int main(int argc, char **argv)
{
SCANNED_ARG *scanned;
SDDS_TABLE inputPage, *copiedPage, outputPage;
long copiedPages;
char *inputfile, *outputfile;
char **column, **excludeColumn=NULL;
int32_t columns;
long excludeColumns;
char *indParameterName;
char **copyColumn;
int32_t copyColumns;
long verbose;
long slopeErrors;
long iArg,i;
double *indVar;
char *indVarUnits;
char **intColumn,**slopeColumn,**slopeSigmaColumn;
char *Units,*slopeUnits;
double *depVar;
long order;
double *coef,*coefsigma,*weight,*diff,chi;
long iCol,iRow,iPage;
long rows;
double *slope, slope2, slopeAve, slopeSigma;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long generateIndex;
short columnMajorOrder=-1;
copiedPage = NULL;
slopeSigmaColumn = NULL;
slopeUnits = Units = indVarUnits = NULL;
rows = 0;
slope = NULL;
slope2 = 0;
coef = coefsigma = weight = diff = slope = NULL;
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
indParameterName = NULL;
verbose = 0;
slopeErrors = 0;
pipeFlags = 0;
tmpfile_used=0;
noWarnings=0;
for (iArg = 1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type == OPTION) {
delete_chars(scanned[iArg].list[0], "_");
switch (match_string(scanned[iArg].list[0], commandline_option, COMMANDLINE_OPTIONS, UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
scanned[iArg].n_items--;
if (scanned[iArg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_INDEPENDENT_PARAMETER:
if (!(indParameterName = scanned[iArg].list[1]))
SDDS_Bomb("no string given for option -independentVariable");
break;
case CLO_COLUMNS:
if (columns)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
column = tmalloc(sizeof(*column)*(columns = scanned[iArg].n_items-1));
for (i = 0; i<columns; i++)
column[i] = scanned[iArg].list[i+1];
break;
case CLO_EXCLUDE:
if (excludeColumns)
SDDS_Bomb("only one -excludecolumns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -excludecolumns syntax");
excludeColumn = tmalloc(sizeof(*excludeColumn)*(excludeColumns = scanned[iArg].n_items-1));
for (i = 0; i<excludeColumns; i++)
excludeColumn[i] = scanned[iArg].list[i+1];
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_SLOPE_ERRORS:
slopeErrors = 1;
break;
default:
SDDS_Bomb("unrecognized option given");
break;
}
}
else {
if (!inputfile)
inputfile = scanned[iArg].list[0];
else if (!outputfile)
outputfile = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames given");
}
}
processFilenames("sddsvslopes", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (!indParameterName)
SDDS_Bomb("independentVariable not given");
if (!excludeColumns) {
excludeColumn = defaultExcludedColumn;
excludeColumns = DEFAULT_EXCLUDED_COLUMNS;
}
if (verbose)
fprintf(stderr,"Reading file %s.\n",inputfile);
SDDS_InitializeInput(&inputPage, inputfile);
copiedPages = 0;
while (SDDS_ReadTable(&inputPage)>0) {
if (!copiedPages) {
copiedPage = (SDDS_TABLE*)malloc(sizeof(SDDS_TABLE));
rows = SDDS_CountRowsOfInterest(&inputPage);
}
else {
copiedPage = (SDDS_TABLE*)realloc(copiedPage, (copiedPages+1)*sizeof(SDDS_TABLE));
}
if (!SDDS_InitializeCopy(&copiedPage[copiedPages], &inputPage, NULL, "m"))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (!SDDS_CopyTable(&copiedPage[copiedPages], &inputPage))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
copiedPages++;
}
if (copiedPages<2) {
fprintf(stderr,"Insufficient data (i.e. number of data pages) to fit a straight line.\n");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Rootname", NULL, SDDS_STRING, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Index", NULL, SDDS_LONG, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
generateIndex = 0;
break;
case SDDS_CHECK_NONEXISTENT:
generateIndex = 1;
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
/****************\
* make array of independent variable
\**************/
indVar = (double*)malloc(sizeof(*indVar)*copiedPages);
switch(SDDS_CheckParameter(&inputPage, indParameterName, NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with parameter %s.\n", indParameterName);
exit(1);
}
for (iPage = 0; iPage<copiedPages; iPage++) {
if (!SDDS_GetParameter(&copiedPage[iPage],indParameterName,&indVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!SDDS_GetParameterInformation(&inputPage, "units", &indVarUnits, SDDS_GET_BY_NAME, indParameterName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!indVarUnits) {
indVarUnits = (char *) malloc(sizeof(*indVarUnits));
indVarUnits[0] = 0;
}
/************************************\
* get columns of interest. use set_multicolumn_flags to simply
* return new values for array column.
