diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/h5findshd.c | 288 | ||||
| -rw-r--r-- | tools/h5toh4.c | 1005 | ||||
| -rw-r--r-- | tools/testh5toh4 | 18 |
3 files changed, 1051 insertions, 260 deletions
diff --git a/tools/h5findshd.c b/tools/h5findshd.c index a18e2ac..b5cd0f9 100644 --- a/tools/h5findshd.c +++ b/tools/h5findshd.c @@ -5,7 +5,7 @@ typedef struct shared_obj_t{ unsigned long objno[2]; char objname[1024]; -int displayed; +int objflag; } shared_obj_t; typedef struct table_t{ @@ -26,6 +26,11 @@ extern int search_obj (table_t, unsigned long *); extern void add_obj (table_t *, unsigned long *, char *); extern void dump_tables(void); extern herr_t find_shared_objs(hid_t , char *, void *); +extern herr_t H5findobj_once(hid_t , char *, void *); +extern int get_table_idx(int, unsigned long *); +extern int get_tableflag(int, int); +extern int set_tableflag(int, int); +extern char* get_objectname(int, int); /*------------------------------------------------------------------------- * Function: init_table @@ -53,17 +58,17 @@ int i; for (i = 0; i < group_table.size; i++) { group_table.objs[i].objno[0] = group_table.objs[i].objno[1] = 0; - group_table.objs[i].displayed = 0; + group_table.objs[i].objflag = 0; } for (i = 0; i < dset_table.size; i++) { dset_table.objs[i].objno[0] = dset_table.objs[i].objno[1] = 0; - dset_table.objs[i].displayed = 0; + dset_table.objs[i].objflag = 0; } for (i = 0; i < type_table.size; i++) { dset_table.objs[i].objno[0] = dset_table.objs[i].objno[1] = 0; - dset_table.objs[i].displayed = 0; + dset_table.objs[i].objflag = 0; } prefix = (char *) HDmalloc(prefix_len * sizeof (char)); @@ -145,7 +150,7 @@ int i; table->objs = HDrealloc (table->objs, table->size*sizeof(shared_obj_t)); for (i = table->nobjs; i < table->size; i++) { table->objs[i].objno[0] = table->objs[i].objno[1] = 0; - table->objs[i].displayed = 0; + table->objs[i].objflag = 0; } } @@ -178,21 +183,21 @@ int i; printf ("%lu %lu %s %d\n", group_table.objs[i].objno[0], group_table.objs[i].objno[1], group_table.objs[i].objname, - group_table.objs[i].displayed); + group_table.objs[i].objflag); printf("\ndset_table: # of entries = %d\n", dset_table.nobjs); for ( i = 0; i < dset_table.nobjs; i++) printf ("%lu %lu %s %d\n", dset_table.objs[i].objno[0], dset_table.objs[i].objno[1], dset_table.objs[i].objname, - dset_table.objs[i].displayed); + dset_table.objs[i].objflag); printf("\ntype_table: # of entries = %d\n", type_table.nobjs); for ( i = 0; i < type_table.nobjs; i++) printf ("%lu %lu %s %d\n", type_table.objs[i].objno[0], type_table.objs[i].objno[1], type_table.objs[i].objname, - type_table.objs[i].displayed); + type_table.objs[i].objflag); } @@ -266,7 +271,7 @@ int i; H5Gget_objinfo(type, ".", TRUE, &statbuf); if (search_obj (type_table, statbuf.objno) < 0) { add_obj (&type_table, statbuf.objno, tmp) ; - type_table.objs[type_table.nobjs-1].displayed = 0; + type_table.objs[type_table.nobjs-1].objflag = 0; } } H5Tclose(type); @@ -283,10 +288,10 @@ int i; i = search_obj (type_table, statbuf.objno); if (i < 0) { add_obj (&type_table, statbuf.objno, tmp) ; - type_table.objs[type_table.nobjs-1].displayed = 1; /* named data type */ + type_table.objs[type_table.nobjs-1].objflag = 1; /* named data type */ } else { strcpy (type_table.objs[i].objname, tmp); - type_table.objs[i].displayed = 1; /* named data type */ + type_table.objs[i].objflag = 1; /* named data type */ } status = SUCCEED; break; @@ -300,3 +305,264 @@ int i; return status; } +/*------------------------------------------------------------------------- + * Function: H5findobj_once + * + * Purpose: Find objects only once and store them in tables + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Paul Harten + * + * Modifications: + * + *-----------------------------------------------------------------------*/ +herr_t +H5findobj_once(hid_t group, char *name, void __unused__ *op_data) +{ +hid_t obj, type; +H5G_stat_t statbuf; +char *tmp; +int status=SUCCEED; +int i; + + H5Gget_objinfo(group, name, TRUE, &statbuf); + + tmp = (char *) HDmalloc ((strlen(prefix)+strlen(name)+2) * sizeof(char)); + + strcpy(tmp, prefix); + + switch (statbuf.type) { + + case H5G_GROUP: + if ((obj=H5Gopen (group, name))>=0) { + + if (prefix_len < (int)(strlen(prefix) + strlen(name) + 2)) { + prefix_len *= 2; + prefix = HDrealloc (prefix, prefix_len * sizeof(char)); + } + strcat(strcat(prefix,"/"), name); + + if (search_obj (group_table, statbuf.objno) < 0) { + add_obj (&group_table, statbuf.objno, prefix); + status = H5Giterate (obj, ".", NULL, (H5G_operator_t)H5findobj_once, NULL); + } + + strcpy(prefix, tmp); + H5Gclose (obj); + + } else + status = FAIL; + + break; + + case H5G_DATASET: + + strcat(tmp,"/"); + strcat(tmp,name); /* absolute name of the data set */ + if (search_obj (dset_table, statbuf.objno) < 0) + add_obj (&dset_table, statbuf.objno, tmp); + + if ((obj=H5Dopen (group, name))>=0) { + type = H5Dget_type (obj); + if (H5Tcommitted(type) > 0 ) { + H5Gget_objinfo(type, ".", TRUE, &statbuf); + if (search_obj (type_table, statbuf.objno) < 0) { + add_obj (&type_table, statbuf.objno, tmp) ; + type_table.objs[type_table.nobjs-1].objflag = 0; + } + } + H5Tclose(type); + H5Dclose (obj); + status = SUCCEED; + } else + status = FAIL; + + break; + + case H5G_TYPE: + strcat(tmp,"/"); + strcat(tmp,name); /* absolute name of the type */ + i = search_obj (type_table, statbuf.objno); + if (i < 0) { + add_obj (&type_table, statbuf.objno, tmp) ; + type_table.objs[type_table.nobjs-1].objflag = 1; /* named data type */ + } else { + strcpy (type_table.objs[i].objname, tmp); + type_table.objs[i].objflag = 1; /* named data type */ + } + status = SUCCEED; + break; + + default: + break; + } + + HDfree (tmp); + + return status; + +} +/*------------------------------------------------------------------------- + * Function: get_table_idx + * + * Purpose: Determine if objects are in a link loop + * + * Return: Success: table index of object detected to be in loop + * + * Failure: FAIL + * + * Programmer: Paul Harten + * + *-----------------------------------------------------------------------*/ +int +get_table_idx(int type, unsigned long *objno) +{ +int idx; + + switch (type) { + + case H5G_GROUP: + + idx = search_obj(group_table, objno); + break; + + case H5G_DATASET: + + idx = search_obj(dset_table, objno); + break; + + case H5G_TYPE: + + idx = search_obj(type_table, objno); + break; + + default: + + idx = -1; + + } + + return idx; + +} +/*------------------------------------------------------------------------- + * Function: Get table flag setting + * + * Purpose: Keep the structures and variables used private to + * this file. + * + * Return: Success: Boolean setting of the i'th element of the + * object table flag + * + * Failure: FAIL + * + * Programmer: Paul Harten + * + *-----------------------------------------------------------------------*/ +int +get_tableflag(int type, int idx) +{ + + switch (type) { + + case H5G_GROUP: + + return group_table.objs[idx].objflag; + + case H5G_DATASET: + + return dset_table.objs[idx].objflag; + + case H5G_TYPE: + + return type_table.objs[idx].objflag; + + default: + + return -1; + + } + +} +/*------------------------------------------------------------------------- + * Function: Set table flag setting + * + * Purpose: Keep the structures and variables used private to + * this file. + * + * Return: Success: Boolean setting of the i'th element of the + * object table flag + * + * Failure: FAIL + * + * Programmer: Paul Harten + * + *-----------------------------------------------------------------------*/ +int +set_tableflag(int type, int idx) +{ + + switch (type) { + + case H5G_GROUP: + + group_table.objs[idx].objflag = TRUE; + return SUCCEED; + + case H5G_DATASET: + + dset_table.objs[idx].objflag = TRUE; + return SUCCEED; + + case H5G_TYPE: + + type_table.objs[idx].objflag = TRUE; + return SUCCEED; + + default: + + return FAIL; + + } + +} +/*------------------------------------------------------------------------- + * Function: Get name of i'th object in table + * + * Purpose: + * + * Return: Success: strdup() of object name character string + * + * Failure: NULL + * + * Programmer: Paul Harten + * + *-----------------------------------------------------------------------*/ +char * +get_objectname(int type, int idx) +{ + + switch (type) { + + case H5G_GROUP: + + return strdup(group_table.objs[idx].objname); + + case H5G_DATASET: + + return strdup(dset_table.objs[idx].objname); + + case H5G_TYPE: + + return strdup(type_table.objs[idx].objname); + + default: + + return NULL; + + } + +} diff --git a/tools/h5toh4.c b/tools/h5toh4.c index 5aee126..e46f0a5 100644 --- a/tools/h5toh4.c +++ b/tools/h5toh4.c @@ -30,13 +30,19 @@ extern herr_t convert_group(hid_t, char *, op_data_t *); extern herr_t convert_dataset(hid_t, char *, op_data_t *); extern herr_t convert_all(hid_t, char *, op_data_t *); extern herr_t convert_attr(hid_t, char *, op_data_t *); +extern herr_t convert_shared_dataset(hid_t, int, op_data_t *); +extern herr_t convert_shared_group(hid_t, int, op_data_t *); extern int32 h5type_to_h4type(hid_t); extern hid_t h4type_to_memtype(int32); extern void init_table(void); extern void free_table(void); extern void dump_tables(void); -extern herr_t find_shared_objs(hid_t , char *, void *); +extern herr_t H5findobj_once(hid_t , char *, void *); +extern int get_table_idx(int, unsigned long *); +extern int get_tableflag(int, int); +extern int set_tableflag(int, int); +extern char* get_objectname(int, int); extern int optind; extern void perror(const char *); @@ -285,20 +291,20 @@ int h5toh4(h5_filename, h4_filename) hid_t fid, gid; hid_t plist=H5P_DEFAULT; int status = 0; - int32 hfile_id; - int32 sd_id; + int32 hfile_id; + int32 sd_id; op_data_t op_data; void *edata; hid_t (*func)(void*); - /* open hdf5 file */ + /* open hdf5 file */ if ((fid = H5Fopen (h5_filename, H5F_ACC_RDONLY, plist)) <= 0) { fprintf(stderr,"Error: Unable to open file %s\n",h5_filename); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "h5toh4", __FILE__, __LINE__); return (fid); } - /* open root group */ + /* open root group */ if ((gid = H5Gopen (fid, "/")) <= 0 ) { fprintf(stderr,"Error: Unable to open root group\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "h5toh4", __FILE__, __LINE__); @@ -325,15 +331,15 @@ int h5toh4(h5_filename, h4_filename) status = FAIL; } - /* allocate and initialize internal data structure */ - init_table(); + /* allocate and initialize internal data structure */ + init_table(); /* Disable error reporting */ H5Eget_auto (&func, &edata); H5Eset_auto (NULL, NULL); - /* find all shared objects */ - if ((status = H5Giterate(fid, "/", NULL, (H5G_operator_t)find_shared_objs, NULL)) != SUCCEED ) { + /* find all objects one time */ + if ((status = H5Giterate(fid, "/", NULL, (H5G_operator_t)H5findobj_once, NULL)) != SUCCEED ) { fprintf(stderr,"Error: Unable to iterate over all of the groups\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "h5toh4", __FILE__, __LINE__); } @@ -342,13 +348,13 @@ int h5toh4(h5_filename, h4_filename) H5Eset_auto (func, edata); #ifdef H5DUMP_DEBUG - dump_tables(); + dump_tables(); #endif - if (status != SUCCEED) { - fprintf(stderr,"Error: internal error! \n"); - goto done; - } + if (status != SUCCEED) { + fprintf(stderr,"Error: internal error! \n"); + goto done; + } op_data.hfile_id = hfile_id; op_data.sd_id = sd_id; @@ -364,7 +370,7 @@ int h5toh4(h5_filename, h4_filename) /* Terminate access to Vgroup interface */ if ((status = Vend(hfile_id)) != SUCCEED) { fprintf(stderr,"Error: Unable to terminate Vgroup interface\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "h5toh4", __FILE__, __LINE__); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "h5toh4", __FILE__, __LINE__); status = FAIL; } } @@ -412,7 +418,7 @@ done: * * Purpose: Dump everything within the specified group * - * Return: void + * Return: status * * Programmer: Paul Harten * @@ -427,6 +433,7 @@ H5G_stat_t statbuf; int32 vgroup_id; int32 obj_idx; int32 status; + int idx, flag; hfile_id = op_data->hfile_id; @@ -458,30 +465,80 @@ H5G_stat_t statbuf; } } op_data->vgroup_id = vgroup_id; - op_data->sds_id = 0; - op_data->vdata_id = 0; + op_data->sds_id = 0; + op_data->vdata_id = 