fix #155 support for ADCIRC file

lutraconsulting · Sep 12, 2019 · 594d6eb · 594d6eb
1 parent 52cf319
commit 594d6eb
Show file tree

Hide file tree

Showing 5 changed files with 74 additions and 4 deletions.
diff --git a/mdal/frmts/mdal_cf.cpp b/mdal/frmts/mdal_cf.cpp
@@ -185,6 +185,34 @@ std::shared_ptr<MDAL::Dataset> MDAL::DriverCF::createFace2DDataset( std::shared_
   return dataset;
 }
 
+std::shared_ptr<MDAL::Dataset> MDAL::DriverCF::createVertex2DDataset( std::shared_ptr<MDAL::DatasetGroup> group,
+    size_t ts, const MDAL::CFDatasetGroupInfo &dsi,
+    const std::vector<double> &vals_x,
+    const std::vector<double> &vals_y,
+    double fill_val_x, double fill_val_y )
+{
+  assert( dsi.outputType == CFDimensions::Vertex2D );
+  size_t nVertices2D = mDimensions.size( CFDimensions::Vertex2D );
+
+  std::shared_ptr<MDAL::MemoryDataset> dataset = std::make_shared<MDAL::MemoryDataset>( group.get() );
+
+  for ( size_t i = 0; i < nVertices2D; ++i )
+  {
+    size_t idx = ts * nVertices2D + i;
+    populate_vals( dsi.is_vector,
+                   dataset->values(),
+                   i,
+                   vals_x,
+                   vals_y,
+                   idx,
+                   fill_val_x,
+                   fill_val_y );
+
+  }
+
+  return dataset;
+}
+
 void MDAL::DriverCF::addDatasetGroups( MDAL::Mesh *mesh, const std::vector<double> &times, const MDAL::cfdataset_info_map &dsinfo_map )
 {
   /* PHASE 2 - add dataset groups */
@@ -199,7 +227,16 @@ void MDAL::DriverCF::addDatasetGroups( MDAL::Mesh *mesh, const std::vector<doubl
           dsi.name
         );
     group->setIsScalar( !dsi.is_vector );
-    group->setIsOnVertices( false );
+
+    if ( dsi.outputType == CFDimensions::Vertex2D )
+      group->setIsOnVertices( true );
+    else if ( dsi.outputType == CFDimensions::Face2D )
+      group->setIsOnVertices( false );
+    else
+    {
+      // unsupported
+      continue;
+    }
 
     // read X data
     double fill_val_x = mNcFile.getFillValue( dsi.ncid_x );
@@ -225,6 +262,13 @@ void MDAL::DriverCF::addDatasetGroups( MDAL::Mesh *mesh, const std::vector<doubl
       if ( dsi.outputType == CFDimensions::Face2D )
       {
         dataset = createFace2DDataset( group, ts, dsi, vals_x, vals_y, fill_val_x, fill_val_y );
+      }
+      else     // Vertex2D
+      {
+        dataset = createVertex2DDataset( group, ts, dsi, vals_x, vals_y, fill_val_x, fill_val_y );
+      }
+      if ( dataset )
+      {
         dataset->setTime( time );
         dataset->setStatistics( MDAL::calculateStatistics( dataset ) );
         group->datasets.push_back( dataset );

diff --git a/mdal/frmts/mdal_cf.hpp b/mdal/frmts/mdal_cf.hpp
@@ -94,6 +94,14 @@ namespace MDAL
         const std::vector<double> &vals_y,
         double fill_val_x, double fill_val_y );
 
+      std::shared_ptr<MDAL::Dataset> createVertex2DDataset(
+        std::shared_ptr<MDAL::DatasetGroup> group,
+        size_t ts,
+        const MDAL::CFDatasetGroupInfo &dsi,
+        const std::vector<double> &vals_x,
+        const std::vector<double> &vals_y,
+        double fill_val_x, double fill_val_y );
+
       void addDatasetGroups( Mesh *mesh,
                              const std::vector<double> &times,
                              const cfdataset_info_map &dsinfo_map );

diff --git a/mdal/frmts/mdal_netcdf.cpp b/mdal/frmts/mdal_netcdf.cpp
@@ -82,6 +82,19 @@ std::vector<std::string> NetCDFFile::readArrNames() const
   return res;
 }
 
+bool NetCDFFile::hasAttrInt( const std::string &name, const std::string &attr_name ) const
+{
+  assert( mNcid != 0 );
+
+  int arr_id;
+  if ( nc_inq_varid( mNcid, name.c_str(), &arr_id ) != NC_NOERR ) return false;
+
+  int val;
+  if ( nc_get_att_int( mNcid, arr_id, attr_name.c_str(), &val ) ) return false;
+
+  return true;
+}
+
 int NetCDFFile::getAttrInt( const std::string &name, const std::string &attr_name ) const
 {
   assert( mNcid != 0 );

diff --git a/mdal/frmts/mdal_netcdf.hpp b/mdal/frmts/mdal_netcdf.hpp
@@ -26,6 +26,7 @@ class NetCDFFile
     bool hasArr( const std::string &name ) const;
     std::vector<std::string> readArrNames() const;
 
+    bool hasAttrInt( const std::string &name, const std::string &attr_name ) const;
     int getAttrInt( const std::string &name, const std::string &attr_name ) const;
     double getAttrDouble( int varid, const std::string &attr_name ) const;
     /**

diff --git a/mdal/frmts/mdal_ugrid.cpp b/mdal/frmts/mdal_ugrid.cpp
@@ -209,7 +209,9 @@ void MDAL::DriverUgrid::populateFaces( MDAL::Faces &faces )
   const std::string mesh2dFaceNodeConnectivity = mNcFile.getAttrStr( mMesh2dName, "face_node_connectivity" );
 
   size_t verticesInFace = mDimensions.size( CFDimensions::MaxVerticesInFace );
-  int fill_val = mNcFile.getAttrInt( mesh2dFaceNodeConnectivity, "_FillValue" );
+  int fill_val = -1;
+  if ( mNcFile.hasAttrInt( mesh2dFaceNodeConnectivity, "_FillValue" ) )
+    fill_val = mNcFile.getAttrInt( mesh2dFaceNodeConnectivity, "_FillValue" );
   int start_index = mNcFile.getAttrInt( mesh2dFaceNodeConnectivity, "start_index" );
   std::vector<int> face_nodes_conn = mNcFile.readIntArr( mesh2dFaceNodeConnectivity, faceCount * verticesInFace );
 
@@ -352,16 +354,18 @@ void MDAL::DriverUgrid::parseNetCDFVariableMetadata( int varid, const std::strin
   }
   else
   {
-    if ( MDAL::contains( long_name, ", x-component" ) )
+    if ( MDAL::contains( long_name, ", x-component" ) || MDAL::contains( long_name, "u component of " ) )
     {
       *is_vector = true;
       name = MDAL::replace( long_name, ", x-component", "" );
+      name = MDAL::replace( name, "u component of ", "" );
     }
-    else if ( MDAL::contains( long_name, ", y-component" ) )
+    else if ( MDAL::contains( long_name, ", y-component" ) || MDAL::contains( long_name, "v component of " ) )
     {
       *is_vector = true;
       *is_x = false;
       name = MDAL::replace( long_name, ", y-component", "" );
+      name = MDAL::replace( name, "v component of ", "" );
     }
     else
     {