H5Object & H5ReferenceData::getData(const unsigned int size, const unsigned int * index) const
{
char * cdata = static_cast<char *>(data) + offset;
void ** ref = 0;
unsigned int pos = 0;
unsigned int cumprod = 1;
H5O_info_t info;
H5Object * hobj;
hid_t obj;
hid_t file;
ssize_t ssize;
char * name = 0;
std::string _name;
for (unsigned int i = 0; i < size; i++)
{
pos += cumprod * index[i];
}
if (pos >= totalSize)
{
throw H5Exception(__LINE__, __FILE__, _("Invalid index."));
}
cdata += pos * (stride ? stride : dataSize);
file = getFile().getH5Id();
ref = &(((void **)cdata)[0]);
obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);
if (obj < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot open object at the given position."));
}
ssize = H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, 0, 0);
name = new char[ssize + 1];
H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, name, ssize + 1);
_name = std::string(name);
delete[] name;
H5Oget_info(obj, &info);
switch (info.type)
{
case H5O_TYPE_GROUP:
hobj = new H5Group(getParent(), obj, _name);
break;
case H5O_TYPE_DATASET:
hobj = new H5Dataset(getParent(), obj, _name);
break;
case H5O_TYPE_NAMED_DATATYPE:
hobj = new H5Type(getParent(), obj, _name);
break;
case H5O_TYPE_UNKNOWN:
default:
H5Oclose(obj);
throw H5Exception(__LINE__, __FILE__, _("Unknown HDF5 object"));
}
return *hobj;
}
/************************************************************
Operator function. Prints the name and type of the object
being examined.
************************************************************/
static herr_t op_func_v1(hid_t loc_id, const char *name, const H5L_info_t *info, void *operator_data)
{
H5O_info_t oinfo;
herr_t status = 0;
int *pDataSetId = (int*)operator_data;
hid_t obj = H5Oopen(loc_id, name, H5P_DEFAULT);
if (obj < 0)
{
return -1;
}
/*
* Get type of the object and return only datasetId
* through operator_data.
*/
status = H5Oget_info(obj, &oinfo);
if (status < 0)
{
H5Oclose(obj);
return -1;
}
if (oinfo.type == H5O_TYPE_DATASET)
{
*pDataSetId = obj;
}
else
{
H5Oclose(obj);
}
return 0;
}
extern hid_t get_attribute_handle(hid_t parent, char *name)
{
char buf[MAX_ATTR_NAME+1];
int nattr, i, len;
hid_t aid;
H5O_info_t object_info;
if (parent < 0) {
debug3("PROFILE: parent is not HDF5 object");
return -1;
}
H5Oget_info(parent, &object_info);
nattr = object_info.num_attrs;
for (i = 0; (nattr>0) && (i<nattr); i++) {
aid = H5Aopen_by_idx(parent, ".", H5_INDEX_NAME, H5_ITER_INC,
i, H5P_DEFAULT, H5P_DEFAULT);
// Get the name of the attribute.
len = H5Aget_name(aid, MAX_ATTR_NAME, buf);
if (len < MAX_ATTR_NAME) {
if (strcmp(buf, name) == 0) {
return aid;
}
}
H5Aclose(aid);
}
debug3("PROFILE: failed to find HDF5 attribute=%s\n", name);
return -1;
}
//--------------------------------------------------------------------------
// Function: H5Object::getNumAttrs
///\brief Returns the number of attributes attached to this HDF5 object.
///\return Number of attributes
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
int H5Object::getNumAttrs() const
{
H5O_info_t oinfo; /* Object info */
if(H5Oget_info(getId(), &oinfo) < 0)
throw AttributeIException(inMemFunc("getNumAttrs"), "H5Oget_info failed");
else
return( (int)oinfo.num_attrs );
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Oget_info
* Signature: (J)Lhdf/hdf5lib/structs/H5O_info_t;
*/
JNIEXPORT jobject JNICALL
Java_hdf_hdf5lib_H5_H5Oget_1info
(JNIEnv *env, jclass clss, jlong loc_id)
{
herr_t status = -1;
H5O_info_t infobuf;
jvalue args[12];
jobject hdrinfobuf;
jobject ihinfobuf1;
jobject ihinfobuf2;
jobject ret_obj = NULL;
status = H5Oget_info((hid_t)loc_id, &infobuf);
if (status < 0) {
h5libraryError(env);
} /* end if */
else {
args[0].i = (jint)infobuf.hdr.version;
args[1].i = (jint)infobuf.hdr.nmesgs;
args[2].i = (jint)infobuf.hdr.nchunks;
args[3].i = (jint)infobuf.hdr.flags;
args[4].j = (jlong)infobuf.hdr.space.total;
args[5].j = (jlong)infobuf.hdr.space.meta;
args[6].j = (jlong)infobuf.hdr.space.mesg;
args[7].j = (jlong)infobuf.hdr.space.free;
args[8].j = (jlong)infobuf.hdr.mesg.present;
args[9].j = (jlong)infobuf.hdr.mesg.shared;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5O_hdr_info_t", "(IIIIJJJJJJ)V", args);
hdrinfobuf = ret_obj;
args[0].j = (jlong)infobuf.meta_size.obj.index_size;
args[1].j = (jlong)infobuf.meta_size.obj.heap_size;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5_ih_info_t", "(JJ)V", args);
ihinfobuf1 = ret_obj;
args[0].j = (jlong)infobuf.meta_size.attr.index_size;
args[1].j = (jlong)infobuf.meta_size.attr.heap_size;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5_ih_info_t", "(JJ)V", args);
ihinfobuf2 = ret_obj;
args[0].j = (jlong)infobuf.fileno;
args[1].j = (jlong)infobuf.addr;
args[2].i = infobuf.type;
args[3].i = (jint)infobuf.rc;
args[4].j = (jlong)infobuf.num_attrs;
args[5].j = infobuf.atime;
args[6].j = infobuf.mtime;
args[7].j = infobuf.ctime;
args[8].j = infobuf.btime;
args[9].l = hdrinfobuf;
args[10].l = ihinfobuf1;
args[11].l = ihinfobuf2;
CALL_CONSTRUCTOR("hdf/hdf5lib/structs/H5O_info_t", "(JJIIJJJJJLhdf/hdf5lib/structs/H5O_hdr_info_t;Lhdf/hdf5lib/structs/H5_ih_info_t;Lhdf/hdf5lib/structs/H5_ih_info_t;)V", args);
}
return ret_obj;
} /* end Java_hdf_hdf5lib_H5_H5Oget_1info */
herr_t H5Group::getLsInfo(hid_t g_id, const char * name, const H5L_info_t * info, void * op_data)
{
H5O_info_t oinfo;
herr_t err;
hid_t obj;
OpDataGetLs & opdata = *(OpDataGetLs *)op_data;
switch (info->type)
{
case H5L_TYPE_SOFT:
opdata.name->push_back(name);
opdata.type->push_back("soft");
break;
case H5L_TYPE_EXTERNAL:
opdata.name->push_back(name);
opdata.type->push_back("external");
break;
case H5L_TYPE_HARD:
obj = H5Oopen_by_addr(g_id, info->u.address);
if (obj < 0)
{
return (herr_t) - 1;
}
err = H5Oget_info(obj, &oinfo);
H5Oclose(obj);
if (err < 0)
{
return (herr_t) - 1;
}
switch (oinfo.type)
{
case H5O_TYPE_GROUP:
opdata.name->push_back(name);
opdata.type->push_back("group");
break;
case H5O_TYPE_DATASET:
opdata.name->push_back(name);
opdata.type->push_back("dataset");
break;
case H5O_TYPE_NAMED_DATATYPE:
opdata.name->push_back(name);
opdata.type->push_back("type");
break;
default:
return (herr_t) - 1;
}
break;
default:
return (herr_t) - 1;
}
return (herr_t)0;
}
/*-------------------------------------------------------------------------
* Function: trav_fileinfo_add
*
* Purpose: Add a file addr & fileno to info struct
*
* Return: void
*
*-------------------------------------------------------------------------
*/
void
trav_fileinfo_add(trav_info_t *info, hid_t loc_id)
{
H5O_info_t oinfo;
size_t idx = info->nused - 1;
if ( info->paths[idx].path && HDstrcmp(info->paths[idx].path, "."))
