Skip to content

GitLab

Commit 7979647d authored by Ben Boeckel's avatar Ben Boeckel
Browse files

avtMFIXCDFFileFormat: remove netcdf dependency

parent 75bf26ba
Hide whitespace changes
Inline Side-by-side
README.kitware.md
View file @ 7979647d
......@@ -25,3 +25,4 @@ within a single process.
* Comment out unused functions in `RC_cpp_lib`.
* Updating avtANSYSFileFormat reader to read in 10-noded tetras.
* Read PFLOTRAN files with big-endian floating-point arrays.
* Port MFIXCDF from netcdfcpp to netcdf
databases/MFIXCDF/avtMFIXCDFFileFormat.C
View file @ 7979647d
......@@ -89,24 +89,54 @@ using std::auto_ptr;
using std::vector;
using std::ostringstream;
void checkFile(NcFile* ncFile, const char* fname, int iSz, int jSz, int kSz)
void checkFile(int ncid, const char* fname, int iSz, int jSz, int kSz)
{
NcDim* iDim= ncFile->get_dim("x");
if (iDim->size() != iSz-1)
int dimid;
size_t dimlen;
if (nc_inq_dimid(ncid, "x", &dimid) != NC_NOERR)
{
debug5 << "No x dimension" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "x dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (dimlen != iSz-1)
{
debug5 << "File has wrong x dimension size" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
NcDim* jDim= ncFile->get_dim("y");
if (jDim->size() != jSz-1)
if (nc_inq_dimid(ncid, "y", &dimid) != NC_NOERR)
{
debug5 << "No y dimension" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "y dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (dimlen != jSz-1)
{
debug5 << "File has wrong y dimension size" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
NcDim* kDim= ncFile->get_dim("z");
if (kDim->size() == 1)
if (nc_inq_dimid(ncid, "z", &dimid) != NC_NOERR)
{
debug5 << "No z dimension" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "z dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,fname);
}
if (dimlen == 1)
{
if (kSz != 1)
{
......@@ -116,7 +146,7 @@ void checkFile(NcFile* ncFile, const char* fname, int iSz, int jSz, int kSz)
}
else
{
if (kDim->size() != kSz-1)
if (dimlen != kSz-1)
{
debug5 << "File has wrong z dimension size" << endl;
EXCEPTION1(InvalidFilesException,fname);
......@@ -125,16 +155,22 @@ void checkFile(NcFile* ncFile, const char* fname, int iSz, int jSz, int kSz)
debug5 << "checkFile succeeded for " << fname << endl;
}
NcFile* openFile( const char* filename )
int openFile( const char* filename )
{
NcFile* ncFile= new NcFile(filename, NcFile::ReadOnly);
if (!ncFile->is_valid())
int mode = NC_NOWRITE | NC_64BIT_OFFSET | NC_NETCDF4 | NC_CLASSIC_MODEL;
int ncid;
if (nc_open(filename, mode, &ncid) != NC_NOERR)
{
debug5 << "NcFile constructor failed for " << filename << endl;
debug5 << "Failed to open " << filename << endl;
EXCEPTION1(InvalidFilesException,filename);
}
int nAttr= ncFile->num_atts();
int nAttr;
if (nc_inq_natts(ncid, &nAttr) != NC_NOERR)
{
debug5 << "Failed to get attribute count" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
if (nAttr != 0)
{
debug5 << "Unexpectedly found " << nAttr <<
......@@ -142,44 +178,56 @@ NcFile* openFile( const char* filename )
EXCEPTION1(InvalidFilesException,filename);
}
NcDim* iDim= ncFile->get_dim("x");
if (!iDim->is_valid())
int dimid;
size_t dimlen;
if (nc_inq_dimid(ncid, "x", &dimid) != NC_NOERR)
{
debug5 << "No x dimension" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "Invalid dim 'x'" << endl;
debug5 << "x dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
debug5 << "Size of " << filename << " " << iDim->name()
<< " is " << iDim->size() << endl;
if (iDim->size()<2)
debug5 << "Size of " << filename << " x is " << dimlen << endl;
if (dimlen<2)
{
debug5 << "dimension of 1 in x is too small" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
NcDim* jDim= ncFile->get_dim("y");
if (!jDim->is_valid())
if (nc_inq_dimid(ncid, "y", &dimid) != NC_NOERR)
{
