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-rw-r--r--tools/h5repack/h5repack_parse.c616
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diff --git a/tools/h5repack/h5repack_parse.c b/tools/h5repack/h5repack_parse.c
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-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- * Copyright by The HDF Group. *
- * Copyright by the Board of Trustees of the University of Illinois. *
- * All rights reserved. *
- * *
- * This file is part of HDF5. The full HDF5 copyright notice, including *
- * terms governing use, modification, and redistribution, is contained in *
- * the files COPYING and Copyright.html. COPYING can be found at the root *
- * of the source code distribution tree; Copyright.html can be found at the *
- * root level of an installed copy of the electronic HDF5 document set and *
- * is linked from the top-level documents page. It can also be found at *
- * http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
- * access to either file, you may request a copy from help@hdfgroup.org. *
- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-
-#include "h5repack.h"
-#include "h5tools.h"
-#include "h5tools_utils.h"
-
-/*-------------------------------------------------------------------------
- * Function: parse_filter
- *
- * Purpose: read filter information
- *
- * Return: a list of names, the number of names and its compression type
- *
- * <name of filter> can be:
- * GZIP, to apply the HDF5 GZIP filter (GZIP compression)
- * SZIP, to apply the HDF5 SZIP filter (SZIP compression)
- * SHUF, to apply the HDF5 shuffle filter
- * FLET, to apply the HDF5 checksum filter
- * NBIT, to apply the HDF5 NBIT filter (NBIT compression)
- * SOFF, to apply the HDF5 scale+offset filter (compression)
- * UD, to apply a User Defined filter k,m,n1[,…,nm]
- * NONE, to remove the filter
- *
- * Examples:
- * "GZIP=6"
- * "A,B:NONE"
- *-------------------------------------------------------------------------
- */
-obj_list_t* parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
- pack_opt_t *options, int *is_glb) {
- size_t i, m, u;
- char c;
- size_t len = HDstrlen(str);
- int k, l, p, q, end_obj = -1, no_param = 0;
- unsigned j, n;
- char sobj[MAX_NC_NAME];
- char scomp[10];
- char stype[6];
- char smask[3];
- obj_list_t* obj_list = NULL;
- unsigned pixels_per_block;
-
- /* initialize compression info */
- HDmemset(filt, 0, sizeof(filter_info_t));
- *is_glb = 0;
-
- /* check for the end of object list and number of objects */
- for (i = 0, n = 0; i < len; i++) {
- c = str[i];
- if (c == ':')
- end_obj = (int) i;
- if (c == ',')
- n++;
- }
-
- /* Check for missing : */
- if (end_obj == -1) {
- /* apply to all objects */
- options->all_filter = 1;
- *is_glb = 1;
- }
-
- n++;
- obj_list = (obj_list_t *) HDmalloc(n * sizeof(obj_list_t));
- if (obj_list == NULL) {
- error_msg("could not allocate object list\n");
- return NULL;
- }
- *n_objs = n;
-
- /* get object list */
- if (end_obj > 0)
- for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
- c = str[j];
- sobj[k] = c;
- if (c == ',' || j == (unsigned) (end_obj - 1)) {
- if (c == ',')
- sobj[k] = '\0';
- else
- sobj[k + 1] = '\0';
- HDstrcpy(obj_list[n].obj, sobj);
- HDmemset(sobj, 0, sizeof(sobj));
- n++;
- k = -1;
- }
- }
- /* nothing after : */
- if (end_obj + 1 == (int) len) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("input Error: Invalid compression type in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
-
- /* get filter additional parameters */
- m = 0;
- for (i = (size_t)(end_obj + 1), k = 0, j = 0; i < len; i++, k++) {
- c = str[i];
- scomp[k] = c;
- if (c == '=' || i == len - 1) {
- if (c == '=') { /*one more parameter */
- scomp[k] = '\0'; /*cut space */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- * szip has the format SZIP=<pixels per block,coding>
- * pixels per block is a even number in 2-32 and coding method is 'EC' or 'NN'
- * example SZIP=8,NN
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(scomp, "SZIP") == 0) {
- l = -1; /* mask index check */