0; op_data->obj_idx = obj_idx; /* hard link */ - if ((status = H5Gget_objinfo(gid, ".", TRUE, &statbuf)) != SUCCEED ) { + if ((status = H5Gget_objinfo(gid, ".", TRUE, &statbuf)) != SUCCEED ) { fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); return (status); - } - - if ((status = H5Aiterate(gid, NULL, (H5G_operator_t)convert_attr, op_data)) != SUCCEED ) { - fprintf(stderr,"Error: Unable to iterate over all of the attributes\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); - status = FAIL; } - if ((status = H5Giterate(gid, ".", NULL, (H5G_operator_t)convert_all, op_data)) != SUCCEED ) { - fprintf(stderr,"Error: Unable to iterate over all of the groups\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); - status = FAIL; + if (strcmp(name,"/") == 0) { /* this is the root group, just iterate */ + + if ((status = H5Aiterate(gid, NULL, (H5A_operator_t)convert_attr, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to iterate over all of the attributes\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + if ((status = H5Giterate(gid, ".", NULL, (H5G_operator_t)convert_all, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to iterate over all of the groups\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + } else { + + if ((idx = get_table_idx(H5G_GROUP, statbuf.objno)) < 0 ) { + + fprintf(stderr,"Error: object not found, %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + status = FAIL; + + } else if((flag = get_tableflag(H5G_GROUP,idx)) < 0 ) { + + fprintf(stderr,"Error: get_tableflag() should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + status = FAIL; + + } else if(flag == TRUE ) { /* this has already been converted, don't convert the attributes again */ + + if ((status = H5Giterate(gid, ".", NULL, (H5G_operator_t)convert_all, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to iterate over all of the groups\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + } else { /* flag == FALSE */ + + /* this is now being converted */ + if ((status = set_tableflag(H5G_GROUP,idx)) < 0 ) { + fprintf(stderr,"Error: set_tableflag should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + if ((status = H5Aiterate(gid, NULL, (H5A_operator_t)convert_attr, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to iterate over all of the attributes\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + if ((status = H5Giterate(gid, ".", NULL, (H5G_operator_t)convert_all, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to iterate over all of the groups\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); + return(status); + } + + } + } + if ((status = Vdetach(vgroup_id)) != SUCCEED ) { fprintf(stderr,"Error: Unable to detach the new Vgroup\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_group", __FILE__, __LINE__); @@ -496,9 +553,9 @@ H5G_stat_t statbuf; /*------------------------------------------------------------------------- * Function: convert_dataset * - * Purpose: Dump the specified data set + * Purpose: Convert the specified data set * - * Return: void + * Return: status * * Programmer: Paul Harten * @@ -508,7 +565,7 @@ H5G_stat_t statbuf; herr_t convert_dataset (hid_t did, char *name, op_data_t *op_data) { hid_t type, space, class, mem_type, type2; -H5G_stat_t statbuf; +/* H5G_stat_t statbuf; */ size_t typesize; int i, idx; int32 dim_sizes[32], start[32], edges[32]; @@ -521,6 +578,7 @@ int32 hfile_id; int32 sd_id; int32 sds_id; int32 vdata_id; +int32 vgroup_id; int32 n_values; int32 status; int32 h4_type; @@ -533,15 +591,19 @@ char *fieldname; hid_t fieldtype; int32 order; off_t offset; +off_t offset_array[512]; +hid_t h4type_array[512], memtype_array[512]; +int32 order_array[512]; - sd_id = op_data->sd_id; /* hard link */ +/* if ((status = H5Gget_objinfo(did, ".", TRUE, &statbuf)) != SUCCEED ) { fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); return (status); } +*/ if ((type = H5Dget_type(did)) <= 0) { fprintf(stderr, "Error: H5Dget_type() didn't return appropriate value.\n"); @@ -581,6 +643,7 @@ off_t offset; switch (class) { case H5T_INTEGER: case H5T_FLOAT: + sd_id = op_data->sd_id; if ((h4_type = h5type_to_h4type(type)) == FAIL ) { fprintf(stderr, "Error: Problems translating h5 type to h4 type\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); @@ -635,7 +698,7 @@ off_t offset; fprintf(stderr, "Error: Unable to write SDS %s.\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); } - if ((status = H5Aiterate(did, NULL, (H5G_operator_t)convert_attr, op_data)) < 0 ) { + if ((status = H5Aiterate(did, NULL, (H5A_operator_t)convert_attr, op_data)) < 0 ) { fprintf(stderr,"Error: iterate over attributes\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); } @@ -645,20 +708,16 @@ off_t offset; } break; case H5T_TIME: - fprintf(stderr,"Error: H5T_TIME not yet implemented.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + fprintf(stderr,"Warning: H5T_TIME not yet implemented.\n"); break; case H5T_STRING: - fprintf(stderr,"Error: H5T_STRING not yet implemented.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + fprintf(stderr,"Warning: H5T_STRING not yet implemented.\n"); break; case H5T_BITFIELD: - fprintf(stderr,"Error: H5T_BITFIELD not yet implemented.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + fprintf(stderr,"Warning: H5T_BITFIELD not yet implemented.\n"); break; case H5T_OPAQUE: - fprintf(stderr,"Error: H5T_OPAQUE not yet implemented.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + fprintf(stderr,"Warning: H5T_OPAQUE not yet implemented.\n"); break; case H5T_COMPOUND: if (ndims==1) { @@ -667,20 +726,73 @@ off_t offset; DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; } + + offset = 0; for (idx=0;idx<nmembers;idx++) { - if ((ndimf = H5Tget_member_dims(type, idx, dimf, permf)) > 1 ) { - fprintf(stdout,"Warning: H5 datasets of H5T_COMPOUND type with ndims = 1, whose members\n"); - fprintf(stdout,"Warning: of the H5T_COMPOUND type have rank > 1 are not converted.