/****************************************************************
**
** Giterate(): Group iteration routine.
**
****************************************************************/
PyObject *Giterate(hid_t parent_id, hid_t loc_id, const char *name) {
hsize_t i=0;
PyObject *t, *tgroup, *tleave, *tlink, *tunknown;
PyObject *info[4];
info[0] = tgroup = PyList_New(0);
info[1] = tleave = PyList_New(0);
info[2] = tlink = PyList_New(0);
info[3] = tunknown = PyList_New(0);
/* Iterate over all the childs behind loc_id (parent_id+loc_id).
* NOTE: using H5_INDEX_CRT_ORDER instead of H5_INDEX_NAME causes failures
* in the test suite */
H5Literate_by_name(parent_id, name, H5_INDEX_NAME, H5_ITER_NATIVE,
&i, litercb, info, H5P_DEFAULT);
/* Create the tuple with the list of Groups and Datasets */
t = PyTuple_New(4);
PyTuple_SetItem(t, 0, tgroup);
PyTuple_SetItem(t, 1, tleave);
PyTuple_SetItem(t, 2, tlink);
PyTuple_SetItem(t, 3, tunknown);
return t;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Literate_by_name
* Signature: (JLjava/lang/String;IIJLjava/lang/Object;Ljava/lang/Object;J)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Literate_1by_1name
(JNIEnv *env, jclass clss, jlong grp_id, jstring name, jint idx_type, jint order,
jlong idx, jobject callback_op, jobject op_data, jlong access_id)
{
hsize_t start_idx = (hsize_t)idx;
herr_t status = -1;
const char *lName;
ENVPTR->GetJavaVM(ENVPAR &jvm);
cb_wrapper wrapper = {callback_op, op_data};
if ((op_data == NULL) || (callback_op == NULL)) {
h5nullArgument(env, "H5Literate_by_name: op_data or callback_op is NULL");
} /* end if */
else {
PIN_JAVA_STRING(name, lName);
if (lName != NULL) {
status = H5Literate_by_name((hid_t)grp_id, lName, (H5_index_t)idx_type, (H5_iter_order_t)order, (hsize_t*)&start_idx, (H5L_iterate_t)H5L_iterate_cb, (void*)&wrapper, (hid_t)access_id);
UNPIN_JAVA_STRING(name, lName);
if (status < 0)
h5libraryError(env);
}
} /* end else */
return status;
} /* end Java_hdf_hdf5lib_H5_H5Literate_1by_1name */
herr_t op_func_group (hid_t loc_id, const char* objname, const H5L_info_t* /*info*/, void* /*ppar*/) {
//struct param glopar;
struct param* ppar;
ppar = &glopar;
int err;
hid_t h5fi;
hid_t h5fo;
hid_t gid;
H5G_stat_t statbuf;
err = H5Gget_objinfo (loc_id, objname, 0, &statbuf); CHKERR(err);
/* if object is group, open containers, create group, iterate over datasets, close */
if (statbuf.type == H5G_GROUP) {
h5fi = H5Fopen(((struct param *)ppar)->conti, H5F_ACC_RDONLY, H5P_DEFAULT); CHKRTN(h5fi < 0, FILEERR);
h5fo = H5Fopen(((struct param *)ppar)->conto, H5F_ACC_RDWR, H5P_DEFAULT); CHKRTN(h5fo < 0, FILEERR);
gid = H5Gcreate(h5fo, objname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); CHKRTN(gid < 0, ERR);
strncpy(((struct param *)ppar)->grupi, objname, sizeof(((struct param *)ppar)->grupi) - 1);
strncpy(((struct param *)ppar)->grupo, objname, sizeof(((struct param *)ppar)->grupo) - 1);
err = H5Literate_by_name (h5fi, objname, H5_INDEX_NAME, H5_ITER_NATIVE, NULL, op_func_dset, (void *) ppar, NULL); CHKERR(err);
err = H5Fclose(h5fo); CHKERR(err);
err = H5Fclose(h5fi); CHKERR(err);
}
return EXIT_SUCCESS;
}
/*------------------------------------------------------------------------- * Function: traverse * * Purpose: Iterate over all the objects/links in a file. Conforms to the * "visitor" pattern. * * Return: 0 on success, -1 on failure * * Programmer: Quincey Koziol, [email protected] * * Date: September 1, 2007 * *------------------------------------------------------------------------- */ static int traverse(hid_t file_id, const char *grp_name, hbool_t visit_start, hbool_t recurse, const trav_visitor_t *visitor) { H5O_info_t oinfo; /* Object info for starting group */ /* Get info for starting object */ if(H5Oget_info_by_name(file_id, grp_name, &oinfo, H5P_DEFAULT) < 0) return -1; /* Visit the starting object */ if(visit_start && visitor->visit_obj) (*visitor->visit_obj)(grp_name, &oinfo, NULL, visitor->udata); /* Go visiting, if the object is a group */ if(oinfo.type == H5O_TYPE_GROUP) { trav_addr_t seen; /* List of addresses seen */ trav_ud_traverse_t udata; /* User data for iteration callback */ /* Init addresses seen */ seen.nused = seen.nalloc = 0; seen.objs = NULL; /* Check for multiple links to top group */ if(oinfo.rc > 1) trav_addr_add(&seen, oinfo.addr, grp_name); /* Set up user data structure */ udata.seen = &seen; udata.visitor = visitor; udata.is_absolute = (*grp_name == '/'); udata.base_grp_name = grp_name; /* Check for iteration of links vs. visiting all links recursively */ if(recurse) { /* Visit all links in group, recursively */ if(H5Lvisit_by_name(file_id, grp_name, trav_index_by, trav_index_order, traverse_cb, &udata, H5P_DEFAULT) < 0) return -1; } /* end if */ else { /* Iterate over links in group */ if(H5Literate_by_name(file_id, grp_name, trav_index_by, trav_index_order, NULL, traverse_cb, &udata, H5P_DEFAULT) < 0) return -1; } /* end else */ /* Free visited addresses table */ if(seen.objs) { size_t u; /* Local index variable */ /* Free paths to objects */ for(u = 0; u < seen.nused; u++) HDfree(seen.objs[u].path); HDfree(seen.objs); } /* end if */ } /* end if */ return 0; }
int convertimagebatch(param par) {
//struct param glopar;
int err;
hid_t h5fi = -1;
hid_t h5fo = -1;
/* open source container */
h5fi = H5Fopen(par.conti, H5F_ACC_RDONLY, H5P_DEFAULT); CHKRTN(h5fi < 0, FILEERR);
/* create empty container. TRUNC overwrite it if exists. */
h5fo = H5Fcreate(par.conto, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* iterate over groups */
glopar = par;
err = H5Literate_by_name (h5fi, ".", H5_INDEX_NAME, H5_ITER_NATIVE, NULL, op_func_group, (void *) &par, NULL); CHKERR(err);
/* close containers */
err = H5Fclose(h5fi); CHKERR(err);
return EXIT_SUCCESS;
}
value hdf5_h5l_iterate_by_name(value loc_v, value group_name_v, value index_type_v,
value order_v, value idx_v, value op_v, value lapl_v, value op_data_v)
{
CAMLparam5(loc_v, group_name_v, index_type_v, order_v, idx_v);
CAMLxparam3(op_v, lapl_v, op_data_v);
CAMLlocal1(exception);
struct operator_data op_data;
hsize_t idx, ret;
op_data.callback = &op_v;
op_data.operator_data = &op_data_v;
op_data.exception = &exception;
idx = Is_block(idx_v) ? Int_val(Field(Field(idx_v, 0), 0)) : 0;
exception = Val_unit;
ret = H5Literate_by_name(Hid_val(loc_v), String_val(group_name_v),
H5_index_val(index_type_v), H5_iter_order_val(order_v),
Is_block(idx_v) ? &idx : NULL, hdf5_h5l_operator, &op_data, H5P_opt_val(lapl_v));
if (Is_block(idx_v))
Store_field(Field(idx_v, 0), 0, Val_int(idx));
if (exception != Val_unit)
caml_raise(exception);
CAMLreturn(Val_h5_iter(ret));
}
int main (void)
{
hid_t file;
hid_t grp;
hid_t dataset, dataspace;
hid_t plist;
herr_t status;
hsize_t dims[2];
hsize_t cdims[2];
int idx_f, idx_g;
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a group in the file.
*/
grp = H5Gcreate(file, "/Data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataset "Compressed Data" in the group using absolute
* name. Dataset creation property list is modified to use
* GZIP compression with the compression effort set to 6.
* Note that compression can be used only when dataset is chunked.
*/
dims[0] = 1000;
dims[1] = 20;
cdims[0] = 20;
cdims[1] = 20;
dataspace = H5Screate_simple(RANK, dims, NULL);
plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(plist, 2, cdims);
H5Pset_deflate( plist, 6);
dataset = H5Dcreate(file, "/Data/Compressed_Data", H5T_NATIVE_INT,
dataspace, H5P_DEFAULT, plist, H5P_DEFAULT);
/*
* Close the first dataset .