\*************************************/
if (!set_multicolumn_flags(&inputPage, &column, &columns, excludeColumn, excludeColumns)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/************************************\
* make column names for the output
\*************************************/
intColumn = (char**)malloc((sizeof(char*)*columns));
slopeColumn = (char**)malloc((sizeof(char*)*columns));
if (slopeErrors)
slopeSigmaColumn = (char**)malloc((sizeof(char*)*columns));
for (i=0; i<columns; i++) {
intColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Intercept")+1)));
strcat(strcpy(intColumn[i], column[i]), "Intercept");
slopeColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Slope")+1)));
strcat(strcpy(slopeColumn[i], column[i]), "Slope");
if (slopeErrors) {
slopeSigmaColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("SlopeSigma")+1)));
strcat(strcpy(slopeSigmaColumn[i], column[i]), "SlopeSigma");
}
}
/************************************\
* Write layout for output file
\*************************************/
if (verbose)
fprintf(stderr,"Opening file %s.\n",outputfile);
if(!SDDS_InitializeOutput(&outputPage,SDDS_BINARY,1,
"lsf of sddsvexperiment",NULL,outputfile) ||
0>SDDS_DefineParameter(&outputPage, "InputFile", "InputFile", NULL,
"InputFile", NULL, SDDS_STRING, 0) ||
0>SDDS_DefineParameter(&outputPage, "IndependentVariable", "IndependentVariable", NULL,
"IndependentVariable", NULL, SDDS_STRING, 0) ||
(0>SDDS_DefineColumn(&outputPage,"Index",NULL,NULL,"Rootname index",NULL,SDDS_LONG,0))||
(0>SDDS_DefineColumn(&outputPage,"Rootname",NULL,NULL,NULL,NULL,SDDS_STRING,0)))
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (columnMajorOrder!=-1)
outputPage.layout.data_mode.column_major = columnMajorOrder;
else
outputPage.layout.data_mode.column_major = inputPage.layout.data_mode.column_major;
for (iCol=0; iCol<columns; iCol++) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &Units, SDDS_GET_BY_NAME,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!Units) {
Units = (char*) malloc(sizeof(*Units));
Units[0] = 0;
}
if (0>SDDS_DefineColumn(&outputPage, intColumn[iCol], NULL, Units, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* units for slopes columns */
if (strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+strlen(indVarUnits)+2));
strcat( strcat( strcpy(slopeUnits, Units), "/"), indVarUnits);
}
if (strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(indVarUnits)+2));
strcat( strcpy( slopeUnits, "1/"), indVarUnits);
}
if (!strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+2));
strcpy( slopeUnits, indVarUnits);
}
if (!strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits));
strcpy( slopeUnits, "");
}
if (0>SDDS_DefineColumn(&outputPage, slopeColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (slopeErrors) {
if (0>SDDS_DefineColumn(&outputPage, slopeSigmaColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(slopeUnits);
}
if(!SDDS_WriteLayout(&outputPage) ||
!SDDS_StartTable(&outputPage,rows) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile",inputfile?inputfile:"pipe",NULL) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
"IndependentVariable", indParameterName, NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/************************************\
* Copy columns to output file (usually columns Index and Rootname)
\*************************************/
copyColumns = DEFAULT_COPY_COLUMNS;
copyColumn = defaultCopyColumn;
if (!set_multicolumn_flags(&inputPage, ©Column, ©Columns, NULL, 0)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
if(!SDDS_CopyColumns(&outputPage, &inputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
depVar = (double*)malloc(sizeof(*depVar)*copiedPages);
weight = (double*)malloc(sizeof(*weight)*copiedPages);
diff = (double*)malloc(sizeof(*weight)*copiedPages);
order=1;
coef = (double*)malloc(sizeof(*coef)*(order+1));
coefsigma = (double*)malloc(sizeof(*coefsigma)*(order+1));
if(slopeErrors)
slope = (double*)malloc(sizeof(*slope)*copiedPages);