debug5 << "Invalid dim 'y'" << endl;
debug5 << "No y dimension" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
debug5 << "Size of " << filename << " " << jDim->name()
<< " is " << jDim->size() << endl;
if (jDim->size()<2)
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "y dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
debug5 << "Size of " << filename << " y is " << dimlen << endl;
if (dimlen<2)
{
debug5 << "dimension of 1 in y is too small" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
NcDim* kDim= ncFile->get_dim("z");
if (!kDim->is_valid())
if (nc_inq_dimid(ncid, "z", &dimid) != NC_NOERR)
{
debug5 << "No z dimension" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
if (nc_inq_dimlen(ncid, dimid, &dimlen) != NC_NOERR)
{
debug5 << "Invalid dim 'z'" << endl;
debug5 << "z dimension has no size" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
debug5 << "Size of " << filename << " " << kDim->name()
<< " is " << kDim->size() << endl;
debug5 << "Size of " << filename << " z is " << dimlen << endl;
return ncFile;
return ncid;
}
// ****************************************************************************
......@@ -210,9 +258,43 @@ avtMFIXCDFFileFormat::avtMFIXCDFFileFormat(const char *filename, DBOptionsAttrib
// Open the file, or try
dataFile= openFile(filename);
filePath= new std::string(filename);
iSz= dataFile->get_dim("x")->size()+1;
jSz= dataFile->get_dim("y")->size()+1;
kSz= dataFile->get_dim("z")->size()+1;
int xdimid, ydimid, zdimid;
if (nc_inq_dimid(dataFile, "x", &xdimid) != NC_NOERR)
{
debug5 << "Missing x dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
if (nc_inq_dimid(dataFile, "y", &ydimid) != NC_NOERR)
{
debug5 << "Missing y dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
if (nc_inq_dimid(dataFile, "z", &zdimid) != NC_NOERR)
{
debug5 << "Missing z dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
size_t xdimlen, ydimlen, zdimlen;
if (nc_inq_dimlen(dataFile, xdimid, &xdimlen) != NC_NOERR)
{
debug5 << "No size for x dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
if (nc_inq_dimlen(dataFile, ydimid, &ydimlen) != NC_NOERR)
{
debug5 << "No size for y dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
if (nc_inq_dimlen(dataFile, zdimid, &zdimlen) != NC_NOERR)
{
debug5 << "No size for z dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
iSz= xdimlen+1;
jSz= ydimlen+1;
kSz= zdimlen+1;
if (kSz==2)
{
kSz= 1; // special case of 2D
......@@ -227,14 +309,31 @@ avtMFIXCDFFileFormat::avtMFIXCDFFileFormat(const char *filename, DBOptionsAttrib
par_rank = PAR_Rank();
// Get coordCode, which specifies coordinate system type
NcDim* coordDim= dataFile->get_dim("coordinates");
if (!coordDim->is_valid() || coordDim->size()!=1)
int coordDim;
if (nc_inq_dimid(dataFile, "coordinates", &coordDim) != NC_NOERR)
{
debug5 << "Missing coordinates dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
size_t coorddimlen;
if (nc_inq_dimlen(dataFile, coordDim, &coorddimlen) != NC_NOERR)
{
debug5 << "No size for coordinates dimension" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
if (coorddimlen!=1)
{
debug5 << "Invalid dim 'coordinates' or size!=1" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
NcVar* coordVar= dataFile->get_var("coordinates");
if (!coordVar->get(&coordCode,1L))
int coordVar;
if (nc_inq_varid(dataFile, "coordinates", &coordVar) != NC_NOERR)
{
debug5 << "Missing coordinates variable" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
size_t coordStart[] = {0};
if (nc_get_var1_int(dataFile, coordVar, coordStart, &coordVar) != NC_NOERR)
{
debug5 << "'coordinates' data is not an int" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
......@@ -257,13 +356,14 @@ avtMFIXCDFFileFormat::avtMFIXCDFFileFormat(const char *filename, DBOptionsAttrib
// }
// We will keep a copy of the time.
