Changeset 782 for XIOS/trunk/src/io

Timestamp:

11/12/15 16:33:03 (8 years ago)

Author:

mhnguyen

Message:

Reading attributes of curvilinear grid from file

+) Correct some minor bugs detecting type of grid
+) Use constant string for attributes conforming to CF convention
+) Add part of code to read attributes of curvilinear grid

Test
+) On Curie
+) test_remap passes

Location:

XIOS/trunk/src/io

Files:

• inetcdf4.cpp (modified) (16 diffs)
• inetcdf4.hpp (modified) (1 diff)
• inetcdf4_decl.cpp (added)
• inetcdf4_impl.hpp (added)
• nc4_data_input.cpp (modified) (7 diffs)
• nc4_data_input.hpp (modified) (2 diffs)
• netCdfInterface.cpp (modified) (2 diffs)
• netCdf_cf_constant.hpp (added)

XIOS/trunk/src/io/inetcdf4.cpp

@@ -1 +1 @@
 #include "inetcdf4.hpp"
 #include "netCdfInterface.hpp"
+#include "netCdf_cf_constant.hpp"
 
 #include <boost/algorithm/string.hpp>
@@ -302 +303 @@
     {
       const StdString& attname = *it;
-      if (attname.compare(name) == 0)
+      if (attname.compare(0, name.size(), name) == 0)
         return retvalue;
       retvalue++;
@@ -326 +327 @@
     {
       const StdString& attname = *it;
-      if (attname.compare(name) == 0) return true;
+      if (attname.compare(0, name.size(), name) == 0) return true;
     }
     return false;
@@ -339 +340 @@
     {
       const StdString& varname = *it;
-      if (varname.compare(name) == 0) return true;
+      if (varname.compare(0, name.size(), name) == 0) return true;
     }
     return false;
@@ -347 +348 @@
                                  const CVarPath* const path)
   {
-    return this->hasAttribute("coordinates", &name, path);
+    return this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path);
   }
 
@@ -353 +354 @@
                             const CVarPath* const path)
   {
-    return this->hasAttribute("bounds", &name, path);
+    return this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path);
   }
 
@@ -441 +442 @@
   {
     StdString retvalue;
-    if (this->hasAttribute("coordinates", &name, path))
-    {
-      return this->getAttributeValue("coordinates", &name, path);
+    if (this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path))
+    {
+      return this->getAttributeValue(CCFKeywords::XIOS_CF_coordinates, &name, path);
     }
     else
@@ -464 +465 @@
   {
     StdString retvalue;
-    if (this->hasAttribute("bounds", &name, path))
-      retvalue = this->getAttributeValue("bounds", &name, path);
+    if (this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path))
+      retvalue = this->getAttributeValue(CCFKeywords::XIOS_CF_bounds, &name, path);
     return retvalue;
   }
@@ -509 +510 @@
       return false;
 
+    bool isCurVi = true;
+    unsigned int nbLonLat = 0;
     std::list<StdString> coords = this->getCoordinatesIdList(name, path);
     std::list<StdString>::const_iterator it = coords.begin(), end = coords.end();
@@ -514 +517 @@
     {
       const StdString& coord = *it;
-      if (this->hasVariable(coord, path))
+      if (this->hasVariable(coord, path) && !this->isTemporal(coord, path))
       {
         std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path);
-        if (dimvar.size() != 2) return false;
-      }
-      else return false;
-    }
-    return true;
+        if (2 == dimvar.size()) ++nbLonLat;
+      }
+    }
+    if (2 != nbLonLat) isCurVi = false;
+
+    return isCurVi;
   }
 
@@ -538 +542 @@
     {
       const StdString& coord = *it;
-      if (this->hasVariable(coord, path))
+      if (this->hasVariable(coord, path) && !this->isTemporal(coord, path))
       {
         std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path);
@@ -581 +585 @@
       else
       {
-        if (coord.compare(this->getUnlimitedDimensionName()) == 0)
+        StdString unlimitedDimName = this->getUnlimitedDimensionName();
+        if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0)
           continue;
         i++;
@@ -612 +617 @@
         else
         {
-          if (coord.compare(this->getUnlimitedDimensionName()) == 0)
+          StdString unlimitedDimName = this->getUnlimitedDimensionName();
+          if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0)
             continue;
           return false;
@@ -712 +718 @@
                           const CVarPath* const path, StdSize record);
 
-  template <>
-  void CINetCDF4::getData(CArray<double, 1>& data, const StdString& var,
-                          bool collective, StdSize record,
-                          const std::vector<StdSize>* start /*= NULL*/,
-                          const std::vector<StdSize>* count /*= NULL*/)
-  {
-    int varid = this->getVariable(var);
-
-    if (this->mpi && collective)
-      CNetCdfInterface::varParAccess(ncidp, varid, NC_COLLECTIVE);
-    else if (this->mpi && !collective)
-      CNetCdfInterface::varParAccess(ncidp, varid, NC_INDEPENDENT);
-
-    std::vector<StdSize> sstart, scount;
-    StdSize array_size = 1;
-    this->getDataInfo(var, NULL, record, sstart, scount, array_size, start, count);
-
-    if (data.numElements() != array_size)
-    {
-      ERROR("CONetCDF4::getData(...)",
-            << "[ Array size = " << data.numElements()
-            << ", Data size = "  << array_size
-            << " ] Invalid array size");
-    }
-
-    CNetCdfInterface::getVaraType(ncidp, varid, &sstart[0], &scount[0], data.dataFirst());
-  }
-
   //---------------------------------------------------------------
 
