static void soft_link_example(void)
{
hid_t file_id;
hid_t group_id;
/* Define the link class that we'll use to register "user-defined soft
* links" using the callbacks we defined above.
* A link class can have NULL for any callback except its traverse
* callback.
*/
const H5L_class_t UD_soft_class[1] = {{
H5L_LINK_CLASS_T_VERS, /* Version number for this struct.
* This field is always H5L_LINK_CLASS_T_VERS */
(H5L_type_t)UD_SOFT_CLASS, /* Link class id number. This can be any
* value between H5L_TYPE_UD_MIN (64) and
* H5L_TYPE_MAX (255). It should be a
* value that isn't already being used by
* another kind of link. We'll use 65. */
"UD_soft_link", /* Link class name for debugging */
NULL, /* Creation callback */
NULL, /* Move callback */
NULL, /* Copy callback */
UD_soft_traverse, /* The actual traversal function */
NULL, /* Deletion callback */
NULL /* Query callback */
}};
/* First, create a file and an object within the file for the link to
* point to.
*/
file_id = H5Fcreate(SOFT_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
group_id = H5Gcreate2(file_id, TARGET_GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group_id);
/* This is how we create a normal soft link to the group.
*/
H5Lcreate_soft(TARGET_GROUP, file_id, SOFT_LINK_NAME, H5P_DEFAULT, H5P_DEFAULT);
/* To do the same thing using a user-defined link, we first have to
* register the link class we defined.
*/
H5Lregister(UD_soft_class);
/* Now create a user-defined link. We give it the path to the group
* as its udata.1
*/
H5Lcreate_ud(file_id, UD_SOFT_LINK_NAME, (H5L_type_t)UD_SOFT_CLASS, TARGET_GROUP,
strlen(TARGET_GROUP) + 1, H5P_DEFAULT, H5P_DEFAULT);
/* We can access the group through the UD soft link like we would through
* a normal soft link. This link will still dangle if the object's
* original name is changed or unlinked.
*/
group_id = H5Gopen2(file_id, UD_SOFT_LINK_NAME, H5P_DEFAULT);
/* The group is now open normally. Don't forget to close it! */
H5Gclose(group_id);
H5Fclose(file_id);
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Lcreate_soft
* Signature: (Ljava/lang/String;JLjava/lang/String;JJ)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Lcreate_1soft
(JNIEnv *env, jclass clss, jstring cur_name, jlong dst_loc_id,
jstring dst_name, jlong create_id, jlong access_id)
{
herr_t status = -1;
const char *lCurName;
const char *lDstName;
PIN_JAVA_STRING_TWO(cur_name, lCurName, dst_name, lDstName);
if (lCurName != NULL && lDstName != NULL) {
status = H5Lcreate_soft(lCurName, (hid_t)dst_loc_id, lDstName, (hid_t)create_id, (hid_t)access_id);
UNPIN_JAVA_STRING_TWO(cur_name, lCurName, dst_name, lDstName);
if (status < 0)
h5libraryError(env);
}
} /* end Java_hdf_hdf5lib_H5_H5Lcreate_1soft */
CXI_Data_Reference * cxi_create_data_link(CXI_Entry * entry, CXI_Dataset * data){
if(!entry || ! data){
return NULL;
}
if(entry->handle <= 0 || data->handle <= 0){
return NULL;
}
CXI_Data * root_data = calloc(sizeof(CXI_Data),1);
CXI_Data_Reference * data_ref = cxi_create_data(entry->handle,root_data);
if(!data_ref) return NULL;
char path[1024];
if(H5Iget_name(data->handle, path, 1024) <= 0){
return NULL;
}
if(H5Lcreate_soft(path, root_data->handle, "data", H5P_DEFAULT, H5P_DEFAULT) < 0){
return NULL;
}
return data_ref;
}
//--------------------------------------------------------------------------
// Function: CommonFG::link
///\brief Creates a link of the specified type from \a new_name to
/// \a curr_name.
///\param link_type - IN: Link type; possible values are
/// \li \c H5G_LINK_HARD
/// \li \c H5G_LINK_SOFT
///\param curr_name - IN: Name of the existing object if link is a hard
/// link; can be anything for the soft link
///\param new_name - IN: New name for the object
///\exception H5::FileIException or H5::GroupIException
///\par Description
/// Note that both names are interpreted relative to the
/// specified location.