H5Oget_info_by_name(loc_id, info->paths[idx].path, &oinfo, H5P_DEFAULT);
else
H5Oget_info(loc_id, &oinfo);
info->paths[idx].objno = oinfo.addr;
info->paths[idx].fileno = oinfo.fileno;
} /* end trav_fileinfo_add() */
herr_t H5Group::printLsInfo(hid_t g_id, const char * name, const H5L_info_t * info, void * op_data)
{
H5O_info_t oinfo;
herr_t err;
H5Object * hobj = 0;
hid_t obj = 0;
OpDataPrintLs & opdata = *(OpDataPrintLs *)op_data;
switch (info->type)
{
case H5L_TYPE_SOFT:
hobj = new H5SoftLink(*opdata.parent, name);
break;
case H5L_TYPE_EXTERNAL:
hobj = new H5ExternalLink(*opdata.parent, name);
break;
case H5L_TYPE_HARD:
obj = H5Oopen(g_id, name, H5P_DEFAULT);
err = H5Oget_info(obj, &oinfo);
H5Oclose(obj);
if (err < 0)
{
return (herr_t) - 1;
}
switch (oinfo.type)
{
case H5O_TYPE_GROUP:
hobj = new H5Group(*opdata.parent, name);
break;
case H5O_TYPE_DATASET:
hobj = new H5Dataset(*opdata.parent, name);
break;
case H5O_TYPE_NAMED_DATATYPE:
hobj = new H5Type(*opdata.parent, name);
break;
default:
return (herr_t) - 1;
}
break;
default:
return (herr_t) - 1;
}
hobj->printLsInfo(*opdata.os);
delete hobj;
return (herr_t)0;
}
/****if* H5Of/H5Oget_info_c
* NAME
* H5Oget_info_c
* PURPOSE
* Calls H5Oget_info
* INPUTS
* object_id - Identifier for target object.
* OUTPUTS
* object_info - Buffer in which to return object information.
*
* RETURNS
* 0 on success, -1 on failure
* AUTHOR
* M. Scot Breitenfeld
* May 16, 2012
* SOURCE
*/
int_f
h5oget_info_c (hid_t_f *object_id, H5O_info_t_f *object_info)
/******/
{
int_f ret_value = 0; /* Return value */
H5O_info_t Oinfo;
/*
* Call H5Oinfo_by_name function.
*/
if(H5Oget_info((hid_t)*object_id, &Oinfo) < 0)
HGOTO_DONE(FAIL);
ret_value = fill_h5o_info_t_f(Oinfo,object_info);
done:
return ret_value;
}
/*-------------------------------------------------------------------------
* Function: flush_verification
*
* Purpose: This function tries to open target object in the test file.
* It compares the success of the open function to the expected
* value, and succeeds if they are equal and fails if they differ.
*
* Note that full path to the object must be provided as the
* obj_pathname argument.
*
* Return: 0 on Success, 1 on Failure
*
* Programmer: Mike McGreevy
* July 16, 2010
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t flush_verification(const char * obj_pathname, const char * expected)
{
/* Variables */
hid_t oid,fid,status = 0;
H5O_info_t oinfo;
/* Try to open the testfile and then obj_pathname within the file */
H5E_BEGIN_TRY {
fid = H5Fopen(FILENAME, H5F_ACC_SWMR_READ, H5P_DEFAULT);
oid = H5Oopen(fid, obj_pathname, H5P_DEFAULT);
status = H5Oget_info(oid, &oinfo);
} H5E_END_TRY;
/* Compare to expected result */
if (strcmp(expected, FLUSHED) == 0) {
if ((oid < 0) || (status < 0)) {
HDfprintf(stderr, "Error! %s should be on disk, but was NOT!\n", obj_pathname);
PROCESS_ERROR;
} /* end if */
} else if (strcmp(expected, NOT_FLUSHED) == 0) {
if ((oid > 0) || (status > 0)) {
HDfprintf(stderr, "Error! %s not expected to be flushed, but it was found on disk!\n", obj_pathname);
PROCESS_ERROR;
} /* end if */
} else {
HDfprintf(stderr, "Error! Bad verification parameters. %s is an invalid expected outcome.\n", expected);
PROCESS_ERROR;
} /* end if */
/* Cleanup */
H5E_BEGIN_TRY {
H5Oclose(oid);
H5Fclose(fid);
} H5E_END_TRY;
return SUCCEED;
error:
return FAIL;
} /* flush_verification */
std::vector<std::string> list_attributes(hdf5dataset& hdataset)
{
H5O_info_t info;
H5Oget_info(hdataset.handle(), &info);
std::size_t num_attr = info.num_attrs;
std::vector<std::string> result(num_attr);
const int MAX_LEN = 256;
char attr_name[MAX_LEN];
for(std::size_t i = 0; i < num_attr; ++i)
{
hid_t attribute_id = H5Aopen_idx(hdataset.handle(), i);
H5Aget_name(attribute_id, MAX_LEN, attr_name);
result[i] = std::string(attr_name);
H5Aclose(attribute_id);
}
return result;
}
/*
* To exercise the coding for the re-read of the object header for SWMR access.
* When the object header is read in H5O_load() of H5Ocache.c, the library initially reads
* 512 bytes for decoding, then reads the remaining bytes later if the object header is
* greater than 512 bytes. For SWMR access, the read should be done all at one time.
