cmake --install build
         source python-venv/bin/activate
-        python -m pip install ./wheel/bagPy-*.whl
+        python -m pip install ./wheel/bag[pP]y-*.whl
         deactivate
 
     - name: Tests

.github/workflows/testreporting.yml

@@ -8,6 +8,7 @@ on:
       - README.*
       - '*.md'
       - '*.svg'
+      - .github/workflows/testmatrix.yml
       - .github/workflows/testwindows.yml
     branches: [ "master" ]
   pull_request:
@@ -50,15 +51,15 @@ jobs:
     # Get current banch name to use it as dest directory
     - name: Extract branch name
       shell: bash
-      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+      run: echo "branch=$(echo ${GITHUB_REF#refs/heads/})" >> $GITHUB_OUTPUT
       id: extract_branch
 
     - name: Prepare environment
       id: coverage
       run: |
         # Output values to be used by other steps
-        echo "##[set-output name=path;]${BADGE_PATH}"
-        echo "##[set-output name=branch;]${BRANCH}"
+        echo "path=${BADGE_PATH}" >> $GITHUB_OUTPUT
+        echo "branch=${BRANCH}" >> $GITHUB_OUTPUT
       env:
         BADGE_PATH: ${{ steps.extract_branch.outputs.branch }}/coverage.svg
         BRANCH: badges
@@ -79,7 +80,7 @@ jobs:
       run: |
         export CC=${{env.CC}}
         export CXX=${{env.CXX}}
-        cmake -G Ninja -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -B build -S . -DCMAKE_INSTALL_PREFIX=/usr/local -DBAG_BUILD_TESTS:BOOL=ON -DBAG_CODE_COVERAGE:BOOL=ON
+        cmake -G Ninja -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -B build -S . -DCMAKE_INSTALL_PREFIX=/usr/local -DBAG_BUILD_EXAMPLES:BOOL=ON -DBAG_BUILD_TESTS:BOOL=ON -DBAG_CODE_COVERAGE:BOOL=ON
 
     - name: Build
       # Build your program with the given configuration
@@ -90,7 +91,7 @@ jobs:
 
     - name: Run tests
       run: |
-        BAG_SAMPLES_PATH=${{github.workspace}}/examples/sample-data ./build/tests/bag_tests_d -r junit -o build/tests/bag_tests-testreport.xml
+        BAG_SAMPLES_PATH=${{github.workspace}}/examples/sample-data ./build/tests/bag_tests_d -r junit | tee build/tests/bag_tests-testreport.xml
 
     - name: Test Reporter
       uses: mikepenz/action-junit-report@v5

.github/workflows/testwindows.yml

@@ -46,7 +46,7 @@ jobs:
             SDK: release-1911
             MSVC_VER: 1920
             ZLIB_URL: "https://github.com/madler/zlib/releases/download/v1.3/zlib13.zip"
-            LIBXML2_URL: "https://gitlab.gnome.org/GNOME/libxml2/-/archive/v2.13.5/libxml2-v2.13.5.zip"
+            LIBXML2_URL: "https://download.gnome.org/sources/libxml2/2.13/libxml2-2.13.9.tar.xz"
             HDF5_URL: "https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_1.14.5.zip"
             CATCH2_URL: "https://github.com/catchorg/Catch2/archive/refs/tags/v3.4.0.zip"
 