/// For information on creating hard link and soft link, please
/// refer to the C layer Reference Manual at:
/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateHard and
/// http://hdfgroup.org/HDF5/doc/RM/RM_H5L.html#Link-CreateSoft
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5L APIs - BMR
//--------------------------------------------------------------------------
void CommonFG::link( H5L_type_t link_type, const char* curr_name, const char* new_name ) const
{
herr_t ret_value = -1;
switch(link_type) {
case H5L_TYPE_HARD:
ret_value = H5Lcreate_hard( getLocId(), curr_name, H5L_SAME_LOC, new_name, H5P_DEFAULT, H5P_DEFAULT );
break;
case H5L_TYPE_SOFT:
ret_value = H5Lcreate_soft( curr_name, getLocId(), new_name, H5P_DEFAULT, H5P_DEFAULT );
break;
default:
throwException("link", "unknown link type");
break;
} /* end switch */
if( ret_value < 0 ) {
throwException("link", "creating link failed");
}
}
/****************************************************************
**
** test_links(): Test soft and hard link iteration
**
****************************************************************/
static void test_links(hid_t fapl)
{
hid_t file; /* File ID */
char obj_name[NAMELEN]; /* Names of the object in group */
ssize_t name_len; /* Length of object's name */
hid_t gid, gid1;
H5G_info_t ginfo; /* Buffer for querying object's info */
hsize_t i;
herr_t ret; /* Generic return value */
/* Output message about test being performed */
MESSAGE(5, ("Testing Soft and Hard Link Iteration Functionality\n"));
/* Create the test file with the datasets */
file = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
CHECK(file, FAIL, "H5Fcreate");
/* create groups */
gid = H5Gcreate2(file, "/g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(gid, FAIL, "H5Gcreate2");
gid1 = H5Gcreate2(file, "/g1/g1.1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(gid1, FAIL, "H5Gcreate2");
/* create soft and hard links to the group "/g1". */
ret = H5Lcreate_soft("something", gid, "softlink", H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Lcreate_soft");
ret = H5Lcreate_hard(gid, "/g1", H5L_SAME_LOC, "hardlink", H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Lcreate_hard");
ret = H5Gget_info(gid, &ginfo);
CHECK(ret, FAIL, "H5Gget_info");
VERIFY(ginfo.nlinks, 3, "H5Gget_info");
/* Test these two functions, H5Oget_info_by_idx and H5Lget_name_by_idx */
for(i = 0; i < ginfo.nlinks; i++) {
H5O_info_t oinfo; /* Object info */
H5L_info_t linfo; /* Link info */
/* Get link name */
name_len = H5Lget_name_by_idx(gid, ".", H5_INDEX_NAME, H5_ITER_INC, i, obj_name, (size_t)NAMELEN, H5P_DEFAULT);
CHECK(name_len, FAIL, "H5Lget_name_by_idx");
/* Get link type */
ret = H5Lget_info_by_idx(gid, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)i, &linfo, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Lget_info_by_idx");
/* Get object type */
if(linfo.type == H5L_TYPE_HARD) {
ret = H5Oget_info_by_idx(gid, ".", H5_INDEX_NAME, H5_ITER_INC, (hsize_t)i, &oinfo, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Oget_info_by_idx");
} /* end if */
if(!HDstrcmp(obj_name, "g1.1"))
VERIFY(oinfo.type, H5O_TYPE_GROUP, "H5Lget_name_by_idx");
else if(!HDstrcmp(obj_name, "hardlink"))
VERIFY(oinfo.type, H5O_TYPE_GROUP, "H5Lget_name_by_idx");
else if(!HDstrcmp(obj_name, "softlink"))
VERIFY(linfo.type, H5L_TYPE_SOFT, "H5Lget_name_by_idx");
else
CHECK(0, 0, "unknown object name");
} /* end for */
ret = H5Gclose(gid);
CHECK(ret, FAIL, "H5Gclose");
ret = H5Gclose(gid1);
CHECK(ret, FAIL, "H5Gclose");
ret = H5Fclose(file);
CHECK(ret, FAIL, "H5Fclose");
} /* test_links() */
static void