*/
static herr_t
test_ohdr_swmr(void)
{
hid_t fid = -1; /* File ID */
hid_t fapl = -1; /* File access property list */
hid_t did = -1; /* Dataset ID */
hid_t sid = -1; /* Dataspace ID */
hid_t plist = -1; /* Dataset creation property list */
size_t compact_size = 1024; /* The size of compact dataset */
int wbuf[1024]; /* Buffer for writing */
hsize_t dims[1]; /* Dimension sizes */
unsigned int n = 0, u; /* Locatl index variable */
H5O_info_t obj_info; /* Information for the object */
TESTING("exercise the coding for the re-read of the object header for SWMR access");
/* File access property list */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
FAIL_STACK_ERROR
/* Set to use latest library format */
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
FAIL_STACK_ERROR
/* Initialize data */
for(u = 0; u < compact_size; u++)
wbuf[u] = n++;
/* Create the file with the latest format (ensure version 2 object header for SWMR) */
if((fid = H5Fcreate(FILE_OHDR_SWMR, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR
/* Create a small data space for compact dataset */
dims[0] = (hsize_t)compact_size;
if((sid = H5Screate_simple(1, dims, NULL)) < 0)
FAIL_STACK_ERROR
/* Create property list for compact dataset creation */
if((plist = H5Pcreate(H5P_DATASET_CREATE)) < 0)
FAIL_STACK_ERROR
/* Set the layout for the compact dataset */
if(H5Pset_layout(plist, H5D_COMPACT) < 0)
FAIL_STACK_ERROR
/* Create a compact dataset */
if((did = H5Dcreate2(fid, DSET_NAME, H5T_NATIVE_INT, sid, H5P_DEFAULT, plist, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Write to the compact dataset */
if(H5Dwrite(did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf) < 0)
FAIL_STACK_ERROR
/* Close the dataset */
if(H5Dclose(did) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(H5Fclose(fid) < 0)
FAIL_STACK_ERROR
/* Open the file for SWMR write and latest format */
if((fid = H5Fopen(FILE_OHDR_SWMR, H5F_ACC_RDWR|H5F_ACC_SWMR_WRITE, fapl)) < 0)
FAIL_STACK_ERROR
/* Open the compact dataset */
if((did = H5Dopen2(fid, DSET_NAME, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Get the object information */
if(H5Oget_info(did, &obj_info) < 0)
FAIL_STACK_ERROR
/* The size of object header should be greater than the speculative read size of 512 */
/* This will exercise the coding for the re-read of the object header for SWMR access */
if(obj_info.hdr.space.total < 512)
TEST_ERROR;
/* Close the dataset */
if(H5Dclose(did) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(H5Fclose(fid) < 0)
FAIL_STACK_ERROR
/* Close the dataspace */
if(H5Sclose(sid) < 0)
FAIL_STACK_ERROR
/* Close the dataset creation property list */
if(H5Pclose(plist) < 0)
FAIL_STACK_ERROR
/* Close the file access property list */
if(H5Pclose(fapl) < 0)
FAIL_STACK_ERROR
/* Remove the test file */
if(HDremove(FILE_OHDR_SWMR) < 0)
FAIL_STACK_ERROR
PASSED();
return 0;
error:
H5E_BEGIN_TRY {
H5Fclose(fid);
H5Dclose(did);
H5Sclose(sid);
H5Pclose(plist);
H5Pclose(fapl);
HDremove(FILE_OHDR_SWMR);
} H5E_END_TRY;
return -1;
} /* test_ohdr_swmr() */
u::logic HDF5FormatLib::GetHDF5StructFile(QString filePathJson1, QString filePathHdf)
{
hid_t file;
herr_t status;
H5O_info_t infobuf;
struct opdata od;
filePathJson = filePathJson1;
try
{
FILE *pfile1;
pfile1 = fopen(filePathJson1.toStdString().c_str(), "w");
if (!pfile1)
{
throw GenericExc(QObject::tr("Ошибка открытия json файла"));
}
fprintf(pfile1, "%s", "{\n");
fclose(pfile1);
file = H5Fopen (filePathHdf.toStdString().c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (file < 0)
{
throw GenericExc(QObject::tr("Ошибка открытия файла"));
}
status = H5Oget_info (file, &infobuf);
if (status < 0)
{
throw GenericExc(QObject::tr("Ошибка получения информации о файле"));
}
od.recurs = 0;
od.prev = NULL;
od.addr = infobuf.addr;
status = H5Literate (file, H5_INDEX_NAME, H5_ITER_NATIVE, NULL, op_func,
(void *) &od);
if (status < 0)
{
throw GenericExc(QObject::tr("Ошибка получения структуры файла"));
}
status = H5Fclose (file);
if (status < 0)
{
throw GenericExc(QObject::tr("Ошибка закрытия файла"));
}
pfile1 = fopen(filePathJson.toStdString().c_str(), "a");
if (!pfile1)
{
throw GenericExc(QObject::tr("Ошибка открытия json файла"));
}
fprintf(pfile1, "%s", "}");
fclose(pfile1);
return true;
} catch (const GenericExc& exc)
{
m_errDescription = exc.GetWhat();
return false;
} catch (...)
{
m_errDescription = QObject::tr("Неизвестная ошибка при получении структуры данных");
return false;
}
}
/*-------------------------------------------------------------------------
* Function: build_match_list_attrs
*
* Purpose: get list of matching attribute name from obj1 and obj2
*
* Note:
* Find common attribute; the algorithm for search is referred from
* build_match_list() in h5diff.c .
*
* Parameter:
* table_out [OUT] : return the list
*
* Programmer: Jonathan Kim
*
* Date: March 15, 2011
*------------------------------------------------------------------------*/
static herr_t build_match_list_attrs(hid_t loc1_id, hid_t loc2_id, table_attrs_t ** table_out, diff_opt_t *options)
{
H5O_info_t oinfo1, oinfo2; /* Object info */
hid_t attr1_id=-1; /* attr ID */
hid_t attr2_id=-1; /* attr ID */
size_t curr1 = 0;
size_t curr2 = 0;
unsigned infile[2];
char name1[ATTR_NAME_MAX];
char name2[ATTR_NAME_MAX];
int cmp;
unsigned i;
table_attrs_t *table_lp = NULL;
if(H5Oget_info(loc1_id, &oinfo1) < 0)
goto error;
if(H5Oget_info(loc2_id, &oinfo2) < 0)
goto error;
table_attrs_init( &table_lp );
/*--------------------------------------------------
* build the list
*/
while(curr1 < oinfo1.num_attrs && curr2 < oinfo2.num_attrs)
{
/*------------------
* open attribute1 */
if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr1_id, (size_t)ATTR_NAME_MAX, name1) < 0)
goto error;
/*------------------
* open attribute2 */
if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr2_id, (size_t)ATTR_NAME_MAX, name2) < 0)
goto error;
/* criteria is string compare */
cmp = HDstrcmp(name1, name2);
if(cmp == 0)
{
infile[0] = 1;
infile[1] = 1;
table_attr_mark_exist(infile, name1, table_lp);
curr1++;
curr2++;
}
else if(cmp < 0)
{
infile[0] = 1;
infile[1] = 0;
table_attr_mark_exist(infile, name1, table_lp);
table_lp->nattrs_only1++;
curr1++;
}
else
{
infile[0] = 0;
infile[1] = 1;
table_attr_mark_exist(infile, name2, table_lp);
table_lp->nattrs_only2++;
curr2++;
}
/* close for next turn */
H5Aclose(attr1_id);
attr1_id = -1;
H5Aclose(attr2_id);
attr2_id = -1;
} /* end while */
/* list1 did not end */
infile[0] = 1;
infile[1] = 0;
while(curr1 < oinfo1.num_attrs)
{
/*------------------
* open attribute1 */
if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr1, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr1_id, (size_t)ATTR_NAME_MAX, name1) < 0)
goto error;
table_attr_mark_exist(infile, name1, table_lp);
table_lp->nattrs_only1++;
curr1++;
/* close for next turn */
H5Aclose(attr1_id);
attr1_id = -1;
}
/* list2 did not end */
infile[0] = 0;
infile[1] = 1;
while(curr2 < oinfo2.num_attrs)
{
/*------------------
* open attribute2 */
if((attr2_id = H5Aopen_by_idx(loc2_id, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)curr2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr2_id, (size_t)ATTR_NAME_MAX, name2) < 0)
goto error;
table_attr_mark_exist(infile, name2, table_lp);
table_lp->nattrs_only2++;
curr2++;
/* close for next turn */
H5Aclose(attr2_id);
}
/*------------------------------------------------------
* print the list
*/
if(options->m_verbose_level == 2)
{
/* if '-v2' is detected */
parallel_print(" obj1 obj2\n");
parallel_print(" --------------------------------------\n");
for(i = 0; i < (unsigned int) table_lp->nattrs; i++)
{
char c1, c2;
c1 = (table_lp->attrs[i].exist[0]) ? 'x' : ' ';
c2 = (table_lp->attrs[i].exist[1]) ? 'x' : ' ';
parallel_print("%5c %6c %-15s\n", c1, c2, table_lp->attrs[i].name);
} /* end for */
}
if(options->m_verbose_level >= 1)
{
parallel_print("Attributes status: %d common, %d only in obj1, %d only in obj2\n", table_lp->nattrs - table_lp->nattrs_only1 - table_lp->nattrs_only2, table_lp->nattrs_only1, table_lp->nattrs_only2 );
}
*table_out = table_lp;
return 0;
error:
if (0 < attr1_id)
H5Aclose(attr1_id);
if (0 < attr2_id)
H5Aclose(attr2_id);
return -1;
}
/*-------------------------------------------------------------------------
* Function: main
*
* Purpose: H5O_mtime_decode() test.
