update to MDAL 0.3.2

external/mdal/frmts/mdal_3di.cpp

@@ -20,24 +20,24 @@ MDAL::Driver3Di *MDAL::Driver3Di::create()
   return new Driver3Di();
 }
 
-MDAL::CFDimensions MDAL::Driver3Di::populateDimensions( const NetCDFFile &ncFile )
+MDAL::CFDimensions MDAL::Driver3Di::populateDimensions( )
 {
   CFDimensions dims;
   size_t count;
   int ncid;
 
   // 2D Mesh
-  ncFile.getDimension( "nMesh2D_nodes", &count, &ncid );
+  mNcFile.getDimension( "nMesh2D_nodes", &count, &ncid );
   dims.setDimension( CFDimensions::Face2D, count, ncid );
 
-  ncFile.getDimension( "nCorner_Nodes", &count, &ncid );
+  mNcFile.getDimension( "nCorner_Nodes", &count, &ncid );
   dims.setDimension( CFDimensions::MaxVerticesInFace, count, ncid );
 
   // Vertices count is populated later in populateFacesAndVertices
   // it is not known from the array dimensions
 
   // Time
-  ncFile.getDimension( "time", &count, &ncid );
+  mNcFile.getDimension( "time", &count, &ncid );
   dims.setDimension( CFDimensions::Time, count, ncid );
 
   return dims;
@@ -111,7 +111,7 @@ void MDAL::Driver3Di::populateFacesAndVertices( Vertices &vertices, Faces &faces
   mDimensions.setDimension( CFDimensions::Vertex2D, vertices.size() );
 }
 
-void MDAL::Driver3Di::addBedElevation( MDAL::Mesh *mesh )
+void MDAL::Driver3Di::addBedElevation( MemoryMesh *mesh )
 {
   assert( mesh );
   if ( 0 == mesh->facesCount() )
@@ -189,12 +189,6 @@ std::set<std::string> MDAL::Driver3Di::ignoreNetCDFVariables()
   return ignore_variables;
 }
 
-std::string MDAL::Driver3Di::nameSuffix( MDAL::CFDimensions::Type type )
-{
-  MDAL_UNUSED( type );
-  return "";
-}
-
 void MDAL::Driver3Di::parseNetCDFVariableMetadata( int varid, const std::string &variableName, std::string &name, bool *is_vector, bool *is_x )
 {
   *is_vector = false;

external/mdal/frmts/mdal_3di.hpp

@@ -44,12 +44,11 @@ namespace MDAL
       Driver3Di *create() override;
 
     private:
-      CFDimensions populateDimensions( const NetCDFFile &ncFile ) override;
+      CFDimensions populateDimensions( ) override;
       void populateFacesAndVertices( Vertices &vertices, Faces &faces ) override;
-      void addBedElevation( Mesh *mesh ) override;
+      void addBedElevation( MemoryMesh *mesh ) override;
       std::string getCoordinateSystemVariableName() override;
       std::set<std::string> ignoreNetCDFVariables() override;
-      std::string nameSuffix( CFDimensions::Type type ) override;
       void parseNetCDFVariableMetadata( int varid, const std::string &variableName,
                                         std::string &name, bool *is_vector, bool *is_x ) override;
 

external/mdal/frmts/mdal_cf.cpp

@@ -79,16 +79,13 @@ MDAL::cfdataset_info_map MDAL::DriverCF::parseDatasetGroupInfo()
         continue;
 
       size_t arr_size = mDimensions.size( mDimensions.type( dimid ) ) * nTimesteps;
-      std::string suffix = nameSuffix( mDimensions.type( dimid ) );
 
       // Get name, if it is vector and if it is x or y
       std::string name;
       bool is_vector = true;
       bool is_x = false;
 
       parseNetCDFVariableMetadata( varid, variable_name, name, &is_vector, &is_x );
-      if ( !suffix.empty() )
-        name = name + " (" + suffix + ")";
 