NcVar* timeVar= dataFile->get_var("t");
if (!timeVar)
int timeVar;
if (nc_inq_varid(dataFile, "t", &timeVar) != NC_NOERR)
{
debug5 << "Data file has no 'time' variable" << endl;
EXCEPTION1(InvalidFilesException,filename);
}
if (!(timeVar->get(&timeNow,1L)))
size_t timeStart[] = {0};
if (nc_get_var1_double(dataFile, timeVar, timeStart, &timeNow) != NC_NOERR)
{
debug5 << "failed to read 1 double from the 'time' variable" << endl;
EXCEPTION2(UnexpectedValueException,"get failed","t");
......@@ -280,7 +380,7 @@ avtMFIXCDFFileFormat::avtMFIXCDFFileFormat(const char *filename, DBOptionsAttrib
avtMFIXCDFFileFormat::~avtMFIXCDFFileFormat()
{
debug5 << "destructor for time " << timeNow << endl;
delete dataFile;
nc_close(dataFile);
delete filePath;
}
......@@ -333,8 +433,8 @@ avtMFIXCDFFileFormat::FreeUpResources(void)
Lz->Delete();
Lz= NULL;
}
delete dataFile;
dataFile= NULL;
nc_close(dataFile);
dataFile= -1;
}
double
......@@ -392,7 +492,7 @@ avtMFIXCDFFileFormat::GetAuxiliaryData(const char * var,
int *matnos = NULL;
int nmats = 0;
char** names = NULL;
NcFile* meshFile = NULL;
int meshFile = -1;
TRY
{
int dims[3] = {1,1,1}, ndims = 1, nzvals = 0;
......@@ -445,7 +545,7 @@ avtMFIXCDFFileFormat::GetAuxiliaryData(const char * var,
char* ind= strrchr(meshFileName,'_');
*ind= '\0'; // string now ends before '_'
strncat(meshFileName,"_MESH.nc",sizeof(meshFileName)-1);
meshFile= openFile(meshFileName);
meshFile = openFile(meshFileName);
checkFile(meshFile, meshFileName, iSz, jSz, kSz);
getBlockOfInts3D( meshFile, "flag", matlist,
offsets[0], widths[0]+2,
......@@ -479,7 +579,7 @@ avtMFIXCDFFileFormat::GetAuxiliaryData(const char * var,
);
// Clean up.
delete meshFile;
nc_close(meshFile);
delete [] matlist;
delete [] matnos;
for(int i = 0; i < nmats; ++i) delete [] names[i];
......@@ -491,7 +591,7 @@ avtMFIXCDFFileFormat::GetAuxiliaryData(const char * var,
CATCH(InvalidFilesException)
{
// Clean up.
delete meshFile;
nc_close(meshFile);
delete [] matlist;
delete [] matnos;
for(int i = 0; i < nmats; ++i) delete [] names[i];
......@@ -502,7 +602,7 @@ avtMFIXCDFFileFormat::GetAuxiliaryData(const char * var,
CATCHALL
{
// Clean up.
delete meshFile;
nc_close(meshFile);
delete [] matlist;
delete [] matnos;
for(int i = 0; i < nmats; ++i) delete [] names[i];
......@@ -799,7 +899,6 @@ avtMFIXCDFFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md)
mesh->name = "Mesh";
checkCoordArrays();
int nVar= dataFile->num_vars();
if (coordCode==0)
mesh->meshType = AVT_RECTILINEAR_MESH;
......@@ -851,23 +950,59 @@ avtMFIXCDFFileFormat::PopulateDatabaseMetaData(avtDatabaseMetaData *md)
AddScalarVarToMetaData(md, "flagclass_var", "Mesh", AVT_ZONECENT);
std::set<std::string> varNames;
int nVar;
int vars[NC_MAX_VARS];
if (nc_inq_varids(dataFile, &nVar, vars) != NC_NOERR)
{
debug5 << "Failed to get variable ids" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
char t[NC_MAX_NAME + 1];
for (int i=0; i<nVar; i++)
{
NcVar* v= dataFile->get_var(i);
NcToken t= v->name();
int var = vars[i];
if (nc_inq_varname(dataFile, var, t) != NC_NOERR)
{
debug5 << "Failed to get variable name" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
nc_type vartype;
if (nc_inq_vartype(dataFile, var, &vartype) != NC_NOERR)
{
debug5 << "Failed to get variable type" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
std::string typeNames[]= {"nat","byte","char","short","int","float","double"};
debug5 << "Variable " << v->name() << " is of type "
<< typeNames[v->type()] << endl;
debug5 << "Variable " << t << " is of type "
<< typeNames[vartype] << endl;
if (strcmp(t,"x") && strcmp(t,"y") && strcmp(t,"z")
&& strcmp(t,"coordinates") && strcmp(t,"t"))
{
// Well, I guess this must be a real variable, then.
