/* * Copyright © 1998 NCSA * All rights reserved. * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Purpose: A library for displaying the values of a dataset in a human * readable format. */ #include #include #include #include #include #include #include #include #include /* taken from h5dumputil.c */ int indent = 0; int compound_data=0; int nCols = 80; static void display_numeric_data(hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t dim_n_size, hsize_t elmtno, hid_t container); static void display_string(hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t dim_n_size, hsize_t elmtno); static void display_compound_data(hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t elmtno); int h5dump_attr(hid_t oid, hid_t ptype); int print_data(hid_t oid, hid_t _p_type, int obj_data); /* * If REPEAT_VERBOSE is defined then character strings will be printed so * that repeated character sequences like "AAAAAAAAAA" are displayed as * * 'A' repeates 9 times * * Otherwise the format is more Perl-like * * 'A'*10 * */ #define REPEAT_VERBOSE /* * The output functions need a temporary buffer to hold a piece of the * dataset while it's being printed. This constant sets the limit on the * size of that temporary buffer in bytes. For efficiency's sake, choose the * largest value suitable for your machine (for testing use a small value). */ #if 1 #define H5DUMP_BUFSIZE (1024*1024) #else #define H5DUMP_BUFSIZE (1024) #endif #define OPT(X,S) ((X)?(X):(S)) #define ALIGN(A,Z) ((((A)+(Z)-1)/(Z))*(Z)) #define START_OF_DATA 0x0001 #define END_OF_DATA 0x0002 /* Special strings embedded in the output */ #define OPTIONAL_LINE_BREAK "\001" /* Variable length string datatype */ #define STR_INIT_LEN 4096 /*initial length */ typedef struct h5dump_str_t { char *s; /*allocate string */ size_t len; /*length of actual value */ size_t nalloc; /*allocated size of string */ } h5dump_str_t; /* Output variables */ typedef struct h5dump_context_t { size_t cur_column; /*current column for output */ size_t cur_elmt; /*current element/output line */ int need_prefix; /*is line prefix needed? */ int ndims; /*dimensionality */ hsize_t p_min_idx[H5S_MAX_RANK]; /*min selected index */ hsize_t p_max_idx[H5S_MAX_RANK]; /*max selected index */ int prev_multiline; /*was prev datum multiline? */ size_t prev_prefix_len;/*length of previous prefix */ int continuation; /*continuation of previous data?*/ int size_last_dim; /*the size of the last dimension. needed so we can break after each row*/ int indent_level; /*the number of times we need some extra indentation*/ } h5dump_context_t; typedef herr_t (*H5G_operator_t)(hid_t, const char*, void*); extern void init_prefix(char **temp, int length); extern void init_table(table_t **table); extern void free_table(table_t **table); extern void dump_table(char *name, table_t* table); extern herr_t find_objs(hid_t group, const char *name, void *op_data); extern int search_obj (table_t *temp, unsigned long *); extern int get_table_idx(table_t *table, unsigned long *); extern int get_tableflag(table_t*, int); extern int set_tableflag(table_t*, int); extern char* get_objectname(table_t*, int); /*------------------------------------------------------------------------- * Function: h5dump_str_close * * Purpose: Closes a string by releasing it's memory and setting the size * information to zero. * * Return: void * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static void h5dump_str_close(h5dump_str_t *str) { if (str && str->nalloc) { free(str->s); memset(str, 0, sizeof(h5dump_str_t)); } } /*------------------------------------------------------------------------- * Function: h5dump_str_len * * Purpose: Returns the length of the string, not counting the null * terminator. * * Return: Success: Length of string * * Failure: 0 * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static size_t h5dump_str_len(h5dump_str_t *str) { return str->len; } /*------------------------------------------------------------------------- * Function: h5dump_str_append * * Purpose: Formats variable arguments according to printf() format * string and appends the result to variable length string STR. * * Return: Success: Pointer to buffer containing result. * * Failure: NULL * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_str_append(h5dump_str_t *str/*in,out*/, const char *fmt, ...) { va_list ap; va_start(ap, fmt); /* Make sure we have some memory into which to print */ if (!str->s || str->nalloc<=0) { str->nalloc = STR_INIT_LEN; str->s = malloc(str->nalloc); assert(str->s); str->s[0] = '\0'; str->len = 0; } while (1) { size_t avail = str->nalloc - str->len; size_t nchars = HDvsnprintf(str->s+str->len, avail, fmt, ap); if (ncharslen += nchars; break; } /* Try again with twice as much space */ str->nalloc *= 2; str->s = realloc(str->s, str->nalloc); assert(str->s); } va_end(ap); return str->s; } /*------------------------------------------------------------------------- * Function: h5dump_str_reset * * Purpose: Reset the string to the empty value. If no memory is * allocated yet then initialize the h5dump_str_t struct. * * Return: Success: Ptr to the buffer which contains a null * character as the first element. * * Failure: NULL * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_str_reset(h5dump_str_t *str/*in,out*/) { if (!str->s || str->nalloc<=0) { str->nalloc = STR_INIT_LEN; str->s = malloc(str->nalloc); assert(str->s); } str->s[0] = '\0'; str->len = 0; return str->s; } /*------------------------------------------------------------------------- * Function: h5dump_str_trunc * * Purpose: Truncate a string to be at most SIZE characters. * * Return: Success: Pointer to the string * * Failure: NULL * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_str_trunc(h5dump_str_t *str/*in,out*/, size_t size) { if (sizelen) { str->len = size; str->s[size] = '\0'; } return str->s; } /*------------------------------------------------------------------------- * Function: h5dump_str_fmt * * Purpose: Reformat a string contents beginning at character START * according to printf format FMT. FMT should contain no format * specifiers except possibly the `%s' variety. For example, if * the input string is `hello' and the format is "<<%s>>" then * the output value will be "<>". * * Return: Success: A pointer to the resulting string. * * Failure: NULL * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_str_fmt(h5dump_str_t *str/*in,out*/, size_t start, const char *fmt) { char _temp[1024], *temp=_temp; /* If the format string is simply "%s" then don't bother doing anything */ if (!strcmp(fmt, "%s")) return str->s; /* * Save the input value if there is a `%' anywhere in FMT. Otherwise * don't bother because we don't need a temporary copy. */ if (strchr(fmt, '%')) { if ((str->len-start)+1>sizeof _temp) { temp = malloc((str->len-start)+1); assert(temp); } strcpy(temp, str->s+start); } /* Reset the output string and append a formatted version */ h5dump_str_trunc(str, start); h5dump_str_append(str, fmt, temp); /* Free the temp buffer if we allocated one */ if (temp != _temp) free(temp); return str->s; } /*------------------------------------------------------------------------- * Function: h5dump_prefix * * Purpose: Renders the line prefix value into string STR. * * Return: Success: Pointer to the prefix. * * Failure: NULL * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_prefix(h5dump_str_t *str/*in,out*/, const h5dump_t *info, hsize_t elmtno, int ndims, hsize_t min_idx[], hsize_t max_idx[]) { hsize_t p_prod[H5S_MAX_RANK], p_idx[H5S_MAX_RANK]; hsize_t n, i=0; h5dump_str_reset(str); if (ndims>0) { /* * Calculate the number