@@ -102,7 +102,7 @@ jobs:
           cd downloads
           $env:ZLIB_ZIP="zlib.zip"
           if(-Not (Test-Path -Path $env:ZLIB_ZIP -PathType Leaf)) { Invoke-WebRequest "$env:ZLIB_URL" -OutFile "$env:ZLIB_ZIP" }
-          $env:LIBXML2_ZIP="libxml2.zip"
+          $env:LIBXML2_ZIP="libxml2.tar.xz"
           if(-Not (Test-Path -Path $env:LIBXML2_ZIP -PathType Leaf)) { Invoke-WebRequest "$env:LIBXML2_URL" -OutFile "$env:LIBXML2_ZIP" }
           $env:HDF5_ZIP="hdf5.zip"
           if(-Not (Test-Path -Path $env:HDF5_ZIP -PathType Leaf)) { Invoke-WebRequest "$env:HDF5_URL" -OutFile "$env:HDF5_ZIP" }
@@ -121,8 +121,8 @@ jobs:
           cmake --build build --config Release --target install -- /nologo /verbosity:minimal 
           cd ..
           # libxml2
-          exec { 7z x ..\downloads\$env:LIBXML2_ZIP }
-          cd libxml2-v2.13.5
+          exec { tar xf ..\downloads\$env:LIBXML2_ZIP }
+          cd libxml2-2.13.9
           if(-Not (Test-Path -Path build)) { mkdir build }
           cmake -B build -G $env:VS_VERSION -S . $env:CMAKE_INSTALL_PREFIX -DCMAKE_BUILD_TYPE=Release `
             -DLIBXML2_WITH_ZLIB=ON -DLIBXML2_WITH_ICONV=OFF -DLIBXML2_WITH_LZMA=OFF -DLIBXML2_WITH_PYTHON=OFF

api/bag.cpp

@@ -824,7 +824,7 @@ BagError bagGetErrorString(
         strncpy(str, "Metadata One or more elements of the requested coverage are missing from the XML file", MAX_STR-1);
         break;
     case BAG_METADTA_INVLID_DIMENSIONS:
-        sprintf(str, "Metadata The number of dimensions is incorrect (not equal to %d)", RANK);
+        snprintf(str, MAX_STR, "Metadata The number of dimensions is incorrect (not equal to %d)", RANK);
         break;
     case BAG_METADTA_BUFFER_EXCEEDED:
         strncpy(str, "Metadata supplied buffer is too large to be stored in the internal array", MAX_STR-1);
@@ -866,7 +866,7 @@ BagError bagGetErrorString(
         strncpy(str, "HDF Bag is not an HDF5 File", MAX_STR-1);
         break;
     case BAG_HDF_RANK_INCOMPATIBLE:
-        sprintf(str, "HDF Bag's rank is incompatible with expected Rank of the Datasets: %d", RANK);
+        snprintf(str, MAX_STR, "HDF Bag's rank is incompatible with expected Rank of the Datasets: %d", RANK);
         break;
     case BAG_HDF_TYPE_NOT_FOUND:
         strncpy(str, "HDF Bag surface Datatype parameter not available", MAX_STR-1);

api/bag_dataset.cpp

@@ -502,12 +502,12 @@ void Dataset::createDataset(
 
     // Mandatory Layers
     // Elevation
-    this->addLayer(SimpleLayer::create(*this, Elevation, chunkSize,
-        compressionLevel));
+    this->addLayer(SimpleLayer::create(*this, Elevation, m_pMetadata->rows(), m_pMetadata->columns(),
+        chunkSize, compressionLevel));
 
     // Uncertainty
-    this->addLayer(SimpleLayer::create(*this, Uncertainty, chunkSize,
-        compressionLevel));
+    this->addLayer(SimpleLayer::create(*this, Uncertainty, m_pMetadata->rows(), m_pMetadata->columns(),
+        chunkSize, compressionLevel));
 }
 
