//-*****************************************************************************
void
CopyWrittenArray( hid_t iGroup,
const std::string &iName,
WrittenArraySampleIDPtr iRef )
{
ABCA_ASSERT( ( bool )iRef,
"CopyWrittenArray() passed a bogus ref" );
hid_t fid = H5Iget_file_id(iGroup);
ABCA_ASSERT( fid >= 0,
"CopyWrittenArray() Could not get file ID from iGroup" );
hid_t did = H5Dopen( fid,
iRef->getObjectLocation().c_str(), H5P_DEFAULT );
DsetCloser dcloser(did);
// We have a reference. Create a link to it.
// We are manually getting the source dataset instead of using
// fid and iName because of a bug in HDF5 1.8.5 and earlier.
// Files written using that approach would sometimes be corrupted.
herr_t status = H5Lcreate_hard( did,
".",
iGroup,
iName.c_str(),
H5P_DEFAULT,
H5P_DEFAULT );
H5Fclose( fid );
ABCA_ASSERT( status >= 0,
"H5Lcreate_hard failed!" << std::endl
<< "Dset obj id: " << did << std::endl
<< "Link loc id: " << iGroup << std::endl
<< "Link name: " << iName );
}
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Iget_1file_1id
(JNIEnv *env, jclass clss, jlong obj_id)
{
hid_t file_id = -1;
file_id = H5Iget_file_id((hid_t)obj_id);
if (file_id < 0)
h5libraryError(env);
return (jlong) file_id;
} /* end Java_hdf_hdf5lib_H5_H5Iget_1file_1id */
/****if* H5If/h5iget_file_id_c
* NAME
* h5iget_file_id_c
* PURPOSE
* Call H5Iget_file_id to obtain file identifier from object identifier
* INPUTS
* obj_id - object identifier
* OUTPUTS
* file_id - file identifier
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* Elena Pourmal
* Tuesday, August 24, 2004
*
* SOURCE
*/
int_f
h5iget_file_id_c(hid_t_f *obj_id, hid_t_f *file_id)
/******/
{
int ret_value;
hid_t c_file_id;
/*
* Call H5Iget_file_id
*/
if ((c_file_id = H5Iget_file_id(*obj_id)) < 0)
HGOTO_DONE(FAIL);
/* Set output & return values */
*file_id=(hid_t_f)c_file_id;
ret_value=0;
done:
return ret_value;
}
hid_t file() const {
MPQC_FILE_THREADSAFE;
return H5Iget_file_id(id_);
}
/* Test basic functionality of registering and deleting types and IDs */
static int basic_id_test(void)
{
H5I_type_t myType = H5I_BADID;
hid_t arrayID = H5I_INVALID_HID;
void* testObj = NULL;
void* testPtr = NULL;
char nameString[10];
hid_t testID;
ssize_t testSize = -1;
herr_t err;
int num_ref;
hsize_t num_members;
/* Try to register an ID with ficticious types */
H5E_BEGIN_TRY
arrayID = H5Iregister((H5I_type_t) 420, testObj);
H5E_END_TRY
VERIFY(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID != H5I_INVALID_HID)
goto out;
H5E_BEGIN_TRY
arrayID = H5Iregister((H5I_type_t) -1, testObj);
H5E_END_TRY
VERIFY(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID != H5I_INVALID_HID)
goto out;
/* Try to access IDs with ficticious types */
H5E_BEGIN_TRY
testPtr = H5Iobject_verify((hid_t)100, (H5I_type_t) 0);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
H5E_BEGIN_TRY
testPtr = H5Iobject_verify((hid_t)700, (H5I_type_t) 700);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
/* Register a type */
myType = H5Iregister_type((size_t)64, 0, (H5I_free_t) free );
CHECK(myType, H5I_BADID, "H5Iregister_type");
if(myType == H5I_BADID)
goto out;
/* Register an ID and retrieve the object it points to.
