sdds2math.c File Reference

Detailed Description

Converts SDDS files to a Mathematica-compatible format.

This program reads an SDDS (Self Describing Data Sets) file and converts it into a format that can be easily imported and used within Mathematica. The output is structured as a single Mathematica variable containing descriptions, column definitions, parameter definitions, array definitions, associations, and tables of data.

The output Mathematica variable has the following structure:

sdds = {description, coldef, pardef, arraydef, associates, tables}

• description: Contains text and contents descriptions.
• coldef: Defines columns with name, units, symbol, format, type, field length, and description.
• pardef: Defines parameters with name, fixed value, units, symbol, type, and description.
• arraydef: Defines arrays with name, units, symbol, format, type, field length, group, and description.
• associates: Lists associations with SDDS flag, filename, path, contents, and description.
• tables: Contains data tables with parameters and row data.

Usage

sdds2math [<SDDSfilename>] [<outputname>]
          [-pipe[=in][,out]]
          [-comments]
          [-verbose]
          [-format=<format-string>]

Options

Option	Description
-pipe	Standard SDDS Toolkit pipe option.
-comments	Include helpful Mathematica comments in the output file.
-format	Specify the format for double precision numbers (Default: g).
-verbose	Display header information to the terminal similar to sddsquery.

Specific Requirements

• If -format=<format-string> is used, <format-string> must be a valid printf-style format.

Copyright

• (c) 2002 The University of Chicago, as Operator of Argonne National Laboratory.
• (c) 2002 The Regents of the University of California, as Operator of Los Alamos National Laboratory.

License

This file is distributed under the terms of the Software License Agreement found in the file LICENSE included with this distribution.

Author

K. Evans, C. Saunders, M. Borland, R. Soliday

Definition in file sdds2math.c.

#include <stdio.h>
#include <string.h>
#include <math.h>
#include "mdb.h"
#include "SDDS.h"
#include "scan.h"

Go to the source code of this file.

Functions
int	main (int argc, char **argv)

Function Documentation

main()

int main	(	int	argc,
		char **	argv )

Definition at line 104 of file sdds2math.c.

                                {
  FILE *outfile;
  SDDS_TABLE SDDS_table;
  SDDS_LAYOUT *layout;
  COLUMN_DEFINITION *coldef;
  PARAMETER_DEFINITION *pardef;
  ARRAY_DEFINITION *arraydef;
  char s[256];
  char *input, *output;
  long i, i_arg, ntable;
  int64_t nrows, j;
  SCANNED_ARG *s_arg;
  char *text, *contents, *ss, *ptr, *iformat = FORMAT, *format, *rformat;
  long verbose = 0, comments = 0, addquotes = 1;
  short nexp;
  double dd, ddred;
  float ff, ffred;
  void *data;
  unsigned long pipeFlags;
 
  SDDS_RegisterProgramName(argv[0]);
 
  input = output = NULL;
  pipeFlags = 0;
 
  argc = scanargs(&s_arg, argc, argv);
  if (argc == 1) {
    fprintf(stderr, "%s", USAGE);
    exit(EXIT_FAILURE);
  }
 
  for (i_arg = 1; i_arg < argc; i_arg++) {
    if (s_arg[i_arg].arg_type == OPTION) {
      switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
      case SET_COMMENTS:
        comments = 1;
        break;
      case SET_FORMAT:
        if (s_arg[i_arg].n_items < 2)
          SDDS_Bomb("Invalid -format syntax");
        iformat = s_arg[i_arg].list[1]; /* Input format */
        break;
      case SET_VERBOSE:
        verbose = 1;
        break;
      case SET_PIPE:
        if (!processPipeOption(s_arg[i_arg].list + 1, s_arg[i_arg].n_items - 1, &pipeFlags))
          SDDS_Bomb("Invalid -pipe syntax");
        break;
      default:
        fprintf(stderr, "Unknown option: %s\n", s_arg[i_arg].list[0]);
        fprintf(stderr, "%s", USAGE);
        exit(EXIT_FAILURE);
      }
    } else {
      if (input == NULL)
        input = s_arg[i_arg].list[0];
      else if (output == NULL)
        output = s_arg[i_arg].list[0];
      else
        SDDS_Bomb("Too many filenames provided.");
    }
  }
 
  processFilenames("sdds2math", &input, &output, pipeFlags, 0, NULL);
 
  if (output) {
    outfile = fopen(output, "w");
    if (!outfile) {
      fprintf(stderr, "Error: Cannot open output file '%s'\n", output);
      exit(EXIT_FAILURE);
    }
  } else {
    outfile = stdout;
  }
 