gent_ub(const char * filename, size_t ub_size, size_t ub_fill)
{
hid_t fid, group, attr, dataset, space;
hid_t create_plist;
hsize_t dims[2];
int data[2][2], dset1[10][10], dset2[20];
char buf[BUF_SIZE];
int i, j;
size_t u;
float dset2_1[10], dset2_2[3][5];
int fd;
char *bp;
if(ub_size > 0)
{
create_plist = H5Pcreate(H5P_FILE_CREATE);
H5Pset_userblock(create_plist, (hsize_t)ub_size);
fid = H5Fcreate(filename, H5F_ACC_TRUNC, create_plist, H5P_DEFAULT);
}
else
{
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
}
/* create groups */
group = H5Gcreate2(fid, "/g1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
group = H5Gcreate2(fid, "/g2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
group = H5Gcreate2(fid, "/g1/g1.1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
group = H5Gcreate2(fid, "/g1/g1.2", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
group = H5Gcreate2(fid, "/g1/g1.2/g1.2.1", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
/* root attributes */
group = H5Gopen2(fid, "/", H5P_DEFAULT);
dims[0] = 10;
space = H5Screate_simple(1, dims, NULL);
attr = H5Acreate2(group, "attr1", H5T_STD_I8BE, space, H5P_DEFAULT, H5P_DEFAULT);
sprintf(buf, "abcdefghi");
H5Awrite(attr, H5T_NATIVE_SCHAR, buf);
H5Sclose(space);
H5Aclose(attr);
dims[0] = 2; dims[1] = 2;
space = H5Screate_simple(2, dims, NULL);
attr = H5Acreate2(group, "attr2", H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT);
data[0][0] = 0; data[0][1] = 1; data[1][0] = 2; data[1][1] = 3;
H5Awrite(attr, H5T_NATIVE_INT, data);
H5Sclose(space);
H5Aclose(attr);
H5Gclose(group);
group = H5Gopen2(fid, "/g1/g1.1", H5P_DEFAULT);
/* dset1.1.1 */
dims[0] = 10; dims[1] = 10;
space = H5Screate_simple(2, dims, NULL);
dataset = H5Dcreate2(group, "dset1.1.1", H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (i = 0; i < 10; i++)
for (j = 0; j < 10; j++)
dset1[i][j] = j*i;
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset1);
H5Sclose(space);
/* attributes of dset1.1.1 */
dims[0] = 27;
space = H5Screate_simple(1, dims, NULL);
attr = H5Acreate2(dataset, "attr1", H5T_STD_I8BE, space, H5P_DEFAULT, H5P_DEFAULT);
sprintf(buf, "1st attribute of dset1.1.1");
H5Awrite(attr, H5T_NATIVE_SCHAR, buf);
H5Sclose(space);
H5Aclose(attr);
dims[0] = 27;
space = H5Screate_simple(1, dims, NULL);
attr = H5Acreate2(dataset, "attr2", H5T_STD_I8BE, space, H5P_DEFAULT, H5P_DEFAULT);
sprintf(buf, "2nd attribute of dset1.1.1");
H5Awrite(attr, H5T_NATIVE_SCHAR, buf);
H5Sclose(space);
H5Aclose(attr);
H5Dclose(dataset);
/* dset1.1.2 */
dims[0] = 20;
space = H5Screate_simple(1, dims, NULL);
dataset = H5Dcreate2(group, "dset1.1.2", H5T_STD_I32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (i = 0; i < 20; i++)
dset2[i] = i;
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2);
H5Sclose(space);
H5Dclose(dataset);
H5Gclose(group);
/* external link */
H5Lcreate_external("somefile", "somepath", fid, "/g1/g1.2/extlink", H5P_DEFAULT, H5P_DEFAULT);
/* soft link */
group = H5Gopen2(fid, "/g1/g1.2/g1.2.1", H5P_DEFAULT);
H5Lcreate_soft("somevalue", group, "slink", H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group);
group = H5Gopen2(fid, "/g2", H5P_DEFAULT);
/* dset2.1 */
dims[0] = 10;
space = H5Screate_simple(1, dims, NULL);
dataset = H5Dcreate2(group, "dset2.1", H5T_IEEE_F32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (i = 0; i < 10; i++)
dset2_1[i] = (float)((float)i * 0.1F + 1.0F);
H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_1);
H5Sclose(space);
H5Dclose(dataset);
/* dset2.2 */
dims[0] = 3; dims[1] = 5;
space = H5Screate_simple(2, dims, NULL);