for (iCol=0; iCol<columns; iCol++) {
for (iPage=0; iPage<copiedPages; iPage++)
weight[iPage]=1;
if (verbose)
fprintf(stderr,"Doing column %s.\n", column[iCol]);
for (iRow=0; iRow<rows; iRow++) {
for (iPage=0; iPage<copiedPages; iPage++) {
if (!SDDS_GetValue(&copiedPage[iPage], column[iCol], iRow, &depVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
if (generateIndex) {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
"Index",iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if(slopeErrors){
/* recalculate the slope with a subset of points */
slopeAve= slope2 = 0;
for (iPage=0; iPage<copiedPages; iPage++) {
weight[iPage] = 1e10;
if(iPage)
weight[iPage-1] = 1;
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
slope[iPage] = coef[1];
slopeAve += slope[iPage];
slope2 += sqr(slope[iPage]);
}
slopeSigma = sqrt(slope2/copiedPages - sqr(slopeAve/copiedPages));
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
slopeSigmaColumn[iCol], slopeSigma, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
if( !SDDS_WriteTable(&outputPage)|| SDDS_Terminate(&inputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (iPage=0; iPage<copiedPages; iPage++) {
if( !SDDS_Terminate(&copiedPage[iPage]) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if( SDDS_Terminate(&outputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
SDDS_FreeStringArray(column, columns);
free(column);
SDDS_FreeStringArray(intColumn, columns);
SDDS_FreeStringArray(slopeColumn, columns);
free(intColumn);
free(slopeColumn);
if (slopeErrors) {
SDDS_FreeStringArray(slopeSigmaColumn, columns);
free(slopeSigmaColumn);
}
free(copiedPage);
free(indVar);
free(depVar);
if (weight)
free(weight);
if (diff)
free(diff);
if (slope)
free(slope);
if (coef) free(coef);
if (coefsigma) free(coefsigma);
if (Units) free(Units);
if (indVarUnits) free(indVarUnits);
free_scanargs(&scanned, argc);
return(0);
}
int main(int argc, char **argv)
{
FILE *outfile;
SDDS_TABLE SDDS_table;
SDDS_LAYOUT *layout;
COLUMN_DEFINITION *coldef;
PARAMETER_DEFINITION *pardef;
ARRAY_DEFINITION *arraydef;
long list_request;
char *input, *output;
long i, j, i_arg, append_units, nrows, ntable;
SCANNED_ARG *s_arg;
char *text, *contents, *delimiter;
long verbose=0, all=0, nvariableparms=0, excel=0, line=0;
void *data;
unsigned long pipeFlags;
#ifdef USE_XLS
workbook *w;
worksheet *ws;
#endif
int ret;
char sheet[256];
char buffer[5];
SDDS_RegisterProgramName(argv[0]);
list_request = -1;
input = output = NULL;
append_units = 0;
delimiter = DELIMITER;
pipeFlags = 0;
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
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_DELIMITER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -delimiter syntax");
delimiter = s_arg[i_arg].list[1];
break;
case SET_ALL:
all = 1;
break;
case SET_EXCEL:
#ifdef USE_XLS
excel = 1;
#else
SDDS_Bomb("-excel option is not available becuase sdds2spreadsheet was not compiled with xlslib support");
#endif
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:
SDDS_Bomb(strcat("Unknown option: ", s_arg[i_arg].list[0]));
break;
}
}
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");
}
}
processFilenames("sdds2spreadsheet", &input, &output, pipeFlags, 0, NULL);
if (output) {
if (!excel) {
outfile=fopen(output,"w");
if(!outfile)
SDDS_Bomb(strcat("Can't open output file ", output));
}
}
else {
if (excel) {
SDDS_Bomb("-pipe=out and -excel options cannot be used together");
}
outfile = stdout;
}
if (input && !excel)
fprintf(outfile,"Created from SDDS file: %s\n", input);
if (!SDDS_InitializeInput(&SDDS_table, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
layout = &SDDS_table.layout;
/* Description */
if(verbose && input)
fprintf(stderr, "\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)
fprintf(stderr, "description: %s\n", text);
if (!excel)
fprintf(outfile,"%s%s\n",text?text:"No description",delimiter);
if (contents)
if (verbose)
fprintf(stderr, "contents: %s\n", contents);
if (!excel)
fprintf(outfile,"%s%s\n",contents?contents:"No description",delimiter);