  /* Calculate formats for converting to Mathematica convention */
  format = (char *)calloc(256, sizeof(char)); /* Whole format */
  if (!format) {
    fprintf(stderr, "Memory allocation error for format.\n");
    exit(EXIT_FAILURE);
  }
 
  rformat = (char *)calloc(256, sizeof(char)); /* Part before e */
  if (!rformat) {
    fprintf(stderr, "Memory allocation error for rformat.\n");
    free(format);
    exit(EXIT_FAILURE);
  }
 
  strcpy(format, iformat);
  if ((ptr = strchr(format, 'E')))
    *ptr = 'e'; /* Convert 'E' to 'e' */
  if ((ptr = strchr(format, 'G')))
    *ptr = 'g'; /* Convert 'G' to 'g' */
  strcpy(rformat, format);
  if ((ptr = strpbrk(rformat, "eg")))
    *ptr = 'f';
 
  /* Initialize SDDS input */
  if (!SDDS_InitializeInput(&SDDS_table, input)) {
    SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
    exit(EXIT_FAILURE);
  }
 
  layout = &SDDS_table.layout;
 
  /* Start top level */
  fprintf(outfile, "{");
 
  /* Description */
  fprintf(outfile, "{");
  if (verbose)
    printf("\nFile '%s' is in SDDS protocol version %" PRId32 "\n", input, layout->version);
 
  if (!SDDS_GetDescription(&SDDS_table, &text, &contents))
    SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors | SDDS_EXIT_PrintErrors);
 
  if (text) {
    if (verbose)
      printf("Description: %s\n", text);
    fprintf(outfile, "\"%s\",", text);
  }
 
  if (contents) {
    if (verbose)
      printf("Contents: %s\n", contents);
    fprintf(outfile, "\"%s\"", contents);
  } else {
    fprintf(outfile, "\"No contents\"");
  }
 
  if (layout->data_mode.mode == SDDS_ASCII) {
    if (verbose)
      printf("\nData is ASCII with %" PRId32 " lines per row and %" PRId32 " additional header lines expected.\n",
             layout->data_mode.lines_per_row, layout->data_mode.additional_header_lines);
    if (verbose)
      printf("Row counts: %s\n", layout->data_mode.no_row_counts ? "No" : "Yes");
  } else if (verbose) {
    printf("\nData is binary\n");
  }
 
  fprintf(outfile, "},\n");
 
  /* Columns */
  fprintf(outfile, " {");
  if (layout->n_columns) {
    if (verbose)
      printf("\n%" PRId32 " columns of data:\n", layout->n_columns);
    if (verbose)
      printf("NAME            UNITS           SYMBOL          FORMAT          TYPE    FIELD  DESCRIPTION\n");
    if (verbose)
      printf("                                                                        LENGTH\n");
    for (i = 0; i < layout->n_columns; i++) {
      if (i > 0)
        fprintf(outfile, ",\n  ");
      coldef = layout->column_definition + i;
      if (verbose)
        printf("%-15s %-15s %-15s %-15s %-7s %-7" PRId32 " %s\n",
               coldef->name ? coldef->name : "No name",
               coldef->units ? coldef->units : "",
               coldef->symbol ? coldef->symbol : "",
               coldef->format_string ? coldef->format_string : "",
               SDDS_type_name[coldef->type - 1],
               coldef->field_length,
               coldef->description ? coldef->description : "No description");
      fprintf(outfile, "{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\",%" PRId32 ",\"%s\"}",
              coldef->name ? coldef->name : "No name",
              coldef->units ? coldef->units : "",
              coldef->symbol ? coldef->symbol : "",
              coldef->format_string ? coldef->format_string : "",
              SDDS_type_name[coldef->type - 1],
              coldef->field_length,
              coldef->description ? coldef->description : "No description");
    }
  }
  fprintf(outfile, "},\n");
 
  /* Parameters */
  fprintf(outfile, " {");
  if (layout->n_parameters) {
    if (verbose)
      printf("\n%" PRId32 " parameters:\n", layout->n_parameters);
    if (verbose)
      printf("NAME                UNITS               SYMBOL              TYPE                DESCRIPTION\n");
    for (i = 0; i < layout->n_parameters; i++) {
      if (i > 0)
        fprintf(outfile, ",\n  ");
      pardef = layout->parameter_definition + i;
      if (verbose)
        printf("%-19s %-19s %-19s %-19s %s\n",
               pardef->name ? pardef->name : "No name",
               pardef->units ? pardef->units : "",
               pardef->symbol ? pardef->symbol : "",
               SDDS_type_name[pardef->type - 1],
               pardef->description ? pardef->description : "No description");
      fprintf(outfile, "{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
              pardef->name ? pardef->name : "No name",
              pardef->fixed_value ? pardef->fixed_value : "",
              pardef->units ? pardef->units : "",
              pardef->symbol ? pardef->symbol : "",
              SDDS_type_name[pardef->type - 1],
              pardef->description ? pardef->description : "No description");
    }
  }
  fprintf(outfile, "},\n");
 