@@ -745 +723 @@
                                        const CVarPath* const path)
   {
+    std::list<StdString>::const_iterator itbList, itList, iteList;
     std::list<StdString> clist = this->getCoordinatesIdList(varname, path);
-    if (this->hasCoordinates(varname, path))
-      return *clist.begin();
-    else
-      return *clist.rbegin();
+    itbList = clist.begin(); iteList = clist.end();
+    for (itList = itbList; itList != iteList; ++itList)
+    {
+      if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path))
+      {
+        StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path);
+        if (CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit))
+          return *itList;
+      }
+    }
   }
 
@@ -755 +740 @@
                                        const CVarPath* const path)
   {
+    std::list<StdString>::const_iterator itbList, itList, iteList;
     std::list<StdString> clist = this->getCoordinatesIdList(varname, path);
-    if (this->hasCoordinates(varname, path))
-      return *(++clist.begin());
-    else
-      return *(++clist.rbegin());
+    itbList = clist.begin(); iteList = clist.end();
+    for (itList = itbList; itList != iteList; ++itList)
+    {
+      if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path))
+      {
+        StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path);
+        if (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit))
+          return *itList;
+      }
+    }
   }
 

XIOS/trunk/src/io/inetcdf4.hpp

@@ -98 +98 @@
                    StdSize record = UNLIMITED_DIM);
 
-      template <class T>
-      void getData(CArray<T, 1>& data, const StdString& var,
+      template <class T, int Ndim>
+      void getData(CArray<T, Ndim>& data, const StdString& var,
                    bool collective, StdSize record,
                    const std::vector<StdSize>* start = NULL,

XIOS/trunk/src/io/nc4_data_input.cpp

@@ -202 +202 @@
     \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file
     \param [in] emelentPosition position of domain in grid
+    \param [in] fieldId id (or name) associated with the grid
   */
   void CNc4DataInput::readDomainAttributeValueFromFile(CDomain* domain, std::map<StdString, StdSize>& dimSizeMap,
@@ -227 +228 @@
     else if (this->isCurvilinear(fieldId))
     {
-
+      int ni = domain->ni;
+      int nj = domain->nj;
+      std::vector<StdSize> nBeginLatLon(2), nSizeLatLon(2);
+      nBeginLatLon[0] = domain->jbegin.getValue(); nBeginLatLon[1] = domain->ibegin.getValue();
+      nSizeLatLon[0]  = nj; nSizeLatLon[1] = ni;
+
+      StdString latName = this->getLatCoordName(fieldId);
+      domain->latvalue_2d.resize(ni,nj);
+      readFieldVariableValue(domain->latvalue_2d, latName, nBeginLatLon, nSizeLatLon);
+      StdString lonName = this->getLonCoordName(fieldId);
+      domain->lonvalue_2d.resize(ni,nj);
+      readFieldVariableValue(domain->lonvalue_2d, lonName, nBeginLatLon, nSizeLatLon);
+
+      StdString boundsLatName = this->getBoundsId(latName);
+      if (0 == boundsLatName.compare(""))
+         ERROR("CNc4DataInput::readDomainAttributeValueFromFile(...)",
+              << "Field '" << fieldId << std::endl
+              << "Trying to read attributes from curvilinear grid."
+              << "Latitude variable " << latName << " does not have bounds.");
+      StdString boundsLonName = this->getBoundsId(lonName);
+      if (0 == boundsLonName.compare(""))
+         ERROR("CNc4DataInput::readDomainAttributeValueFromFile(...)",
+              << "Field '" << fieldId << std::endl
+              << "Trying to read attributes from curvilinear grid."
+              << "Longitude variable " << lonName << " does not have bounds.");
+
+      domain->nvertex.setValue(4);
+      std::vector<StdSize> nBeginBndsLatLon(3), nSizeBndsLatLon(3);
+      nBeginBndsLatLon[0] = domain->jbegin.getValue(); nSizeBndsLatLon[0] = nj;
+      nBeginBndsLatLon[1] = domain->ibegin.getValue(); nSizeBndsLatLon[1] = ni;
+      nBeginBndsLatLon[2] = 0; nSizeBndsLatLon[2] = 4;
+
+      domain->bounds_lat_2d.resize(4,ni,nj);
+      readFieldVariableValue(domain->bounds_lat_2d, boundsLatName, nBeginBndsLatLon, nSizeBndsLatLon);
+      domain->bounds_lon_2d.resize(4,ni,nj);
+      readFieldVariableValue(domain->bounds_lon_2d, boundsLonName, nBeginBndsLatLon, nSizeBndsLatLon);
     }
     else if (this->isUnstructured(fieldId))
@@ -236 +272 @@
 