       // Add it to the map
       auto it = dsinfo_map.find( name );
@@ -136,12 +133,12 @@ static void populate_vals( bool is_vector, double *vals, size_t i,
 {
   if ( is_vector )
   {
-    vals[2 * i] =   MDAL::safeValue( vals_x[idx], fill_val_x );
-    vals[2 * i + 1] =   MDAL::safeValue( vals_y[idx], fill_val_y );
+    vals[2 * i] = MDAL::safeValue( vals_x[idx], fill_val_x );
+    vals[2 * i + 1] = MDAL::safeValue( vals_y[idx], fill_val_y );
   }
   else
   {
-    vals[i] =   MDAL::safeValue( vals_x[idx], fill_val_x );
+    vals[i] = MDAL::safeValue( vals_x[idx], fill_val_x );
   }
 }
 
@@ -190,7 +187,7 @@ void MDAL::DriverCF::addDatasetGroups( MDAL::Mesh *mesh, const std::vector<doubl
 
     // read X data
     double fill_val_x = mNcFile.getFillValue( dsi.ncid_x );
-    std::vector<double> vals_x( dsi.arr_size );
+    std::vector<double> vals_x( dsi.arr_size, std::numeric_limits<double>::quiet_NaN() );
     if ( nc_get_var_double( mNcFile.handle(), dsi.ncid_x, vals_x.data() ) ) CF_THROW_ERR;
 
     // read Y data if vector
@@ -199,7 +196,7 @@ void MDAL::DriverCF::addDatasetGroups( MDAL::Mesh *mesh, const std::vector<doubl
     if ( dsi.is_vector )
     {
       fill_val_y = mNcFile.getFillValue( dsi.ncid_y );
-      vals_y.resize( dsi.arr_size );
+      vals_y.resize( dsi.arr_size, std::numeric_limits<double>::quiet_NaN() );
       if ( nc_get_var_double( mNcFile.handle(), dsi.ncid_y, vals_y.data() ) ) CF_THROW_ERR;
     }
 
@@ -254,7 +251,8 @@ bool MDAL::DriverCF::canRead( const std::string &uri )
   {
     NetCDFFile ncFile;
     ncFile.openFile( uri );
-    populateDimensions( ncFile );
+    mNcFile = ncFile;
+    populateDimensions( );
   }
   catch ( MDAL_Status )
   {
@@ -318,7 +316,7 @@ std::unique_ptr< MDAL::Mesh > MDAL::DriverCF::load( const std::string &fileName,
     mNcFile.openFile( mFileName );
 
     // Parse dimensions
-    mDimensions = populateDimensions( mNcFile );
+    mDimensions = populateDimensions( );
 
     // Create mMesh
     Faces faces;

external/mdal/frmts/mdal_cf.hpp

@@ -63,6 +63,7 @@ namespace MDAL
 
   //! NetCDF Climate and Forecast (CF) Metadata Conventions
   //! http://cfconventions.org
+  //! and http://ugrid-conventions.github.io/ugrid-conventions/
   class DriverCF: public Driver
   {
     public:
@@ -74,12 +75,11 @@ namespace MDAL
       std::unique_ptr< Mesh > load( const std::string &fileName, MDAL_Status *status ) override;
 
     protected:
-      virtual CFDimensions populateDimensions( const NetCDFFile &ncFile ) = 0;
+      virtual CFDimensions populateDimensions( ) = 0;
       virtual void populateFacesAndVertices( Vertices &vertices, Faces &faces ) = 0;
-      virtual void addBedElevation( MDAL::Mesh *mesh ) = 0;
+      virtual void addBedElevation( MDAL::MemoryMesh *mesh ) = 0;
       virtual std::string getCoordinateSystemVariableName() = 0;
       virtual std::set<std::string> ignoreNetCDFVariables() = 0;
-      virtual std::string nameSuffix( CFDimensions::Type type ) = 0;
       virtual void parseNetCDFVariableMetadata( int varid, const std::string &variableName,
           std::string &name, bool *is_vector, bool *is_x ) = 0;
 