AddScalarVarToMetaData(md, v->name(), "Mesh", AVT_ZONECENT);
varNames.insert(v->name());
for (int l=0; l<v->num_dims(); l++)
AddScalarVarToMetaData(md, t, "Mesh", AVT_ZONECENT);
varNames.insert(t);
int ndims;
if (nc_inq_varndims(dataFile, var, &ndims) != NC_NOERR)
{
debug5 << "Variable " << v->name() << " dim " << l << " size is "
<< v->get_dim(l)->size() << endl;
debug5 << "Failed to get variable dimension count" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
int dimids[NC_MAX_VAR_DIMS];
if (nc_inq_vardimid(dataFile, var, dimids) != NC_NOERR)
{
debug5 << "Failed to get variable dimension ids" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
for (int l=0; l<ndims; l++)
{
size_t dimlen;
if (nc_inq_dimlen(dataFile, dimids[l], &dimlen) != NC_NOERR)
{
debug5 << "Failed to get variable dimension len" << endl;
EXCEPTION1(InvalidFilesException,filePath->c_str());
}
debug5 << "Variable " << t << " dim " << l << " size is "
<< dimlen << endl;
}
}
}
......@@ -1606,26 +1741,21 @@ avtMFIXCDFFileFormat::GetVectorVar(int domain, const char *varname)
return arr;
}
//void avtMFIXCDFFileFormat::getBlockOfDoubles1D(NcVar* in, vtkDoubleArray *v,
// long offset, int n)
void avtMFIXCDFFileFormat::getBlockOfDoubles1D(NcFile* file,
void avtMFIXCDFFileFormat::getBlockOfDoubles1D(int ncid,
const char* varname,
double* data,
long offset, int n)
{
NcVar* inVar= file->get_var(varname);
if (!inVar)
int varid;
if (nc_inq_varid(ncid, varname, &varid) != NC_NOERR)
{
debug5 << "Data file nas no variable " << varname << endl;
EXCEPTION1(InvalidVariableException, varname);
}
if (!inVar->set_cur(offset))
{
debug5 << "set_cur failed with offset " << offset << endl;
EXCEPTION2(UnexpectedValueException,"set_cur failed",(int)offset);
}
if (!inVar->get(data,n))
size_t start[] = {static_cast<size_t>(offset)};
size_t count[] = {static_cast<size_t>(n)};
if (nc_get_vara_double(ncid, varid, start, count, data) != NC_NOERR)
{
debug5 << "get failed with offset,n values " << offset
<< " " << n << endl;
......@@ -1635,34 +1765,28 @@ void avtMFIXCDFFileFormat::getBlockOfDoubles1D(NcFile* file,
// << inVar->name() << endl;
}
void avtMFIXCDFFileFormat::getBlockOfFloats3D(NcFile* file,
void avtMFIXCDFFileFormat::getBlockOfFloats3D(int ncid,
const char* varname,
float *data,
long iOffset, int iN,
long jOffset, int jN,
long kOffset, int kN)
{
NcVar* inVar= file->get_var(varname);
if (!inVar)
int varid;
if (nc_inq_varid(ncid, varname, &varid) != NC_NOERR)
{
debug5 << "Data file nas no variable " << varname << endl;
EXCEPTION1(InvalidVariableException, varname);
}
debug5 << "Setting cur for " << inVar->name() << " to " << kOffset
debug5 << "Setting cur for " << varname << " to " << kOffset
<< " " << jOffset << " " << iOffset << endl;
if (!(inVar->set_cur(0,kOffset,jOffset,iOffset)))
{
debug5 << "Failure doing set_cur of " << inVar->name() << " to "
<< kOffset << " " << jOffset << " " << iOffset << endl;
ostringstream oss;
oss << kOffset << " " << jOffset << " " << iOffset;
EXCEPTION2(UnexpectedValueException,"set_cur failed",oss.str());
}
size_t start[] = {static_cast<size_t>(kOffset), static_cast<size_t>(jOffset), static_cast<size_t>(iOffset)};