if (layout->data_mode.mode==SDDS_ASCII) {
if (verbose) {
fprintf(stderr, "\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);
fprintf(stderr, "row counts: %s \n",
layout->data_mode.no_row_counts?"no":"yes");
}
}
else if (verbose)
fprintf(stderr, "\ndata is binary\n");
/* Columns */
if (layout->n_columns) {
if(verbose) {
fprintf(stderr, "\n%" PRId32 " columns of data:\n", layout->n_columns);
fprintf(stderr, "NAME UNITS SYMBOL FORMAT TYPE FIELD DESCRIPTION\n");
fprintf(stderr, " LENGTH\n");
}
if (all && !excel)
fprintf(outfile,
"\nColumns%s\nName%sUnits%sSymbol%sFormat%sType%sField Length%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter,
delimiter);
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
if(verbose)
fprintf(stderr, "%-15s %-15s %-15s %-15s %-7s %-7" PRId32 " %s\n",
coldef->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:"");
if(all && !excel)
fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s%-7" PRId32 "%s%s%s\n",
coldef->name, delimiter,
coldef->units?coldef->units:"", delimiter,
coldef->symbol?coldef->symbol:"", delimiter,
coldef->format_string?coldef->format_string:"", delimiter,
SDDS_type_name[coldef->type-1], delimiter,
coldef->field_length, delimiter,
coldef->description?coldef->description:"", delimiter);
}
}
/* Parameters */
if (layout->n_parameters) {
if (verbose) {
fprintf(stderr, "\n%" PRId32 " parameters:\n", layout->n_parameters);
fprintf(stderr,
"NAME UNITS SYMBOL TYPE DESCRIPTION\n");
}
if(all && !excel)
fprintf(outfile,"\nParameters%s\nName%sFixedValue%sUnits%sSymbol%sType%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
for (i=0; i<layout->n_parameters; i++) {
pardef = layout->parameter_definition+i;
if(!pardef->fixed_value) {
nvariableparms++;
if(!all) continue;
}
if(verbose) fprintf(stderr, "%-19s %-19s %-19s %-19s %s\n",
pardef->name, pardef->units?pardef->units:"", pardef->symbol?pardef->symbol:"",
SDDS_type_name[pardef->type-1], pardef->description?pardef->description:"");
if (!excel) {
if(all) fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s%s%s\n",
pardef->name, delimiter,
pardef->fixed_value?pardef->fixed_value:"", delimiter,
pardef->units?pardef->units:"", delimiter,
pardef->symbol?pardef->symbol:"", delimiter,
SDDS_type_name[pardef->type-1], delimiter,
pardef->description?pardef->description:"", delimiter);
else fprintf(outfile,"%s%s%s%s%s\n",
pardef->name, delimiter, delimiter,
pardef->fixed_value?pardef->fixed_value:"", delimiter);
}
}
}
/* Arrays */
if (layout->n_arrays && all) {
if(verbose) {
fprintf(stderr, "\n%" PRId32 " arrays of data:\n", layout->n_arrays);
fprintf(stderr, "NAME UNITS SYMBOL"
" FORMAT TYPE FIELD GROUP DESCRIPTION\n");
fprintf(stderr, " LENGTH NAME\n");
}
if (!excel) {
fprintf(outfile,"\nArrays%s\nName%sUnits%sSymbol%sFormat%sType%sField Length%sGroup Name%sDescription%s\n", delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
}
for (i=0; i<layout->n_arrays; i++) {
arraydef = layout->array_definition+i;
if(verbose) fprintf(stderr, "%-15s %-15s %-15s %-7s %-8s*^%-5" PRId32 " %-7" PRId32 " %-15s %s\n",
arraydef->name, arraydef->units, arraydef->symbol,
arraydef->format_string, SDDS_type_name[arraydef->type-1], arraydef->dimensions,
arraydef->field_length, arraydef->group_name, arraydef->description);
if (!excel) {
fprintf(outfile,"%s%s%s%s%s%s%s%s%s*^%-5" PRId32 "%s%-7" PRId32 "%s%s%s%s%s\n",
arraydef->name, delimiter,
arraydef->units, delimiter,
arraydef->symbol, delimiter,
arraydef->format_string, delimiter,
SDDS_type_name[arraydef->type-1], arraydef->dimensions, delimiter,
arraydef->field_length, delimiter,
arraydef->group_name, delimiter,
arraydef->description, delimiter);
}
}
}
/* Associates */
/*
if (layout->n_associates && all) {
if(verbose) {
fprintf(stderr, "\n%ld associates:\n", layout->n_associates);
fprintf(stderr, "SDDS FILENAME PATH CONTENTS DESCRIPTION\n");
}
fprintf(outfile,"\nAssociates%s\nType%sFilename%sPath%sContents%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
for (i=0; i<layout->n_associates; i++)