*
* Return: Success:
*
* Failure:
*
* Programmer: Robb Matzke
* Thursday, July 30, 1998
*
* Modifications:
* Added checks for old and new modification time messages
* in pre-created datafiles (generated with gen_old_mtime.c and
* gen_new_mtime.c).
* Quincey Koziol
* Friday, January 3, 2003
*
*-------------------------------------------------------------------------
*/
int
main(void)
{
hid_t fapl, file, space, dset;
hsize_t size[1] = {2};
time_t now;
struct tm *tm;
H5O_info_t oi1, oi2;
signed char buf1[32], buf2[32];
char filename[1024];
h5_reset();
fapl = h5_fileaccess();
TESTING("modification time messages");
/* Create the file, create a dataset, then close the file */
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0)
TEST_ERROR;
if((space = H5Screate_simple(1, size, NULL)) < 0) TEST_ERROR;
if((dset = H5Dcreate2(file, "dset", H5T_NATIVE_SCHAR, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
TEST_ERROR;
now = HDtime(NULL);
if(H5Dclose(dset) < 0) TEST_ERROR;
if(H5Sclose(space) < 0) TEST_ERROR;
if(H5Fclose(file) < 0) TEST_ERROR;
/*
* Open the file and get the modification time. We'll test the
* H5Oget_info() arguments too: being able to stat something without
* knowing its name.
*/
h5_fixname(FILENAME[0], fapl, filename, sizeof filename);
if((file = H5Fopen(filename, H5F_ACC_RDONLY, fapl)) < 0) TEST_ERROR;
if(H5Oget_info_by_name(file, "dset", &oi1, H5P_DEFAULT) < 0) TEST_ERROR;
if((dset = H5Dopen2(file, "dset", H5P_DEFAULT)) < 0) TEST_ERROR;
if(H5Oget_info(dset, &oi2) < 0) TEST_ERROR;
if(H5Dclose(dset) < 0) TEST_ERROR;
if(H5Fclose(file) < 0) TEST_ERROR;
/* Compare addresses & times from the two ways of calling H5Oget_info() */
if(oi1.addr != oi2.addr || oi1.mtime != oi2.mtime) {
H5_FAILED();
puts(" Calling H5Oget_info() with the dataset ID returned");
puts(" different values than calling it with a file and dataset");
puts(" name.");
goto error;
}
/* Compare times -- they must be within 60 seconds of one another */
if(0 == oi1.mtime) {
SKIPPED();
puts(" The modification time could not be decoded on this OS.");
puts(" Modification times will be mantained in the file but");
puts(" cannot be queried on this system. See H5O_mtime_decode().");
return 0;
} else if(HDfabs(HDdifftime(now, oi1.mtime)) > 60.0) {
H5_FAILED();
tm = HDlocaltime(&(oi1.mtime));
HDstrftime((char*)buf1, sizeof buf1, "%Y-%m-%d %H:%M:%S", tm);
tm = HDlocaltime(&now);
HDstrftime((char*)buf2, sizeof buf2, "%Y-%m-%d %H:%M:%S", tm);
printf(" got: %s\n ans: %s\n", buf1, buf2);
goto error;
}
PASSED();
/* Check opening existing file with old-style modification time information
* and make certain that the time is correct
*/
TESTING("accessing old modification time messages");
{
char testfile[512]="";
char *srcdir = HDgetenv("srcdir");
if(srcdir && ((HDstrlen(srcdir) + strlen(TESTFILE1) + 1) < sizeof(testfile))){
HDstrcpy(testfile, srcdir);
HDstrcat(testfile, "/");
}
HDstrcat(testfile, TESTFILE1);
file = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT);
if(file >= 0){
if(H5Oget_info_by_name(file, "/Dataset1", &oi1, H5P_DEFAULT) < 0)
TEST_ERROR;
if(oi1.mtime != MTIME1) {
H5_FAILED();
/* If this fails, examine H5Omtime.c. Modification time is very
* system dependant (e.g., on Windows DST must be hardcoded). */
puts(" Old modification time incorrect");
goto error;
}
if(H5Fclose(file) < 0) TEST_ERROR;
}
else {
H5_FAILED();
printf("***cannot open the pre-created old modification test file (%s)\n",
testfile);
goto error;
} /* end else */
}
PASSED();
/* Check opening existing file with new-style modification time information
* and make certain that the time is correct
*/
TESTING("accessing new modification time messages");
{
char testfile[512]="";
char *srcdir = HDgetenv("srcdir");
if(srcdir && ((HDstrlen(srcdir) + strlen(TESTFILE2) + 1) < sizeof(testfile))){
HDstrcpy(testfile, srcdir);
HDstrcat(testfile, "/");
}
HDstrcat(testfile, TESTFILE2);
file = H5Fopen(testfile, H5F_ACC_RDONLY, H5P_DEFAULT);
if(file >= 0){
if(H5Oget_info_by_name(file, "/Dataset1", &oi2, H5P_DEFAULT) < 0)
TEST_ERROR;
if(oi2.mtime != MTIME2) {
H5_FAILED();
puts(" Modification time incorrect.");
goto error;
}
if(H5Fclose(file) < 0) TEST_ERROR;
}
else {
H5_FAILED();
printf("***cannot open the pre-created old modification test file (%s)\n",
testfile);
goto error;
} /* end else */
}
PASSED();
/* All looks good */
puts("All modification time tests passed.");
h5_cleanup(FILENAME, fapl);
return 0;
/* Something broke */
error:
return 1;
}
/*-------------------------------------------------------------------------
* Function: refresh_verification
*
* Purpose: This function opens the specified object, and checks to see
* that is does not have any attributes on it. It then sends
* a signal to the main process, which will flush the object
* (putting an attribute on the object on disk). This function
* will then refresh the object, and verify that it has picked
* up the new metadata reflective of the added attribute.