of elements represented by a unit change in a * certain index position. */ for (i=ndims-1, p_prod[ndims-1]=1; i>0; --i) { p_prod[i-1] = (max_idx[i]-min_idx[i]) * p_prod[i]; } /* * Calculate the index values from the element number. */ for (i=0, n=elmtno; i<(hsize_t)ndims; i++) { p_idx[i] = n / p_prod[i] + min_idx[i]; n %= p_prod[i]; } /* * Print the index values. */ for (i=0; i<(hsize_t)ndims; i++) { if (i) h5dump_str_append(str, "%s", OPT(info->idx_sep, ",")); h5dump_str_append(str, OPT(info->idx_n_fmt, "%lu"), (unsigned long)p_idx[i]); } } else { /* Scalar */ h5dump_str_append(str, OPT(info->idx_n_fmt, "%lu"), (unsigned long)0); } /* * Add prefix and suffix to the index. */ return h5dump_str_fmt(str, 0, OPT(info->idx_fmt, "%s: ")); } /*------------------------------------------------------------------------- * Function: h5dump_escape * * Purpose: Changes all "funny" characters in S into standard C escape * sequences. If ESCAPE_SPACES is non-zero then spaces are * escaped by prepending a backslash. * * Return: Success: S * * Failure: NULL if the buffer would overflow. The * buffer has as many left-to-right escapes as * possible before overflow would have happened. * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static char * h5dump_escape(char *s/*in,out*/, size_t size, int escape_spaces) { size_t n = strlen(s); size_t i; const char *escape; char octal[8]; for (i=0; isize) return NULL; /*would overflow*/ memmove(s+i+esc_size, s+i, (n-i)+1); /*make room*/ memcpy(s+i, escape, esc_size); /*insert*/ n += esc_size; i += esc_size - 1; } } return s; } /*------------------------------------------------------------------------- * Function: h5dump_is_zero * * Purpose: Determines if memory is initialized to all zero bytes. * * Return: TRUE if all bytes are zero; FALSE otherwise * * Programmer: Robb Matzke * Monday, June 7, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static hbool_t h5dump_is_zero(const void *_mem, size_t size) { const unsigned char *mem = (const unsigned char*)_mem; while (size-- > 0) { if (mem[size]) return FALSE; } return TRUE; } /*------------------------------------------------------------------------- * Function: h5dump_region * * Purpose: Prints information about a dataspace region by appending * the information to the specified string. * * Return: Success: 0 * * Failure: NULL * * Programmer: Robb Matzke * Monday, June 7, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static int h5dump_region(hid_t region, h5dump_str_t *str/*in,out*/, const h5dump_t *info) { hssize_t nblocks, npoints, i; hsize_t *ptdata; int j; int ndims = H5Sget_simple_extent_ndims(region); /* * These two functions fail if the region does not have blocks or points, * respectively. They do not currently know how to translate from one to * the other. */ H5E_BEGIN_TRY { nblocks = H5Sget_select_hyper_nblocks(region); npoints = H5Sget_select_elem_npoints(region); } H5E_END_TRY; h5dump_str_append(str, "{"); /* Print block information */ if (nblocks>0) { ptdata = malloc(nblocks*ndims*2*sizeof(ptdata[0])); H5Sget_select_hyper_blocklist(region, 0, nblocks, ptdata); for (i=0; idset_blockformat_pre, i?","OPTIONAL_LINE_BREAK" ":"", (unsigned long)i); /* Start coordinates and opposite corner */ for (j=0; j0) { ptdata = malloc(npoints*ndims*sizeof(ptdata[0])); H5Sget_select_elem_pointlist(region, 0, npoints, ptdata); for (i=0; idset_ptformat_pre , i?","OPTIONAL_LINE_BREAK" ":"", (unsigned long)i); for (j=0; jraw is non-zero * then data is printed in hexadecimal format. * *------------------------------------------------------------------------- */ static char * h5dump_sprint(h5dump_str_t *str/*in,out*/, const h5dump_t *info, hid_t container, hid_t type, void *vp, h5dump_context_t *ctx) { size_t i, n, offset, size, dims[H5S_MAX_RANK], nelmts, start; char *name, quote='\0'; hid_t memb, obj, region; int nmembs, x, j, k, ndims, otype; static char fmt_llong[8], fmt_ullong[8]; H5T_str_t pad; H5G_stat_t sb; /* Build default formats for long long types */ if (!fmt_llong[0]) { sprintf(fmt_llong, "%%%sd", PRINTF_LL_WIDTH); sprintf(fmt_ullong, "%%%su", PRINTF_LL_WIDTH); } /* Append value depending on data type */ start = h5dump_str_len(str); if (info->raw) { h5dump_str_append(str, "0x"); n = H5Tget_size(type); for (i=0; ifmt_raw, "%02x"), ((unsigned char*)vp)[i]); } } else if (H5Tequal(type, H5T_NATIVE_DOUBLE)) { h5dump_str_append(str, OPT(info->fmt_double, "%g"), *((double*)vp)); } else if (H5Tequal(type, H5T_NATIVE_FLOAT)) { h5dump_str_append(str, OPT(info->fmt_double, "%g"), *((float*)vp)); } else if (info->ascii && (H5Tequal(type, H5T_NATIVE_SCHAR) || H5Tequal(type, H5T_NATIVE_UCHAR))) { if (ESCAPE_HTML==info->str_locale) { if (*((char*)vp)<=' ' || *((char*)vp)>'~') { h5dump_str_append(str, "%%%02X", *((unsigned char*)vp)); } else { h5dump_str_append(str, "%c", *((char*)vp)); } } else { switch (*((char*)vp)) { case '"': h5dump_str_append(str, "\\\""); break; case '\\': h5dump_str_append(str, "\\\\"); break; case '\b': h5dump_str_append(str, "\\b"); break; case '\f': h5dump_str_append(str, "\\f"); break; case '\n': h5dump_str_append(str, "\\n"); break; case '\r': h5dump_str_append(str, "\\r"); break; case '\t': h5dump_str_append(str, "\\t"); break; default: if (isprint(*((char*)vp))) { h5dump_str_append(str, "%c", *((char*)vp)); } else { h5dump_str_append(str, "\\%03o", *((unsigned char*)vp)); } break; } } } else if (H5T_STRING==H5Tget_class(type)) { size = H5Tget_size(type); quote = '\0'; pad = H5Tget_strpad(type); for (i=0; istr_repeat>0) { while (i+jstr_repeat>0 && j>info->str_repeat) { if (quote) h5dump_str_append(str, "%c", quote); quote = '\''; h5dump_str_append(str, "%s%c", i?" ":"", quote); } else if (!quote) { quote = '"'; h5dump_str_append(str, "%s%c", i?" ":"", quote); } /* Print the character */ if (ESCAPE_HTML==info->str_locale) { if (((char*)vp)[i]<=' ' || ((char*)vp)[i]>'~') { h5dump_str_append(str, "%%%02X", ((unsigned char*)vp)[i]); } else { h5dump_str_append(str, "%c", ((char*)vp)[i]); } } else { switch (((char*)vp)[i]) { case '"': h5dump_str_append(str, "\\\""); break; case '\\': h5dump_str_append(str, "\\\\"); break; case '\b': h5dump_str_append(str, "\\b"); break; case '\f': h5dump_str_append(str, "\\f"); break; case '\n': h5dump_str_append(str, "\\n"); break; case '\r': h5dump_str_append(str, "\\r"); break; case '\t': h5dump_str_append(str, "\\t"); break; default: if (isprint(((char*)vp)[i])) { h5dump_str_append(str, "%c", ((char*)vp)[i]); } else { h5dump_str_append(str, "\\%03o", ((unsigned char*)vp)[i]); } break; } } /* Print the repeat count */ if (info->str_repeat && j>info->str_repeat) { #ifdef REPEAT_VERBOSE h5dump_str_append(str, "%c repeats %d times", quote, j-1); #else h5dump_str_append(str, "%c*%d", quote, j-1); #endif quote = '\0'; i += j-1; } } if (quote) h5dump_str_append(str, "%c", quote); if (0==i) { h5dump_str_append(str, "\"\""); /*empty string*/ } } else if (H5Tequal(type, H5T_NATIVE_INT)) { h5dump_str_append(str, OPT(info->fmt_int, "%d"), *((int*)vp)); } else if (H5Tequal(type, H5T_NATIVE_UINT)) { h5dump_str_append(str, OPT(info->fmt_uint, "%u"), *((unsigned*)vp)); } else if (H5Tequal(type, H5T_NATIVE_SCHAR)) { h5dump_str_append(str, OPT(info->fmt_schar, "%d"), *((signed char*)vp)); } else if (H5Tequal(type, H5T_NATIVE_UCHAR)) { h5dump_str_append(str, OPT(info->fmt_uchar, "%u"), *((unsigned char*)vp)); } else if (H5Tequal(type, H5T_NATIVE_SHORT)) { h5dump_str_append(str, OPT(info->fmt_short, "%d"), *((short*)vp)); } else if (H5Tequal(type, H5T_NATIVE_USHORT)) { h5dump_str_append(str, OPT(info->fmt_ushort, "%u"), *((unsigned short*)vp)); } else if (H5Tequal(type, H5T_NATIVE_LONG)) { h5dump_str_append(str, OPT(info->fmt_long, "%ld"), *((long*)vp)); } else if (H5Tequal(type, H5T_NATIVE_ULONG)) { h5dump_str_append(str, OPT(info->fmt_ulong, "%lu"), *((unsigned long*)vp)); } else if (H5Tequal(type, H5T_NATIVE_LLONG)) { h5dump_str_append(str, OPT(info->fmt_llong, fmt_llong), *((long_long*)vp)); } else if (H5Tequal(type, H5T_NATIVE_ULLONG)) { h5dump_str_append(str, OPT(info->fmt_ullong, fmt_ullong), *((unsigned long_long*)vp)); } else if (H5Tequal(type, H5T_NATIVE_HSSIZE)) { if (sizeof(hssize_t)==sizeof(int)) { h5dump_str_append(str, OPT(info->fmt_int, "%d"), *((int*)vp)); } else if (sizeof(hssize_t)==sizeof(long)) { h5dump_str_append(str, OPT(info->fmt_long, "%ld"), *((long*)vp)); } else { h5dump_str_append(str, OPT(info->fmt_llong, fmt_llong), *((int64_t*)vp)); } } else if (H5Tequal(type, H5T_NATIVE_HSIZE)) { if (sizeof(hsize_t)==sizeof(int)) { h5dump_str_append(str, OPT(info->fmt_uint, "%u"), *((unsigned*)vp)); } else if (sizeof(hsize_t)==sizeof(long)) { h5dump_str_append(str, OPT(info->fmt_ulong, "%lu"), *((unsigned long*)vp)); } else { h5dump_str_append(str, OPT(info->fmt_ullong, fmt_ullong), *((uint64_t*)vp)); } } else if (H5T_COMPOUND==H5Tget_class(type)) { nmembs = H5Tget_nmembers(type); h5dump_str_append(str, "%s", OPT(info->cmpd_pre, "{")); for (j=0; jcmpd_sep, ", " OPTIONAL_LINE_BREAK)); /*put code to indent compound type elemnts here*/ if (ctx->indent_level >= 0) { h5dump_str_append(str, "%s", OPT(info->line_pre, "")); } for (x=0; x < ctx->indent_level + 1; x++){ h5dump_str_append(str,"%s",OPT(info->line_indent,"")); } /* The name */ name = H5Tget_member_name(type, j); h5dump_str_append(str, OPT(info->cmpd_name, ""), name); free(name); /* The value */ offset = H5Tget_member_offset(type, j); memb = H5Tget_member_type(type, j); size = H5Tget_size(memb); ndims = H5Tget_member_dims(type, j, dims, NULL); assert(ndims>=0 && ndims<=H5S_MAX_RANK); for (k=0, nelmts=1; k1) { h5dump_str_append(str, "%s", OPT(info->arr_pre, "[")); } for (i=0; iarr_sep, "," OPTIONAL_LINE_BREAK)); } if ((ndims > 0) &&(info->arr_linebreak) && i && (i%dims[ndims-1] == 0)) { h5dump_str_append(str, "%s", "\n"); /*need to indent some more here*/ if (ctx->indent_level >= 0) { h5dump_str_append(str, "%s", OPT(info->line_pre, "")); } for (x=0; x < ctx->indent_level+1; x++){ h5dump_str_append(str,"%s",OPT(info->line_indent,"")); } } h5dump_sprint(str, info, container, memb, (char*)vp+offset+i*size, ctx); } if (nelmts>1) { h5dump_str_append(str, "%s", OPT(info->arr_suf, "]")); } H5Tclose(memb); } h5dump_str_append(str, "%s", OPT(info->cmpd_end, "")); /*put code to indent compound type elemnts here*/ if (ctx->indent_level >= 0) { h5dump_str_append(str, "%s", OPT(info->line_pre, "")); } for (x=0; x < ctx->indent_level; x++){ h5dump_str_append(str,"%s",OPT(info->line_indent,"")); } h5dump_str_append(str, "%s", OPT(info->cmpd_suf, "}")); } else if (H5T_ENUM==H5Tget_class(type)) { char enum_name[1024]; if (H5Tenum_nameof(type, vp, enum_name, sizeof enum_name)>=0) { h5dump_str_append(str, h5dump_escape(enum_name, sizeof enum_name, TRUE)); } else { h5dump_str_append(str, "0x"); n = H5Tget_size(type); for (i=0; idset_hidefileno){ h5dump_str_append(str, info->dset_format, sb.objno[1], sb.objno[0]); } else { h5dump_str_append(str, info->dset_format, sb.fileno[1], sb.fileno[0], sb.objno[1], sb.objno[0]); } h5dump_region(region, str, info); H5Sclose(region); H5Dclose(obj); } } else if (H5Tequal(type, H5T_STD_REF_OBJ)) { /* * Object references -- show the type and OID of the referenced * object. */ if (h5dump_is_zero(vp, H5Tget_size(type))) { h5dump_str_append(str, "NULL"); } else { otype = H5Rget_object_type(container, vp); obj = H5Rdereference(container, H5R_OBJECT, vp); H5Gget_objinfo(obj, ".", FALSE, &sb); /* Print object type and close object */ switch (otype) { case H5G_GROUP: h5dump_str_append(str, GROUPNAME); H5Gclose(obj); break; case H5G_DATASET: h5dump_str_append(str, DATASET); H5Dclose(obj); break; case H5G_TYPE: h5dump_str_append(str, DATATYPE); H5Tclose(obj); break; default: h5dump_str_append(str, "%u-", otype); break; } /* Print OID */ if (info->obj_hidefileno){ h5dump_str_append(str, info->obj_format, sb.objno[1], sb.objno[0]); } else { h5dump_str_append(str, info->obj_format, sb.fileno[1], sb.fileno[0], sb.objno[1], sb.objno[0]); } } } else { /* All other types get printed as hexadecimal */ h5dump_str_append(str, "0x"); n = H5Tget_size(type); for (i=0; ielmt_fmt, "%s")); } /*------------------------------------------------------------------------- * Function: h5dump_ncols * * Purpose: Count the number of columns in a string. This is the number * of characters in the string not counting line-control * characters. * * Return: Success: Width of string. * * Failure: 0 * * Programmer: Robb Matzke * Tuesday, April 27, 1999 * * Modifications: * *------------------------------------------------------------------------- */ static size_t h5dump_ncols(const char *s) { size_t i; for (i=0; *s; s++) if (*s>=' ') i++; return i; } /*------------------------------------------------------------------------- * Function: h5dump_simple_prefix * * Purpose: If ctx->need_prefix is set then terminate the current line * (if applicable), calculate the prefix string, and display it * at the start of a line. * * Return: void * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * Robb Matzke, 1999-09-29 * If a new prefix is printed then the current element number is * set back to zero. *------------------------------------------------------------------------- */ static void h5dump_simple_prefix(FILE *stream, const h5dump_t *info, h5dump_context_t *ctx, hsize_t elmtno, int secnum) { h5dump_str_t prefix; int i, templength = 0; int indentlevel = 0; memset(&prefix, 0, sizeof(h5dump_str_t)); if (!ctx->need_prefix) return; /* Terminate previous line, if any */ if (ctx->cur_column) { fputs(OPT(info->line_suf, ""), stream); /*if (info->line_ncols != ctx->cur_column) { putc('\n', stream); }*/ putc('\n',stream); fputs(OPT(info->line_sep, ""), stream); } /* Calculate new prefix */ h5dump_prefix(&prefix, info, elmtno, ctx->ndims, ctx->p_min_idx, ctx->p_max_idx); /* Write new prefix to output */ if (ctx->indent_level >= 0) { if (0==elmtno && 0==secnum && info->line_1st) { fputs(h5dump_str_fmt(&prefix, 0, info->line_1st), stream); } else if (secnum && info->line_cont) { fputs(h5dump_str_fmt(&prefix, 0, info->line_cont), stream); } else { fputs(h5dump_str_fmt(&prefix, 0, info->line_pre), stream); } templength = h5dump_str_len(&prefix); indentlevel = ctx->indent_level; } else { indentlevel = 2; /*this is because sometimes we dont print out all the header info for the data(like the tattr-2.ddl example. if that happens the ctx->indent_level a negative so we need to skip the above and just print out 2 indent levels. maybe the 2 should be a value of the ctx struct?? */ } for (i = 0; i < indentlevel; i++){ fputs(h5dump_str_fmt(&prefix, 0, info->line_indent), stream); templength += h5dump_str_len(&prefix); } ctx->cur_column = ctx->prev_prefix_len = templength; ctx->cur_elmt = 0; ctx->need_prefix = 0; /* Free string */ h5dump_str_close(&prefix); } /*------------------------------------------------------------------------- * Function: h5dump_simple_data * * Purpose: Prints some (NELMTS) data elements to output STREAM. The * elements are stored in _MEM as type TYPE and are printed * according to the format described in INFO. The CTX struct * contains context information shared between calls to this * function. The FLAGS is a bit field that indicates whether * the data supplied in this call falls at the beginning or end * of the total