  /* Arrays */
  fprintf(outfile, " {");
  if (layout->n_arrays) {
    if (verbose)
      printf("\n%" PRId32 " arrays of data:\n", layout->n_arrays);
    if (verbose)
      printf("NAME            UNITS           SYMBOL          FORMAT  TYPE            FIELD   GROUP           DESCRIPTION\n");
    if (verbose)
      printf("                                                                        LENGTH  NAME\n");
    for (i = 0; i < layout->n_arrays; i++) {
      if (i > 0)
        fprintf(outfile, ",\n  ");
      arraydef = layout->array_definition + i;
      if (verbose)
        printf("%-15s %-15s %-15s %-7s %-8s*^%-5" PRId32 " %-7" PRId32 " %-15s %s\n",
               arraydef->name ? arraydef->name : "No name",
               arraydef->units ? arraydef->units : "",
               arraydef->symbol ? arraydef->symbol : "",
               arraydef->format_string ? arraydef->format_string : "",
               SDDS_type_name[arraydef->type - 1],
               arraydef->dimensions,
               arraydef->field_length,
               arraydef->group_name ? arraydef->group_name : "",
               arraydef->description ? arraydef->description : "No description");
      fprintf(outfile, "{\"%s\",\"%s\",\"%s\",\"%s\",\"%s*^%" PRId32 "\",%" PRId32 ",\"%s\",\"%s\"}",
              arraydef->name ? arraydef->name : "No name",
              arraydef->units ? arraydef->units : "",
              arraydef->symbol ? arraydef->symbol : "",
              arraydef->format_string ? arraydef->format_string : "",
              SDDS_type_name[arraydef->type - 1],
              arraydef->dimensions,
              arraydef->field_length,
              arraydef->group_name ? arraydef->group_name : "",
              arraydef->description ? arraydef->description : "No description");
    }
  }
  fprintf(outfile, "},\n");
 
  /* Associates */
  fprintf(outfile, " {");
  if (layout->n_associates) {
    if (verbose)
      printf("\n%" PRId32 " associates:\n", layout->n_associates);
    if (verbose)
      printf("SDDS  FILENAME            PATH                          CONTENTS            DESCRIPTION\n");
    for (i = 0; i < layout->n_associates; i++) {
      if (i > 0)
        fprintf(outfile, ",\n  ");
      if (verbose)
        printf("%-5s %-19s %-29s %-19s %s\n",
               layout->associate_definition[i].sdds ? "True" : "False",
               layout->associate_definition[i].filename ? layout->associate_definition[i].filename : "",
               layout->associate_definition[i].path ? layout->associate_definition[i].path : "",
               layout->associate_definition[i].contents ? layout->associate_definition[i].contents : "",
               layout->associate_definition[i].description ? layout->associate_definition[i].description : "No description");
      fprintf(outfile, "{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
              layout->associate_definition[i].sdds ? "True" : "False",
              layout->associate_definition[i].filename ? layout->associate_definition[i].filename : "",
              layout->associate_definition[i].path ? layout->associate_definition[i].path : "",
              layout->associate_definition[i].contents ? layout->associate_definition[i].contents : "",
              layout->associate_definition[i].description ? layout->associate_definition[i].description : "No description");
    }
  }
  fprintf(outfile, "},\n");
 
  /* Process tables */
  fprintf(outfile, " {"); /* Start of array of tables */
  while ((ntable = SDDS_ReadTable(&SDDS_table)) > 0) {
    if (ntable > 1)
      fprintf(outfile, ",\n  ");
    if (comments)
      fprintf(outfile, "(*Table %ld*)", ntable);
    fprintf(outfile, "{\n"); /* Start of this table */
 
    /* Variable parameters */
    fprintf(outfile, "   {"); /* Start of parameters */
    for (i = 0; i < layout->n_parameters; i++) {
      if (i > 0)
        fprintf(outfile, ",\n    ");
      pardef = layout->parameter_definition + i;
      if (!(data = SDDS_GetParameter(&SDDS_table, pardef->name, NULL))) {
        SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
        exit(EXIT_FAILURE);
      }
 