 //! Create an optional simple layer.
@@ -546,8 +546,8 @@ Layer& Dataset::createSimpleLayer(
     case Num_Soundings:  //[[fallthrough]];
     case Average_Elevation:  //[[fallthrough]];
     case Nominal_Elevation:
-        return this->addLayer(SimpleLayer::create(*this, type, chunkSize,
-            compressionLevel));
+        return this->addLayer(SimpleLayer::create(*this, type,
+            m_pMetadata->rows(), m_pMetadata->columns(), chunkSize, compressionLevel));
     case Surface_Correction:  //[[fallthrough]];
     case Georef_Metadata:  //[[fallthrough]];
     default:
@@ -1073,10 +1073,17 @@ void Dataset::readDataset(
     OpenMode openMode)
 {
     signal(SIGABRT, handleAbrt);
-    m_pH5file = std::unique_ptr<::H5::H5File, DeleteH5File>(new ::H5::H5File{
-        fileName.c_str(),
-        (openMode == BAG_OPEN_READONLY) ? H5F_ACC_RDONLY : H5F_ACC_RDWR},
-        DeleteH5File{});
+    try {
+        m_pH5file = std::unique_ptr<::H5::H5File, DeleteH5File>(new ::H5::H5File{
+                                                                        fileName.c_str(),
+                                                                        (openMode == BAG_OPEN_READONLY) ? H5F_ACC_RDONLY : H5F_ACC_RDWR},
+                                                                DeleteH5File{});
+    }
+    catch( ::H5::FileIException& e )
+    {
+        std::cerr << "Unable to read BAG file, error was: " << e.getCDetailMsg() << std::endl;
+        e.printErrorStack();
+    }
 
     m_pMetadata = std::make_unique<Metadata>(*this);
 
@@ -1103,7 +1110,10 @@ void Dataset::readDataset(
 
         H5Dclose(id);
 
-        auto layerDesc = SimpleLayerDescriptor::open(*this, layerType);
+        // Pre-stage the layer-specific desciptor.  Note that we don't need to specify the
+        // dimensions of the layer here, since they're set from the HDF5 dataset when it
+        // gets opened with SimpleLayer::open().
+        auto layerDesc = SimpleLayerDescriptor::open(*this, layerType, 0, 0);
         this->addLayer(SimpleLayer::open(*this, *layerDesc));
     }
 
@@ -1166,7 +1176,10 @@ void Dataset::readDataset(
         }
 
         {
-            auto descriptor = VRRefinementsDescriptor::open(*this);
+            // Pre-stage the layer-specific descriptor for the refinements; note that this
+            // doesn't have to have specific dimensions since they're set when the refinements
+            // layer is read in VRRefinements::open().
+            auto descriptor = VRRefinementsDescriptor::open(*this, 0, 0);
             this->addLayer(VRRefinements::open(*this, *descriptor));
         }
 
@@ -1176,7 +1189,10 @@ void Dataset::readDataset(
         {
             H5Dclose(id);
 
-            auto descriptor = VRNodeDescriptor::open(*this);
+            // Pre-stage the layer-specific descriptor for the nodes; note that this doesn't
+            // have to have specific dimensions since they're set when the nodes layer is
+            // read in VRNode::open().
+            auto descriptor = VRNodeDescriptor::open(*this, 0, 0);
             this->addLayer(VRNode::open(*this, *descriptor));
         }
     }

api/bag_exceptions.h

@@ -441,7 +441,7 @@ struct BAG_API InvalidVRRefinementDimensions final : virtual std::exception
 {
     const char* what() const noexcept override
     {
-        return "The variable resolution refinement layer is not 1 dimensional.";
+        return "The variable resolution refinement layer is inconsistent with specification.";
     }
 };
 

api/bag_georefmetadatalayer.cpp

@@ -104,8 +104,13 @@ std::shared_ptr<GeorefMetadataLayer> GeorefMetadataLayer::create(
         keyType != DT_UINT64)
         throw InvalidKeyType{};
 
+    // The keys array should be the same dimensions as the mandatory elevation layer, so read
+    // from the file global descriptor, and set.
+    uint32_t rows = 0, cols = 0;
+    std::tie<uint32_t, uint32_t>(rows, cols) = dataset.getDescriptor().getDims();
     auto pDescriptor = GeorefMetadataLayerDescriptor::create(dataset, name, profile, keyType,
-                                                             definition, chunkSize, compressionLevel);
+                                                             definition, rows, cols,
+                                                             chunkSize, compressionLevel);
 