if(verbose) fprintf(stderr, "%-5s %-19s %-29s %-19s %s\n",
layout->associate_definition[i].sdds?"SDDS":"Non-SDDS",
layout->associate_definition[i].filename, layout->associate_definition[i].path,
layout->associate_definition[i].contents, layout->associate_definition[i].description);
fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s\n",
layout->associate_definition[i].sdds?"yes":"no", delimiter,
layout->associate_definition[i].filename, delimiter,
layout->associate_definition[i].path, delimiter,
layout->associate_definition[i].contents, delimiter,
layout->associate_definition[i].description, delimiter);
}
*/
#ifdef USE_XLS
w = xlsNewWorkbook();
#ifdef __APPLE__
xlsWorkbookIconvInType(w, "UCS-4-INTERNAL");
#endif
#endif
/* Process tables */
while ((ntable=SDDS_ReadTable(&SDDS_table))>0) {
line=0;
#ifdef USE_XLS
if (excel) {
sprintf(sheet, "Sheet%d", ntable);
ws = xlsWorkbookSheet(w, sheet);
} else
fprintf(outfile,"\nTable %ld\n",ntable);
#else
fprintf(outfile,"\nTable %ld\n",ntable);
#endif
/* Variable parameters */
if (nvariableparms) {
for (i=0; i<layout->n_parameters; i++) {
pardef = layout->parameter_definition+i;
if(pardef->fixed_value) continue;
if (!(data=SDDS_GetParameter(&SDDS_table, pardef->name, NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef USE_XLS
if (excel) {
xlsWorksheetLabel(ws, line, 0, pardef->name, NULL);
switch(pardef->type) {
case SDDS_DOUBLE:
xlsWorksheetNumberDbl(ws, line, 1, *((double*)data), NULL);
break;
case SDDS_FLOAT:
xlsWorksheetNumberDbl(ws, line, 1, *((float*)data), NULL);
break;
case SDDS_ULONG:
xlsWorksheetNumberInt(ws, line, 1, *((uint32_t*)data), NULL);
break;
case SDDS_LONG:
xlsWorksheetNumberInt(ws, line, 1, *((int32_t*)data), NULL);
break;
case SDDS_USHORT:
xlsWorksheetNumberInt(ws, line, 1, *((unsigned short*)data), NULL);
break;
case SDDS_SHORT:
xlsWorksheetNumberInt(ws, line, 1, *((short*)data), NULL);
break;
case SDDS_STRING:
xlsWorksheetLabel(ws, line, 1, *((char**)data), NULL);
break;
case SDDS_CHARACTER:
sprintf(buffer, "%c", *((char*)data));
xlsWorksheetLabel(ws, line, 1, buffer, NULL);
break;
default:
break;
}
line++;
} else {
#endif
fprintf(outfile,"%s%s%s",pardef->name,delimiter,delimiter);
SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
fprintf(outfile,"%s\n",delimiter);
#ifdef USE_XLS
}
#endif
}
line++;
}
/* Columns */
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(1);
}
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
#ifdef USE_XLS
if (excel) {
xlsWorksheetLabel(ws, line, i, coldef->name, NULL);
}
else
fprintf(outfile,"%s%s",coldef->name,delimiter);
#else
fprintf(outfile,"%s%s",coldef->name,delimiter);
#endif
}
line++;
if (!excel)
fprintf(outfile,"\n");
if (nrows) {
for (j=0; j<nrows; j++) {
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
if (!(data=SDDS_GetValue(&SDDS_table, coldef->name,j,NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef USE_XLS
if (excel) {
switch(coldef->type) {
case SDDS_DOUBLE:
xlsWorksheetNumberDbl(ws, line, i, *((double*)data), NULL);
break;
case SDDS_FLOAT:
xlsWorksheetNumberDbl(ws, line, i, *((float*)data), NULL);
break;
case SDDS_ULONG:
xlsWorksheetNumberInt(ws, line, i, *((uint32_t*)data), NULL);
break;
case SDDS_LONG:
xlsWorksheetNumberInt(ws, line, i, *((int32_t*)data), NULL);
break;
case SDDS_USHORT:
xlsWorksheetNumberInt(ws, line, i, *((unsigned short*)data), NULL);
break;
case SDDS_SHORT:
xlsWorksheetNumberInt(ws, line, i, *((short*)data), NULL);
break;
case SDDS_STRING:
xlsWorksheetLabel(ws, line, i, *((char**)data), NULL);
break;
case SDDS_CHARACTER:
sprintf(buffer, "%c", *((char*)data));
xlsWorksheetLabel(ws, line, i, buffer, NULL);
break;
default:
break;
}
} else {
#endif
switch(coldef->type) {
case SDDS_DOUBLE:
fprintf(outfile, "%.*g", DBL_DIG, *((double*)data));
break;
case SDDS_FLOAT:
fprintf(outfile, "%.*g", FLT_DIG, *((float*)data));
break;
default:
SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
break;
}
fprintf(outfile,delimiter);
#ifdef USE_XLS
}
#endif
}
if (!excel)
fprintf(outfile,"\n");
line++;
}
}
}
}
#ifdef USE_XLS