dataset = H5Dcreate2(group, "dset2.2", H5T_IEEE_F32BE, space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for (i = 0; i < 3; i++)
for (j = 0; j < 5; j++)
dset2_2[i][j] = (float)(((float)i + 1.0F) * (float)j * 0.1F);
H5Dwrite(dataset, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset2_2);
H5Sclose(space);
H5Dclose(dataset);
H5Gclose(group);
/* user-defined link */
H5Lregister(UD_link_class);
H5Lcreate_ud(fid, "/g2/udlink", (H5L_type_t)MY_LINKCLASS, NULL, (size_t)0, H5P_DEFAULT, H5P_DEFAULT);
H5Fclose(fid);
/* If a user block is being used, write to it here */
if(ub_size > 0)
{
ssize_t nbytes;
HDassert(ub_size <= BUF_SIZE);
fd = HDopen(filename, O_RDWR);
HDassert(fd >= 0);
/* fill buf with pattern */
HDmemset(buf, '\0', ub_size);
bp = buf;
for (u = 0; u < ub_fill; u++)
*bp++ = pattern[u % 10];
nbytes = HDwrite(fd, buf, ub_size);
HDassert(nbytes >= 0);
HDclose(fd);
}
}
/*
* Actually save the powder pattern to file
*/
void savePowderPattern(cGlobal *global, int detIndex, int powderClass) {
// Dereference common variables
cPixelDetectorCommon *detector = &(global->detector[detIndex]);
long nframes = detector->nPowderFrames[powderClass];
// Define buffer variables
double *powderBuffer;
double *powderSquaredBuffer;
double *powderSigmaBuffer;
double *bufferPeaks;
char sBuffer[1024];
/*
* Filename
*/
char filename[1024];
char filenamebase[1024];
sprintf(filenamebase,"r%04u-detector%ld-class%d", global->runNumber, global->detector[detIndex].detectorID, powderClass);
sprintf(filename,"%s-sum.h5",filenamebase);
printf("%s\n",filename);
/*
* Mess of stuff for writing the compound HDF5 file
*/
#ifdef H5F_ACC_SWMR_WRITE
pthread_mutex_lock(&global->swmr_mutex);
#endif
hid_t fh, gh, sh, dh; /* File, group, dataspace and data handles */
//herr_t r;
hsize_t size[2];
//hsize_t max_size[2];
hid_t h5compression;
// Create file
fh = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if ( fh < 0 ) {
ERROR("Couldn't create HDF5 file: %s\n", filename);
}
gh = H5Gcreate(fh, "data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if ( gh < 0 ) {
ERROR("Couldn't create HDF5 group\n");
H5Fclose(fh);
}
// Setting compression level
if (global->h5compress) {
h5compression = H5Pcreate(H5P_DATASET_CREATE);
}
else {
h5compression = H5P_DEFAULT;
}
FOREACH_DATAFORMAT_T(i_f, cDataVersion::DATA_FORMATS) {
if (isBitOptionSet(global->detector[detIndex].powderFormat, *i_f)) {
cDataVersion dataV(NULL, &global->detector[detIndex], global->detector[detIndex].powderVersion, *i_f);
while (dataV.next()) {
if (*i_f != cDataVersion::DATA_FORMAT_RADIAL_AVERAGE) {
// size for 2D data
size[0] = dataV.pix_ny;
size[1] = dataV.pix_nx;
sh = H5Screate_simple(2, size, NULL);
// Compression for 1D
if (global->h5compress) {
H5Pset_chunk(h5compression, 2, size);
H5Pset_deflate(h5compression, global->h5compress); // Compression levels are 0 (none) to 9 (max)
}
}
else {
// size for 1D data (radial average)
size[0] = dataV.pix_nn;
size[1] = 0;
sh = H5Screate_simple(1, size, NULL);
// Compression for 1D
h5compression = H5P_DEFAULT;
}
double *powder = dataV.getPowder(powderClass);
double *powder_squared = dataV.getPowderSquared(powderClass);
long *powder_counter = dataV.getPowderCounter(powderClass);
pthread_mutex_t *mutex = dataV.getPowderMutex(powderClass);
// Copy powder pattern to buffer
powderBuffer = (double*) calloc(dataV.pix_nn, sizeof(double));
if (global->threadSafetyLevel > 0)
pthread_mutex_lock(mutex);
memcpy(powderBuffer, powder, dataV.pix_nn*sizeof(double));
if (global->threadSafetyLevel > 0)
pthread_mutex_unlock(mutex);
// Masked powders require a per-pixel correction
if(global->detector[detIndex].savePowderMasked != 0 && powder_counter != NULL) {
