diff options
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/h5dump/h5dump.c | 92 | ||||
| -rw-r--r-- | tools/h5dump/h5dumpgentest.c | 54 | ||||
| -rwxr-xr-x | tools/h5dump/testh5dump.sh | 4 | ||||
| -rw-r--r-- | tools/lib/h5tools.c | 33 | ||||
| -rw-r--r-- | tools/lib/h5tools_str.c | 6 | ||||
| -rw-r--r-- | tools/testfiles/tvlstr.ddl | 41 | ||||
| -rw-r--r-- | tools/testfiles/tvlstr.h5 | bin | 0 -> 8192 bytes | |||
| -rw-r--r-- | tools/testfiles/tvlstr.h5.xml | 51 |
8 files changed, 245 insertions, 36 deletions
diff --git a/tools/h5dump/h5dump.c b/tools/h5dump/h5dump.c index d751d25..36250d3 100644 --- a/tools/h5dump/h5dump.c +++ b/tools/h5dump/h5dump.c @@ -677,12 +677,14 @@ print_datatype(hid_t type) char *fname; hid_t nmembers, mtype, str_type; int i, j, ndims, perm[H5DUMP_MAX_RANK]; - size_t size; + size_t size=0; hsize_t dims[H5DUMP_MAX_RANK]; H5T_str_t str_pad; H5T_cset_t cset; H5G_stat_t statbuf; hid_t super; + hid_t tmp_type; + htri_t is_vlstr=FALSE; switch (H5Tget_class(type)) { case H5T_INTEGER: @@ -770,15 +772,23 @@ print_datatype(hid_t type) break; case H5T_STRING: - size = H5Tget_size(type); - str_pad = H5Tget_strpad(type); - cset = H5Tget_cset(type); + /* Make a copy of type in memory in case when TYPE is on disk, the size + * will be bigger than in memory. This makes it easier to compare + * types in memory. */ + tmp_type = H5Tcopy(type); + size = H5Tget_size(tmp_type); + str_pad = H5Tget_strpad(tmp_type); + cset = H5Tget_cset(tmp_type); + is_vlstr = H5Tis_variable_str(tmp_type); printf("H5T_STRING %s\n", dump_header_format->strblockbegin); indent += COL; indentation(indent + COL); - printf("%s %d;\n", STRSIZE, (int) size); + if(is_vlstr) + printf("%s H5T_VARIABLE;\n", STRSIZE); + else + printf("%s %d;\n", STRSIZE, (int) size); indentation(indent + COL); printf("%s ", STRPAD); @@ -800,14 +810,17 @@ print_datatype(hid_t type) printf("unknown_cset;\n"); str_type = H5Tcopy(H5T_C_S1); + if(is_vlstr) + H5Tset_size(str_type, H5T_VARIABLE); + else + H5Tset_size(str_type, size); H5Tset_cset(str_type, cset); - H5Tset_size(str_type, size); H5Tset_strpad(str_type, str_pad); indentation(indent + COL); printf("%s ", CTYPE); - if (H5Tequal(type, str_type)) { + if (H5Tequal(tmp_type, str_type)) { printf("H5T_C_S1;\n"); H5Tclose(str_type); } else { @@ -817,7 +830,7 @@ print_datatype(hid_t type) H5Tset_size(str_type, size); H5Tset_strpad(str_type, str_pad); - if (H5Tequal(type, str_type)) { + if (H5Tequal(tmp_type, str_type)) { printf("H5T_FORTRAN_S1;\n"); } else { printf("unknown_one_character_type;\n "); @@ -827,6 +840,8 @@ print_datatype(hid_t type) H5Tclose(str_type); } + H5Tclose(tmp_type); + indent -= COL; indentation(indent + COL); printf("%s", dump_header_format->strblockend); @@ -1887,13 +1902,14 @@ dump_data(hid_t obj_id, int obj_data, struct subset_t *sset) alloc_size = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); assert(alloc_size == (hsize_t)((size_t)alloc_size)); /*check for overflow*/ + buf = malloc((size_t)alloc_size); assert(buf); if (H5Aread(obj_id, p_type, buf) >= 0) status = h5tools_dump_mem(stdout, outputformat, obj_id, p_type, - space, buf, depth); - + space, buf, depth); + free(buf); H5Tclose(p_type); H5Sclose(space); @@ -2857,10 +2873,25 @@ done: d_status = EXIT_FAILURE; free_handler(hand, argc); - + + for(i=0; i<info.group_table->nobjs; i++) { + if(info.group_table->objs[i].objname) + free(info.group_table->objs[i].objname); + } free(group_table->objs); + + for(i=0; i<info.dset_table->nobjs; i++) { + if(info.dset_table->objs[i].objname) + free(info.dset_table->objs[i].objname); + } free(dset_table->objs); + + for(i=0; i<info.type_table->nobjs; i++) { + if(info.type_table->objs[i].objname) + free(info.type_table->objs[i].objname); + } free(type_table->objs); + free(prefix); free(info.prefix); @@ -4557,12 +4588,14 @@ xml_print_strs(hid_t did, int source) { herr_t e; hid_t type, space; - char *buf; + void *buf; char *bp; char *onestring; hsize_t ssiz; - size_t tsiz; + size_t tsiz, str_size; size_t i; + htri_t is_vlstr; + if (source == DATASET_DATA) { type = H5Dget_type(did); } else if (source == ATTRIBUTE_DATA) { @@ -4575,12 +4608,14 @@ xml_print_strs(hid_t did, int source) /* return an error */ return FAIL; } + is_vlstr = H5Tis_variable_str(type); + if (source == DATASET_DATA) { space = H5Dget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); - buf = calloc((size_t)ssiz, sizeof(char)); + buf = malloc((size_t)ssiz); if (buf == NULL) { return FAIL; @@ -4596,11 +4631,12 @@ xml_print_strs(hid_t did, int source) space = H5Aget_space(did); ssiz = H5Sget_simple_extent_npoints(space); ssiz *= H5Tget_size(type); - - buf = calloc((size_t)ssiz, sizeof(char)); + + buf = malloc((size_t)ssiz); if (buf == NULL) { return FAIL; } + e = H5Aread(did, type, buf); if (e < 0) { free(buf); @@ -4611,28 +4647,36 @@ xml_print_strs(hid_t did, int source) return FAIL; } -/* pull out each string... */ + /* pull out each string... */ ssiz = H5Sget_simple_extent_npoints(space); tsiz = H5Tget_size(type); - onestring = (char *) calloc((size_t)tsiz, sizeof(char)); - bp = buf; + bp = (char*)buf; + if(!is_vlstr) + onestring = (char *) calloc(tsiz, sizeof(char)); for (i = 0; i < ssiz; i++) { - strncpy(onestring, bp, tsiz); + if(is_vlstr) { + onestring = *(char **)bp; + str_size = (size_t)strlen(onestring); + } else { + strncpy(onestring, bp, tsiz); + str_size = tsiz; + } indentation(indent + COL); if (!onestring) { printf("\"%s\"\n", "NULL"); } else { - char *t_onestring = xml_escape_the_string(onestring, (int)tsiz); + char *t_onestring = xml_escape_the_string(onestring, (int)str_size); - printf("\"%s\"\n", xml_escape_the_string(onestring, (int)tsiz)); + printf("\"%s\"\n", t_onestring); free(t_onestring); } - - bp += tsiz; + + bp += tsiz; } + return SUCCEED; } diff --git a/tools/h5dump/h5dumpgentest.c b/tools/h5dump/h5dumpgentest.c index 8f6e3bc..f0e9515 100644 --- a/tools/h5dump/h5dumpgentest.c +++ b/tools/h5dump/h5dumpgentest.c @@ -63,6 +63,7 @@ #define FILE35 "tfamily%05d.h5" #define FILE36 "tmulti" #define FILE37 "tlarge_objname.h5" +#define FILE38 "tvlstr.h5" #define LENSTR 50 #define LENSTR2 11 @@ -108,6 +109,9 @@ typedef struct s1_t { #define ARRAY3_DIM1 6 #define ARRAY3_DIM2 3 +/* VL string datatype name */ +#define VLSTR_TYPE "vl_string_type" + static void gent_group(void) { hid_t fid, group; @@ -2838,6 +2842,55 @@ static void gent_large_objname(void) H5Fclose(fid); } +static void gent_vlstr(void) +{ + const char *wdata[SPACE1_DIM1]= { + "Four score and seven years ago our