ret = xlsWorkbookDump(w, output);
xlsDeleteWorkbook(w);
#endif
/*
QUIT:
*/
fflush(stdout);
if (!SDDS_Terminate(&SDDS_table)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return(0);
}
/**************************** main ****************************************/
int main(int argc, char **argv)
{
FILE *outfile;
SDDS_TABLE SDDS_table;
SDDS_LAYOUT *layout;
COLUMN_DEFINITION *coldef;
PARAMETER_DEFINITION *pardef;
ARRAY_DEFINITION *arraydef;
long list_request;
char s[256];
char *input, *output;
long i, j, i_arg, append_units, nrows, ntable, len;
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]);
list_request = -1;
input = output = NULL;
append_units = 0;
pipeFlags = 0;
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
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:
SDDS_Bomb(strcat("Unknown option: ", s_arg[i_arg].list[0]));
break;
}
}
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");
}
}
processFilenames("sdds2math", &input, &output, pipeFlags, 0, NULL);
if (output) {
outfile=fopen(output,"w");
if(!outfile)
SDDS_Bomb(strcat("Can't open output file ", output));
}
else {
outfile = stdout;
}
/* Calculate formats for converting to Mathematica convention */
len=strlen(iformat); /* Inputformat */
format=(char *)calloc(256,sizeof(char)); /* Whole format */
rformat=(char *)calloc(256,sizeof(char)); /* Part before e */
strcpy(format,iformat);
if((ptr=strchr(format,'E'))) *ptr='e'; /* Aren't going to use E or G anyway */
if((ptr=strchr(format,'G'))) *ptr='g';
strcpy(rformat,format);
if((ptr=strpbrk(rformat,"eg"))) *ptr='f';
/* fprintf(outfile,"Created from SDDS file: %s\n",filename[file]); */
if (!SDDS_InitializeInput(&SDDS_table, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
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);
if (text)
fprintf(outfile,"\"%s\",",text?text:"No description\t");
if (contents)
if(verbose) printf("contents: %s\n", contents);
fprintf(outfile,"\"%s\"",contents?contents:"No description\t");
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->units, coldef->symbol,
coldef->format_string, SDDS_type_name[coldef->type-1], coldef->field_length, coldef->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->units, pardef->symbol,
SDDS_type_name[pardef->type-1], pardef->description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
pardef->name?pardef->name:"No name",
pardef->fixed_value?pardef->units:"",
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->units, arraydef->symbol,
arraydef->format_string, SDDS_type_name[arraydef->type-1], arraydef->dimensions,
arraydef->field_length, arraydef->group_name, arraydef->description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s*^%" PRId32 "\",%-7" 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->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?"SDDS":"Non-SDDS",
layout->associate_definition[i].filename, layout->associate_definition[i].path,
layout->associate_definition[i].contents, layout->associate_definition[i].description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
layout->associate_definition[i].sdds?"True":"False",
layout->associate_definition[i].filename,
layout->associate_definition[i].path,
layout->associate_definition[i].contents,
layout->associate_definition[i].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(1);
}
/* 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);
}
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);
}
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(1);
}
/* for (i=0; i<layout->n_columns; i++) { */
/* coldef = layout->column_definition+i; */
/* fprintf(outfile,"%s%s",coldef->name,delimiter); */
/* } */
/* fprintf(outfile,"\n"); */
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(1);
}
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);
}
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);
}
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 */
/*
QUIT:
*/
fflush(stdout);
if (!SDDS_Terminate(&SDDS_table)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return(0);
}