*
* Return: 0 on Success, 1 on Failure
*
* Programmer: Mike McGreevy
* July 16, 2010
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
herr_t refresh_verification(const char * obj_pathname)
{
/* Variables */
hid_t oid,fid,status = 0;
H5O_info_t flushed_oinfo;
H5O_info_t refreshed_oinfo;
/* Open Object */
if ((fid = H5Fopen(FILENAME, H5F_ACC_SWMR_READ, H5P_DEFAULT)) < 0) PROCESS_ERROR;
if ((oid = H5Oopen(fid, obj_pathname, H5P_DEFAULT)) < 0) PROCESS_ERROR;
/* Get Object info */
if ((status = H5Oget_info(oid, &flushed_oinfo)) < 0) PROCESS_ERROR;
/* Make sure there are no attributes on the object. This is just a sanity
check to ensure we didn't erroneously flush the attribute before
starting the verification. */
if (flushed_oinfo.num_attrs != 0) PROCESS_ERROR;
/* Send Signal to MAIN PROCESS indicating that it can go ahead and modify the
object. */
send_signal(SIGNAL_BETWEEN_PROCESSES_1, NULL, NULL);
/* Wait for Signal from MAIN PROCESS indicating that it's modified the
object and we can run verification now. */
if (wait_for_signal(SIGNAL_BETWEEN_PROCESSES_2) < 0) PROCESS_ERROR;
/* Get object info again. This will NOT reflect what's on disk, only what's
in the cache. Thus, all values will be unchanged from above, despite
newer information being on disk. */
if ((status = H5Oget_info(oid, &refreshed_oinfo)) < 0) PROCESS_ERROR;
/* Verify that before doing a refresh, getting the object info returns stale
information. (i.e., unchanged from above, despite new info on disk). */
if (flushed_oinfo.addr != refreshed_oinfo.addr) PROCESS_ERROR;
if (flushed_oinfo.type != refreshed_oinfo.type) PROCESS_ERROR;
if (flushed_oinfo.hdr.version != refreshed_oinfo.hdr.version) PROCESS_ERROR;
if (flushed_oinfo.hdr.flags != refreshed_oinfo.hdr.flags) PROCESS_ERROR;
if (flushed_oinfo.num_attrs != refreshed_oinfo.num_attrs) PROCESS_ERROR;
if (flushed_oinfo.hdr.nmesgs != refreshed_oinfo.hdr.nmesgs) PROCESS_ERROR;
if (flushed_oinfo.hdr.nchunks != refreshed_oinfo.hdr.nchunks) PROCESS_ERROR;
if (flushed_oinfo.hdr.space.total != refreshed_oinfo.hdr.space.total) PROCESS_ERROR;
/* Refresh object */
/* The H5*refresh function called depends on which object we are trying
* to refresh. (MIKE: add desired refresh call as parameter so adding new
* test cases is easy). */
if ((strcmp(obj_pathname, D1) == 0) ||
(strcmp(obj_pathname, D2) == 0)) {
if (H5Drefresh(oid) < 0) PROCESS_ERROR;
} /* end if */
else if ((strcmp(obj_pathname, G1) == 0) ||
(strcmp(obj_pathname, G2) == 0)) {
if (H5Grefresh(oid) < 0) PROCESS_ERROR;
} /* end if */
else if ((strcmp(obj_pathname, T1) == 0) ||
(strcmp(obj_pathname, T2) == 0)) {
if (H5Trefresh(oid) < 0) PROCESS_ERROR;
} /* end if */
else if ((strcmp(obj_pathname, D3) == 0) ||
(strcmp(obj_pathname, G3) == 0) ||
(strcmp(obj_pathname, T3) == 0)) {
if (H5Orefresh(oid) < 0) PROCESS_ERROR;
} /* end if */
else {
HDfprintf(stdout, "Error. %s is an unrecognized object.\n", obj_pathname);
PROCESS_ERROR;
} /* end else */
/* Get object info. This should now accurately reflect the refreshed object on disk. */
if ((status = H5Oget_info(oid, &refreshed_oinfo)) < 0) PROCESS_ERROR;
/* Confirm following attributes are the same: */
if (flushed_oinfo.addr != refreshed_oinfo.addr) PROCESS_ERROR;
if (flushed_oinfo.type != refreshed_oinfo.type) PROCESS_ERROR;
if (flushed_oinfo.hdr.version != refreshed_oinfo.hdr.version) PROCESS_ERROR;
if (flushed_oinfo.hdr.flags != refreshed_oinfo.hdr.flags) PROCESS_ERROR;
/* Confirm following attributes are different */
if (flushed_oinfo.num_attrs == refreshed_oinfo.num_attrs) PROCESS_ERROR;
if (flushed_oinfo.hdr.nmesgs == refreshed_oinfo.hdr.nmesgs) PROCESS_ERROR;
if (flushed_oinfo.hdr.nchunks == refreshed_oinfo.hdr.nchunks) PROCESS_ERROR;
if (flushed_oinfo.hdr.space.total == refreshed_oinfo.hdr.space.total) PROCESS_ERROR;
/* Close objects */
if (H5Oclose(oid) < 0) PROCESS_ERROR;
if (H5Fclose(fid) < 0) PROCESS_ERROR;
/* Return */
return SUCCEED;
error:
return FAIL;
} /* refresh_verification */
unsigned int LocID::referenceCount() const {
H5O_info_t oInfo;
HErr res = H5Oget_info(hid, &oInfo);
res.check("LocID:referenceCount: Coud not get object info");
return oInfo.rc;
}
int
main (void)
{
hid_t file, dataset; /* File and dataset identifiers */
hid_t fid; /* Dataspace identifier */
hid_t attr1, attr2, attr3; /* Attribute identifiers */
hid_t attr;
hid_t aid1, aid2, aid3; /* Attribute dataspace identifiers */
hid_t atype, atype_mem; /* Attribute type */
H5T_class_t type_class;
hsize_t fdim[] = {SIZE};
hsize_t adim[] = {ADIM1, ADIM2}; /* Dimensions of the first attribute */
float matrix[ADIM1][ADIM2]; /* Attribute data */
herr_t ret; /* Return value */
H5O_info_t oinfo; /* Object info */
unsigned i, j; /* Counters */
char string_out[80]; /* Buffer to read string attribute back */
int point_out; /* Buffer to read scalar attribute back */
/*
* Data initialization.