data to be printed (START_OF_DATA and * END_OF_DATA). * * Return: void * * Programmer: Robb Matzke * Monday, April 26, 1999 * * Modifications: * Robb Matzke, 1999-06-04 * The `container' argument is the optional dataset for * reference types. * * Robb Matzke, 1999-09-29 * Understands the `per_line' property which indicates that * every Nth element should begin a new line. * *------------------------------------------------------------------------- */ static void h5dump_simple_data(FILE *stream, const h5dump_t *info, hid_t container, h5dump_context_t *ctx/*in,out*/, unsigned flags, hsize_t nelmts, hid_t type, void *_mem) { unsigned char *mem = (unsigned char*)_mem; hsize_t i; /*element counter */ char *s, *section; /*a section of output */ int secnum; /*section sequence number */ size_t size; /*size of each datum */ size_t ncols=80; /*available output width */ h5dump_str_t buffer; /*string into which to render */ int multiline; /*datum was multiline */ int elmt_counter = 0; /*counts the # elements printed. I needed something that isnt going to get reset when a new line is formed. i'm going to use this var to count elements and break after we see a number equal to the ctx->size_last_dim*/ /* Setup */ memset(&buffer, 0, sizeof(h5dump_str_t)); size = H5Tget_size(type); if (info->line_ncols>0) ncols = info->line_ncols; h5dump_simple_prefix(stream, info, ctx, 0, 0); for (i=0; icur_elmt++, elmt_counter++){ /* Render the element */ h5dump_str_reset(&buffer); h5dump_sprint(&buffer, info, container, type, mem+i*size, ctx); if (i+1elmt_suf1, ",")); } s = h5dump_str_fmt(&buffer, 0, "%s"); /* * If the element would split on multiple lines if printed at our * current location... */ if (1==info->line_multi_new && (ctx->cur_column + h5dump_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(OPT(info->line_suf, ""))) > ncols) { if (ctx->prev_multiline) { /* * ... and the previous element also occupied more than one * line, then start this element at the beginning of a line. */ ctx->need_prefix = TRUE; } else if ((ctx->prev_prefix_len + h5dump_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(OPT(info->line_suf, ""))) <= ncols) { /* * ...but *could* fit on one line otherwise, then we * should end the current line and start this element on its * own line. */ ctx->need_prefix = TRUE; } } /*we need to break after each row of a dimension---> we should break at the end of the each last dimension well that is the way the dumper did it before*/ if (info->arr_linebreak && ctx->cur_elmt){ if ((ctx->cur_elmt%ctx->size_last_dim) == 0){ ctx->need_prefix = TRUE; } if (elmt_counter==ctx->size_last_dim){ ctx->need_prefix = TRUE; elmt_counter = 0; } } /* * If the previous element occupied multiple lines and this element * is too long to fit on a line then start this element at the * beginning of the line. */ if (1==info->line_multi_new && ctx->prev_multiline && (ctx->cur_column + h5dump_ncols(s) + strlen(OPT(info->elmt_suf2, " ")) + strlen(OPT(info->line_suf, ""))) > ncols) { ctx->need_prefix = TRUE; } /* * If too many elements have already been printed then we need to * start a new line. */ if (info->line_per_line>0 && ctx->cur_elmt>=info->line_per_line) { ctx->need_prefix = TRUE; } /* * Each OPTIONAL_LINE_BREAK embedded in the rendered string can cause * the data to split across multiple lines. We display the sections * one-at a time. */ for (secnum=0, multiline=0; (section=strtok(secnum?NULL:s, OPTIONAL_LINE_BREAK)); secnum++) { /* * If the current section plus possible suffix and end-of-line * information would cause the output to wrap then we need to * start a new line. */ /*added the info->skip_first because the dumper does not want this check to happen for the first line */ if ((!(info->skip_first && i == 0)) && (ctx->cur_column + strlen(section) + strlen(OPT(info->elmt_suf2, " ")) + strlen(OPT(info->line_suf, ""))) > ncols) { ctx->need_prefix = 1; } /* * Print the prefix or separate the beginning of this element * from the previous element. */ if (ctx->need_prefix) { if (secnum) multiline++; h5dump_simple_prefix(stream, info, ctx, i, secnum); } else if ((i || ctx->continuation) && 0==secnum) { fputs(OPT(info->elmt_suf2, " "), stream); ctx->cur_column += strlen(OPT(info->elmt_suf2, " ")); } /* Print the section */ fputs(section, stream); ctx->cur_column += strlen(section); } ctx->prev_multiline = multiline; } h5dump_str_close(&buffer); } /*------------------------------------------------------------------------- * Function: h5dump_simple_dset * * Purpose: Print some values from a dataset with a simple data space. * This is a special case of h5dump_dset(). This function only * intended for dumping datasets -- it does strip mining and * some other things which are unnecessary for smaller objects * such as attributes (to print small objects like attributes * simply read the attribute and call h5dump_simple_mem()). * * Return: Success: 0 * * Failure: -1 * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static int h5dump_simple_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t p_type, int indentlevel) { hid_t f_space; /*file data space */ hsize_t elmtno, i; /*counters */ int carry; /*counter carry value */ hssize_t zero[8]; /*vector of zeros */ unsigned flags; /*buffer extent flags */ hsize_t total_size[H5S_MAX_RANK];/*total size of dataset*/ /* Print info */ h5dump_context_t ctx; /*print context */ size_t p_type_nbytes; /*size of memory type */ hsize_t p_nelmts; /*total selected elmts */ /* Stripmine info */ hsize_t sm_size[H5S_MAX_RANK]; /*stripmine size */ hsize_t sm_nbytes; /*bytes per stripmine */ 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 */ hsize_t hs_nelmts; /*elements in request */ hsize_t dim_n_size; /* * Check that everything looks okay. The dimensionality must not be too * great and the dimensionality of the items selected for printing must * match the dimensionality of the dataset. */ memset(&ctx, 0, sizeof ctx); ctx.indent_level = indentlevel; ctx.need_prefix = 1; f_space = H5Dget_space(dset); ctx.ndims = H5Sget_simple_extent_ndims(f_space); if ((size_t)(ctx.ndims)>NELMTS(sm_size)) return -1; /* Assume entire data space to be printed */ for (i=0; i<(hsize_t)(ctx.ndims); i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(f_space, total_size, NULL); for (i=0, p_nelmts=1; i<(hsize_t)(ctx.ndims); i++) { p_nelmts *= total_size[i]; } if (0==p_nelmts) return 0; /*nothing to print*/ ctx.size_last_dim = total_size[ctx.ndims-1]; /* * Determine the strip mine size and allocate a buffer. The strip mine is * a hyperslab whose size is manageable. */ p_type_nbytes = H5Tget_size(p_type); for (i=ctx.ndims, sm_nbytes=p_type_nbytes; i>0; --i) { sm_size[i-1] = MIN (total_size[i-1], H5DUMP_BUFSIZE/sm_nbytes); sm_nbytes *= sm_size[i-1]; assert(sm_nbytes>0); } sm_buf = malloc(sm_nbytes); sm_nelmts = sm_nbytes/p_type_nbytes; sm_space = H5Screate_simple(1, &sm_nelmts, NULL); /* The stripmine loop */ memset(hs_offset, 0, sizeof hs_offset); memset(zero, 0, sizeof zero); for (elmtno=0; elmtno0) { for (i=0, hs_nelmts=1; i<(hsize_t)(ctx.ndims); i++) { hs_size[i] = MIN(total_size[i]-hs_offset[i], sm_size[i]); ctx.p_max_idx[i] = ctx.p_min_idx[i] + hs_size[i]; hs_nelmts *= hs_size[i]; } H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL); H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL); dim_n_size = total_size[ctx.ndims-1]; } else { H5Sselect_all(f_space); H5Sselect_all(sm_space); hs_nelmts = 1; dim_n_size = 1; } /* Read the data */ if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf)<0) { return -1; } /* Print the data */ flags = ((0==elmtno ? START_OF_DATA : 0) | (elmtno+hs_nelmts>=p_nelmts ? END_OF_DATA : 0)); h5dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts, p_type, sm_buf); /* if (programtype == UNKNOWN){ return FAIL; } else if (programtype == H5LS){ h5dump_simple_data(stream, info, dset, &ctx, flags, hs_nelmts, p_type, sm_buf); } else if (programtype == H5DUMP){ switch (H5Tget_class(p_type)) { case H5T_INTEGER: display_numeric_data (hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno, dset); break; case H5T_FLOAT: display_numeric_data (hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno, dset); break; case H5T_TIME: break; case H5T_STRING: display_string (hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno); break; case H5T_BITFIELD: break; case H5T_OPAQUE: break; case H5T_COMPOUND: compound_data = 1; display_compound_data (hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, elmtno); compound_data = 0; break; case H5T_REFERENCE: display_numeric_data(hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno, dset); break; #if 0 display_reference_data(hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno, dset); #endif case H5T_ENUM: display_numeric_data(hs_nelmts, p_type, sm_buf, p_type_nbytes, p_nelmts, dim_n_size, elmtno, dset); break; default: break; } } */ /* Calculate the next hyperslab offset */ for (i=ctx.ndims, carry=1; i>0 && carry; --i) { ctx.p_min_idx[i-1] = ctx.p_max_idx[i-1]; hs_offset[i-1] += hs_size[i-1]; if (hs_offset[i-1]==(hssize_t)(total_size[i-1])) { hs_offset[i-1] = 0; } else { carry = 0; } } ctx.continuation++; } /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } H5Sclose(sm_space); H5Sclose(f_space); if (sm_buf) free(sm_buf); return 0; } /*------------------------------------------------------------------------- * Function: h5dump_simple_mem * * Purpose: Print some values from memory with a simple data space. * This is a special case of h5dump_mem(). * * Return: Success: 0 * * Failure: -1 * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * *------------------------------------------------------------------------- */ static int h5dump_simple_mem(FILE *stream, const h5dump_t *info, hid_t type, hid_t space, void *mem, int indentlevel) { hsize_t i; /*counters */ hsize_t nelmts; /*total selected elmts */ h5dump_context_t ctx; /*printing context */ /* * Check that everything looks okay. The dimensionality must not be too * great and the dimensionality of the items selected for printing must * match the dimensionality of the dataset. */ memset(&ctx, 0, sizeof ctx); ctx.indent_level = indentlevel; ctx.need_prefix = 1; ctx.ndims = H5Sget_simple_extent_ndims(space); if ((size_t)(ctx.ndims)>NELMTS(ctx.p_min_idx)) return -1; /* Assume entire data space to be printed */ for (i=0; i<(hsize_t)(ctx.ndims); i++) ctx.p_min_idx[i] = 0; H5Sget_simple_extent_dims(space, ctx.p_max_idx, NULL); for (i=0, nelmts=1; i<(hsize_t)(ctx.ndims); i++) { nelmts *= ctx.p_max_idx[i] - ctx.p_min_idx[i]; } if (0==nelmts) return 0; /*nothing to print*/ ctx.size_last_dim = ctx.p_max_idx[ctx.ndims-1]; ctx.indent_level = indentlevel; /* Print it */ h5dump_simple_data(stream, info, -1/*no dataset*/, &ctx, START_OF_DATA|END_OF_DATA, nelmts, type, mem); /* Terminate the output */ if (ctx.cur_column) { fputs(OPT(info->line_suf, ""), stream); putc('\n', stream); fputs(OPT(info->line_sep, ""), stream); } return 0; } /*------------------------------------------------------------------------- * Function: h5dump_fixtype * * Purpose: Given a file data type choose a memory data type which is * appropriate for printing the data. * * Return: Success: Memory data type * * Failure: FAIL * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * Robb Matzke, 1999-06-04 * Added support for references. * *------------------------------------------------------------------------- */ hid_t h5dump_fixtype(hid_t f_type) { hid_t m_type = FAIL, f_memb; hid_t *memb = NULL; char **name = NULL; int nmembs = 0, i, j, *ndims = NULL; size_t size, offset, *dims = NULL, nelmts; H5T_str_t strpad; size = H5Tget_size(f_type); switch (H5Tget_class(f_type)) { case H5T_INTEGER: /* * Use the smallest native integer type of the same sign as the file * such that the memory type is at least as large as the file type. * If there is no memory type large enough then use the largest * memory type available. */ if (size<=sizeof(char)) { m_type = H5Tcopy(H5T_NATIVE_SCHAR); } else if (size<=sizeof(short)) { m_type = H5Tcopy(H5T_NATIVE_SHORT); } else if (size<=sizeof(int)) { m_type = H5Tcopy(H5T_NATIVE_INT); } else if (size<=sizeof(long)) { m_type = H5Tcopy(H5T_NATIVE_LONG); } else { m_type = H5Tcopy(H5T_NATIVE_LLONG); } H5Tset_sign(m_type, H5Tget_sign(f_type)); break; case H5T_FLOAT: /* * Use the smallest native floating point type available such that * its size is at least as large as the file type. If there is not * native type large enough then use the largest native type. */ if (size<=sizeof(float)) { m_type = H5Tcopy(H5T_NATIVE_FLOAT); } else if (size<=sizeof(double)) { m_type = H5Tcopy(H5T_NATIVE_DOUBLE); } else { m_type = H5Tcopy(H5T_NATIVE_LDOUBLE); } break; case H5T_STRING: /* * This is needed because the function in dumputil.c is the case where * 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); break; case H5T_COMPOUND: /* * We have to do this in two steps. The first step scans the file * type and converts the members to native types and remembers all * their names and sizes, computing the size of the memory compound * type at the same time. Then we create the memory compound type * and add the members. */ nmembs = H5Tget_nmembers(f_type); memb = calloc(nmembs, sizeof(hid_t)); name = calloc(nmembs, sizeof(char*)); ndims = calloc(nmembs, sizeof(int)); dims = calloc(nmembs*4, sizeof(size_t)); for (i=0, size=0; i=0 && ndims[i]<=4); for (j=0, nelmts=1; j=0) H5Tclose(memb[i]); if (name[i]) free(name[i]); } free(memb); free(name); free(ndims); free(dims); } return m_type; } /*------------------------------------------------------------------------- * Function: h5dump_dset * * Purpose: Print some values from a dataset DSET to the file STREAM * after converting all types to P_TYPE (which should be a * native type). If P_TYPE is a negative value then it will be * computed from the dataset type using only native types. * * Note: This function is intended only for datasets since it does * some things like strip mining which are unnecessary for * smaller objects such as attributes. The easiest way to print * small objects is to read the object into memory and call * h5dump_mem(). * * Return: Success: 0 * * Failure: -1 * * Programmer: Robb Matzke * Thursday, July 23, 1998 * * Modifications: * Robb Matzke, 1999-06-07 * If info->raw is set then the memory datatype will be the same * as the file datatype. * *------------------------------------------------------------------------- */ int h5dump_dset(FILE *stream, const h5dump_t *info, hid_t dset, hid_t _p_type, int indentlevel) { hid_t f_space; hid_t p_type = _p_type; hid_t f_type; int status; h5dump_t info_dflt; /* Use default values */ if (!stream) stream = stdout; if (!info) { memset(&info_dflt, 0, sizeof info_dflt); info = &info_dflt; } if (p_type<0) { f_type = H5Dget_type(dset); if (info->raw) { p_type = H5Tcopy(f_type); } else { p_type = h5dump_fixtype(f_type); } H5Tclose(f_type); if (p_type<0) return -1; } /* Check the data space */ f_space = H5Dget_space(dset); if (H5Sis_simple(f_space)<=0) return -1; H5Sclose(f_space); /* Print the data */ status = h5dump_simple_dset(stream, info, dset, p_type, indentlevel); if (p_type!