\n"); - break; + if ((ndimf = H5Tget_member_dims(type, idx, dimf, permf)) < 0 || ndimf > 4 ) { + fprintf(stderr, "Error: rank of members of compound type should not be %d\n",ndimf); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + return FAIL; } + if ((fieldtype = H5Tget_member_type(type, idx)) < 0 ) { + fprintf(stderr,"Error: H5 datasets of H5T_COMPOUND type with fieldtype %d, idx %d.\n",fieldtype,idx); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + break; + } + if ((h4_type = h5type_to_h4type(fieldtype)) < 0 ) { + fprintf(stderr, "Error: Problems translating h5 type to h4 type\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + break; + } + if ((mem_type = h4type_to_memtype(h4_type)) == FAIL ) { + fprintf(stderr, "Error: Problems translating h4 type to mem type\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + return FAIL; + } + if ((typesize = H5Tget_size(mem_type)) <= 0) { + fprintf(stderr, "Error: H5Tget_size() didn't return appropriate value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + status = FAIL; + break; + } + order = 1; + if (ndimf > 0) { + order *= dimf[permf[0]]; + if (ndimf > 1) { + order *= dimf[permf[1]]; + if (ndimf > 2) { + order *= dimf[permf[2]]; + if (ndimf > 3) { + order *= dimf[permf[3]]; + } + } + } + } + h4type_array[idx] = h4_type; /* used for VSfdefine */ + memtype_array[idx] = mem_type; /* used during the build of the memory compound type */ + offset_array[idx] = offset; /* used during the build of the memory compound type */ + order_array[idx] = order; /* used for VSfdefine */ + + offset += order * typesize; /* calculating packed size of memory compound type */ } hfile_id = op_data->hfile_id; + vgroup_id = op_data->vgroup_id; if ((vdata_id = VSattach(hfile_id, -1, "w")) <= 0 ) { fprintf(stderr, "Error: Unable to create vdata %s.\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); status = FAIL; break; } +/* + * This step is done during the convert_shared_dataset() call instead of here. + * + if ((idx = Vinsert(vgroup_id, vdata_id)) < 0 ) { + fprintf(stderr, "Error: Unable to insert vdata %s.\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + status = FAIL; + break; + } +*/ op_data->vdata_id = vdata_id; if ((status = VSsetname(vdata_id, name)) != SUCCEED ) { fprintf(stderr, "Error: Unable to set vdata name %s.\n",name); @@ -692,40 +804,42 @@ off_t offset; DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; } + if ((type2 = H5Tcreate(H5T_COMPOUND, (size_t)offset)) <= 0 ) { + fprintf(stderr, "Error: unable to execute H5Tcreate()\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + break; + } for (idx=0;idx<nmembers;idx++) { - if ((ndimf = H5Tget_member_dims(type, idx, dimf, NULL)) < 0 ) { - fprintf(stderr, "Error: field rank for H5T_COMPOUND type %d, idx %d < 0\n", type, idx); + if ((ndimf = H5Tget_member_dims(type, idx, dimf, permf)) < 0 || ndimf > 4 ) { + fprintf(stderr, "Error: rank of members of compound type should not be %d\n",ndimf); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; + return FAIL; } if ((fieldname = H5Tget_member_name(type, idx)) == NULL ) { fprintf(stderr, "Error: Unable to get fieldname for compound type %d, idx %d\n", type, idx); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; } - if ((fieldtype = H5Tget_member_type(type, idx)) < 0 ) { - fprintf(stderr,"Error: H5 datasets of H5T_COMPOUND type with fieldtype %d, idx %d.\n",fieldtype,idx); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; - } - if ((h4_type = h5type_to_h4type(fieldtype)) < 0 ) { - fprintf(stderr, "Error: Problems translating h5 type to h4 type\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; - } -/* - if ((mem_type = h4type_to_memtype(h4_type)) == FAIL ) { - fprintf(stderr, "Error: Problems translating h4 type to mem type\n"); + if ((offset = H5Tget_offset(memtype_array[idx])) < 0 || offset >= 128 ) { + fprintf(stderr, "Error: H5Tget_offset() is returning a bad value %d\n",(int)offset); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); return FAIL; } -*/ if (ndimf == 0 ) { - order = 1; + if ((status = H5Tinsert(type2,fieldname,offset_array[idx]+offset,memtype_array[idx])) != SUCCEED ) { + fprintf(stderr, "Error: Problems inserting field into compound datatype\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + return FAIL; + } } else { - order = dimf[0]; + if ((status = H5Tinsert_array(type2,fieldname,offset_array[idx]+offset,ndimf,dimf,permf, + memtype_array[idx])) != SUCCEED ) { + fprintf(stderr, "Error: Problems inserting array field into compound datatype\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); + return FAIL; + } } - if ((status = VSfdefine(vdata_id, fieldname, h4_type, order)) != SUCCEED ) { + if ((status = VSfdefine(vdata_id, fieldname, h4type_array[idx], order_array[idx])) != SUCCEED ) { fprintf(stderr, "Error: Unable to set field %d\n", idx); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; @@ -747,17 +861,6 @@ off_t offset; DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; } - - if ((type2 = H5Tcopy(type)) <= 0 ) { - fprintf(stderr, "Error: H5Tcopy did not SUCCEED, type %d\n", type2); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; - } - if ((status = H5Tpack(type2)) != SUCCEED ) { - fprintf(stderr, "Error: H5Tpack did not SUCCEED, status %d\n", (int)status); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; - } if ((recsize = H5Tget_size(type2)) <= 0 ) { fprintf(stderr, "Error: Unable to get record size %d\n", (int)recsize); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); @@ -790,8 +893,9 @@ off_t offset; DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); break; } + /* there are only vdata attributes, no field attributes */ - if ((status = H5Aiterate(did, NULL, (H5G_operator_t)convert_attr, op_data)) < 0 ) { + if ((status = H5Aiterate(did, NULL, (H5A_operator_t)convert_attr, op_data)) < 0 ) { fprintf(stderr,"Error: iterate over attributes\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); } @@ -801,13 +905,10 @@ off_t offset; break; } - if ((status = H5Tclose(type2)) != SUCCEED ) { - fprintf(stderr, "Error: H5Tclose did not SUCCEED, status %d\n", (int)status); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_dataset", __FILE__, __LINE__); - break; - } } else { + fprintf(stdout,"Warning: H5 datasets of H5T_COMPOUND type with ndims > 1 are not converted.