external/mdal/frmts/mdal_flo2d.cpp

@@ -109,6 +109,7 @@ void MDAL::DriverFlo2D::parseCADPTSFile( const std::string &datFileName, std::ve
   // CADPTS.DAT - COORDINATES OF CELL CENTERS (ELEM NUM, X, Y)
   while ( std::getline( cadptsStream, line ) )
   {
+    line = MDAL::rtrim( line );
     std::vector<std::string> lineParts = MDAL::split( line, ' ' );
     if ( lineParts.size() != 3 )
     {
@@ -140,6 +141,7 @@ void MDAL::DriverFlo2D::parseFPLAINFile( std::vector<double> &elevations,
 
   while ( std::getline( fplainStream, line ) )
   {
+    line = MDAL::rtrim( line );
     std::vector<std::string> lineParts = MDAL::split( line, ' ' );
     if ( lineParts.size() != 7 )
     {
@@ -220,6 +222,7 @@ void MDAL::DriverFlo2D::parseTIMDEPFile( const std::string &datFileName, const s
 
   while ( std::getline( inStream, line ) )
   {
+    line = MDAL::rtrim( line );
     std::vector<std::string> lineParts = MDAL::split( line, ' ' );
     if ( lineParts.size() == 1 )
     {
@@ -301,6 +304,7 @@ void MDAL::DriverFlo2D::parseDEPTHFile( const std::string &datFileName, const st
   // DEPTH.OUT - COORDINATES (ELEM NUM, X, Y, MAX DEPTH)
   while ( std::getline( depthStream, line ) )
   {
+    line = MDAL::rtrim( line );
     if ( vertex_idx == nVertices ) throw MDAL_Status::Err_IncompatibleMesh;
 
     std::vector<std::string> lineParts = MDAL::split( line, ' ' );
@@ -348,6 +352,7 @@ void MDAL::DriverFlo2D::parseVELFPVELOCFile( const std::string &datFileName )
     {
       if ( vertex_idx == nVertices ) throw MDAL_Status::Err_IncompatibleMesh;
 
+      line = MDAL::rtrim( line );
       std::vector<std::string> lineParts = MDAL::split( line, ' ' );
       if ( lineParts.size() != 4 )
       {
@@ -378,6 +383,7 @@ void MDAL::DriverFlo2D::parseVELFPVELOCFile( const std::string &datFileName )
     {
       if ( vertex_idx == nVertices ) throw MDAL_Status::Err_IncompatibleMesh;
 
+      line = MDAL::rtrim( line );
       std::vector<std::string> lineParts = MDAL::split( line, ' ' );
       if ( lineParts.size() != 4 )
       {

external/mdal/frmts/mdal_gdal.cpp

@@ -396,47 +396,6 @@ void MDAL::DriverGdal::addDataToOutput( GDALRasterBandH raster_band, std::shared
   }
 }
 
-void MDAL::DriverGdal::activateFaces( std::shared_ptr<MemoryDataset> tos )
-{
-  // only for data on vertices
-  if ( !tos->group()->isOnVertices() )
-    return;
-
-  bool isScalar = tos->group()->isScalar();
-
-  // Activate only Faces that do all Vertex's outputs with some data
-  int *active = tos->active();
-  const double *values = tos->constValues();
-
-  for ( unsigned int idx = 0; idx < meshGDALDataset()->mNVolumes; ++idx )
-  {
-    Face elem = mMesh->faces.at( idx );
-    for ( size_t i = 0; i < 4; ++i )
-    {
-      const size_t vertexIndex = elem[i];
-      if ( isScalar )
-      {
-        double val = values[vertexIndex];
-        if ( std::isnan( val ) )
-        {
-          active[idx] = 0; //NOT ACTIVE
-          break;
-        }
-      }
-      else
-      {
-        double x = values[2 * vertexIndex];
-        double y = values[2 * vertexIndex + 1];
-        if ( std::isnan( x ) || std::isnan( y ) )
-        {
-          active[idx] = 0; //NOT ACTIVE
-          break;
-        }
-      }
-    }
-  }
-}
-
 void MDAL::DriverGdal::addDatasetGroups()
 {
   // Add dataset to mMesh
@@ -465,7 +424,7 @@ void MDAL::DriverGdal::addDatasetGroups()
       {
         addDataToOutput( raster_bands[i], dataset, is_vector, i == 0 );
       }
-      activateFaces( dataset );
+      MDAL::activateFaces( mMesh.get(), dataset );
       dataset->setStatistics( MDAL::calculateStatistics( dataset ) );
       group->datasets.push_back( dataset );
     }