* Once the ID has been registered, testObj will be freed when
* its ID type is destroyed. */
testObj = HDmalloc(7 * sizeof(int));
arrayID = H5Iregister(myType, testObj);
CHECK(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID == H5I_INVALID_HID)
{
HDfree(testObj);
goto out;
}
testPtr = (int *) H5Iobject_verify(arrayID, myType);
VERIFY(testPtr, testObj, "H5Iobject_verify");
if(testPtr != testObj)
goto out;
/* Ensure that H5Iget_file_id and H5Iget_name() fail, since this
* is an hid_t for the wrong kind of object */
H5E_BEGIN_TRY
testID = H5Iget_file_id(arrayID);
H5E_END_TRY
VERIFY(testID, H5I_INVALID_HID, "H5Iget_file_id");
if(testID != H5I_INVALID_HID)
goto out;
H5E_BEGIN_TRY
testSize = H5Iget_name(arrayID, nameString, (size_t)9);
H5E_END_TRY
VERIFY(testSize, -1, "H5Iget_name");
if(testSize != -1)
goto out;
/* Make sure H5Iremove_verify catches objects of the wrong type */
H5E_BEGIN_TRY
testPtr = (int*) H5Iremove_verify(arrayID, (H5I_type_t) 0);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iremove_verify");
if(testPtr != NULL)
goto out;
H5E_BEGIN_TRY
testPtr = (int*) H5Iremove_verify(arrayID, (H5I_type_t) ((int) myType-1));
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iremove_verify");
if(testPtr != NULL)
goto out;
/* Remove an ID and make sure we can't access it */
testPtr = (int*) H5Iremove_verify(arrayID, myType);
CHECK(testPtr, NULL, "H5Iremove_verify");
if(testPtr == NULL)
goto out;
H5E_BEGIN_TRY
testPtr = (int*) H5Iobject_verify(arrayID, myType);
H5E_END_TRY
VERIFY(testPtr, NULL, "H5Iobject_verify");
if(testPtr != NULL)
goto out;
/* Delete the type and make sure we can't access objects within it */
arrayID = H5Iregister(myType, testObj);
err = H5Idestroy_type(myType);
VERIFY(err, 0, "H5Idestroy_type");
if( err != 0)
goto out;
VERIFY(H5Itype_exists(myType), 0, "H5Itype_exists");
if(H5Itype_exists(myType) != 0)
goto out;
H5E_BEGIN_TRY
VERIFY(H5Inmembers(myType, NULL), -1, "H5Inmembers");
if(H5Inmembers(myType, NULL) != -1)
goto out;
H5E_END_TRY
/* Register another type and another object in that type */
myType = H5Iregister_type((size_t)64, 0, (H5I_free_t) free );
CHECK(myType, H5I_BADID, "H5Iregister_type");
if(myType == H5I_BADID)
goto out;
/* The memory that testObj pointed to should already have been
* freed when the previous type was destroyed. Allocate new
* memory for it.
*/
testObj = HDmalloc(7 * sizeof(int));
arrayID = H5Iregister(myType, testObj);
CHECK(arrayID, H5I_INVALID_HID, "H5Iregister");
if(arrayID == H5I_INVALID_HID)
{
HDfree(testObj);
goto out;
}
err = H5Inmembers(myType, &num_members);
CHECK(err, -1, "H5Inmembers");
if (err < 0)
goto out;
VERIFY(num_members, 1, "H5Inmembers");
if(num_members != 1)
goto out;
/* Increment references to type and ensure that dec_type_ref
doesn't destroy the type */
num_ref = H5Iinc_type_ref(myType);
VERIFY(num_ref, 2, "H5Iinc_type_ref");
if( num_ref != 2)
goto out;
num_ref = H5Idec_type_ref(myType);
VERIFY(num_ref, 1, "H5Idec_type_ref");
if(num_ref != 1)
goto out;
err = H5Inmembers(myType, &num_members);
CHECK(err, -1, "H5Inmembers");
if (err < 0)
goto out;
VERIFY(num_members, 1, "H5Inmembers");
if(num_members != 1)
goto out;
/* This call to dec_type_ref should destroy the type */
num_ref = H5Idec_type_ref(myType);
VERIFY(num_ref, 0, "H5Idec_type_ref");
if(num_ref != 0)
goto out;
VERIFY(H5Itype_exists(myType), 0, "H5Itype_exists");
if (H5Itype_exists(myType) != 0)
goto out;
H5E_BEGIN_TRY
err = H5Inmembers(myType, &num_members);
if(err >= 0)
goto out;
H5E_END_TRY
return 0;
out:
/* Clean up type if it has been allocated and free memory used
* by testObj */
if(myType >= 0)
H5Idestroy_type(myType);
return -1;
}
File Object::file () const {
return File (Exception::check ("H5Iget_file_id", H5Iget_file_id (handle ())));
}
hid_t HdfGroup::file_id() const { return H5Iget_file_id( d->id ); }
/*-------------------------------------------------------------------------
* Function: copy_attr
*
* Purpose: copy attributes located in LOC_IN, which is obtained either from
* loc_id = H5Gopen2( fid, name);
* loc_id = H5Dopen2( fid, name);
* loc_id = H5Topen2( fid, name);
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
int
copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
trav_table_t *travt, pack_opt_t *options)
{
int ret_value = 0;
hid_t attr_id = -1; /* attr ID */
hid_t attr_out = -1; /* attr ID */
hid_t space_id = -1; /* space ID */
hid_t ftype_id = -1; /* file type ID */
hid_t wtype_id = -1; /* read/write type ID */
size_t msize; /* size of type */
void *buf = NULL; /* data buffer */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