\n"); + } break; default: @@ -850,7 +951,7 @@ off_t offset; herr_t convert_attr (hid_t attr, char *attr_name, op_data_t *op_data) { -hid_t attr_id, type, space, mem_type; +hid_t attr_id, type, space, mem_type, class; size_t typesize; char *attr_values; int32 status; @@ -870,93 +971,131 @@ int32 n_values; fprintf(stderr, "Error: H5Dget_type() didn't return appropriate value.\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); status = FAIL; - return status; + return status; } - if ((space = H5Aget_space(attr_id)) <= 0) { - fprintf(stderr, "Error: H5Dget_space() didn't return appropriate value.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr2", __FILE__, __LINE__); - status = FAIL; - return status; - } - - if ((n_values = H5Sget_simple_extent_npoints(space)) <= 0) { - fprintf(stderr, "Error: H5sget_simple_extent_npoints() didn't return correct value.\n"); + if ((class = H5Tget_class(type)) < 0 ) { + fprintf(stderr,"Error: problem with getting class\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } + status = class; + return status; + } - if ((h4_type = h5type_to_h4type(type)) == FAIL ) { - fprintf(stderr, "Error: Problems translating h5 type to h4 type\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } + switch (class) { + case H5T_INTEGER: + case H5T_FLOAT: - if ((mem_type = h4type_to_memtype(h4_type)) == FAIL ) { - fprintf(stderr, "Error: Problems translating h4 type to mem type\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - return status; - } - if ((typesize = H5Tget_size(mem_type)) <= 0) { - fprintf(stderr, "Error: H5Tget_size() didn't return appropriate value.\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } + if ((space = H5Aget_space(attr_id)) <= 0) { + fprintf(stderr, "Error: H5Dget_space() didn't return appropriate value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr2", __FILE__, __LINE__); + status = FAIL; + return status; + } - if ((attr_values = HDmalloc(n_values*typesize)) == NULL) { - fprintf(stderr, "Error: Problems with HDmalloc of memory space\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } + if ((n_values = H5Sget_simple_extent_npoints(space)) <= 0) { + fprintf(stderr, "Error: H5sget_simple_extent_npoints() didn't return correct value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } - if ((status = H5Aread(attr_id, mem_type, attr_values)) != SUCCEED) { - fprintf(stderr, "Error: Problems with H5Aread\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } - - if (sds_id != 0) { - if ((status = SDsetattr(sds_id, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { - fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + if ((h4_type = h5type_to_h4type(type)) == FAIL ) { + fprintf(stderr, "Error: Problems translating h5 type to h4 type\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); status = FAIL; + return status; } - } else if (vdata_id != 0) { - if ((status = VSsetattr(vdata_id, -1, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { - fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + + if ((mem_type = h4type_to_memtype(h4_type)) == FAIL ) { + fprintf(stderr, "Error: Problems translating h4 type to mem type\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); status = FAIL; + return status; } - } else { - if ((status = Vsetattr(vgroup_id, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { - fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + + if ((typesize = H5Tget_size(mem_type)) <= 0) { + fprintf(stderr, "Error: H5Tget_size() didn't return appropriate value.\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); status = FAIL; + return status; } - - } - if ((status = H5Tclose(type)) != SUCCEED ) { - fprintf(stderr, "Error: Problems closing H5Tclose\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } - if ((status = H5Sclose(space)) != SUCCEED ) { - fprintf(stderr, "Error: Problems closing H5Sclose\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } - if ((status = H5Aclose(attr_id)) != SUCCEED ) { - fprintf(stderr, "Error: Problems closing H5Aclose\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); - status = FAIL; - } + if ((attr_values = HDmalloc(n_values*typesize)) == NULL) { + fprintf(stderr, "Error: Problems with HDmalloc of memory space\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } - HDfree(attr_values); + if ((status = H5Aread(attr_id, mem_type, attr_values)) != SUCCEED) { + fprintf(stderr, "Error: Problems with H5Aread\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + + if (sds_id != 0) { + if ((status = SDsetattr(sds_id, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { + fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + } else if (vdata_id != 0) { + if ((status = VSsetattr(vdata_id, -1, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { + fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + } else { + if ((status = Vsetattr(vgroup_id, attr_name, h4_type, n_values, attr_values)) != SUCCEED ) { + fprintf(stderr, "Error: Unable to set %s attribute.\n",attr_name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + } - status = SUCCEED; + if ((status = H5Sclose(space)) != SUCCEED ) { + fprintf(stderr, "Error: Problems closing H5Sclose\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + if ((status = H5Aclose(attr_id)) != SUCCEED ) { + fprintf(stderr, "Error: Problems closing H5Aclose\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + + HDfree(attr_values); + + status = SUCCEED; + break; + + case H5T_TIME: + fprintf(stderr,"Warning: H5T_TIME attribute not yet implemented.\n"); + break; + case H5T_STRING: + fprintf(stderr,"Warning: H5T_STRING attribute not yet implemented.\n"); + break; + case H5T_BITFIELD: + fprintf(stderr,"Warning: H5T_BITFIELD attribute not yet implemented.\n"); + break; + case H5T_OPAQUE: + fprintf(stderr,"Warning: H5T_OPAQUE attribute not yet implemented.\n"); + break; + case H5T_COMPOUND: + fprintf(stderr,"Warning: H5T_COMPOUND attribute not implemented.