*/
int vector[] = {1, 2, 3, 4, 5, 6, 7}; /* Dataset data */
int point = 1; /* Value of the scalar attribute */
char string[] = "ABCD"; /* Value of the string attribute */
for (i=0; i < ADIM1; i++) { /* Values of the array attribute */
for (j=0; j < ADIM2; j++)
matrix[i][j] = -1.;
}
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create the dataspace for the dataset in the file.
*/
fid = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(fid, RANK, fdim, NULL);
/*
* Create the dataset in the file.
*/
dataset = H5Dcreate2(file, "Dataset", H5T_NATIVE_INT, fid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
ret = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT, vector);
/*
* Create dataspace for the first attribute.
*/
aid1 = H5Screate(H5S_SIMPLE);
ret = H5Sset_extent_simple(aid1, ARANK, adim, NULL);
/*
* Create array attribute.
*/
attr1 = H5Acreate2(dataset, ANAME, H5T_NATIVE_FLOAT, aid1, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write array attribute.
*/
ret = H5Awrite(attr1, H5T_NATIVE_FLOAT, matrix);
/*
* Create scalar attribute.
*/
aid2 = H5Screate(H5S_SCALAR);
attr2 = H5Acreate2(dataset, "Integer attribute", H5T_NATIVE_INT, aid2,
H5P_DEFAULT, H5P_DEFAULT);
/*
* Write scalar attribute.
*/
ret = H5Awrite(attr2, H5T_NATIVE_INT, &point);
/*
* Create string attribute.
*/
aid3 = H5Screate(H5S_SCALAR);
atype = H5Tcopy(H5T_C_S1);
H5Tset_size(atype, 5);
H5Tset_strpad(atype,H5T_STR_NULLTERM);
attr3 = H5Acreate2(dataset, ANAMES, atype, aid3, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write string attribute.
*/
ret = H5Awrite(attr3, atype, string);
/*
* Close attribute and file dataspaces, and datatype.
*/
ret = H5Sclose(aid1);
ret = H5Sclose(aid2);
ret = H5Sclose(aid3);
ret = H5Sclose(fid);
ret = H5Tclose(atype);
/*
* Close the attributes.
*/
ret = H5Aclose(attr1);
ret = H5Aclose(attr2);
ret = H5Aclose(attr3);
/*
* Close the dataset.
*/
ret = H5Dclose(dataset);
/*
* Close the file.
*/
ret = H5Fclose(file);
/*
* Reopen the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT);
/*
* Open the dataset.
*/
dataset = H5Dopen2(file, "Dataset", H5P_DEFAULT);
/*
* Attach to the scalar attribute using attribute name, then read and
* display its value.
*/
attr = H5Aopen(dataset, "Integer attribute", H5P_DEFAULT);
ret = H5Aread(attr, H5T_NATIVE_INT, &point_out);
printf("The value of the attribute \"Integer attribute\" is %d \n", point_out);
ret = H5Aclose(attr);
/*
* Find string attribute by iterating through all attributes
*/
ret = H5Oget_info(dataset, &oinfo);
for(i = 0; i < (unsigned)oinfo.num_attrs; i++) {
attr = H5Aopen_by_idx(dataset, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)i, H5P_DEFAULT, H5P_DEFAULT);
atype = H5Aget_type(attr);
type_class = H5Tget_class(atype);
if (type_class == H5T_STRING) {
atype_mem = H5Tget_native_type(atype, H5T_DIR_ASCEND);
ret = H5Aread(attr, atype_mem, string_out);
printf("Found string attribute; its index is %d , value = %s \n", i, string_out);
ret = H5Tclose(atype_mem);
}
ret = H5Aclose(attr);
ret = H5Tclose(atype);
}
/*
* Get attribute info using iteration function.
*/
ret = H5Aiterate2(dataset, H5_INDEX_NAME, H5_ITER_INC, NULL, attr_info, NULL);
/*
* Close the dataset and the file.
*/
H5Dclose(dataset);
H5Fclose(file);
return 0;
}
/*-------------------------------------------------------------------------
* Function: copy_named_datatype
*
* Purpose: Copies the specified datatype anonymously, and returns an open
* id for that datatype in the output file. The first time this
* is called it scans every named datatype in travt into a
* private stack, afterwards it simply scans that stack. The id
* returned must be closed after it is no longer needed.
* named_datatype_free must be called before the program exits
* to free the stack.
*-------------------------------------------------------------------------
*/
hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
hid_t ret_value = -1; /* The identifier of the named dtype in the out file */
if (H5Oget_info(type_in, &oinfo) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Oget_info failed");
if (*named_dt_head_p) {
/* Stack already exists, search for the datatype */
while (dt && dt->addr_in != oinfo.addr)
dt = dt->next;
dt_ret = dt;
}
else {
/* Create the stack */
size_t i;
for (i = 0; i < travt->nobjs; i++) {
if (travt->objs[i].type == H5TRAV_TYPE_NAMED_DATATYPE) {
/* Push onto the stack */
if (NULL == (dt = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
dt->next = *named_dt_head_p;
*named_dt_head_p = dt;
/* Update the address and id */
dt->addr_in = travt->objs[i].objno;
dt->id_out = -1;
/* Check if this type is the one requested */
if (oinfo.addr == dt->addr_in) {
dt_ret = dt;
} /* end if */
} /* end if */
} /* end for */
} /* end else */
/* Handle the case that the requested datatype was not found. This is
* possible if the datatype was committed anonymously in the input file. */
if (!dt_ret) {
/* Push the new datatype onto the stack */
if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "buffer allocation failed failed");
dt_ret->next = *named_dt_head_p;
*named_dt_head_p = dt_ret;
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
} /* end if */
/* If the requested datatype does not yet exist in the output file, copy it
* anonymously */
if (dt_ret->id_out < 0) {
if (options->use_native == 1)
dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
else
dt_ret->id_out = H5Tcopy(type_in);
if (dt_ret->id_out < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
} /* end if */
/* Set return value */
ret_value = dt_ret->id_out;
/* Increment the ref count on id_out, because the calling function will try to close it */
if(H5Iinc_ref(ret_value) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iinc_ref failed");
done:
return ret_value;
} /* end copy_named_datatype */
/*-------------------------------------------------------------------------
* 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() */
void H5ReferenceData::printData(std::ostream & os, const unsigned int pos, const unsigned int indentLevel) const
{
char * cdata = static_cast<char *>(data) + offset + pos * (stride ? stride : dataSize);
void ** ref = &(((void **)cdata)[0]);