for (long i=0; i<dataV.pix_nn; i++) {
if(powder_counter[i] != 0)
powderBuffer[i] /= powder_counter[i];
else
powderBuffer[i] = 0;
}
}
// Write powder to dataset
dh = H5Dcreate(gh, dataV.name, H5T_NATIVE_DOUBLE, sh, H5P_DEFAULT, h5compression, H5P_DEFAULT);
if (dh < 0) ERROR("Could not create dataset.\n");
H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, powderBuffer);
H5Dclose(dh);
// Fluctuations (sigma)
powderSquaredBuffer = (double*) calloc(dataV.pix_nn, sizeof(double));
powderSigmaBuffer = (double*) calloc(dataV.pix_nn, sizeof(double));
if (global->threadSafetyLevel > 0)
pthread_mutex_lock(mutex);
memcpy(powderSquaredBuffer, powder_squared, dataV.pix_nn*sizeof(double));
if (global->threadSafetyLevel > 0)
pthread_mutex_unlock(mutex);
// Masked powders require a per-pixel correction
if(global->detector[detIndex].savePowderMasked != 0 && powder_counter != NULL) {
for (long i=0; i<dataV.pix_nn; i++) {
if(powder_counter[i] != 0)
powderSigmaBuffer[i] = sqrt(powderSquaredBuffer[i]/powder_counter[i] - powderBuffer[i]*powderBuffer[i]);
}
}
else {
for (long i=0; i<dataV.pix_nn; i++) {
powderSigmaBuffer[i] = sqrt(powderSquaredBuffer[i]/nframes - (powderBuffer[i]/nframes)*(powderBuffer[i]/nframes));
}
}
// Write to data set
sprintf(sBuffer,"%s_sigma",dataV.name);
dh = H5Dcreate(gh, sBuffer, H5T_NATIVE_DOUBLE, sh, H5P_DEFAULT, h5compression, H5P_DEFAULT);
if (dh < 0) ERROR("Could not create dataset.\n");
H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, powderSigmaBuffer);
H5Dclose(dh);
// Soft link if main data set
if (dataV.isMainDataset) {
// Create symbolic link if this is the main dataset
sprintf(sBuffer,"/data/%s",dataV.name);
H5Lcreate_soft(sBuffer, fh, "/data/data",0,0);
H5Lcreate_soft(sBuffer, fh, "/data/correcteddata",0,0);
}
free(powderBuffer);
free(powderSquaredBuffer);
free(powderSigmaBuffer);
H5Sclose(sh);
}
}
}
// Peak powder
size[0] = detector->pix_ny;
size[1] = detector->pix_nx;
sh = H5Screate_simple(2, size, NULL);
bufferPeaks = (double*) calloc(detector->pix_nn, sizeof(double));
pthread_mutex_lock(&detector->powderPeaks_mutex[powderClass]);
memcpy(bufferPeaks, detector->powderPeaks[powderClass], detector->pix_nn*sizeof(double));
pthread_mutex_unlock(&detector->powderPeaks_mutex[powderClass]);
dh = H5Dcreate(gh, "peakpowder", H5T_NATIVE_DOUBLE, sh, H5P_DEFAULT, h5compression, H5P_DEFAULT);
if (dh < 0) ERROR("Could not create dataset.\n");
H5Dwrite(dh, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, bufferPeaks);
H5Dclose(dh);
H5Sclose(sh);
free(bufferPeaks);
// Save frame count
size[0] = 1;
sh = H5Screate_simple(1, size, NULL );
dh = H5Dcreate(gh, "nframes", H5T_NATIVE_LONG, sh, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dh < 0) ERROR("Could not create dataset.\n");
H5Dwrite(dh, H5T_NATIVE_LONG, H5S_ALL, H5S_ALL, H5P_DEFAULT, &detector->nPowderFrames[powderClass] );
H5Dclose(dh);
H5Sclose(sh);
// Clean up stale HDF5 links
H5Gclose(gh);
int n_ids;
hid_t ids[256];
n_ids = H5Fget_obj_ids(fh, H5F_OBJ_ALL, 256, ids);
for ( int i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP ) H5Gclose(id);
if ( type == H5I_DATASET ) H5Dclose(id);
if ( type == H5I_DATATYPE ) H5Tclose(id);
if ( type == H5I_DATASPACE ) H5Sclose(id);
if ( type == H5I_ATTR ) H5Aclose(id);
}
H5Fclose(fh);
#ifdef H5F_ACC_SWMR_WRITE
pthread_mutex_unlock(&global->swmr_mutex);
#endif
/*
* Clean up stuff
*/
for(long i=0; i<global->nPowderClasses; i++) {
fflush(global->powderlogfp[i]);
fflush(global->framelist[i]);
}
}
/*-------------------------------------------------------------------------
* Function: main
*
* Generate an HDF5 file with groups, datasets and symbolic links.
