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Merged
markcmiller86 merged 11 commits into from
Oct 26, 2025
Merged

Unify python objects between hdf5 and pdb drivers #380

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1b2277d
Handle intermediate mini-array types
markcmiller86 Jun 23, 2024
dc564da
Use multi-component add methods
markcmiller86 Jun 23, 2024
2e83148
fix multi-comp add methods
markcmiller86 Jun 23, 2024
5854dbc
add mini-array types
markcmiller86 Jun 23, 2024
02ecf67
Remove unused var, typestr
markcmiller86 Jun 23, 2024
de8d899
Handle mini-array types
markcmiller86 Jun 23, 2024
bb707ea
Handle mini-array data indirections
markcmiller86 Jun 23, 2024
c1d600a
WS change to trigger ci
markcmiller86 Oct 26, 2025
2002c2a
Merge branch 'main' into mcm86-22jun24-unify-pyobjs
markcmiller86 Oct 26, 2025
c3773bb
fix mem error
markcmiller86 Oct 26, 2025
305e31a
Merge remote-tracking branch 'origin/mcm86-22jun24-unify-pyobjs' into…
markcmiller86 Oct 26, 2025
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48 changes: 11 additions & 37 deletions src/hdf5_drv/silo_hdf5.c
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Original file line number Diff line number Diff line change
Expand Up @@ -7173,10 +7173,10 @@ db_hdf5_GetComponentStuff(DBfile *_dbfile, char const *objname, char const *comp
UNWIND();
}

for (i=0, mult=1; i<ndims; i++) mult *= dim[i];

if (just_get_datatype == 0)
{
for (i=0, mult=1; i<ndims; i++) mult *= dim[i];

/* Allocate the return value */
if (NULL==(retval=calloc(mult, db_GetMachDataSize(datatype)))) {
db_perror(compname, E_CALLFAIL, me);
Expand Down Expand Up @@ -7214,6 +7214,15 @@ db_hdf5_GetComponentStuff(DBfile *_dbfile, char const *objname, char const *comp
else
{
*just_get_datatype = datatype;
if (mult > 1)
{
if (datatype == DB_INT)
*just_get_datatype = DB_INTA;
else if (datatype == DB_FLOAT)
*just_get_datatype = DB_FLOATA;
else if (datatype == DB_DOUBLE)
*just_get_datatype = DB_DOUBLEA;
}
}
}

Expand Down Expand Up @@ -8836,18 +8845,7 @@ db_hdf5_GetObject(DBfile *_dbfile, char const *name)
H5T_NATIVE_INT);
memcpy(mem_value, file_value, H5Tget_size(atype));
H5Tconvert(atype, mtype, 1, mem_value, bkg, H5P_DEFAULT);
#if 0
DBAddIntNComponent(obj, name, nelmts, (int*)mem_value);
#else
if (1==nelmts) {
DBAddIntComponent(obj, name, *((int*)mem_value));
} else {
for (j=0; (size_t)j<nelmts; j++) {
sprintf(bigname, "%s%d", name, j+1);
DBAddIntComponent(obj, bigname, ((int*)mem_value)[j]);
}
}
#endif
break;

case H5T_FLOAT:
Expand All @@ -8857,35 +8855,11 @@ db_hdf5_GetObject(DBfile *_dbfile, char const *name)
H5Tconvert(atype, mtype, 1, mem_value, bkg, H5P_DEFAULT);
if (4 == (int) H5Tget_size(member_type))
{
#if 0
DBAddFltNComponent(obj, name, nelmts, (double*)mem_value);
#else
if (1==nelmts) {
DBAddFltComponent(obj, name, *((double*)mem_value));
} else {
for (j=0; (size_t)j<nelmts; j++) {
sprintf(bigname, "%s%d", name, j+1);
DBAddFltComponent(obj, bigname,
((double*)mem_value)[j]);
}
}
#endif
}
else
{
#if 0
DBAddDblNComponent(obj, name, nelmts, (double*)mem_value);
#else
if (1==nelmts) {
DBAddDblComponent(obj, name, *((double*)mem_value));
} else {
for (j=0; (size_t)j<nelmts; j++) {
sprintf(bigname, "%s%d", name, j+1);
DBAddDblComponent(obj, bigname,
((double*)mem_value)[j]);
}
}
#endif
}
break;