hid_t file = getFile().getH5Id();
hid_t obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);
if (obj < 0)
{
os << "NULL";
return;
}
ssize_t size = H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, 0, 0);
char * name = 0;
H5O_info_t info;
if (size != -1)
{
name = new char[size + 1];
H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, name, size + 1);
if (datasetReference == H5R_OBJECT)
{
H5Oget_info(obj, &info);
H5Oclose(obj);
switch (info.type)
{
case H5O_TYPE_GROUP:
os << "GROUP ";
break;
case H5O_TYPE_DATASET:
os << "DATASET ";
break;
case H5O_TYPE_NAMED_DATATYPE:
os << "DATATYPE ";
break;
case H5O_TYPE_UNKNOWN:
default:
if (size != -1)
{
delete[] name;
}
throw H5Exception(__LINE__, __FILE__, _("Unknown HDF5 object"));
}
os << (haddr_t)(*ref) << " " << name;
}
else
{
hid_t space = H5Rget_region(file, H5R_DATASET_REGION, ref);
hssize_t npoints = H5Sget_select_elem_npoints(space);
hsize_t ndims = H5Sget_simple_extent_dims(space, 0, 0);
H5Oclose(obj);
os << "DATASET " << name << " {";
if (npoints >= 0)
{
const hsize_t N = ndims * npoints;
hsize_t * buf = new hsize_t[N];
herr_t err = H5Sget_select_elem_pointlist(space, 0, npoints, buf);
for (hssize_t i = 0; i < (hssize_t)N; i += ndims)
{
os << "(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + j] << ",";
}
os << buf[i + ndims - 1] << ")";
if (i != N - ndims)
{
os << ", ";
}
else
{
os << "}";
}
}
delete[] buf;
}
else
{
hssize_t nblocks = H5Sget_select_hyper_nblocks(space);
if (nblocks >= 0)
{
const hsize_t N = 2 * ndims * nblocks;
hsize_t * buf = new hsize_t[N];
herr_t err = H5Sget_select_hyper_blocklist(space, 0, nblocks, buf);
for (hssize_t i = 0; i < (hssize_t)N; i += 2 * ndims)
{
os << "(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + j] << ",";
}
os << buf[i + ndims - 1] << ")-(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + ndims + j] << ",";
}
os << buf[i + 2 * ndims - 1] << ")";
if (i != N - 2 * ndims)
{
os << ", ";
}
else
{
os << "}";
}
}
delete[] buf;
}
}
H5Sclose(space);
}
delete[] name;
}
}
int VsFilter::visitLinks(hid_t locId, const char* name,
const H5L_info_t *linfo, void* opdata) {
VsLog::debugLog() <<"VsFilter::visitLinks() - looking at object " <<name <<std::endl;
switch (linfo->type) {
case H5L_TYPE_HARD: {
H5O_info_t objinfo;
/* Stat the object */
if(H5Oget_info_by_name(locId, name, &objinfo, H5P_DEFAULT) < 0) {
VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open object with name " <<name <<std::endl;
VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
return 0;
}
switch(objinfo.type)
{
case H5O_TYPE_GROUP:
return visitGroup( locId, name, opdata );
break;
case H5O_TYPE_DATASET:
return visitDataset( locId, name, opdata );
break;
default:
VsLog::debugLog() << "VsFilter::visitLinks: node '" << name <<
"' has an unknown type " << objinfo.type << std::endl;
break;
}
}
break;
//end of case H5L_TYPE_HARD
case H5L_TYPE_EXTERNAL: {
char *targbuf = (char*) malloc( linfo->u.val_size );
if (H5Lget_val(locId, name, targbuf, linfo->u.val_size, H5P_DEFAULT) < 0) {
VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open external link with name " <<targbuf <<std::endl;
VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
return 0;
}
const char *filename;
const char *targname;
if (H5Lunpack_elink_val(targbuf, linfo->u.val_size, 0, &filename, &targname) < 0) {
VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open external file with name " <<filename <<std::endl;
VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
return 0;
}
VsLog::debugLog() << "VsFilter::visitLinks(): node '" << name << "' is an external link." << std::endl;
VsLog::debugLog() << "VsFilter::visitLinks(): node '" << targname << "' is an external target group." << std::endl;
free(targbuf);
targbuf = NULL;
// Get info of the linked object.
H5O_info_t objinfo;
#ifndef H5_USE_16_API
hid_t obj_id = H5Oopen(locId, name, H5P_DEFAULT);
#else
hid_t obj_id = H5Oopen(locId, name);
#endif
if (obj_id < 0) {
VsLog::errorLog() <<"VsFilter::visitLinks() - unable to get id for external object " <<name <<std::endl;
VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
return 0;
}
//Test-open the linked object
if (H5Oget_info (obj_id, &objinfo) < 0) {
VsLog::errorLog() <<"VsFilter::visitLinks() - unable to open external object " <<name <<std::endl;
VsLog::errorLog() <<"VsFilter::visitLinks() - this object and all children will be dropped." <<std::endl;
return 0;
}
//Close the linked object to release hdf5 id
H5Oclose( obj_id );
//Finally, decide what to do depending on what type of object this is
switch(objinfo.type)
{
case H5O_TYPE_GROUP:
return visitGroup( locId, name, opdata );
break;
case H5O_TYPE_DATASET:
return visitDataset( locId, name, opdata );
break;
default:
VsLog::debugLog() << "VsFilter::visitLinks: node '" << name <<
"' has an unknown type " << objinfo.type << std::endl;
break;
}
}
break;
//END OF CASE H5L_TYPE_EXTERNAL
default:
VsLog::debugLog() << "VsFilter::visitLinks: node '" << name <<
"' has an unknown object type " << linfo->type << std::endl;
break;
}
return 0;
}
hsize_t diff_attr(hid_t loc1_id,
hid_t loc2_id,
const char *path1,
const char *path2,
diff_opt_t *options)
{
hid_t attr1_id=-1; /* attr ID */
hid_t attr2_id=-1; /* attr ID */
hid_t space1_id=-1; /* space ID */
hid_t space2_id=-1; /* space ID */
hid_t ftype1_id=-1; /* file data type ID */
hid_t ftype2_id=-1; /* file data type ID */
hid_t mtype1_id=-1; /* memory data type ID */
hid_t mtype2_id=-1; /* memory data type ID */
size_t msize1; /* memory size of memory type */
size_t msize2; /* memory size of memory type */
void *buf1=NULL; /* data buffer */
void *buf2=NULL; /* data buffer */
hsize_t nelmts1; /* number of elements in dataset */
int rank1; /* rank of dataset */
int rank2; /* rank of dataset */
hsize_t dims1[H5S_MAX_RANK];/* dimensions of dataset */
hsize_t dims2[H5S_MAX_RANK];/* dimensions of dataset */
char name1[512];
char name2[512];
char np1[512];
char np2[512];
H5O_info_t oinfo1, oinfo2; /* Object info */
unsigned u; /* Local index variable */
hsize_t nfound = 0;
hsize_t nfound_total = 0;
int j;
if(H5Oget_info(loc1_id, &oinfo1) < 0)
goto error;
if(H5Oget_info(loc2_id, &oinfo2) < 0)
goto error;
if(oinfo1.num_attrs != oinfo2.num_attrs)