- for (m = 0, u = i + 1; u < len; u++, m++) {
- if (str[u] == ',') {
- stype[m] = '\0'; /* end digit of szip */
- l = 0; /* start EC or NN search */
- u++; /* skip ',' */
- }
- c = str[u];
- if (!HDisdigit(c) && l == -1) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("compression parameter not digit in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- if (l == -1)
- stype[m] = c;
- else {
- smask[l] = c;
- l++;
- if (l == 2) {
- smask[l] = '\0';
- i = len - 1; /* end */
- (*n_objs)--; /* we counted an extra ',' */
- if (HDstrcmp(smask,"NN") == 0)
- filt->cd_values[j++] = H5_SZIP_NN_OPTION_MASK;
- else if (HDstrcmp(smask,"EC") == 0)
- filt->cd_values[j++] = H5_SZIP_EC_OPTION_MASK;
- else {
- error_msg("szip mask must be 'NN' or 'EC' \n");
- HDexit(EXIT_FAILURE);
- }
- }
- }
- } /* u */
- } /*if */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SCALEOFFSET
- * scaleoffset has the format SOFF=<scale_factor,scale_type>
- * scale_type can be
- * integer datatype, H5Z_SO_INT (IN)
- * float datatype using D-scaling method, H5Z_SO_FLOAT_DSCALE (DS)
- * float datatype using E-scaling method, H5Z_SO_FLOAT_ESCALE (ES) , not yet implemented
- * for integer datatypes, scale_factor denotes Minimum Bits
- * for float datatypes, scale_factor denotes decimal scale factor
- * examples
- * SOFF=31,IN
- * SOFF=3,DF
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "SOFF") == 0) {
- l = -1; /* mask index check */
- for (m = 0, u = i + 1; u < len; u++, m++) {
- if (str[u] == ',') {
- stype[m] = '\0'; /* end digit */
- l = 0; /* start 'IN' , 'DS', or 'ES' search */
- u++; /* skip ',' */
- }
- c = str[u];
- if (!HDisdigit(c) && l == -1) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("compression parameter is not a digit in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- if (l == -1)
- stype[m] = c;
- else {
- smask[l] = c;
- l++;
- if (l == 2) {
- smask[l] = '\0';
- i = len - 1; /* end */
- (*n_objs)--; /* we counted an extra ',' */
- if (HDstrcmp(smask,"IN") == 0)
- filt->cd_values[j++] = H5Z_SO_INT;
- else if (HDstrcmp(smask, "DS") == H5Z_SO_FLOAT_DSCALE)
- filt->cd_values[j++] = H5Z_SO_FLOAT_DSCALE;
- else {
- error_msg("scale type must be 'IN' or 'DS' \n");
- HDexit(EXIT_FAILURE);
- }
- }
- }
- } /* u */
- } /*if */
-
- /*-------------------------------------------------------------------------
- * User Defined
- * has the format UD=<filter_number,cd_value_count,value_1[,value_2,...,value_N]>
- * BZIP2 example
- * UD=307,1,9
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "UD") == 0) {
- l = -1; /* filter number index check */
- p = -1; /* CD_VAL count check */
- for (m = 0, q = 0, u = i + 1; u < len; u++, m++, q++) {
- if (str[u] == ',') {
- stype[q] = '\0'; /* end digit */
- if (l == -1) {
- filt->filtn = HDatoi(stype);
- l = 0;
- }
- else if (p == -1) {
- filt->cd_nelmts = HDstrtoull(stype, NULL, 0);
- p = 0;
- }
- else
- filt->cd_values[j++] = (unsigned)HDstrtoul(stype, NULL, 0);
- q = 0;
- u++; /* skip ',' */
- }
- c = str[u];
- if (!HDisdigit(c) && l == -1) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("filter number parameter is not a digit in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- stype[q] = c;
- } /* for u */
- stype[q] = '\0';
- } /*if */
-
- /*-------------------------------------------------------------------------
- * all other filters
- *-------------------------------------------------------------------------
- */
- else {
- /* here we could have 1 or 2 digits */
- for (m = 0, u = i + 1; u < len; u++, m++) {
- c = str[u];
- if (!HDisdigit(c)) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("compression parameter is not a digit in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- stype[m] = c;
- } /* u */
-
- stype[m] = '\0';
- } /*if */
-
- filt->cd_values[j++] = (unsigned) HDstrtoul(stype, NULL, 0);
- if(filt->cd_nelmts == 0)
- j = 0;
- i += m; /* jump */
- }
- else if (i == len - 1) { /*no more parameters */
- scomp[k + 1] = '\0';
- no_param = 1;
- }
-
- /*-------------------------------------------------------------------------
- * translate from string to filter symbol