Expand Down
8 changes: 5 additions & 3 deletions src/silo/silo.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3283,7 +3283,7 @@ DBAddIntNComponent(DBobject *object, const char *compname, int n, int const *ii)
int i;
char tmp[256];

API_BEGIN("DBAddIntComponent", int, -1) {
API_BEGIN("DBAddIntNComponent", int, -1) {
if (!object)
API_ERROR("object pointer", E_BADARGS);
if (!compname || !*compname)
Expand Down Expand Up @@ -3367,7 +3367,7 @@ DBAddFltNComponent(DBobject *object, const char *compname, int n, double const *
int i;
char tmp[256];

API_BEGIN("DBAddFltComponent", int, -1) {
API_BEGIN("DBAddFltNComponent", int, -1) {
if (!object)
API_ERROR("object pointer", E_BADARGS);
if (!compname || !*compname)
Expand All @@ -3387,6 +3387,7 @@ DBAddFltNComponent(DBobject *object, const char *compname, int n, double const *
{
char tmp2[32];
snprintf(tmp2, sizeof(tmp2), ",%g", ff[i]);
strcat(tmp, tmp2);
}
strcat(tmp, "'");

Expand Down Expand Up @@ -3436,7 +3437,7 @@ DBAddDblNComponent(DBobject *object, const char *compname, int n, double const *
int i;
char tmp[256];

API_BEGIN("DBAddDblComponent", int, -1) {
API_BEGIN("DBAddDblNComponent", int, -1) {
if (!object)
API_ERROR("object pointer", E_BADARGS);
if (!compname || !*compname)
Expand All @@ -3456,6 +3457,7 @@ DBAddDblNComponent(DBobject *object, const char *compname, int n, double const *
{
char tmp2[64];
snprintf(tmp2, sizeof(tmp2), ",%.30g", dd[i]);
strcat(tmp,tmp2);
}
strcat(tmp, "'");

Expand Down
8 changes: 7 additions & 1 deletion src/silo/silo.h.in
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Original file line number Diff line number Diff line change
Expand Up @@ -357,7 +357,13 @@ typedef enum {
DB_DOUBLE=20,
DB_CHAR=21,
DB_LONG_LONG=22,
DB_NOTYPE=25 /*unknown type */

/* mini-array types for things like dims[3] or min_extents[3] */
DB_INTA=23,
DB_FLOATA=24,
DB_DOUBLEA=25,

DB_NOTYPE=26 /*unknown type */
} DBdatatype;

/* Flags for DBCreate (used only in DBCreate) */
Expand Down
45 changes: 30 additions & 15 deletions tools/python/pydbfile.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -352,13 +352,13 @@ static PyObject *DBfile_DBGetVarInfo(PyObject *self, PyObject *args)
PyDict_SetItemString(retval, "type", PyString_FromString(silo_obj->type));
for (int i=0; i<silo_obj->ncomponents; i++)
{
PyObject *tmpTuple;
string compname = silo_obj->comp_names[i];
string pdbname = silo_obj->pdb_names[i];
int type = DBGetComponentType(db, str, compname.c_str());
void *comp = 0;