* After the file is generated, write bad offset values to
* the heap at 3 locations in the file:
* (A) Open the file:
* fd = HDopen(TESTFILE, O_RDWR, 0663);
* (B) Position the file at:
* (1) HDlseek(fd, (HDoff_t)880, SEEK_SET);
* "/group1/group2": replace heap offset "8" by bad offset
* (2) HDlseek(fd, (HDoff_t)1512, SEEK_SET);
* "/dsetA": replace name offset into private heap "72" by bad offset
* (3) HDlseek(fd, (HDoff_t)1616, SEEK_SET);
* /soft_one: replace link value offset in the scratch pad "32" by bad offset
* (C) Write the bad offset value to the file for (1), (2) and (3):
* write(fd, &val, sizeof(val));
*
* Note: if the groups/datasets/symbolic links are changed in the file,
* the above locations need to be adjusted accordingly.
*
* Return: EXIT_SUCCESS/EXIT_FAILURE
*
*-------------------------------------------------------------------------
*/
int
main(void)
{
hid_t fid = -1, gid1 = -1, gid2 = -1; /* File and group IDs */
hid_t did = -1, sid = -1; /* Dataset and dataspace IDs */
int fd = -1; /* File descriptor */
int64_t val = 999; /* Bad offset value */
/* Create the test file */
if((fid = H5Fcreate(TESTFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Create two groups */
if((gid1 = H5Gcreate2(fid, GRP1, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
if((gid2 = H5Gcreate2(gid1, GRP2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Close the groups */
if(H5Gclose(gid1) < 0)
FAIL_STACK_ERROR
if(H5Gclose(gid2) < 0)
FAIL_STACK_ERROR
/* Create soft links to the groups */
if(H5Lcreate_soft("/group1", fid, SOFT1, H5P_DEFAULT, H5P_DEFAULT) < 0)
FAIL_STACK_ERROR
if(H5Lcreate_soft("/group1/group2", fid, SOFT2, H5P_DEFAULT, H5P_DEFAULT) < 0)
FAIL_STACK_ERROR
/* Create a dataset */
if((sid = H5Screate(H5S_SCALAR)) < 0)
FAIL_STACK_ERROR
if((did = H5Dcreate2(fid, DSET, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)) < 0)
FAIL_STACK_ERROR
/* Close the dataset */
if(H5Dclose(did) < 0)
FAIL_STACK_ERROR
/* Close the dataspace */
if(H5Sclose(sid) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(H5Fclose(fid) < 0)
FAIL_STACK_ERROR
/*
* Write bad offset values at 3 locations in the file
*/
/* Open the file */
if((fd = HDopen(TESTFILE, O_RDWR, 0663)) < 0)
FAIL_STACK_ERROR
/* Position the file for /group1/group2: replace heap offset "8" by bad offset */
if(HDlseek(fd, (HDoff_t)880, SEEK_SET) < 0)
FAIL_STACK_ERROR
/* Write the bad offset value to the file */
if(HDwrite(fd, &val, sizeof(val)) < 0)
FAIL_STACK_ERROR
/* Position the file for /dsetA: replace name offset into private heap "72" by bad offset */
if(HDlseek(fd, (HDoff_t)1512, SEEK_SET) < 0)
FAIL_STACK_ERROR
/* Write the bad offset value to the file */
if(HDwrite(fd, &val, sizeof(val)) < 0)
FAIL_STACK_ERROR
/* Position the file for /soft_one: replace link value offset in the scratch pad "32" by bad offset */
if(HDlseek(fd, (HDoff_t)1616, SEEK_SET) < 0)
FAIL_STACK_ERROR
/* Write the bad offset value to the file */
if(HDwrite(fd, &val, sizeof(val)) < 0)
FAIL_STACK_ERROR
/* Close the file */
if(HDclose(fd) < 0)
FAIL_STACK_ERROR
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
H5Gclose(gid1);
H5Gclose(gid2);
H5Dclose(did);
H5Sclose(sid);
H5Fclose(fid);
} H5E_END_TRY;
return EXIT_FAILURE;
} /* end main() */