\n"); + break; + default: + fprintf(stderr,"Error: %d class not found\n",class); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + } } else { @@ -964,6 +1103,13 @@ int32 n_values; } + if ((status = H5Tclose(type)) != SUCCEED ) { + fprintf(stderr, "Error: Problems closing H5Tclose\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_attr", __FILE__, __LINE__); + status = FAIL; + return status; + } + return status; } @@ -987,157 +1133,538 @@ herr_t convert_all (hid_t group, char *name, op_data_t *op_data) { hid_t obj; - H5G_stat_t statbuf; + H5G_stat_t statbuf, statbuf2; int status; - op_data_t op_data_save; - int32 vgroup_id; - char *sds_name; - int32 sd_id; - int32 sds_id; - int32 sds_ref; - int32 sds_index; - void *edata; - hid_t (*func)(void*); + op_data_t op_data_save; + int32 vgroup_id; + int32 sd_id; + int32 sds_id; + int idx, flag; + void *edata; + hid_t (*func)(void*); - op_data_save = *op_data; + op_data_save = *op_data; - vgroup_id = op_data->vgroup_id; - sd_id = op_data->sd_id; - sds_id = op_data->sds_id; + vgroup_id = op_data->vgroup_id; + sd_id = op_data->sd_id; + sds_id = op_data->sds_id; if ((status = H5Gget_objinfo(group, name, FALSE, &statbuf)) != SUCCEED ) { - fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (status); + fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (status); } + statbuf2 = statbuf; switch (statbuf.type) { - case H5G_LINK: + case H5G_LINK: /* this is a soft link only */ - if (statbuf.nlink==0) { - /* Disable error reporting */ - H5Eget_auto (&func, &edata); - H5Eset_auto (NULL, NULL); + /* Disable error reporting */ + H5Eget_auto (&func, &edata); + H5Eset_auto (NULL, NULL); - /* test to see if object exists */ - if ((status = H5Gget_objinfo(group, name, TRUE, NULL)) != SUCCEED ) { - fprintf(stdout,"Warning: the object pointed to by the symbolic link \"%s\" does not exist.\n",name); - } + /* test to see if object exists */ + if ((status = H5Gget_objinfo(group, name, TRUE, NULL)) != SUCCEED ) { + fprintf(stdout,"Warning: the object pointed to by the symbolic link \"%s\" does not exist.\n",name); + } - /* Enable error reporting */ - H5Eset_auto (func, edata); + /* Enable error reporting */ + H5Eset_auto (func, edata); - if (status != SUCCEED) { - break; - } + if (status != SUCCEED) { + break; + } - } - /* follow link */ + /* follow link for type */ if ((status = H5Gget_objinfo(group, name, TRUE, &statbuf)) != SUCCEED ) { - fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (status); + fprintf(stderr,"Error: H5Gget_objinfo() did not work\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (status); } - if (statbuf.type==H5G_DATASET) { + if (statbuf.type==H5G_DATASET ) { - sds_name = HDmalloc (statbuf.linklen*sizeof(char)); - if ((status = H5Gget_linkval (group, name, statbuf.linklen, sds_name)) != SUCCEED ) { - fprintf (stderr,"Error: unable to get link value.\n"); + if ((idx = get_table_idx(H5G_DATASET, statbuf.objno)) < 0 ) { + + fprintf(stderr,"Error: object not found\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if((flag = get_tableflag(H5G_DATASET,idx)) < 0 ) { + + fprintf(stderr,"Error: get_tableflag() should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if(flag == TRUE ) { /* this has already been converted, add as a tag/ref */ + + if ((obj = H5Dopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open H5 dataset\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (status); - } - if ((sds_index = SDnametoindex(sd_id, sds_name)) < 0 ) { - fprintf (stderr,"Error: Problem with SDnametoindex().\n"); + return (obj); + } else { + if ((status = convert_shared_dataset(obj, idx, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to convert to tag/ref\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + } + } + if ((status = H5Dclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close H5 dataset %s\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (sds_index); - } - if ((sds_id = SDselect(sd_id, sds_index)) < 0 ) { - fprintf (stderr,"Error: Problem with SDselect().\n"); + status = FAIL; + break; + } + + } else { /* flag == FALSE */ + + if ((obj = H5Dopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open H5 dataset\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (sds_id); - } - if ((sds_ref = SDidtoref(sds_id)) < 0 ) { - fprintf (stderr,"Error: Problem with SDidtoref().\n"); + return (obj); + } else { + if (( status = convert_dataset (obj, name, op_data)) != SUCCEED) { + fprintf(stderr,"Error: convert_dataset did not work for %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + if ((status = convert_shared_dataset(obj, idx, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to convert to tag/ref\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + } + if(( status = set_tableflag(H5G_DATASET,idx)) != SUCCEED ) { + fprintf(stderr,"Error: set_tableflag() did not work for %s\n", name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + break; + } + } + if ((status = H5Dclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close H5 dataset %s\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (sds_ref); - } - if ((status = Vaddtagref(vgroup_id, DFTAG_NDG, sds_ref)) != SUCCEED ) { - fprintf (stderr,"Error: Problem with Vaddtagref().\n"); + status = FAIL; + break; + } + + } + + } else if (statbuf.type==H5G_GROUP ) { + + if ((idx = get_table_idx(H5G_GROUP, statbuf.objno)) < 0 ) { + + fprintf(stderr,"Error: object not found\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if((flag = get_tableflag(H5G_GROUP,idx)) < 0 ) { + + fprintf(stderr,"Error: get_tableflag() should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if(flag == TRUE ) { + + if (( status = convert_shared_group (group, idx, op_data)) != SUCCEED) { + fprintf(stderr,"Error: convert_group did not work for %s\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (status); - } + status = FAIL; + break; + } - free (sds_name); + } else { /* flag == FALSE */ + + if ((obj = H5Gopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open group\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (obj); + } else { + if (( status = convert_group (obj, name, op_data)) != SUCCEED) { + fprintf(stderr,"Error: convert_group did not work for %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + } + if ((status = H5Gclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close group %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } } + } + break; case H5G_GROUP: - if ((obj = H5Gopen (group, name)) <= 0 ) { - fprintf(stderr,"Error: Unable to open group\n"); + + if ((idx = get_table_idx(H5G_GROUP, statbuf.objno)) < 0 ) { + + fprintf(stderr,"Error: object not found\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (obj); - } else { - if (( status = convert_group (obj, name, op_data)) != SUCCEED) { + status = FAIL; + + } else if((flag = get_tableflag(H5G_GROUP,idx)) < 0 ) { + + fprintf(stderr,"Error: get_tableflag() should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if(flag == TRUE ) { + + if (( status = convert_shared_group (group, idx, op_data)) != SUCCEED) { fprintf(stderr,"Error: convert_group did not work for %s\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); status = FAIL; break; } - } - if ((status = H5Gclose(obj)) != SUCCEED) { - fprintf(stderr,"Error: Unable to close group %s\n",name); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - status = FAIL; - break; - } - break; - case H5G_DATASET: + } else { /* flag == FALSE */ - if ((obj = H5Dopen (group, name)) <= 0 ) { - fprintf(stderr,"Error: Unable to open H5 dataset %s\n",name); - DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); - return (obj); - } else { - if (( status = convert_dataset (obj, name, op_data)) != SUCCEED) { - fprintf(stderr,"Error: convert_dataset did not work for %s\n",name); + if ((obj = H5Gopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open group\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (obj); + } else { + if (( status = convert_group (obj, name, op_data)) != SUCCEED) { + fprintf(stderr,"Error: convert_group did not work for %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + } + if ((status = H5Gclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close group %s\n",name); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); status = FAIL; break; } + } - if ((status = H5Dclose(obj)) != SUCCEED) { - fprintf(stderr,"Error: Unable to close H5 dataset %s\n",name); + + break; + + case H5G_DATASET: + + if ((idx = get_table_idx(H5G_DATASET, statbuf.objno)) < 0 ) { + + fprintf(stderr,"Error: object not found\n"); DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); status = FAIL; - break; + + } else if((flag = get_tableflag(H5G_DATASET,idx)) < 0 ) { + + fprintf(stderr,"Error: get_tableflag() should never return < 0\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + + } else if(flag == TRUE ) { /* this has already been converted, add as a tag/ref */ + + if ((obj = H5Dopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open H5 dataset\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (obj); + } else { + if ((status = convert_shared_dataset(obj, idx, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to convert to tag/ref\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + } + } + if ((status = H5Dclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close H5 dataset %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + + } else { /* flag == FALSE */ + + if ((obj = H5Dopen (group, name)) <= 0 ) { + fprintf(stderr,"Error: Unable to open H5 dataset\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + return (obj); + } else { + if (( status = convert_dataset (obj, name, op_data)) != SUCCEED) { + fprintf(stderr,"Error: convert_dataset did not work for %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + if ((status = convert_shared_dataset(obj, idx, op_data)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to convert to tag/ref\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + } + if(( status = set_tableflag(H5G_DATASET,idx)) != SUCCEED ) { + fprintf(stderr,"Error: set_tableflag() did not work for %s\n", name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + break; + } + } + if ((status = H5Dclose(obj)) != SUCCEED) { + fprintf(stderr,"Error: Unable to close H5 dataset %s\n",name); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_all", __FILE__, __LINE__); + status = FAIL; + break; + } + } - break; + + break; case H5G_TYPE: - /* object is ignored */ + /* object is ignored */ break; default: fprintf (stderr,"Unknown Object %s\n", name); - status = 1; - return FAIL; + status = FAIL; + return status; break; } - *op_data = op_data_save; + *op_data = op_data_save; return SUCCEED; } +/*------------------------------------------------------------------------- + * Function: convert_shared_dataset + * + * Purpose: Handle a shared dataset which has already been converted. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Paul Harten + * + * Modifications: + * + *-----------------------------------------------------------------------*/ +herr_t +convert_shared_dataset(hid_t did, int idx, op_data_t *op_data) +{ + int status=SUCCEED; + int32 vgroup_id; + char *dataset_name, *dataset_name2; + int32 hfile_id; + int32 sd_id; + int32 sds_id; + int32 sds_ref; + int32 vdata_ref; + int32 sds_index; + int32 numtagref; + hid_t type, space, class; + hsize_t dims[32], maxdims[32]; + int n_values, ndims; + + vgroup_id = op_data->vgroup_id; + + if ((dataset_name = get_objectname(H5G_DATASET, idx)) == NULL ) { + fprintf(stderr,"Error: get_objectname() did not work\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (status); + } + + if ((dataset_name2 = strrchr(dataset_name,'/')) == NULL) { /* find last "/" in dataset_name */ + dataset_name2 = dataset_name; /* no "/"s were found */ + } else { + dataset_name2 = dataset_name2 + sizeof(char); /* 1 character past last "/" */ + } + + if ((type = H5Dget_type(did)) <= 0) { + fprintf(stderr, "Error: H5Dget_type() didn't return appropriate value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = FAIL; + return status; + } + + if ((space = H5Dget_space(did)) <= 0) { + fprintf(stderr, "Error: H5Dget_space() didn't return appropriate value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = FAIL; + return status; + } + + if ((n_values = H5Sget_simple_extent_npoints(space)) <= 0) { + fprintf(stderr, "Error: H5Sget_simple_extent_npoints() returned inappropriate value.