forefathers brought forth on this continent a new nation,", + "conceived in liberty and dedicated to the proposition that all men are created equal.", + "Now we are engaged in a great civil war,", + "testing whether that nation or any nation so conceived and so dedicated can long endure." + }; /* Information to write */ + char *string_att= "This is the string for the attribute"; + hid_t fid1; /* HDF5 File IDs */ + hid_t dataset, root; /* Dataset ID */ + hid_t sid1, dataspace;/* Dataspace ID */ + hid_t tid1, att; /* Datatype ID */ + hsize_t dims1[] = {SPACE1_DIM1}; + + /* Create file */ + fid1 = H5Fcreate(FILE38, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + + sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL); + + /* Create a VL string datatype to refer to */ + tid1 = H5Tcopy (H5T_C_S1); + H5Tset_size (tid1,H5T_VARIABLE); + + /* Create a dataset and write VL string to it. */ + dataset=H5Dcreate(fid1,"Dataset1",tid1,sid1,H5P_DEFAULT); + H5Dwrite(dataset,tid1,H5S_ALL,H5S_ALL,H5P_DEFAULT,wdata); + H5Dclose(dataset); + + /* Create a named VL string type. Change padding of datatype */ + H5Tset_strpad(tid1, H5T_STR_NULLPAD); + H5Tcommit(fid1, "vl_string_type", tid1); + + /* Create an group attribute of VL string type */ + root = H5Gopen(fid1, "/"); + dataspace = H5Screate(H5S_SCALAR); + + att = H5Acreate(root, "test_scalar", tid1, dataspace, H5P_DEFAULT); + H5Awrite(att, tid1, &string_att); + + /* Close */ + H5Tclose(tid1); + H5Sclose(sid1); + H5Sclose(dataspace); + H5Aclose(att); + H5Gclose(root); + H5Fclose(fid1); +} + int main(void) { gent_group(); @@ -2888,6 +2941,7 @@ int main(void) gent_multi(); gent_large_objname(); + gent_vlstr(); return 0; } diff --git a/tools/h5dump/testh5dump.sh b/tools/h5dump/testh5dump.sh index ec22362..99c1a89 100755 --- a/tools/h5dump/testh5dump.sh +++ b/tools/h5dump/testh5dump.sh @@ -144,6 +144,9 @@ TOOLTEST tvldtypes2.ddl tvldtypes2.h5 TOOLTEST tvldtypes3.ddl tvldtypes3.h5 TOOLTEST tvldtypes4.ddl tvldtypes4.h5 +#test for file with variable length string data +TOOLTEST tvlstr.ddl tvlstr.h5 + # test for files with array data TOOLTEST tarray1.ddl tarray1.h5 TOOLTEST tarray2.ddl tarray2.h5 @@ -218,6 +221,7 @@ TOOLTEST tarray7.h5.xml --xml tarray7.h5 TOOLTEST tvldtypes1.h5.xml --xml tvldtypes1.h5 TOOLTEST tvldtypes2.h5.xml --xml tvldtypes2.h5 TOOLTEST tvldtypes3.h5.xml --xml tvldtypes3.h5 +TOOLTEST tvlstr.h5.xml --xml tvlstr.h5 TOOLTEST tsaf.h5.xml --xml tsaf.h5 TOOLTEST tempty.h5.xml --xml tempty.h5 diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c index b2c4cec..fbdb38a 100644 --- a/tools/lib/h5tools.c +++ b/tools/lib/h5tools.c @@ -457,6 +457,7 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, *this var to count elements and *break after we see a number equal *to the ctx->size_last_dim. */ + unsigned char *tmp=NULL; /* Setup */ memset(&buffer, 0, sizeof(h5tools_str_t)); @@ -470,7 +471,12 @@ h5tools_dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, for (i = 0; i < nelmts; i++, ctx->cur_elmt++, elmt_counter++) { /* Render the element */ h5tools_str_reset(&buffer); - h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx); + if(H5Tis_variable_str(type)) { + tmp = ((unsigned char**)mem)[i]; + h5tools_str_sprint(&buffer, info, container, type, tmp, ctx); + + } else + h5tools_str_sprint(&buffer, info, container, type, mem + i * size, ctx); if (i + 1 < nelmts || (flags & END_OF_DATA) == 0) h5tools_str_append(&buffer, "%s", OPT(info->elmt_suf1, ",")); @@ -785,7 +791,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, hsize_t sm_nelmts; /*elements per stripmine*/ unsigned char *sm_buf = NULL; /*buffer for raw data */ hid_t sm_space; /*stripmine data space */ - + /* Hyperslab info */ hssize_t hs_offset[H5S_MAX_RANK];/*starting offset */ hsize_t hs_size[H5S_MAX_RANK]; /*size this pass */ @@ -820,9 +826,6 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(f_space, total_size, NULL); - /* printf("total_size[ctx.ndims-1]%d\n",total_size[ctx.ndims-1]); - printf("total_size cast %d\n",(int)(total_size[ctx.ndims-1])); */ - /*assert(total_size[ctx.ndims - 1]==(hsize_t)((int)(total_size[ctx.ndims - 1])));*/ ctx.size_last_dim = (total_size[ctx.ndims - 1]); /* calculate the number of elements we're going to print */ @@ -858,6 +861,7 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, assert(sm_nbytes == (hsize_t)((size_t)sm_nbytes)); /*check for overflow*/ sm_buf = malloc((size_t)sm_nbytes); + sm_nelmts = sm_nbytes / p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); @@ -896,10 +900,10 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, flags = (elmtno == 0) ? START_OF_DATA : 0; flags |= ((elmtno + hs_nelmts) >= p_nelmts) ? END_OF_DATA : 0; h5tools_dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts, - p_type, sm_buf); + p_type, sm_buf); /* Reclaim any VL memory, if necessary */ - if (vl_data) + if(vl_data) H5Dvlen_reclaim(p_type, sm_space, H5P_DEFAULT, sm_buf); /* Calculate the next hyperslab offset */ @@ -925,7 +929,9 @@ h5tools_dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, H5Sclose(sm_space); H5Sclose(f_space); + free(sm_buf); + return SUCCEED; } @@ -967,7 +973,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, ctx.indent_level = indentlevel; ctx.need_prefix = 1; - + /* Assume entire data space to be printed */ for (i = 0; i < (hsize_t)ctx.ndims; i++) ctx.p_min_idx[i] = 0; @@ -976,7 +982,7 @@ h5tools_dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t obj_id, for (i = 0, nelmts = 1; ctx.ndims != 0 && i < (hsize_t)ctx.ndims; i++) nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i]; - + if (nelmts == 0) return SUCCEED; /*nothing to print*/ assert(ctx.p_max_idx[ctx.ndims - 1]==(hsize_t)((int)ctx.p_max_idx[ctx.ndims - 1])); @@ -1075,8 +1081,13 @@ h5tools_fixtype(hid_t f_type) * strDUAction == TRUE. if it is false we will do the original action * here. */ - m_type = H5Tcopy(f_type); - H5Tset_cset(m_type, H5T_CSET_ASCII); + if(H5Tis_variable_str(f_type)) { + m_type = H5Tcopy(H5T_C_S1); + H5Tset_size(m_type, H5T_VARIABLE); + } else { + m_type = H5Tcopy(f_type); + H5Tset_cset(m_type, H5T_CSET_ASCII); + } break; case H5T_COMPOUND: diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c index 0820cfb..3cacff0 100644 --- a/tools/lib/h5tools_str.c +++ b/tools/lib/h5tools_str.c @@ -545,7 +545,11 @@ h5tools_str_sprint(h5tools_str_t *str, const h5dump_t *info, hid_t container, unsigned int i; quote = '\0'; - size = H5Tget_size(type); + if(H5Tis_variable_str(type)) { + size = HDstrlen(cp_vp); + } else { + size = H5Tget_size(type); + } pad = H5Tget_strpad(type); for (i = 0; i < size && (cp_vp[i] != '\0' || pad != H5T_STR_NULLTERM); i++) { diff --git a/tools/testfiles/tvlstr.ddl b/tools/testfiles/tvlstr.ddl new file mode 100644 index 0000000..93b392e --- /dev/null +++ b/tools/testfiles/tvlstr.ddl @@ -0,0 +1,41 @@ +############################# +Expected output for 'h5dump tvlstr.h5' +############################# +HDF5 "tvlstr.h5" { +GROUP "/" { + ATTRIBUTE "test_scalar" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLPAD; + CSET H5T_CSET_ASCII; + CTYPE H5T_C_S1; + } + DATASPACE SCALAR + DATA { + "This is the string for the attribute" + } + } + DATASET "Dataset1" { + DATATYPE H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLTERM; + CSET H5T_CSET_ASCII; + CTYPE H5T_C_S1; + } + DATASPACE SIMPLE { ( 4 ) / ( 4 ) } + DATA { + "Four score and seven years ago our forefathers brought forth on this continent a new nation,", + "conceived in liberty and dedicated to the proposition that all men are created equal.", + "Now we are engaged in a great civil war,", + "testing whether that nation or any nation so conceived and so dedicated can long endure." + } + } + DATATYPE "vl_string_type" H5T_STRING { + STRSIZE H5T_VARIABLE; + STRPAD H5T_STR_NULLPAD; + CSET H5T_CSET_ASCII; + CTYPE H5T_C_S1; + }; + +} +} diff --git a/tools/testfiles/tvlstr.h5 b/tools/testfiles/tvlstr.h5 Binary files differnew file mode 100644 index 0000000..53f34ef --- /dev/null +++ b/tools/testfiles/tvlstr.h5 diff --git a/tools/testfiles/tvlstr.h5.xml b/tools/testfiles/tvlstr.h5.xml new file mode 100644 index 0000000..3e5b07e --- /dev/null +++ b/tools/testfiles/tvlstr.h5.xml @@ -0,0 +1,51 @@ +############################# +Expected output for 'h5dump --xml tvlstr.h5' +############################# +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE HDF5-File PUBLIC "HDF5-File.dtd" "http://hdf.ncsa.uiuc.edu/DTDs/HDF5-File.dtd"> +<HDF5-File> +<RootGroup OBJ-XID="root"> + <Attribute Name="test_scalar"> + <Dataspace> + <ScalarDataspace /> + </Dataspace> + <DataType> + <AtomicType> + <StringType Cset="H5T_CSET_ASCII" StrSize="4" StrPad="H5T_STR_NULLPAD"/> + </AtomicType> + </DataType> + <Data> + <DataFromFile> + "This is the string for the attribute" + </DataFromFile> + </Data> + </Attribute> + <NamedDataType Name="vl_string_type" OBJ-XID="/vl_string_type" Parents="root"> + <DataType> + <AtomicType> + <StringType Cset="H5T_CSET_ASCII" StrSize="16" StrPad="H5T_STR_NULLPAD"/> + </AtomicType> + </DataType> + </NamedDataType> + <Dataset Name="Dataset1" OBJ-XID="/Dataset1" Parents="root"> + <Dataspace> + <SimpleDataspace Ndims="1"> + <Dimension DimSize="4" MaxDimSize="4"/> + </SimpleDataspace> + </Dataspace> + <DataType> + <AtomicType> + <StringType Cset="H5T_CSET_ASCII" StrSize="4" StrPad="H5T_STR_NULLTERM"/> + </AtomicType> + </DataType> + <Data> + <DataFromFile> + "Four score and seven years ago our forefathers brought forth on this continent a new nation," + "conceived in liberty and dedicated to the proposition that all men are created equal." + "Now we are engaged in a great civil war," + "testing whether that nation or any nation so conceived and so dedicated can long endure." + </DataFromFile> + </Data> + </Dataset> +</RootGroup> +</HDF5-File> |