- *-------------------------------------------------------------------------
- */
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_NONE
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(scomp, "NONE") == 0) {
- filt->filtn = H5Z_FILTER_NONE;
- filt->cd_nelmts = 0;
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_DEFLATE
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "GZIP") == 0) {
- filt->filtn = H5Z_FILTER_DEFLATE;
- filt->cd_nelmts = 1;
- if (no_param) { /*no more parameters, GZIP must have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "SZIP") == 0) {
- filt->filtn = H5Z_FILTER_SZIP;
- filt->cd_nelmts = 2;
- if (no_param) { /*no more parameters, SZIP must have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
-
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SHUFFLE
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "SHUF") == 0) {
- filt->filtn = H5Z_FILTER_SHUFFLE;
- filt->cd_nelmts = 0;
- if (m > 0) { /*shuffle does not have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("extra parameter in SHUF <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_FLETCHER32
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "FLET") == 0) {
- filt->filtn = H5Z_FILTER_FLETCHER32;
- filt->cd_nelmts = 0;
- if (m > 0) { /*shuffle does not have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("extra parameter in FLET <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_NBIT
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "NBIT") == 0) {
- filt->filtn = H5Z_FILTER_NBIT;
- filt->cd_nelmts = 0;
- if (m > 0) { /*nbit does not have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("extra parameter in NBIT <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SCALEOFFSET
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "SOFF") == 0) {
- filt->filtn = H5Z_FILTER_SCALEOFFSET;
- filt->cd_nelmts = 2;
- if (no_param) { /*no more parameters, SOFF must have parameter */
- if (obj_list)
- HDfree(obj_list);
- error_msg("missing compression parameter in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- /*-------------------------------------------------------------------------
- * User Defined Filter
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(scomp, "UD") == 0) {
- /* parameters does not match count */
- if (filt->cd_nelmts != j) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("incorrect number of compression parameters in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- else {
- if (obj_list)
- HDfree(obj_list);
- error_msg("invalid filter type in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- } /*i*/
-
- /*-------------------------------------------------------------------------
- * check valid parameters
- *-------------------------------------------------------------------------
- */
-
- switch (filt->filtn) {
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_DEFLATE
- *-------------------------------------------------------------------------
- */
- case H5Z_FILTER_DEFLATE:
- if (filt->cd_values[0] > 9) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("invalid compression parameter in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- break;
- /*-------------------------------------------------------------------------
- * H5Z_FILTER_SZIP
- *-------------------------------------------------------------------------
- */
- case H5Z_FILTER_SZIP:
- pixels_per_block = filt->cd_values[0];
- if ((pixels_per_block % 2) == 1) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("pixels_per_block is not even in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- if (pixels_per_block > H5_SZIP_MAX_PIXELS_PER_BLOCK) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("pixels_per_block is too large in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- if ((HDstrcmp(smask,"NN") != 0) && (HDstrcmp(smask,"EC") != 0)) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("szip mask must be 'NN' or 'EC' \n");
- HDexit(EXIT_FAILURE);
- }
- break;
- default:
- break;
- };
-
- return obj_list;
-}
-
-
-/*-------------------------------------------------------------------------