external/mdal/frmts/mdal_gdal.hpp

@@ -90,7 +90,6 @@ namespace MDAL
       metadata_hash parseMetadata( GDALMajorObjectH gdalBand, const char *pszDomain = nullptr );
       void addDataToOutput( GDALRasterBandH raster_band, std::shared_ptr<MemoryDataset> tos, bool is_vector, bool is_x );
       bool addSrcProj();
-      void activateFaces( std::shared_ptr<MemoryDataset> tos );
       void addDatasetGroups();
       void createMesh();
       void parseRasterBands( const GdalDataset *cfGDALDataset );

external/mdal/frmts/mdal_netcdf.cpp

@@ -103,21 +103,21 @@ std::string NetCDFFile::getAttrStr( const std::string &name, const std::string &
   return getAttrStr( attr_name, arr_id );
 }
 
-std::string NetCDFFile::getAttrStr( const std::string &name, int varid ) const
+std::string NetCDFFile::getAttrStr( const std::string &attr_name, int varid ) const
 {
   assert( mNcid != 0 );
 
   size_t attlen = 0;
 
-  if ( nc_inq_attlen( mNcid, varid, name.c_str(), &attlen ) )
+  if ( nc_inq_attlen( mNcid, varid, attr_name.c_str(), &attlen ) )
   {
     // attribute is missing
     return std::string();
   }
 
   char *string_attr = static_cast<char *>( malloc( attlen + 1 ) );
 
-  if ( nc_get_att_text( mNcid, varid, name.c_str(), string_attr ) ) throw MDAL_Status::Err_UnknownFormat;
+  if ( nc_get_att_text( mNcid, varid, attr_name.c_str(), string_attr ) ) throw MDAL_Status::Err_UnknownFormat;
   string_attr[attlen] = '\0';
 
   std::string res( string_attr );
@@ -139,6 +139,7 @@ double NetCDFFile::getAttrDouble( int varid, const std::string &attr_name ) cons
   return res;
 }
 
+
 int NetCDFFile::getVarId( const std::string &name )
 {
   int ncid_val;
@@ -153,3 +154,9 @@ void NetCDFFile::getDimension( const std::string &name, size_t *val, int *ncid_v
   if ( nc_inq_dimid( mNcid, name.c_str(), ncid_val ) != NC_NOERR ) throw MDAL_Status::Err_UnknownFormat;
   if ( nc_inq_dimlen( mNcid, *ncid_val, val ) != NC_NOERR ) throw MDAL_Status::Err_UnknownFormat;
 }
+
+bool NetCDFFile::hasDimension( const std::string &name ) const
+{
+  int ncid_val;
+  return nc_inq_dimid( mNcid, name.c_str(), &ncid_val ) == NC_NOERR;
+}

external/mdal/frmts/mdal_netcdf.hpp

@@ -28,11 +28,19 @@ class NetCDFFile
 
     int getAttrInt( const std::string &name, const std::string &attr_name ) const;
     double getAttrDouble( int varid, const std::string &attr_name ) const;
+    /**
+     * Get string attribute
+     * \param name name of the variable
+     * \param attr_name name of the attribute of the variable
+     * \returns empty string if attribute is missing, else attribute value
+     */
     std::string getAttrStr( const std::string &name, const std::string &attr_name ) const;
-    std::string getAttrStr( const std::string &name, int varid ) const;
+    std::string getAttrStr( const std::string &attr_name, int varid ) const;
     double getFillValue( int varid ) const;
     int getVarId( const std::string &name );
     void getDimension( const std::string &name, size_t *val, int *ncid_val ) const;
+    bool hasDimension( const std::string &name ) const;
+
   private:
     int mNcid; // C handle to the file
 };