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = FAIL; + return status; + } + + if ((ndims = H5Sget_simple_extent_dims(space,dims,maxdims)) < 0 ) { + fprintf(stderr, "Error: Problems getting ndims, dims, and maxdims of dataset\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = ndims; + return status; + } + + if ((class = H5Tget_class(type)) < 0 ) { + fprintf(stderr,"Error: problem with getting class\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = class; + return status; + } + + switch (class) { + case H5T_INTEGER: + case H5T_FLOAT: + sd_id = op_data->sd_id; + if ((sds_index = SDnametoindex(sd_id, dataset_name2)) < 0 ) { + fprintf (stderr,"Error: Problem with SDnametoindex().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (sds_index); + } + if ((sds_id = SDselect(sd_id, sds_index)) < 0 ) { + fprintf (stderr,"Error: Problem with SDselect().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (sds_id); + } + if ((sds_ref = SDidtoref(sds_id)) < 0 ) { + fprintf (stderr,"Error: Problem with SDidtoref().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (sds_ref); + } + if ((numtagref = Vaddtagref(vgroup_id, DFTAG_NDG, sds_ref)) < 0 ) { + fprintf (stderr,"Error: Problem with Vaddtagref().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (numtagref); + } + break; + case H5T_TIME: + fprintf(stderr,"Error: H5T_TIME not yet implemented.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + break; + case H5T_STRING: + fprintf(stderr,"Error: H5T_STRING not yet implemented.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + break; + case H5T_BITFIELD: + fprintf(stderr,"Error: H5T_BITFIELD not yet implemented.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + break; + case H5T_OPAQUE: + fprintf(stderr,"Error: H5T_OPAQUE not yet implemented.\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + break; + case H5T_COMPOUND: + hfile_id = op_data->hfile_id; + if (ndims==1) { + if ((vdata_ref = VSfind(hfile_id,dataset_name2)) <= 0 ) { + fprintf (stderr,"Error: Problem with VSfind().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (vdata_ref); + } + if ((numtagref = Vaddtagref(vgroup_id, DFTAG_VH, vdata_ref)) < 0 ) { + fprintf (stderr,"Error: Problem with Vaddtagref().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + return (numtagref); + } + } + break; + default: + fprintf(stderr,"Error: %d class not found\n",class); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_dataset", __FILE__, __LINE__); + status = FAIL; + } + + HDfree (dataset_name); + + return status; + +} + +/*------------------------------------------------------------------------- + * Function: convert_shared_group + * + * Purpose: Handle a shared group which has already been converted. + * + * Return: status + * + * Programmer: Paul Harten + * + * Modifications: + * + *-----------------------------------------------------------------------*/ +herr_t +convert_shared_group (hid_t group, int idx, op_data_t *op_data) { + + int32 hfile_id; + int32 vgroup_id; + int32 vgroup_ref; + int32 numtagref; + int32 status; + char *group_name, *group_name2; + char vgroup_name[VGNAMELENMAX]; + + hfile_id = op_data->hfile_id; + + if ((group_name = get_objectname(H5G_GROUP, idx)) == NULL ) { + fprintf(stderr,"Error: get_objectname() did not work\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return (status); + } + + if ((group_name2 = strrchr(group_name,'/')) == NULL) { /* find last "/" in group_name */ + group_name2 = group_name; /* no "/"s were found */ + } else { + group_name2 = group_name2 + sizeof(char); /* 1 character past last "/" */ + } + + if ((status = Vgetname(op_data->vgroup_id,vgroup_name)) < 0 ) { + fprintf (stderr,"Error: Problem with Vfind().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return (status); + } + + if ((vgroup_ref = Vfind(hfile_id,vgroup_name)) <= 0 ) { + fprintf (stderr,"Error: Problem with Vfind().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return (vgroup_ref); + } + + if ((vgroup_id = Vattach(hfile_id, vgroup_ref, "w")) <= 0 ) { + fprintf(stderr,"Error: Unable to create new vgroup\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return(vgroup_id); + } + + if ((vgroup_ref = Vfind(hfile_id,group_name2)) <= 0 ) { + fprintf (stderr,"Error: Problem with Vfind().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return (vgroup_ref); + } + + if ((numtagref = Vaddtagref(vgroup_id, DFTAG_VG, vgroup_ref)) < 0 ) { + fprintf (stderr,"Error: Problem with Vaddtagref().\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + return (numtagref); + } + + if ((status = Vdetach(vgroup_id)) != SUCCEED ) { + fprintf(stderr,"Error: Unable to detach the new Vgroup\n"); + DEBUG_PRINT("Error detected in %s() [%s line %d]\n", "convert_shared_group", __FILE__, __LINE__); + status = FAIL; + } + + HDfree(group_name); + + return status; + +} + + /***************************************************************************** Routine: h5type_to_h4type(h5type) diff --git a/tools/testh5toh4 b/tools/testh5toh4 index 22ea13b..e78c4fb 100644 --- a/tools/testh5toh4 +++ b/tools/testh5toh4 @@ -151,10 +151,6 @@ TEST() ;; esac -# if [ $noclean -eq 0 ] -# then -# $RM $output -# fi } @@ -236,25 +232,27 @@ MESG 3 "$TestName" $RM ./testfiles/*.hdf ./testfiles/*.tmp TEST tgroup.h5 TEST tdset.h5 -TEST tdset2.h5 TEST tattr.h5 TEST tslink.h5 TEST thlink.h5 -TEST tcompound.h5 -TEST tcompound2.h5 TEST tall.h5 +TEST tdset2.h5 +TEST tcompound2.h5 +TEST tmany.h5 $RM ./testfiles/*.tmp TEST tgroup.h5 tgroup.hdf TEST tdset.h5 tdset.hdf -TEST tdset2.h5 tdset2.hdf TEST tattr.h5 tattr.hdf TEST tslink.h5 tslink.hdf TEST thlink.h5 thlink.hdf TEST tcompound.h5 tcompound.hdf -TEST tcompound2.h5 tcompound2.hdf TEST tall.h5 tall.hdf +TEST tdset2.h5 tdset2.hdf +TEST tcompound2.h5 tcompound2.hdf +TEST tmany.h5 tmany.hdf $RM ./testfiles/*.hdf ./testfiles/*.tmp -TEST -m tgroup.h5 tdset.h5 tdset2.h5 tattr.h5 tslink.h5 thlink.h5 tcompound.h5 tcompound2.h5 tall.h5 +TEST -m tgroup.h5 tdset.h5 tattr.h5 tslink.h5 thlink.h5 tcompound.h5 tall.h5 +TEST -m tdset2.h5 tcompound2.h5 tmany.h5 $RM ./testfiles/*.hdf ./testfiles/*.tmp else MESG 3 "$TestName <<<SKIPPED>>>" |