     // Create the H5 Group to hold keys & values.
     const auto& h5file = dataset.getH5file();
@@ -122,7 +127,8 @@ std::shared_ptr<GeorefMetadataLayer> GeorefMetadataLayer::create(
     auto h5valueDataSet = GeorefMetadataLayer::createH5valueDataSet(dataset, *pDescriptor);
 
     auto layer = std::make_shared<GeorefMetadataLayer>(dataset,
-                                                       *pDescriptor, std::move(h5keyDataSet), std::move(h5vrKeyDataSet),
+                                                       *pDescriptor, std::move(h5keyDataSet),
+                                                       std::move(h5vrKeyDataSet),
                                                        std::move(h5valueDataSet));
 
     layer->setValueTable(std::unique_ptr<ValueTable>(new ValueTable{*layer}));
@@ -150,6 +156,12 @@ std::shared_ptr<GeorefMetadataLayer> GeorefMetadataLayer::open(
         new ::H5::DataSet{h5file.openDataSet(internalPath + COMPOUND_KEYS)},
         DeleteH5dataSet{});
 
+    // The keys array has the dimensions of the layer, so we can read and reset the
+    // descriptor dimensions, in case they were inconsistent (or not set).
+    std::array<hsize_t, kRank> dims;
+    h5keyDataSet->getSpace().getSimpleExtentDims(dims.data(), nullptr);
+    descriptor.setDims(dims[0], dims[1]);
+
     std::unique_ptr<::H5::DataSet, DeleteH5dataSet> h5vrKeyDataSet{};
     if (dataset.getVRMetadata())
         h5vrKeyDataSet = std::unique_ptr<::H5::DataSet, DeleteH5dataSet>(
@@ -161,7 +173,9 @@ std::shared_ptr<GeorefMetadataLayer> GeorefMetadataLayer::open(
         DeleteH5dataSet{});
 
     auto layer = std::make_shared<GeorefMetadataLayer>(dataset,
-                                                       descriptor, std::move(h5keyDataSet), std::move(h5vrKeyDataSet),
+                                                       descriptor,
+                                                       std::move(h5keyDataSet),
+                                                       std::move(h5vrKeyDataSet),
                                                        std::move(h5valueDataSet));
 
     layer->setValueTable(std::unique_ptr<ValueTable>(new ValueTable{*layer}));
@@ -188,7 +202,9 @@ GeorefMetadataLayer::createH5keyDataSet(
     std::unique_ptr<::H5::DataSet, DeleteH5dataSet> pH5dataSet;
 
     {
-        // Use the dimensions from the descriptor.
+        // Use the dimensions from the descriptor.  We could do this from the specific
+        // descriptor for the layer, too, which should mirror the size of the file global
+        // descriptor used here.
         uint32_t dim0 = 0, dim1 = 0;
         std::tie(dim0, dim1) = dataset.getDescriptor().getDims();
         const std::array<hsize_t, kRank> fileDims{dim0, dim1};

api/bag_georefmetadatalayer.h

@@ -64,8 +64,8 @@ class BAG_API GeorefMetadataLayer final : public Layer
 protected:
     static std::shared_ptr<GeorefMetadataLayer> create(DataType keyType,
                                                        const std::string& name, GeorefMetadataProfile profile, Dataset& dataset,
-                                                       const RecordDefinition& definition, uint64_t chunkSize,
-                                                       int compressionLevel);
+                                                       const RecordDefinition& definition,
+                                                       uint64_t chunkSize, int compressionLevel);
     static std::shared_ptr<GeorefMetadataLayer> open(Dataset& dataset,
                                                      GeorefMetadataLayerDescriptor& descriptor);
 