*/
H5Sclose(dataspace);
H5Dclose(dataset);
/*
* Create the second dataset.
*/
dims[0] = 500;
dims[1] = 20;
dataspace = H5Screate_simple(RANK, dims, NULL);
dataset = H5Dcreate(file, "/Data/Float_Data", H5T_NATIVE_FLOAT,
dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
*Close the second dataset and file.
*/
H5Sclose(dataspace);
H5Dclose(dataset);
H5Pclose(plist);
H5Gclose(grp);
H5Fclose(file);
/*
* Now reopen the file and group in the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);
grp = H5Gopen(file, "Data", H5P_DEFAULT);
/*
* Access "Compressed_Data" dataset in the group.
*/
dataset = H5Dopen(grp, "Compressed_Data", H5P_DEFAULT);
if( dataset < 0) printf(" Dataset 'Compressed-Data' is not found. \n");
printf("\"/Data/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Create hard link to the Data group.
*/
status = H5Lcreate_hard(file, "Data", H5L_SAME_LOC, "Data_new", H5P_DEFAULT, H5P_DEFAULT);
/*
* We can access "Compressed_Data" dataset using created
* hard link "Data_new".
*/
dataset = H5Dopen(file, "/Data_new/Compressed_Data", H5P_DEFAULT);
if( dataset < 0) printf(" Dataset is not found. \n");
printf("\"/Data_new/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Use iterator to see the names of the objects in the root group.
*/
idx_f = H5Literate(file, H5_INDEX_NAME, H5_ITER_INC, NULL, file_info, NULL);
/*
* Unlink name "Data" and use iterator to see the names
* of the objects in the file root direvtory.
*/
if(H5Ldelete(file, "Data", H5P_DEFAULT) < 0)
printf(" H5Ldelete failed \n");
else
printf("\"Data\" is unlinked \n");
idx_f = H5Literate(file, H5_INDEX_NAME, H5_ITER_INC, NULL, file_info, NULL);
/*
* Use iterator to see the names of the objects in the group
* /Data_new.
*/
idx_g = H5Literate_by_name(grp, "/Data_new", H5_INDEX_NAME, H5_ITER_INC, NULL, group_info, NULL, H5P_DEFAULT);
/*
* Close the file.
*/
H5Gclose(grp);
H5Fclose(file);
return 0;
}
herr_t op_func (hid_t loc_id, const char *name, const H5L_info_t *info,
void *operator_data)
{
herr_t status, return_val = 0;
H5O_info_t infobuf;
struct opdata *od = (struct opdata *) operator_data;
unsigned spaces = 2*(od->recurs+1);
FILE* pfile;
pfile = fopen(filePathJson.toStdString().c_str(), "a");
if (!pfile)
{
throw GenericExc(QObject::tr("Ошибка открытия json файла"));
}
status = H5Oget_info_by_name (loc_id, name, &infobuf, H5P_DEFAULT);
if (status < 0)
{
throw GenericExc(QObject::tr("Ошибка получения информации о файле"));
}
switch (infobuf.type) {
case H5O_TYPE_GROUP: {
if (countGroup != 0) {
fprintf (pfile, "{\n");
fprintf (pfile, "%*s", spaces, "");
}
fprintf (pfile, "\"%s\" : ", name);
countGroup++;
if ( group_check (od, infobuf.addr) ) {
}
else {
struct opdata nextod;
nextod.recurs = od->recurs + 1;
nextod.prev = od;
nextod.addr = infobuf.addr;
fclose(pfile);
return_val = H5Literate_by_name (loc_id, name, H5_INDEX_NAME,
H5_ITER_NATIVE, NULL, op_func, (void *) &nextod,
H5P_DEFAULT);
}
pfile = fopen(filePathJson.toStdString().c_str(), "a");
if (!pfile)
{
throw GenericExc(QObject::tr("Ошибка открытия json файла"));
}
if (count == 0) {
fprintf (pfile, "%*s}\n", spaces, "");
} else {
fprintf (pfile, "\n%*s]\n", spaces, "");
count = 0;
}
break;
}
case H5O_TYPE_DATASET:
if (count == 0)
{
fprintf (pfile, "[\n");
} else
{
fprintf(pfile, ",\n");
}
fprintf (pfile, "%*s", spaces, "");
fprintf (pfile, "\"%s\"", name);
count++;
countGroup = 0;
break;
default:
break;
}
fclose(pfile);
return return_val;
}
