WIP: 109 layer descriptor shape parameters

.github/workflows/testreporting.yml

@@ -79,7 +79,7 @@ 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 +90,7 @@ 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

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:
@@ -1103,7 +1103,10 @@ 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 +1169,10 @@ 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 +1182,10 @@ 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));
 }

api/bag_interleavedlegacylayerdescriptor.cpp

@@ -20,9 +20,10 @@ namespace BAG {
 InterleavedLegacyLayerDescriptor::InterleavedLegacyLayerDescriptor(
     uint32_t id,
     LayerType layerType,
-    GroupType groupType)
+    GroupType groupType,
+    uint32_t rows, uint32_t cols)
     : LayerDescriptor(id, Layer::getInternalPath(layerType),
-        kLayerTypeMapString.at(layerType), layerType, 0, 0)
+        kLayerTypeMapString.at(layerType), layerType, rows, cols, 0, 0)
     , m_groupType(groupType)
     , m_elementSize(Layer::getElementSize(Layer::getDataType(layerType)))
 {
@@ -45,8 +46,10 @@ InterleavedLegacyLayerDescriptor::InterleavedLegacyLayerDescriptor(
 InterleavedLegacyLayerDescriptor::InterleavedLegacyLayerDescriptor(
     const Dataset& dataset,
     LayerType layerType,
-    GroupType groupType)
+    GroupType groupType,
+    uint32_t rows, uint32_t cols)
     : LayerDescriptor(dataset, layerType,
+        rows, cols,
         groupType == NODE
             ? NODE_GROUP_PATH
             : groupType == ELEVATION
@@ -76,9 +79,11 @@ std::shared_ptr<InterleavedLegacyLayerDescriptor> InterleavedLegacyLayerDescript
     LayerType layerType,
     GroupType groupType)
 {
+    uint32_t rows, cols;
+    std::tie(rows, cols) = dataset.getDescriptor().getDims();
     return std::shared_ptr<InterleavedLegacyLayerDescriptor>(
         new InterleavedLegacyLayerDescriptor{dataset.getNextId(), layerType,
-            groupType});
+            groupType, rows, cols});
 }
 
 //! Open an interleaved layer descriptor.
@@ -99,8 +104,10 @@ std::shared_ptr<InterleavedLegacyLayerDescriptor> InterleavedLegacyLayerDescript
     LayerType layerType,
     GroupType groupType)
 {
+    uint32_t rows, cols;
+    std::tie<uint32_t, uint32_t>(rows, cols) = dataset.getDescriptor().getDims();
     return std::shared_ptr<InterleavedLegacyLayerDescriptor>(
-        new InterleavedLegacyLayerDescriptor{dataset, layerType, groupType});
+        new InterleavedLegacyLayerDescriptor{dataset, layerType, groupType, rows, cols});
 }
 
 

api/bag_interleavedlegacylayerdescriptor.h

@@ -43,9 +43,9 @@ class BAG_API InterleavedLegacyLayerDescriptor final : public LayerDescriptor
 
 protected:
     InterleavedLegacyLayerDescriptor(uint32_t id, LayerType layerType,
-        GroupType groupType);
+        GroupType groupType, uint32_t rows, uint32_t cols);
     InterleavedLegacyLayerDescriptor(const Dataset& dataset, LayerType layerType,
-        GroupType groupType);
+        GroupType groupType, uint32_t rows, uint32_t cols);
 
 private:
     static void validateTypes(LayerType layerType, GroupType groupType);

api/bag_layer.cpp

@@ -208,9 +208,8 @@ UInt8Array Layer::read(
     if (m_pBagDataset.expired())
         throw DatasetNotFound{};
 
-    const auto pDataset = m_pBagDataset.lock();
     uint32_t numRows = 0, numColumns = 0;
-    std::tie(numRows, numColumns) = pDataset->getDescriptor().getDims();
+    std::tie(numRows, numColumns) = m_pLayerDescriptor->getDims();
 
     if (columnEnd >= numColumns || rowEnd >= numRows)
         throw InvalidReadSize{};