if (type == DB_INT || type == DB_SHORT || type == DB_LONG || type == DB_LONG_LONG ||
type == DB_FLOAT || type == DB_DOUBLE || type == DB_CHAR)
if (type != DB_NOTYPE)
{
comp = DBGetComponent(db, str, compname.c_str());
if (!comp)
Expand All @@ -369,59 +369,74 @@ static PyObject *DBfile_DBGetVarInfo(PyObject *self, PyObject *args)
continue;
}
}
string typestr = "";
int ival = -1;
switch (type)
{
case DB_INT:
typestr = "int";
ival = *((int*)comp);
PyDict_SetItemString(retval, compname.c_str(), PyInt_FromLong((long)ival));
break;
case DB_INTA:
tmpTuple = PyTuple_New(3);
PyTuple_SET_ITEM(tmpTuple, 0, PyInt_FromLong((long)((int*)comp)[0]));
PyTuple_SET_ITEM(tmpTuple, 1, PyInt_FromLong((long)((int*)comp)[1]));
PyTuple_SET_ITEM(tmpTuple, 2, PyInt_FromLong((long)((int*)comp)[2]));
PyDict_SetItemString(retval, compname.c_str(), tmpTuple);
break;
case DB_SHORT:
typestr = "short";
ival = *((short*)comp);
PyDict_SetItemString(retval, compname.c_str(), PyInt_FromLong((long)ival));
break;
case DB_LONG:
typestr = "long";
ival = (int) *((long*)comp);
PyDict_SetItemString(retval, compname.c_str(), PyInt_FromLong((long)ival));
break;
case DB_LONG_LONG:
typestr = "long long";
ival = (int) *((long long*)comp);
PyDict_SetItemString(retval, compname.c_str(), PyInt_FromLong((long)ival));
break;
case DB_FLOAT:
typestr = "float";
PyDict_SetItemString(retval, compname.c_str(), PyFloat_FromDouble((double)*((float*)comp)));
break;
case DB_FLOATA:
tmpTuple = PyTuple_New(3);
PyTuple_SET_ITEM(tmpTuple, 0, PyFloat_FromDouble((double)((float*)comp)[0]));
PyTuple_SET_ITEM(tmpTuple, 1, PyFloat_FromDouble((double)((float*)comp)[1]));
PyTuple_SET_ITEM(tmpTuple, 2, PyFloat_FromDouble((double)((float*)comp)[2]));
PyDict_SetItemString(retval, compname.c_str(), tmpTuple);
break;
case DB_DOUBLE:
typestr = "double";
PyDict_SetItemString(retval, compname.c_str(), PyFloat_FromDouble(*((double*)comp)));
break;
case DB_DOUBLEA:
tmpTuple = PyTuple_New(3);
PyTuple_SET_ITEM(tmpTuple, 0, PyFloat_FromDouble((double)((double*)comp)[0]));
PyTuple_SET_ITEM(tmpTuple, 1, PyFloat_FromDouble((double)((double*)comp)[1]));
PyTuple_SET_ITEM(tmpTuple, 2, PyFloat_FromDouble((double)((double*)comp)[2]));
PyDict_SetItemString(retval, compname.c_str(), tmpTuple);
break;
case DB_CHAR:
typestr = "char";
if (*((char*)comp)== 0)
PyDict_SetItemString(retval, compname.c_str(), PyString_FromString(""));
else
PyDict_SetItemString(retval, compname.c_str(), PyString_FromString((char*)comp));
break;
case DB_NOTYPE:
typestr = "notype";
break;
default:
typestr = "var";
string valStr = std::string(pdbname.c_str());
if (pdbname.find("'<s>") == 0)
{
int len = pdbname.length();
valStr = string((const char*)(pdbname.c_str()),4,len-5);
}
if (get_data_flag)
bool is_meta_data = false;
if ((compname == "align") || (compname == "baseindex") || (compname == "dims") ||
(compname == "dtime") || (compname == "max_extents") || (compname == "max_index") ||
(compname == "min_extents") || (compname == "min_index") || (compname == "time"))
is_meta_data = true;
if (get_data_flag || is_meta_data)
{

PyObject *argTuple = PyTuple_New(2);
PyTuple_SET_ITEM(argTuple, 0, PyString_FromString(valStr.c_str()));
PyTuple_SET_ITEM(argTuple, 1, PyString_FromString("dont-throw-errors-in-sanity-checks"));
Expand Down Expand Up @@ -491,7 +506,7 @@ static PyObject *DBfile_DBWrite(PyObject *self, PyObject *args)
double dvar;
char *svar;
char *data = 0;
int dsize[DB_NOTYPE];
int dsize[DB_NOTYPE+1];

dsize[DB_INT] = sizeof(int);
dsize[DB_SHORT] = sizeof(short);
Expand Down