   /*!
-    Read attributes of a domain from a file
+    Read attribute value of a domain from a file
     \param [in] domain domain whose attributes are read from the file
     \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file
     \param [in] emelentPosition position of domain in grid
+    \param [in] fieldId id (or name) associated with the grid
   */
   void CNc4DataInput::readDomainAttributesFromFile(CDomain* domain, std::map<StdString, StdSize>& dimSizeMap,
@@ -251 +288 @@
     itMapNi = itMapNj; ++itMapNi;
 
-    if (this->isRectilinear(fieldId))
+    if (this->isRectilinear(fieldId) || this->isCurvilinear(fieldId))
     {
       domain->nj_glo.setValue(itMapNj->second);
       domain->ni_glo.setValue((itMapNi)->second);
-    }
-    else if (this->isCurvilinear(fieldId))
-    {
-
     }
     else if (this->isUnstructured(fieldId))
@@ -271 +304 @@
     \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file
     \param [in] emelentPosition position of axis in grid
+    \param [in] fieldId id (or name) associated with the grid
   */
   void CNc4DataInput::readAxisAttributesFromFile(CAxis* axis, std::map<StdString, StdSize>& dimSizeMap,
@@ -282 +316 @@
 
   /*!
-    Read attributes of an axis from a file
+    Read attribute value of an axis from a file
     \param [in] axis axis whose attributes are read from the file
     \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file
     \param [in] emelentPosition position of axis in grid
+    \param [in] fieldId id (or name) associated with the grid
   */
   void CNc4DataInput::readAxisAttributeValueFromFile(CAxis* axis, std::map<StdString, StdSize>& dimSizeMap,
@@ -306 +341 @@
   }
 
-  void CNc4DataInput::readFieldVariableValue(CArray<double,1>& var, const StdString& varId,
-                                             const std::vector<StdSize>& nBegin,
-                                             const std::vector<StdSize>& nSize,
-                                             bool forceIndependent)
-  {
-    if (SuperClass::type==MULTI_FILE || !isCollective) return;
-
-    bool openCollective = isCollective;
-    if (forceIndependent) openCollective = !isCollective;
-    switch (SuperClass::type)
-    {
-      case MULTI_FILE:
-        SuperClassWriter::getData(var, varId, openCollective, 0);
-        break;
-      case ONE_FILE:
-      {
-        SuperClassWriter::getData(var, varId, openCollective, 0, &nBegin, &nSize);
-        break;
-      }
-    }
-  }
-
   void CNc4DataInput::closeFile_(void)
   {

XIOS/trunk/src/io/nc4_data_input.hpp

@@ -50 +50 @@
                                         int elementPosition, const StdString& fieldId);
 
-    void readFieldVariableValue(CArray<double,1>& var, const StdString& varId,
+    template <typename T, int Ndim>
+    void readFieldVariableValue(CArray<T, Ndim>& var, const StdString& varId,
                                 const std::vector<StdSize>& nBegin,
                                 const std::vector<StdSize>& nSize,
@@ -65 +66 @@
     bool isCollective;
   }; // class CNc4DataInput
+
+template <typename T, int Ndim>
+void CNc4DataInput::readFieldVariableValue(CArray<T,Ndim>& var, const StdString& varId,
+                                           const std::vector<StdSize>& nBegin,
+                                           const std::vector<StdSize>& nSize,
+                                           bool forceIndependent)
+{
+  if (SuperClass::type==MULTI_FILE || !isCollective) return;
+
+  bool openCollective = isCollective;
+  if (forceIndependent) openCollective = !isCollective;
+  switch (SuperClass::type)
+  {
+    case MULTI_FILE:
+      ERROR("CINetCDF4::readFieldVariableValue(...)",
+            << "Only support attributes reading with one_file mode");
+      break;
+    case ONE_FILE:
+    {
+      SuperClassWriter::getData(var, varId, openCollective, 0, &nBegin, &nSize);
+      break;
+    }
+  }
+}
 } // namespace xios
 

XIOS/trunk/src/io/netCdfInterface.cpp

@@ -603 +603 @@
 int CNetCdfInterface::inqAttName(int ncid, int varid, int attnum, StdString& name)
 {
-  char attName[NC_MAX_NAME + 1];
-  int status = nc_inq_attname(ncid, varid, attnum, attName);
+  std::vector<char> attName(NC_MAX_NAME + 1,' ');
+  int status = nc_inq_attname(ncid, varid, attnum, &attName[0]);
   if (NC_NOERR != status)
   {
@@ -616 +616 @@
     throw CNetCdfException(e);
   }
+
+  int nameSize = 0;
+  while ((nameSize < NC_MAX_NAME) && (' ' != attName[nameSize] )) ++nameSize;
+  name.resize(nameSize);
+//  for (int idx = 0; idx < nameSize; ++idx) name.at(idx) = attName[idx];
+  std::copy(&attName[0], &attName[nameSize-1], name.begin());
 
   return status;