return 1;
for( u = 0; u < (unsigned)oinfo1.num_attrs; u++)
{
/* reset buffers for every attribute, we might goto out and call free */
buf1 = NULL;
buf2 = NULL;
/* open attribute */
if((attr1_id = H5Aopen_by_idx(loc1_id, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto error;
/* get name */
if(H5Aget_name(attr1_id, 255, name1) < 0)
goto error;
/* use the name on the first file to open the second file */
H5E_BEGIN_TRY
{
if((attr2_id = H5Aopen(loc2_id, name1, H5P_DEFAULT)) < 0)
goto error;
} H5E_END_TRY;
/* get name */
if(H5Aget_name(attr2_id, 255, name2) < 0)
goto error;
/* get the datatypes */
if ((ftype1_id = H5Aget_type(attr1_id)) < 0)
goto error;
if ((ftype2_id = H5Aget_type(attr2_id)) < 0)
goto error;
if ((mtype1_id = h5tools_get_native_type(ftype1_id))<0)
goto error;
if ((mtype2_id = h5tools_get_native_type(ftype2_id))<0)
goto error;
if ((msize1 = H5Tget_size(mtype1_id))==0)
goto error;
if ((msize2 = H5Tget_size(mtype2_id))==0)
goto error;
/* get the dataspace */
if ((space1_id = H5Aget_space(attr1_id)) < 0)
goto error;
if ((space2_id = H5Aget_space(attr2_id)) < 0)
goto error;
/* get dimensions */
if ( (rank1 = H5Sget_simple_extent_dims(space1_id, dims1, NULL)) < 0 )
goto error;
if ( (rank2 = H5Sget_simple_extent_dims(space2_id, dims2, NULL)) < 0 )
goto error;
/*-------------------------------------------------------------------------
* check for comparable TYPE and SPACE
*-------------------------------------------------------------------------
*/
if ( msize1 != msize2
||
diff_can_type(ftype1_id,
ftype2_id,
rank1,
rank2,
dims1,
dims2,
NULL,
NULL,
name1,
name2,
options,
0)!=1)
{
if (H5Tclose(ftype1_id)<0)
goto error;
if (H5Tclose(ftype2_id)<0)
goto error;
if (H5Sclose(space1_id)<0)
goto error;
if (H5Sclose(space2_id)<0)
goto error;
if (H5Aclose(attr1_id)<0)
goto error;
if (H5Aclose(attr2_id)<0)
goto error;
if (H5Tclose(mtype1_id)<0)
goto error;
if (H5Tclose(mtype2_id)<0)
goto error;
continue;
}
/*-------------------------------------------------------------------------
* read
*-------------------------------------------------------------------------
*/
nelmts1=1;
for (j=0; j<rank1; j++)
nelmts1*=dims1[j];
buf1=(void *) HDmalloc((unsigned)(nelmts1*msize1));
buf2=(void *) HDmalloc((unsigned)(nelmts1*msize2));
if ( buf1==NULL || buf2==NULL){
parallel_print( "cannot read into memory\n" );
goto error;
}
if (H5Aread(attr1_id,mtype1_id,buf1)<0)
goto error;
if (H5Aread(attr2_id,mtype2_id,buf2)<0)
goto error;
/* format output string */
sprintf(np1,"%s of <%s>",name1,path1);
sprintf(np2,"%s of <%s>",name2,path2);
/*-------------------------------------------------------------------------
* array compare
*-------------------------------------------------------------------------
*/
/* always print name */
if (options->m_verbose)
{
do_print_objname ("attribute", np1, np2);
nfound = diff_array(buf1,
buf2,
nelmts1,
(hsize_t)0,
rank1,
dims1,
options,
np1,
np2,
mtype1_id,
attr1_id,
attr2_id);
print_found(nfound);
}
/* check first if we have differences */
else
{
if (options->m_quiet==0)
{
/* shut up temporarily */
options->m_quiet=1;
nfound = diff_array(buf1,
buf2,
nelmts1,
(hsize_t)0,
rank1,
dims1,
options,
np1,
np2,
mtype1_id,
attr1_id,
attr2_id);
/* print again */
options->m_quiet=0;
if (nfound)
{
do_print_objname ("attribute", np1, np2);
nfound = diff_array(buf1,
buf2,
nelmts1,
(hsize_t)0,
rank1,
dims1,
options,
np1,
np2,
mtype1_id,
attr1_id,
attr2_id);
print_found(nfound);
} /*if*/
} /*if*/
/* in quiet mode, just count differences */
else
{
nfound = diff_array(buf1,
buf2,
nelmts1,
(hsize_t)0,
rank1,
dims1,
options,
np1,
np2,
mtype1_id,
attr1_id,
attr2_id);
} /*else quiet */
} /*else verbose */
/*-------------------------------------------------------------------------
* close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype1_id)<0)
goto error;
if (H5Tclose(ftype2_id)<0)
goto error;
if (H5Sclose(space1_id)<0)
goto error;
if (H5Sclose(space2_id)<0)
goto error;
if (H5Aclose(attr1_id)<0)
goto error;
if (H5Aclose(attr2_id)<0)
goto error;
if (H5Tclose(mtype1_id)<0)
goto error;
if (H5Tclose(mtype2_id)<0)
goto error;
if (buf1)
HDfree(buf1);
if (buf2)
HDfree(buf2);
nfound_total += nfound;
} /* u */
return nfound_total;
error:
H5E_BEGIN_TRY {
H5Tclose(ftype1_id);
H5Tclose(ftype2_id);
H5Tclose(mtype1_id);
H5Tclose(mtype2_id);
H5Sclose(space1_id);
H5Sclose(space2_id);
H5Aclose(attr1_id);
H5Aclose(attr2_id);
if (buf1)
HDfree(buf1);
if (buf2)
HDfree(buf2);
} H5E_END_TRY;
options->err_stat=1;
return nfound_total;
}
/*-------------------------------------------------------------------------
* Function: find_objs_cb
*
* Purpose: Callback to find objects, committed types and store them in tables
*
* Return: Success: SUCCEED
*
* Failure: FAIL
*
* Programmer: Ruey-Hsia Li
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
static herr_t
find_objs_cb(const char *name, const H5O_info_t *oinfo, const char *already_seen,
void *op_data)
{
find_objs_t *info = (find_objs_t*)op_data;
herr_t ret_value = 0;
switch(oinfo->type) {
case H5O_TYPE_GROUP:
if(NULL == already_seen)
add_obj(info->group_table, oinfo->addr, name, TRUE);
break;
case H5O_TYPE_DATASET:
if(NULL == already_seen) {
hid_t dset;
/* Add the dataset to the list of objects */
add_obj(info->dset_table, oinfo->addr, name, TRUE);
/* Check for a dataset that uses a named datatype */
if((dset = H5Dopen2(info->fid, name, H5P_DEFAULT)) >= 0) {
hid_t type = H5Dget_type(dset);
if(H5Tcommitted(type) > 0) {
H5O_info_t type_oinfo;
H5Oget_info(type, &type_oinfo);
if(search_obj(info->type_table, type_oinfo.addr) == NULL)
add_obj(info->type_table, type_oinfo.addr, name, FALSE);
} /* end if */
H5Tclose(type);
H5Dclose(dset);
} /* end if */
else
ret_value = FAIL;
} /* end if */
break;
case H5O_TYPE_NAMED_DATATYPE:
if(NULL == already_seen) {
obj_t *found_obj;
if((found_obj = search_obj(info->type_table, oinfo->addr)) == NULL)
add_obj(info->type_table, oinfo->addr, name, TRUE);
else {
/* Use latest version of name */
HDfree(found_obj->objname);
found_obj->objname = HDstrdup(name);
/* Mark named datatype as having valid name */
found_obj->recorded = TRUE;
} /* end else */
} /* end if */
break;
default:
break;
} /* end switch */
return ret_value;
}