      /* This parameter */
      if (comments)
        fprintf(outfile, "(* %s *)", pardef->name);
 
      addquotes = 1;
      switch (pardef->type) {
      case SDDS_DOUBLE:
        dd = *(double *)data;
        sprintf(s, format, dd);
        if ((ptr = strchr(s, 'e'))) {
          *ptr = ' ';
          sscanf(s, "%lf %hd", &ddred, &nexp);
          fprintf(outfile, rformat, ddred);
          fprintf(outfile, "*10^%d", nexp);
        } else {
          fprintf(outfile, "%s", s);
        }
        break;
      case SDDS_FLOAT:
        ff = *(float *)data;
        sprintf(s, format, ff);
        if ((ptr = strchr(s, 'e'))) {
          *ptr = ' ';
          sscanf(s, "%f %hd", &ffred, &nexp);
          fprintf(outfile, rformat, ffred);
          fprintf(outfile, "*10^%d", nexp);
        } else {
          fprintf(outfile, "%s", s);
        }
        break;
      case SDDS_STRING:
        ss = *(char **)data;
        if (*ss == '"')
          addquotes = 0;
        else if (SDDS_StringIsBlank(ss) || SDDS_HasWhitespace(ss))
          addquotes = 0;
      case SDDS_CHARACTER:
        if (addquotes)
          fprintf(outfile, "\"");
        SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
        if (addquotes)
          fprintf(outfile, "\"");
        break;
      default:
        SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
        break;
      }
    }
    fprintf(outfile, "},\n"); /* End of parameters */
 
    /* Columns */
    fprintf(outfile, "   {"); /* Start of data array */
    if (layout->n_columns) {
      SDDS_SetColumnFlags(&SDDS_table, 1);
      SDDS_SetRowFlags(&SDDS_table, 1);
      if ((nrows = SDDS_CountRowsOfInterest(&SDDS_table)) < 0) {
        SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
        exit(EXIT_FAILURE);
      }
 
      if (nrows) {
        for (j = 0; j < nrows; j++) {
          if (j > 0)
            fprintf(outfile, ",\n    ");
          fprintf(outfile, "{"); /* Start of row */
          for (i = 0; i < layout->n_columns; i++) {
            if (i > 0)
              fprintf(outfile, ",");
            coldef = layout->column_definition + i;
            if (!(data = SDDS_GetValue(&SDDS_table, coldef->name, j, NULL))) {
              SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
              exit(EXIT_FAILURE);
            }
 
            addquotes = 1;
            switch (coldef->type) {
            case SDDS_DOUBLE:
              dd = *(double *)data;
              sprintf(s, format, dd);
              if ((ptr = strchr(s, 'e'))) {
                *ptr = ' ';
                sscanf(s, "%lf %hd", &ddred, &nexp);
                fprintf(outfile, rformat, ddred);
                fprintf(outfile, "*10^%d", nexp);
              } else {
                fprintf(outfile, "%s", s);
              }
              break;
            case SDDS_FLOAT:
              ff = *(float *)data;
              sprintf(s, format, ff);
              if ((ptr = strchr(s, 'e'))) {
                *ptr = ' ';
                sscanf(s, "%f %hd", &ffred, &nexp);
                fprintf(outfile, rformat, ffred);
                fprintf(outfile, "*10^%d", nexp);
              } else {
                fprintf(outfile, "%s", s);
              }
              break;
            case SDDS_STRING:
              ss = *(char **)data;
              if (*ss == '"')
                addquotes = 0;
              else if (SDDS_StringIsBlank(ss) || SDDS_HasWhitespace(ss))
                addquotes = 0;
            case SDDS_CHARACTER:
              if (addquotes)
                fprintf(outfile, "\"");
              SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
              if (addquotes)
                fprintf(outfile, "\"");
              break;
            default:
              SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
              break;
            }
          }
          fprintf(outfile, "}"); /* End of row */
        }
      }
    }
    fprintf(outfile, "}"); /* End of data array */
    fprintf(outfile, "}"); /* End of this table */
  }
  fprintf(outfile, "\n }\n"); /* End of array of tables, last major component */
 
  /* End top level */
  fprintf(outfile, "}\n"); /* End of top level */
 
  /* Clean up and exit */
  fflush(stdout);
  if (!SDDS_Terminate(&SDDS_table)) {
    SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
    exit(EXIT_FAILURE);
  }
 
  free(format);
  free(rformat);
 
  return EXIT_SUCCESS;
}