htri_t is_named; /* Whether the datatype is named */
hsize_t dims[H5S_MAX_RANK];/* dimensions of dataset */
char name[255];
H5O_info_t oinfo; /* object info */
int j;
unsigned u;
hbool_t is_ref = 0;
H5T_class_t type_class = -1;
if (H5Oget_info(loc_in, &oinfo) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
/*-------------------------------------------------------------------------
* copy all attributes
*-------------------------------------------------------------------------
*/
for (u = 0; u < (unsigned) oinfo.num_attrs; u++) {
/* open attribute */
if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
/* get name */
if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
/* get the file datatype */
if ((ftype_id = H5Aget_type(attr_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_type failed");
/* Check if the datatype is committed */
if ((is_named = H5Tcommitted(ftype_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommitted failed");
if (is_named && travt) {
hid_t fidout = -1;
/* Create out file id */
if ((fidout = H5Iget_file_id(loc_out)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iget_file_id failed");
/* Copy named dt */
if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
H5Fclose(fidout);
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
} /* end if */
if (H5Fclose(fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
} /* end if */
else {
if (options->use_native == 1)
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
} /* end else */
/* get the dataspace handle */
if ((space_id = H5Aget_space(attr_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aget_space failed");
/* get dimensions */
if ((rank = H5Sget_simple_extent_dims(space_id, dims, NULL)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_dims failed");
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
if ((msize = H5Tget_size(wtype_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
/*-------------------------------------------------------------------------
* object references are a special case. We cannot just copy the buffers,
* but instead we recreate the reference.
* This is done on a second sweep of the file that just copies the referenced
* objects at copy_refs_attr()
*-------------------------------------------------------------------------
*/
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
if (type_class == H5T_VLEN || type_class == H5T_ARRAY) {
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
if (H5Tclose(base_type) < 0)
H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
}
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id);
for (j = 0; j < nmembers; j++) {
hid_t mtid = H5Tget_member_type(wtype_id, (unsigned)j);
H5T_class_t mtclass = H5Tget_class(mtid);
if (H5Tclose(mtid) < 0)
H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose mtid failed");
if (mtclass == H5T_REFERENCE) {
is_ref = 1;
break;
}
} /* for (j=0; i<nmembers; j++) */
} /* if (type_class == H5T_COMPOUND) */
if (!is_ref) {
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
if (buf == NULL) {
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if (H5Aread(attr_id, wtype_id, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
/*-------------------------------------------------------------------------
* copy
*-------------------------------------------------------------------------
*/
if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Acreate2 failed on ,%s>", name);
if (H5Awrite(attr_out, wtype_id, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Awrite failed");
/*close*/
if (H5Aclose(attr_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
HDfree(buf);
buf = NULL;
} /*H5T_REFERENCE*/
if (options->verbose)
printf(FORMAT_OBJ_ATTR, "attr", name);
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Sclose(space_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
space_id = -1;
if (H5Tclose(wtype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
wtype_id = -1;
if (H5Tclose(ftype_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tclose failed");
ftype_id = -1;
if (H5Aclose(attr_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
attr_id = -1;
} /* for u */
done:
H5E_BEGIN_TRY {
if (buf) {
/* Check if we have VL data and string in the attribute's datatype that must
* be reclaimed */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
/* Free buf */
HDfree(buf);
} /* end if */
H5Aclose(attr_out);
H5Sclose(space_id);
H5Tclose(wtype_id);
H5Tclose(ftype_id);
H5Aclose(attr_id);
} H5E_END_TRY;
return ret_value;
} /* end copy_attr() */