=_p_type) H5Tclose(p_type); return status; } /*------------------------------------------------------------------------- * Function: h5dump_mem * * Purpose: Displays the data contained in MEM. MEM must have the * specified data TYPE and SPACE. Currently only simple data * spaces are allowed and only the `all' selection. * * Return: Success: 0 * * Failure: -1 * * Programmer: Robb Matzke * Wednesday, January 20, 1999 * * Modifications: * *------------------------------------------------------------------------- */ int h5dump_mem(FILE *stream, const h5dump_t *info, hid_t type, hid_t space, void *mem,int indentlevel) { h5dump_t info_dflt; /* Use default values */ if (!stream) stream = stdout; if (!info) { memset(&info_dflt, 0, sizeof info_dflt); info = &info_dflt; } /* Check the data space */ if (H5Sis_simple(space)<=0) return -1; return h5dump_simple_mem(stream, info, type, space, mem, indentlevel); } /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*from h5dumputil.c*/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*************************************************************************/ /*------------------------------------------------------------------------- * Function: display_numeric_data * * Purpose: Display numeric data in ddl format. * * Return: void * * Comment: hs_nelmts number of elements to be printed * p_type memory data type * sm_buf data buffer * p_type_nbytes size of p_type * p_nelmts total number of elements * dim_n_size size of dimemsion n * elmtno element index * *------------------------------------------------------------------------- */ static void display_numeric_data (hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t dim_n_size, hsize_t elmtno, hid_t container) { hsize_t i; /*char p_buf[256]; */ char* out_buf = malloc(sizeof(char) * nCols); struct h5dump_str_t tempstr; hsize_t x; hbool_t isref = FALSE; hsize_t totalspace; hbool_t done; int temp; /******************************************************************************************/ h5dump_t info; /* Set to all default values and then override */ memset(&info, 0, sizeof info); info.idx_fmt = "(%s)"; info.line_ncols = nCols; info.line_multi_new = 1; /* * If a compound datatype is split across multiple lines then add an * ellipsis to the beginning of the continuation line. */ info.line_pre = " %s "; info.line_cont = " %s "; /*********************************************************************************************/ /* i added this too*/ if (H5Tequal(p_type, H5T_STD_REF_DSETREG)) { isref = TRUE; } out_buf[0] = '\0'; if ((indent+COL) > nCols) indent = 0; memset(&tempstr, 0, sizeof(h5dump_str_t)); for (i=0; i (nCols-indent-COL)) { if (isref){ /* i added this */ temp = (int)strlen(out_buf); if ((strlen(out_buf) + 7) < (totalspace)){ /* 7 for the word dataset */ memcpy(out_buf+strlen(out_buf), tempstr.s, totalspace - strlen(out_buf)); out_buf[totalspace] = '\0'; memmove(tempstr.s, tempstr.s+(totalspace - temp), tempstr.len - (totalspace - temp)); tempstr.s[tempstr.len - totalspace + temp] = '\0'; tempstr.len = strlen(tempstr.s); } } /* first row of member */ if (compound_data && (elmtno+i+1) == dim_n_size) printf("%s\n", out_buf); else { indentation(indent+COL); printf("%s\n", out_buf); } strcpy(out_buf, tempstr.s); /* i added this too*/ if (isref) { done = FALSE; while (!done) { if (tempstr.len > totalspace) { /* keep printing until we can fit in the totalspace */ memmove(out_buf,tempstr.s, totalspace); out_buf[totalspace] = '\0'; memmove(tempstr.s,tempstr.s+totalspace, strlen(tempstr.s + totalspace)); tempstr.s[tempstr.len - totalspace] = '\0'; tempstr.len = strlen(tempstr.s); indentation(indent+COL); printf(out_buf); } else { strcpy(out_buf, tempstr.s); done = TRUE; } } } if ((elmtno+i+1) % dim_n_size) strcat(out_buf, ", "); else { /* end of a row, flush out_buf */ indentation(indent+COL); printf("%s", out_buf); if ((elmtno+i+1) != p_nelmts) /* not last element */ printf(",\n"); else if (compound_data) { /* last element of member data*/ if ((nCols-strlen(out_buf)-indent-COL) < 2) { /* 2 for space and ] */ printf("\n"); indentation(indent+COL-3); } } else printf("\n"); /* last row */ *out_buf = '\0'; } } else { strcat(out_buf, tempstr.s); if ((elmtno+i+1) % dim_n_size) { if ((nCols-strlen(out_buf)-indent-COL-1) > 0) strcat(out_buf, ", "); else strcat(out_buf, ","); } else { /* end of a row */ /* 1st row of member data */ if (compound_data && (elmtno+i+1) == dim_n_size) printf("%s", out_buf); else { indentation(indent+COL); printf("%s", out_buf); } /* if it's the last element */ if ((elmtno+i+1) != p_nelmts) printf(",\n"); else if (compound_data) { /* last row of member data*/ /* 2 for space and ] */ if ((nCols-strlen(out_buf)-indent-COL) < 2) { printf("\n"); indentation(indent+COL-3); } } else printf("\n"); /* last row */ *out_buf = '\0'; } } } #if !defined (WIN32) && !defined (_DEBUG) free(out_buf); #endif } /*------------------------------------------------------------------------- * Function: display_string * * Purpose: Display string in ddl format * * Return: void * * Comment: concatenator operator : '//' * separator between elements: ',' * * Modifications: * *------------------------------------------------------------------------- */ static void display_string (hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t dim_n_size, hsize_t elmtno) { hsize_t i, row_size=0; int j, m, x, y, first_row=1; int free_space, long_string = 0; char* out_buf = malloc(sizeof(char) * nCols); struct h5dump_str_t tempstr; int temp; /******************************************************************************************/ h5dump_t info; /* Set to all default values and then override */ memset(&info, 0, sizeof info); info.idx_fmt = "(%s)"; info.line_ncols = nCols; info.line_multi_new = 1; /* * If a compound datatype is split across multiple lines then add an * ellipsis to the beginning of the continuation line. */ info.line_pre = " %s "; info.line_cont = " %s "; /*********************************************************************************************/ out_buf[0] = '\0'; memset(&tempstr, 0, sizeof(h5dump_str_t)); h5dump_str_reset(&tempstr); for (i=0; i free_space) long_string = 1; } else /* 3 for double quotes and one comma */ if (((int)tempstr.len + 3) > free_space) long_string = 1; if (long_string) { if (free_space < 5) { /* 5 for double quotes, one space and two '/'s */ /* flush out_buf */ if (compound_data && first_row) { printf("%s\n", out_buf); first_row = 0; } else { indentation(indent+COL); printf("%s\n", out_buf); } out_buf[0] = '\0'; x = 0 ; } else { x = free_space - 5; if (compound_data && first_row) { printf("%s\"", out_buf); strncpy(out_buf, tempstr.s, x); out_buf[x] = '\0'; printf("%s\" %s\n", out_buf,CONCATENATOR); first_row = 0; out_buf[0] = '\0'; } else { indentation(indent+COL); printf("%s\"", out_buf); memset(out_buf, '\0', nCols); temp = copy_atomic_char(out_buf,tempstr.s,(int)tempstr.len,x); out_buf[x] = '\0'; printf("%s\" %s\n",out_buf,CONCATENATOR); x = temp; } } y = nCols - indent -COL - 5; m = (int)((tempstr.len - x)/y); for (j = 0; j < m - 1 ; j++) { indentation(indent+COL); strncpy(out_buf, tempstr.s+x+j*y, y); out_buf[y] = '\0'; printf("\"%s\" %s\n", out_buf,CONCATENATOR); } if ((elmtno+i+1) == p_nelmts) { /* last element */ if ((int)strlen(tempstr.s+x+j*y) > (nCols - indent - COL -2)) { /* 2 for double quotes */ indentation(indent+COL); strncpy(out_buf, tempstr.s+x+j*y, y); out_buf[y] = '\0'; printf("\"%s\" %s\n", out_buf, CONCATENATOR); indentation(indent+COL); printf("\"%s\"", tempstr.s+x+m*y); if (compound_data) { if ((nCols-strlen(out_buf)-indent-COL) < 2) { printf("\n"); indentation(indent+COL-3); } } else printf("\n"); } else { indentation(indent+COL); printf("\"%s\"", tempstr.s+x+j*y); if (compound_data) { if ((nCols-strlen(out_buf)-indent-COL) < 2) { printf("\n"); indentation(indent+COL-3); } } else printf("\n"); } out_buf[0] = '\0'; } else if ( row_size == dim_n_size) { if ((int)strlen(tempstr.s+x+j*y) > (nCols - indent - COL -3)) { /* 3 for 2 "'s and 1 , */ indentation(indent+COL); strncpy(out_buf, tempstr.s+x+j*y, y); out_buf[y] = '\0'; printf("\"%s\" %s\n", out_buf, CONCATENATOR); indentation(indent+COL); printf("\"%s\",\n", tempstr.s+x+m*y); } else { indentation(indent+COL); printf("\"%s\",\n", tempstr.s+x+j*y); } out_buf[0] = '\0'; row_size = 0; } else { if ((int)strlen(tempstr.s+x+j*y) > (nCols - indent - COL -3)) { /* 3 for 2 "'s and 1 , */ indentation(indent+COL); strncpy(out_buf, tempstr.s+x+j*y, y); out_buf[y] = '\0'; printf("\"%s\" %s\n", out_buf, CONCATENATOR); strcpy(out_buf, "\""); strcat(out_buf, tempstr.s+x+m*y); strcat(out_buf, "\","); if ((int)strlen(out_buf) < (nCols-indent-COL)) strcat(out_buf, " "); } else { strcpy(out_buf, "\""); strcat (out_buf, tempstr.s+x+j*y); strcat(out_buf, "\","); if ((int)strlen(out_buf) < (nCols-indent-COL)) strcat(out_buf, " "); } } long_string = 0; } else { /* flush out_buf if it's end of a row */ if (row_size == dim_n_size) { if (compound_data && (elmtno+i+1) == dim_n_size) { /* 1st row */ printf("%s\"%s\"", out_buf, tempstr.s); first_row = 0; } else { indentation(indent+COL); printf("%s\"%s\"", out_buf, tempstr.s); } if ((elmtno+i+1) != p_nelmts) printf(",\n"); else if (compound_data) { if ((nCols-strlen(out_buf)-tempstr.len-indent-COL) < 2) { /* 2 for space and ] */ printf("\n"); indentation(indent+COL-3); } } else printf("\n"); out_buf[0] = '\0'; row_size = 0; } else { strcat(out_buf, "\""); strcat(out_buf, tempstr.s); strcat(out_buf, "\","); if ((int)strlen(out_buf) < (nCols-indent-COL)) strcat(out_buf, " "); } } } free(out_buf); } /*------------------------------------------------------------------------- * Function: display_compound_data * * Purpose: Display compound data in ddl format * * Return: void * * Modifications: * *------------------------------------------------------------------------- */ static void display_compound_data (hsize_t hs_nelmts, hid_t p_type, unsigned char *sm_buf, size_t p_type_nbytes, hsize_t p_nelmts, hsize_t elmtno) { size_t offset, size, dims[4]; hsize_t nelmts, dim_n_size=0; hid_t memb; int nmembs, i, j, k, ndims, perm[4]; if ((indent+COL) > nCols) indent = 0; for (i=0; i<(int)hs_nelmts && (elmtno+i) < p_nelmts; i++) { nmembs = H5Tget_nmembers(p_type); indentation(indent+COL); printf("{\n"); indent+= COL; for (j=0; j 0) dim_n_size = dims[ndims-1]; else dim_n_size = 1; for (k=0, nelmts=1; k 1) { printf("[ "); } display_numeric_data (nelmts, memb, sm_buf+offset+i*p_type_nbytes, size, nelmts, dim_n_size, 0, -1) ; if (nelmts > 1) { printf(" ]"); } indent -= 2; break; case H5T_FLOAT: indentation(indent+COL); indent += 2; if (nelmts > 1) { printf("[ "); } display_numeric_data (nelmts, memb, sm_buf+offset+i*p_type_nbytes, size, nelmts, dim_n_size, 0, -1) ; if (nelmts > 1) { printf(" ]"); } indent -= 2; break; case H5T_TIME: break; case H5T_STRING: indentation(indent+COL); indent += 2; if (nelmts > 1) { printf("[ "); } display_string (nelmts, memb, sm_buf+offset+i*p_type_nbytes, size, nelmts, dim_n_size, 0 ) ; if (nelmts > 1) { printf(" ]"); } indent -= 2; break; case H5T_BITFIELD: break; case H5T_OPAQUE: break; case H5T_COMPOUND: display_compound_data (nelmts, memb, sm_buf+offset+i*p_type_nbytes, size, nelmts, 0); indentation(indent); break; default: break; } if ( j == nmembs-1) printf("\n"); else printf(",\n"); H5Tclose(memb); } indent-= COL; indentation(indent+COL); if ((elmtno+i+1) == p_nelmts) printf("}\n"); else printf("},\n"); } } /*------------------------------------------------------------------------- * Function: print_data * * Purpose: Print some values from a dataset or an attribute to the * file STREAM after converting all types to P_TYPE (which * should be a native type). If P_TYPE is a negative value * then it will be computed from the dataset/attribute type * using only native types. * * Return: Success: 0 * * Failure: -1 * * Modifications: * *------------------------------------------------------------------------- */ int print_data(hid_t oid, hid_t _p_type, int obj_data) { hid_t f_space; hid_t p_type = _p_type; hid_t f_type; int status = -1; if (p_type < 0) { if (obj_data == DATASET_DATA) f_type = H5Dget_type(oid); else f_type = H5Aget_type(oid); if (f_type < 0) return status; p_type = h5dump_fixtype(f_type); H5Tclose(f_type); if (p_type < 0) return status; } /* Check the data space */ if (obj_data == DATASET_DATA) f_space = H5Dget_space(oid); else f_space = H5Aget_space(oid); if (f_space < 0) return status; if (H5Sis_simple(f_space) >= 0) { if (obj_data == DATASET_DATA) { status = h5dump_simple_dset(NULL,NULL, oid,p_type,0); } else { /*attribute data*/ status = h5dump_attr(oid,p_type); } } H5Sclose(f_space); if (p_type != _p_type) H5Tclose(p_type); return status; } /*------------------------------------------------------------------------- * Function: indentation * * Purpose: Print spaces for indentation * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ void indentation(int x) { if(x < nCols) { while (x>0) { printf(" "); x--; } } else { printf("The indentation exceeds the number of cols. Exiting....\n"); exit(1); } } /*------------------------------------------------------------------------- * Function: copy_atomic_char * * Purpose: copies the atomic characters from 1 string to another * assumes there will be enough room in output for the input string * * Return: returns the number of actual characters copied * * Programmer: Patrick Lu * * Modifications: * *-----------------------------------------------------------------------*/ int copy_atomic_char(char* output, char* input, int numchar, int freespace){ int x = 0; while (freespace || (x == numchar)){ if (input[x] == '\\'){ if (freespace == 1){ break; } else { if ((input[x+1] == '"') || (input[x+1] == '\\') || (input[x+1] == 'b') || (input[x+1] == 'f') || (input[x+1] == 'n') || (input[x+1] == 'r') || (input[x+1] == 't')){ /*escape characters*/ strncat(output,input,2); x += 2; freespace = freespace - 2; } else { /* octal number */ if (freespace < 4){ break; } else { strncat(output,input,4); x += 4; freespace = freespace - 4; } } } } else { strncat(output,input+x,1); freespace = freespace - 1; x++; } } if (x == 0) x = FAIL; return(x); } /*------------------------------------------------------------------------- * Function: h5dump_attr * * Purpose: dumps an attribute * * Return: 0 = succeed or -1 for fail * * Programmer: Patrick Lu * * Modifications: * *-----------------------------------------------------------------------*/ int h5dump_attr(hid_t oid, hid_t p_type){ hid_t f_space; void *sm_buf; hid_t type; hsize_t size[64], nelmts = 1, dim_n_size; size_t p_type_nbytes, need; int ndims, i; int status = -1; f_space = H5Aget_space(oid); /* get the size of the attribute and allocate enough mem*/ type = H5Aget_type(oid); ndims = H5Sget_simple_extent_dims(f_space, size, NULL); if (ndims){ for (i = 0; i < ndims; i++){ nelmts *= size[i]; } dim_n_size = size[ndims - 1]; } else { dim_n_size = 1; } need = nelmts * MAX(H5Tget_size(type), H5Tget_size(p_type)); sm_buf = malloc(need); p_type_nbytes = H5Tget_size(p_type); /*read the attr*/ if (H5Aread(oid, p_type, sm_buf) < 0){ return (status); } status = 0; /*print it*/ switch (H5Tget_class(p_type)) { case H5T_INTEGER: display_numeric_data (nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0, oid); break; case H5T_FLOAT: display_numeric_data (nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0, oid); break; case H5T_TIME: break; case H5T_STRING: display_string (nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0); break; case H5T_BITFIELD: break; case H5T_OPAQUE: break; case H5T_COMPOUND: compound_data = 1; display_compound_data (nelmts, p_type, sm_buf, p_type_nbytes, nelmts, 0); compound_data = 0; break; case H5T_REFERENCE: display_numeric_data(nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0, oid); case H5T_ENUM: display_numeric_data(nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0, oid); /* display_reference_data(nelmts, p_type, sm_buf, p_type_nbytes, nelmts, dim_n_size, 0, oid);*/ break; default: break; } free(sm_buf); return (status); } /* Print the program name and the version information which is */ /* defined the same as the HDF5 library version. */ void print_version(char *program_name) { printf("%s: Version %u.%u.%u%s\n", program_name, H5_VERS_MAJOR, H5_VERS_MINOR, H5_VERS_RELEASE, H5_VERS_SUBRELEASE); } /* THE FUNCTIONS BELOW ARE FROM THE H5FINSHD.C FILE */ /*------------------------------------------------------------------------- * Function: init_table * * Purpose: allocate and initialize tables for shared groups, datasets, * and committed types * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ void init_table (table_t** temp){ int i; table_t *table = malloc(sizeof(table_t)); table->size = 20; table->nobjs = 0; table->objs = (obj_t*) malloc(table->size*sizeof(obj_t)); for (i = 0; i < table->size; i++) { table->objs[i].objno[0] = table->objs[i].objno[1] = 0; table->objs[i].displayed = 0; table->objs[i].recorded = 0; table->objs[i].objflag = 0; } *temp = table; } /*------------------------------------------------------------------------- * Function: init_prefix * * Purpose: allocate and initialize prefix * * Return: void * * Modifications: * *-----------------------------------------------------------------------*/ void init_prefix(char **prefix, int prefix_len){ char *temp; temp = (char *) malloc(prefix_len * sizeof (char)); *temp = '\0'; *prefix = temp; } /*------------------------------------------------------------------------- * Function: free_table * * Purpose: free tables for shared groups, datasets, * and committed types * * Return: void * * Programmer: Paul Harten * * Modifications: * *-----------------------------------------------------------------------*/ void free_table (table_t **table){ table_t *temp = *table; if (temp->objs != NULL) { HDfree(temp->objs); } *table = temp; } /*------------------------------------------------------------------------- * Function: search_obj * * Purpose: search the object specified by objno in the table * * Return: an integer, the location of the object * -1 if object is not found * * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ int search_obj (table_t *table, unsigned long *objno) { int i=0, found=0; while (i < table->nobjs && !found) if (table->objs[i].objno[0] == *(objno) && table->objs[i].objno[1] == *(objno+1) ) found = 1; else i++; if (!found) return -1; else return i; } /*------------------------------------------------------------------------- * Function: add_obj * * Purpose: add a shared object to the table * realloc the table if necessary * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ void add_obj (table_t *table, unsigned long *objno, char *objname) { int i; if (table->nobjs == table->size) { table->size *= 2; table->objs = realloc (table->objs, table->size*sizeof(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].recorded = 0; table->objs[i].objflag = 0; } } i = table->nobjs++; table->objs[i].objno[0] = *objno; table->objs[i].objno[1] = *(objno+1); strcpy (table->objs[i].objname, objname); } /*------------------------------------------------------------------------- * Function: Find_objs * * Purpose: Find objects, committed types and store them in tables * * Return: Success: SUCCEED * * Failure: FAIL * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ herr_t find_objs(hid_t group, const char *name, void *op_data) { hid_t obj, type; H5G_stat_t statbuf; char *tmp; int i; find_objs_t *info = (find_objs_t*)op_data; if (info->threshold > 1) { /*will get an infinite loop if greater than 1*/ return(FAIL); } H5Gget_objinfo(group, name, TRUE, &statbuf); tmp = (char *) malloc ((strlen(info->prefix)+strlen(name)+2) * sizeof(char)); strcpy(tmp, info->prefix); switch (statbuf.type) { case H5G_GROUP: if ((obj=H5Gopen (group, name))>=0) { if (info->prefix_len < (int)(strlen(info->prefix) + strlen(name) + 2)) { info->prefix_len *= 2; info->prefix = realloc (info->prefix, info->prefix_len * sizeof(char)); } strcat(strcat(info->prefix,"/"), name); if (statbuf.nlink > info->threshold) { if (search_obj (info->group_table, statbuf.objno) < 0) { add_obj (info->group_table, statbuf.objno, info->prefix); H5Giterate (obj, ".", NULL, find_objs, (void*)info); } } else H5Giterate (obj, ".", NULL, find_objs, (void*)info); strcpy(info->prefix, tmp); H5Gclose (obj); } else info->status = 1; break; case H5G_DATASET: strcat(tmp,"/"); strcat(tmp,name); /* absolute name of the data set */ if (statbuf.nlink > info->threshold && search_obj (info->dset_table, statbuf.objno) < 0) add_obj (info->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 (info->type_table, statbuf.objno) < 0) { add_obj (info->type_table, statbuf.objno, tmp) ; info->type_table->objs[info->type_table->nobjs - 1].objflag = 0; } } H5Tclose(type); H5Dclose (obj); } else info->status = 1; break; case H5G_TYPE: strcat(tmp,"/"); strcat(tmp,name); /* absolute name of the type */ i = search_obj (info->type_table, statbuf.objno); if (i < 0) { add_obj (info->type_table, statbuf.objno, tmp) ; info->type_table->objs[info->type_table->nobjs-1].recorded = 1; /* named data type */ info->type_table->objs[info->type_table->nobjs-1].objflag = 1; /* named data type */ } else { strcpy (info->type_table->objs[i].objname, tmp); info->type_table->objs[i].recorded = 1; info->type_table->objs[info->type_table->nobjs-1].objflag = 1; /* named data type */ } break; default: break; } free (tmp); return SUCCEED; } /*------------------------------------------------------------------------- * Function: dump_tables * * Purpose: display the contents of tables for debugging purposes * * Return: void * * Programmer: Ruey-Hsia Li * * Modifications: * *-----------------------------------------------------------------------*/ void dump_table(char* tablename, table_t *table) { int i; printf("%s: # of entries = %d\n", tablename,table->nobjs); for ( i = 0; i < table->nobjs; i++) printf ("%lu %lu %s %d\n", table->objs[i].objno[0], table->objs[i].objno[1], table->objs[i].objname, table->objs[i].objflag); } /*------------------------------------------------------------------------- * 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(table_t *table, unsigned long *objno) { int idx = -1; /* 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; } */ idx = search_obj(table, objno); 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(table_t *table, 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; } */ return(table->objs[idx].objflag); } /*------------------------------------------------------------------------- * 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(table_t *table, 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; } */ table->objs[idx].objflag = TRUE; return(SUCCEED); } /*------------------------------------------------------------------------- * 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(table_t* table, 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; } */ return(strdup(table->objs[idx].objname)); }