- * Function: parse_layout
- *
- * Purpose: read layout info
- *
- * Return: a list of names, the number of names and its chunking info for
- * chunked. NULL, on error
- * the layout type can be:
- * CHUNK, to apply chunking layout
- * CONTI, to apply contiguous layout
- * COMPA, to apply compact layout
- *
- * Example:
- * "AA,B,CDE:CHUNK=10X10"
- *
- * Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
- *
- * Date: December 30, 2003
- *
- *-------------------------------------------------------------------------
- */
-obj_list_t* parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about layout needed */
-pack_opt_t *options) {
- obj_list_t* obj_list = NULL;
- unsigned i, j, n;
- char c;
- size_t len = HDstrlen(str);
- int k, end_obj = -1, c_index;
- char sobj[MAX_NC_NAME];
- char sdim[10];
- char slayout[10];
-
- HDmemset(sdim, '\0', sizeof(sdim));
- HDmemset(sobj, '\0', sizeof(sobj));
- HDmemset(slayout, '\0', sizeof(slayout));
-
- /* check for the end of object list and number of objects */
- for (i = 0, n = 0; i < len; i++) {
- c = str[i];
- if (c == ':')
- end_obj = (int) i;
- if (c == ',')
- n++;
- }
-
- if (end_obj == -1) { /* missing : chunk all */
- options->all_layout = 1;
- }
-
- n++;
- obj_list = (obj_list_t*) HDmalloc(n * sizeof(obj_list_t));
- if (obj_list == NULL) {
- error_msg("could not allocate object list\n");
- return NULL;
- }
- *n_objs = n;
-
- /* get object list */
- if (end_obj > 0)
- for (j = 0, k = 0, n = 0; j < (unsigned) end_obj; j++, k++) {
- c = str[j];
- sobj[k] = c;
- if (c == ',' || j == (unsigned) (end_obj - 1)) {
- if (c == ',')
- sobj[k] = '\0';
- else
- sobj[k + 1] = '\0';
- HDstrcpy(obj_list[n].obj, sobj);
- HDmemset(sobj, 0, sizeof(sobj));
- n++;
- k = -1;
- }
- }
-
- /* nothing after : */
- if (end_obj + 1 == (int) len) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("in parse layout, no characters after : in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
-
- /* get layout info */
- for (j = (unsigned) (end_obj + 1), n = 0; n <= 5; j++, n++) {
- if (n == 5) {
- slayout[n] = '\0'; /*cut string */
- if (HDstrcmp(slayout, "COMPA") == 0)
- pack->layout = H5D_COMPACT;
- else if (HDstrcmp(slayout, "CONTI") == 0)
- pack->layout = H5D_CONTIGUOUS;
- else if (HDstrcmp(slayout, "CHUNK") == 0)
- pack->layout = H5D_CHUNKED;
- else {
- error_msg("in parse layout, not a valid layout in <%s>\n", str);
- HDexit(EXIT_FAILURE);
- }
- }
- else {
- c = str[j];
- slayout[n] = c;
- }
- } /* j */
-
- if (pack->layout == H5D_CHUNKED) {
- /*-------------------------------------------------------------------------
- * get chunk info
- *-------------------------------------------------------------------------
- */
- k = 0;
- if (j > len) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("in parse layout, <%s> Chunk dimensions missing\n", str);
- HDexit(EXIT_FAILURE);
- }
-
- for (i = j, c_index = 0; i < len; i++) {
- c = str[i];
- sdim[k] = c;
- k++; /*increment sdim index */
-
- if (!HDisdigit(c) && c != 'x' && c != 'N' && c != 'O' && c != 'N' && c != 'E') {
- if (obj_list)
- HDfree(obj_list);
- error_msg("in parse layout, <%s> Not a valid character in <%s>\n", sdim, str);
- HDexit(EXIT_FAILURE);
- }
-
- if (c == 'x' || i == len - 1) {
- if (c == 'x') {
- sdim[k - 1] = '\0';
- k = 0;
- pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
- if (pack->chunk.chunk_lengths[c_index] == 0) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
- HDexit(EXIT_FAILURE);
- }
- c_index++;
- }
- else if (i == len - 1) { /*no more parameters */
- sdim[k] = '\0';
- k = 0;
- if (HDstrcmp(sdim,"NONE") == 0) {
- pack->chunk.rank = -2;
- }
- else {
- pack->chunk.chunk_lengths[c_index] = HDstrtoull(sdim, NULL, 0);
- if (pack->chunk.chunk_lengths[c_index] == 0) {
- if (obj_list)
- HDfree(obj_list);
- error_msg("in parse layout, <%s> conversion to number in <%s>\n", sdim, str);
- HDexit(EXIT_FAILURE);
- }
- pack->chunk.rank = c_index + 1;
- }
- } /*if */
- } /*if c=='x' || i==len-1 */
- } /*i*/
- } /*H5D_CHUNKED*/
-
- return obj_list;
-}
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