api/bag_georefmetadatalayerdescriptor.cpp

@@ -35,10 +35,11 @@ GeorefMetadataLayerDescriptor::GeorefMetadataLayerDescriptor(
         GeorefMetadataProfile profile,
         DataType keyType,
         RecordDefinition definition,
+        uint32_t rows, uint32_t cols,
         uint64_t chunkSize,
         int compressionLevel)
     : LayerDescriptor(dataset.getNextId(), GEOREF_METADATA_PATH + name, name,
-                      Georef_Metadata, chunkSize, compressionLevel)
+                      Georef_Metadata, rows, cols, chunkSize, compressionLevel)
     , m_pBagDataset(dataset.shared_from_this())
     , m_profile(profile)
     , m_keyType(keyType)
@@ -72,12 +73,14 @@ std::shared_ptr<GeorefMetadataLayerDescriptor> GeorefMetadataLayerDescriptor::cr
             GeorefMetadataProfile profile,
             DataType keyType,
             RecordDefinition definition,
+            uint32_t rows, uint32_t cols,
             uint64_t chunkSize,
             int compressionLevel)
 {
     return std::shared_ptr<GeorefMetadataLayerDescriptor>(
         new GeorefMetadataLayerDescriptor{dataset, name, profile, keyType,
-                                          std::move(definition), chunkSize, compressionLevel});
+                                          std::move(definition), rows, cols,
+                                          chunkSize, compressionLevel});
 }
 
 //! Open an existing georeferenced metadata layer descriptor.
@@ -165,8 +168,13 @@ std::shared_ptr<GeorefMetadataLayerDescriptor> GeorefMetadataLayerDescriptor::op
         profile = UNKNOWN_METADATA_PROFILE;
     }
 
+    std::array<hsize_t, 2> dims;
+    h5dataSet.getSpace().getSimpleExtentDims(dims.data(), nullptr);
+
     return std::shared_ptr<GeorefMetadataLayerDescriptor>(
         new GeorefMetadataLayerDescriptor{dataset, name, profile, keyType, definition,
+                                          static_cast<const uint32_t>(dims[0]),
+                                          static_cast<const uint32_t>(dims[1]),
                                           chunkSize, compressionLevel});
 }
 

api/bag_georefmetadatalayerdescriptor.h

@@ -21,12 +21,13 @@ namespace BAG {
 class BAG_API GeorefMetadataLayerDescriptor final : public LayerDescriptor
 {
 public:
-    static std::shared_ptr<GeorefMetadataLayerDescriptor> create(Dataset& dataset,
-                                                                 const std::string& name, GeorefMetadataProfile profile, DataType keyType,
-                                                                 RecordDefinition definition, uint64_t chunkSize,
-                                                                 int compressionLevel);
-    static std::shared_ptr<GeorefMetadataLayerDescriptor> open(Dataset& dataset,
-                                                               const std::string& name);
+    static std::shared_ptr<GeorefMetadataLayerDescriptor>
+        create(Dataset& dataset,
+            const std::string& name, GeorefMetadataProfile profile, DataType keyType,
+            RecordDefinition definition, uint32_t rows, uint32_t cols,
+            uint64_t chunkSize, int compressionLevel);
+    static std::shared_ptr<GeorefMetadataLayerDescriptor>
+        open(Dataset& dataset, const std::string& name);
 
     GeorefMetadataLayerDescriptor(const GeorefMetadataLayerDescriptor&) = delete;
     GeorefMetadataLayerDescriptor(GeorefMetadataLayerDescriptor&&) = delete;
@@ -52,7 +53,8 @@ class BAG_API GeorefMetadataLayerDescriptor final : public LayerDescriptor
 
 protected:
     GeorefMetadataLayerDescriptor(Dataset& dataset, const std::string& name, GeorefMetadataProfile profile,
-                                  DataType keyType, RecordDefinition definition, uint64_t chunkSize,
+                                  DataType keyType, RecordDefinition definition,
+                                  uint32_t rows, uint32_t cols, uint64_t chunkSize,
                                   int compressionLevel);
 
 private:

api/bag_interleavedlegacylayer.cpp

@@ -51,6 +51,10 @@ std::shared_ptr<InterleavedLegacyLayer> InterleavedLegacyLayer::open(
         descriptor.setMinMax(std::get<1>(possibleMinMax),
             std::get<2>(possibleMinMax));
 
+    std::array<hsize_t, 2> dims;
+    h5dataSet->getSpace().getSimpleExtentDims(dims.data(), nullptr);
+    descriptor.setDims(dims[0], dims[1]);
+
     return std::make_shared<InterleavedLegacyLayer>(dataset,
         descriptor, std::move(h5dataSet));
 }