size_t count[] = {static_cast<size_t>(kN), static_cast<size_t>(jN), static_cast<size_t>(iN)};
debug5 << "Getting " << kN << " " << jN << " " << iN << endl;
if (!(inVar->get(data, 1, kN, jN, iN)))
if (nc_get_vara_float(ncid, varid, start, count, data) != NC_NOERR)
{
debug5 << "Failure doing get from " << inVar->name() << " of "
debug5 << "Failure doing get from " << varname << " of "
<< kN << " " << jN << " " << iN << endl;
ostringstream oss;
oss << kN << " " << jN << " " << iN;
......@@ -1672,15 +1796,15 @@ void avtMFIXCDFFileFormat::getBlockOfFloats3D(NcFile* file,
<< data[2] << " ..." << endl;
}
void avtMFIXCDFFileFormat::getBlockOfInts3D(NcFile* file,
void avtMFIXCDFFileFormat::getBlockOfInts3D(int ncid,
const char* varname,
int *data,
long iOffset, int iN,
long jOffset, int jN,
long kOffset, int kN)
{
NcVar* inVar= file->get_var(varname);
if (!inVar)
int varid;
if (nc_inq_varid(ncid, varname, &varid) != NC_NOERR)
{
debug5 << "Data file nas no variable " << varname << endl;
EXCEPTION1(InvalidVariableException, varname);
......@@ -1688,18 +1812,12 @@ void avtMFIXCDFFileFormat::getBlockOfInts3D(NcFile* file,
// debug5 << "Setting cur to " << kOffset << " " << jOffset << " "
// << iOffset << endl;
if (!(inVar->set_cur(0,kOffset,jOffset,iOffset)))
{
debug5 << "Failure doing set_cur of " << inVar->name() << " to "
<< kOffset << " " << jOffset << " " << iOffset << endl;
ostringstream oss;
oss << kOffset << " " << jOffset << " " << iOffset;
EXCEPTION2(UnexpectedValueException,"set_cur failed",oss.str());
}
size_t start[] = {static_cast<size_t>(kOffset), static_cast<size_t>(jOffset), static_cast<size_t>(iOffset)};
size_t count[] = {static_cast<size_t>(kN), static_cast<size_t>(jN), static_cast<size_t>(iN)};
// debug5 << "Getting " << kN << " " << jN << " " << iN << endl;
if (!(inVar->get(data, 1, kN, jN, iN)))
if (nc_get_vara_int(ncid, varid, start, count, data) != NC_NOERR)
{
debug5 << "Failure doing get from " << inVar->name() << " of "
debug5 << "Failure doing get from " << varname << " of "
<< kN << " " << jN << " " << iN << endl;
ostringstream oss;
oss << kN << " " << jN << " " << iN;
......
databases/MFIXCDF/avtMFIXCDFFileFormat.h
View file @ 7979647d
......@@ -44,7 +44,7 @@
#define AVT_MFIXCDF_FILE_FORMAT_H
#include <avtSTMDFileFormat.h>
#include <vtk_netcdfcpp.h>
#include <vtk_netcdf.h>
#include <string>
#include <set>
......@@ -120,17 +120,17 @@ private:
void decompose_domains(int, int *, int *, int *);
void get_limit(int, int, int, vtkDoubleArray *,
int *, int *, double **);
void getBlockOfDoubles1D(NcFile* file,
void getBlockOfDoubles1D(int ncid,
const char* varname,
double* data,
long offset, int n);
void getBlockOfFloats3D(NcFile* file,
void getBlockOfFloats3D(int ncid,
const char* varname,
float* data,
long iOffset, int iN,
long jOffset, int jN,
long kOffset, int kN);
void getBlockOfInts3D(NcFile* file,
void getBlockOfInts3D(int ncid,
const char* varname,
int* data,
long iOffset, int iN,
......@@ -142,7 +142,7 @@ private:
// These members are initialized in the constructor
std::string* filePath;
NcFile* dataFile;
int dataFile;
double timeNow;
int numXDomains;
int numYDomains;
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment