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);
}
int main(int argc, char **argv)
{
SCANNED_ARG *scanned;
SDDS_TABLE inputPage, outputPage, residualPage;
char *inputfile, *outputfile;
char **column, **excludeColumn;
int32_t columns;
long excludeColumns;
char *indColumnName;
long verbose;
long iArg, i, j, ipage;
double *indVar, *indVarOrig;
char *indVarUnits;
char **intColumn, **slopeColumn, **slopeSigmaColumn, **interceptSigmaColumn;
char *Units,*slopeUnits;
double *depVar, *depVarOrig;
long order;
double *coef, *coefsigma, *weight, *diff, *diffOrig, chi;
long iCol, iRow;
long rows, rowsOrig;
double rmsResidual;
double slopeSigma, interceptSigma;
char **sigmaColumn, **chiSquaredColumn;
long *sigmaColumnExists;
long doSlopeSigma, generateSigma, doPreliminaryFit;
long validSigmas;
double sigmaSum, averageSigma;
long ascii;
char *residualFile;
unsigned long pipeFlags;
long tmpfile_used, noWarnings;
double xMin, xMax;
indVar = indVarOrig = depVar = depVarOrig = coef = coefsigma = weight = diff = NULL;
intColumn = slopeColumn = slopeSigmaColumn = interceptSigmaColumn = sigmaColumn = chiSquaredColumn = NULL;
slopeUnits = NULL;
sigmaColumnExists = NULL;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
indColumnName = NULL;
verbose = 0;
doSlopeSigma = 0;
generateSigma = 0;
doPreliminaryFit = 0;
ascii = 0;
pipeFlags = 0;
tmpfile_used=0;
noWarnings=0;
residualFile = NULL;
xMin = xMax = 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_INDEPENDENT_COLUMN:
if (!(indColumnName = 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_ASCII:
ascii = 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_SIGMA:
doSlopeSigma = 1;
if (scanned[iArg].n_items > 1 ) {
switch (match_string(scanned[iArg].list[1], sigma_option, SIGMA_OPTIONS, UNIQUE_MATCH)) {
case SIGMA_GENERATE:
generateSigma = 1;
break;
default:
SDDS_Bomb("unrecognized sigma option given");
break;
}
}
break;
case CLO_RESIDUAL:
if (!(residualFile=scanned[iArg].list[1])){
fprintf(stderr,"No file specified in -residual option.\n");
exit(1);
}
break;
case CLO_RANGE:
if (scanned[iArg].n_items!=3 ||
1!=sscanf(scanned[iArg].list[1], "%lf", &xMin) ||
1!=sscanf(scanned[iArg].list[2], "%lf", &xMax) ||
xMin>=xMax)
SDDS_Bomb("incorrect -range syntax");
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");
}
}
if (residualFile && outputfile) {
if (!strcmp( residualFile, outputfile)) {
fprintf( stderr, "Residual file can't be the same as the output file.\n");
exit(1);
}
}
processFilenames("sddsslopes", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (!indColumnName) {
fprintf( stderr, "independentVariable not given\n");
exit(1);
}
if (!excludeColumns) {
excludeColumn = defaultExcludedColumn;
excludeColumns = DEFAULT_EXCLUDED_COLUMNS;
}
if (verbose)
fprintf(stderr,"Reading file %s.\n",inputfile);
if ( !SDDS_InitializeInput( &inputPage, inputfile) )
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
while (0 < (ipage=SDDS_ReadTable( &inputPage))) {
if (verbose) {
fprintf(stderr, "working on page %ld\n", ipage);
}
rows = SDDS_CountRowsOfInterest(&inputPage);
rowsOrig = rows;
/*************************************\
* make array of independent variable
\*************************************/
if (ipage==1) {
indVar = (double*) malloc( sizeof(*indVar) * rows);
}
else {
indVar = (double*) realloc( indVar, sizeof(*indVar) * rows);
}
if (ipage==1) {
if (!SDDS_FindColumn(&inputPage, FIND_NUMERIC_TYPE, indColumnName, NULL)){
fprintf(stderr,"Something wrong with column %s.\n", indColumnName);
SDDS_CheckColumn(&inputPage, indColumnName, NULL, SDDS_ANY_NUMERIC_TYPE, stderr);
exit(1);
}
}
/* filter out the specified range in independent variable */
if (xMin!=xMax) {
if (!(indVarOrig = SDDS_GetColumnInDoubles( &inputPage, indColumnName)))
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
for (i=j=0; i<rowsOrig; i++) {
if (indVarOrig[i]<=xMax && indVarOrig[i]>=xMin) {
indVar[j] = indVarOrig[i];
j++;
}
}
rows = j;
}
else {
if (!(indVar = SDDS_GetColumnInDoubles( &inputPage, indColumnName)))
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if ( ipage == 1 ) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &indVarUnits, SDDS_GET_BY_NAME, indColumnName))
SDDS_PrintErrors( stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!indVarUnits) {
indVarUnits = (char *) malloc(sizeof(*indVarUnits));
indVarUnits[0] = 0;
}
}
/************************************\
* initialize residual file
\************************************/
if (residualFile) {
if ( ipage == 1 ) {
if(!SDDS_InitializeOutput(&residualPage,ascii?SDDS_ASCII:SDDS_BINARY,1,
"Residual of 2-term fit",NULL,outputfile) ||
!SDDS_InitializeCopy(&residualPage, &inputPage, residualFile, "w") ||
!SDDS_WriteLayout(&residualPage) )
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_CopyPage(&residualPage,&inputPage))
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/************************************\
* 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
\*************************************/
if (ipage==1) {
intColumn = (char**) malloc((sizeof(char*)*columns));
slopeColumn = (char**) malloc((sizeof(char*)*columns));
if (doSlopeSigma) {
slopeSigmaColumn = (char**) malloc((sizeof(char*)*columns));
interceptSigmaColumn = (char**) malloc((sizeof(char*)*columns));
chiSquaredColumn = (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 (doSlopeSigma) {
slopeSigmaColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("SlopeSigma")+1)));
strcat(strcpy(slopeSigmaColumn[i], column[i]), "SlopeSigma");
interceptSigmaColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("InterceptSigma")+1)));
strcat(strcpy(interceptSigmaColumn[i], column[i]), "InterceptSigma");
chiSquaredColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("ChiSquared")+1)));
strcat(strcpy(chiSquaredColumn[i], column[i]), "ChiSquared");
}
}
}
/************************************\
* Write layout for output file
\*************************************/
if (ipage==1) {
if (verbose)
fprintf(stderr,"Opening file %s.\n",outputfile);
if(!SDDS_InitializeOutput(&outputPage,ascii?SDDS_ASCII:SDDS_BINARY,1,
"2-term fit",NULL,outputfile) ||
0>SDDS_DefineParameter(&outputPage, "InputFile", "InputFile", NULL,
"InputFile", NULL, SDDS_STRING, 0) ||
0>SDDS_DefineColumn(&outputPage, "IndependentVariable", NULL, NULL, NULL, NULL, SDDS_STRING,0) )
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
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 (doSlopeSigma) {
if (0>SDDS_DefineColumn(&outputPage, interceptSigmaColumn[iCol], NULL, Units,
NULL, NULL, SDDS_DOUBLE,0) ||
0>SDDS_DefineColumn(&outputPage, slopeSigmaColumn[iCol], NULL, slopeUnits,
NULL, NULL, SDDS_DOUBLE,0) ||
0>SDDS_DefineColumn(&outputPage, chiSquaredColumn[iCol], NULL, NULL,
NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(slopeUnits);
}
if ( !SDDS_WriteLayout(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ( !SDDS_StartTable(&outputPage,1) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile",inputfile?inputfile:"pipe",NULL) ||
!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
"IndependentVariable", indColumnName, NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* determine which included columns has a Sigma column defined in the input file */
if ( ipage == 1 ) {
sigmaColumn = (char **) malloc( sizeof(*sigmaColumn)*columns);
sigmaColumnExists = (long *) malloc(columns*sizeof(*sigmaColumnExists));
for (iCol=0; iCol<columns; iCol++) {
sigmaColumn[iCol] = (char *) malloc( sizeof(**sigmaColumn) *
(strlen(column[iCol]) + strlen("Sigma") + 1) );
strcat( strcpy(sigmaColumn[iCol], column[iCol]), "Sigma");
switch(SDDS_CheckColumn(&inputPage, sigmaColumn[iCol], NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
sigmaColumnExists[iCol] = 1;
break;
default:
/* try other possible spelling */
strcat( strcpy(sigmaColumn[iCol] ,"Sigma"), column[iCol]);
switch(SDDS_CheckColumn(&inputPage, sigmaColumn[iCol], NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
sigmaColumnExists[iCol] = 1;
break;
default:
sigmaColumnExists[iCol] = 0;
}
break;
}
}
}
if ( ipage == 1 ) {
weight = (double*)malloc(sizeof(*weight)*rows);
diff = (double*)malloc(sizeof(*diff)*rows);
order=1;
coef = (double*)malloc(sizeof(*coef)*(order+1));
coefsigma = (double*)malloc(sizeof(*coefsigma)*(order+1));
}
else {
weight = (double*)realloc( weight, sizeof(*weight)*rows);
diff = (double*)realloc( diff, sizeof(*diff)*rows);
order=1;
coef = (double*)realloc( coef, sizeof(*coef)*(order+1));
coefsigma = (double*)realloc( coefsigma, sizeof(*coefsigma)*(order+1));
}
if (ipage==1) {
depVar = (double*) malloc( sizeof(*depVar) * rows);
}
else {
depVar = (double*) realloc( depVar, sizeof(*depVar) * rows);
}
for (iCol=0; iCol<columns; iCol++) {
if (verbose)
fprintf(stderr,"Doing column %s.\n", column[iCol]);
/* filter out the specified range in independent variable */
if (xMin!=xMax) {
if (!(depVarOrig = (double*) SDDS_GetColumnInDoubles(&inputPage, column[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
for (i=j=0; i<rowsOrig; i++) {
if ( xMin <= indVarOrig[i] && indVarOrig[i] <= xMax ) {
depVar[j] = depVarOrig[i];
j++;
}
}
}
else {
if (!(depVar=SDDS_GetColumnInDoubles(&inputPage, column[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
/*********************
three possibilities:
1) don't do or write slope errors. (doSlopeSigma=0)
do one lsf call with all weights = 1
2) calculated slope errors from sigma columns in the input file.
(doSlopeSigma=1 && generateSigma=0 && sigmaColumnExists[iCol]=1 )
do one lsf call with weights from sigma columns
3) calculate slope errors from generated sigma from a preliminary fit.
(doSlopeSigma=1 && (generateSigma=1 || sigmaColumnExists[iCol]=NULL)
do preliminary fit to generate sigma
*********************/
for (iRow=0; iRow<rows; iRow++)
weight[iRow] = 1;
if (doSlopeSigma) {
/*********************
check validity of sigma column values
*********************/
if( !generateSigma && sigmaColumnExists[iCol]) {
if (verbose)
fprintf(stderr,"\tUsing column %s for sigma.\n",sigmaColumn[iCol]);
if(!(weight=SDDS_GetColumnInDoubles(&inputPage, sigmaColumn[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
/* check for zero weight values which will give lsfn problems */
validSigmas = rows;
sigmaSum = 0;
for (iRow=0; iRow<rows; iRow++) {
sigmaSum += weight[iRow];
if(!weight[iRow]) {
validSigmas--;
/*
fprintf(stderr,"Warning: %s of row number %ld is zero. Using average sigma.\n",sigmaColumn[iCol],iRow); */
}
}
if (!validSigmas) {
fprintf(stderr,"Warning: All sigmas are zero.\n");
doPreliminaryFit = 1;
}
else if (validSigmas!=rows) {
/* fix some sigmas */
averageSigma = sigmaSum/ validSigmas;
fprintf(stderr, "Warning: replacing %ld invalid sigmas with average (%e)\n",
rows-validSigmas, averageSigma);
for (iRow=0; iRow<rows; iRow++) {
if(!weight[iRow]) {
weight[iRow] = averageSigma;
}
}
}
}
else {
doPreliminaryFit = 1;
}
}
if (doPreliminaryFit) {
if (verbose)
fprintf(stderr,"\tGenerating sigmas from rms residual of a preliminary fit.\n");
if (!(lsfn(indVar, depVar, weight, rows, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
rmsResidual = 0;
/* calculate rms residual */
for (iRow=0; iRow<rows; iRow++) {
rmsResidual += sqr(diff[iRow]);
}
rmsResidual = sqrt(rmsResidual/(rows));
for (iRow=0; iRow<rows; iRow++) {
weight[iRow] = rmsResidual;
}
}
if (!(lsfn(indVar, depVar, weight, rows, order, coef, coefsigma, &chi, diff))) {
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (doSlopeSigma) {
interceptSigma = coefsigma[0];
slopeSigma = coefsigma[1];
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
chiSquaredColumn[iCol], chi,
interceptSigmaColumn[iCol], interceptSigma,
slopeSigmaColumn[iCol], slopeSigma, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (residualFile) {
if (xMin!=xMax) {
/* calculate the residuals for the whole column explicitly since there
are points outside the range of which the lsf call did not calculate
the difference. */
diffOrig = (double*) malloc( rowsOrig * sizeof(double) );
for (i=0; i<rowsOrig; i++) {
diffOrig[i] = depVarOrig[i] - coef[0] - coef[1] * indVarOrig[i];
}
if( !SDDS_SetColumnFromDoubles(&residualPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
diffOrig,rowsOrig,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if( !SDDS_SetColumnFromDoubles(&residualPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
diff,rows,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
if (residualFile) {
if (!SDDS_WriteTable(&residualPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteTable(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (residualFile) {
if (!SDDS_Terminate(&residualPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if(!SDDS_Terminate(&inputPage) || !SDDS_Terminate(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
return(0);
}
int main(int argc, char **argv)
{
SCANNED_ARG *s_arg;
SDDS_DATASET inputPage, outputPage;
char *inputfile, *outputfile;
char **inputColumnName, **inputStringColumnName, **inputDoubleColumnName;
char **outputStringColumnName, **outputDoubleColumnName, **matchColumn=NULL;
long inputRows, inputDoubleColumns, inputStringColumns, indexColumn=0, matchColumns=0, noOldColumnNamesColumn=0;
long outputRows, outputDoubleColumns, outputStringColumns;
char **inputParameterName;
int32_t inputParameters, inputColumns;
char *inputDescription, *inputContents;
char *outputDescription;
long i, i_arg, col;
char *buffer;
char **columnOfStrings;
long buffer_size;
#define BUFFER_SIZE_INCREMENT 16384
MATRIX *R, *RInv;
long OldStringColumnsDefined;
char *inputStringRows, *outputStringRows;
char **stringArray, *stringParameter;
long token_length;
long verbose;
char format[32];
long digits;
char *Symbol, *Root;
void *parameterPointer;
long ascii;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long ipage=0, columnType;
char *oldColumnNames, *newColumnNamesColumn;
short columnMajorOrder=-1;
inputColumnName = outputStringColumnName = outputDoubleColumnName = inputParameterName = NULL;
outputRows = outputDoubleColumns = outputStringColumns = OldStringColumnsDefined = 0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
verbose = 0;
Symbol = Root = NULL;
ascii = 0;
digits=3;
pipeFlags = 0;
tmpfile_used = 0;
noWarnings = 0;
oldColumnNames = NULL;
newColumnNamesColumn = NULL;
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], commandline_option, COMMANDLINE_OPTIONS,
UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
s_arg[i_arg].n_items--;
if (s_arg[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, s_arg[i_arg].list+1, &s_arg[i_arg].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_MATCH_COLUMN:
matchColumns = s_arg[i_arg].n_items-1;
matchColumn = s_arg[i_arg].list+1;
break;
case CLO_INDEX_COLUMN:
indexColumn = 1;
break;
case CLO_NO_OLDCOLUMNNAMES:
noOldColumnNamesColumn = 1;
break;
case CLO_VERBOSE:
verbose=1;
break;
case CLO_ASCII:
ascii=1;
break;
case CLO_DIGITS:
if (!(get_long(&digits, s_arg[i_arg].list[1])))
bomb("no string given for option -digits", USAGE);
break;
case CLO_COLUMNROOT:
if (!(Root=s_arg[i_arg].list[1]))
SDDS_Bomb("No root string given");
break;
case CLO_SYMBOL:
if (!(Symbol=s_arg[i_arg].list[1]))
SDDS_Bomb("No symbol string given");
break;
case CLO_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_OLDCOLUMNNAMES:
if (!(oldColumnNames=s_arg[i_arg].list[1]))
SDDS_Bomb("No oldColumnNames string given");
break;
case CLO_NEWCOLUMNNAMES:
if (s_arg[i_arg].n_items!=2 ||
SDDS_StringIsBlank(newColumnNamesColumn = s_arg[i_arg].list[1]))
SDDS_Bomb("Invalid -newColumnNames syntax/value");
break;
default:
bomb("unrecognized option given", USAGE);
}
}
else {
if (!inputfile)
inputfile = s_arg[i_arg].list[0];
else if (!outputfile)
outputfile = s_arg[i_arg].list[0];
else
bomb("too many filenames given", USAGE);
}
}
processFilenames("sddstranpose", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (newColumnNamesColumn && Root)
SDDS_Bomb("-root and -newColumnNames are incompatible");
if (!SDDS_InitializeInput(&inputPage, inputfile) ||
!(inputParameterName=(char**)SDDS_GetParameterNames(&inputPage, &inputParameters)) ||
!SDDS_GetDescription(&inputPage, &inputDescription, &inputContents))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (matchColumns)
inputColumnName = getMatchingSDDSNames(&inputPage, matchColumn, matchColumns, &inputColumns, SDDS_MATCH_COLUMN);
else {
if (!(inputColumnName=(char**)SDDS_GetColumnNames(&inputPage, &inputColumns)))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
inputDoubleColumns=0;
inputStringColumns=0;
inputDoubleColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputStringColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputRows = 0;
/*********** \
* read data *
\***********/
while (0<SDDS_ReadTable(&inputPage)) {
ipage ++;
#if defined(DEBUG)
fprintf(stderr, "working on page %ld\n", ipage);
#endif
if (ipage==1) {
SDDS_DeferSavingLayout(1);
if( !SDDS_SetColumnFlags(&inputPage, 0))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
/* count the string and numerical columns in the input file */
for (i=0;i<inputColumns;i++) {
if ( SDDS_NUMERIC_TYPE( columnType = SDDS_GetColumnType( &inputPage, i))) {
inputDoubleColumnName[inputDoubleColumns]=inputColumnName[i];
inputDoubleColumns++;
}
}
for (i=0; i<inputPage.layout.n_columns; i++) {
if (inputPage.layout.column_definition[i].type == SDDS_STRING ) {
inputStringColumnName[inputStringColumns] = inputPage.layout.column_definition[i].name;
inputStringColumns++;
}
}
if( !(inputRows=SDDS_CountRowsOfInterest(&inputPage)))
SDDS_Bomb("No rows in dataset.");
}
else {
/* these statements are executed on the subsequent pages */
if (inputRows != SDDS_CountRowsOfInterest(&inputPage)) {
SDDS_Bomb("Datasets don't have the same number of rows.\nProcessing stopped before reaching the end of the input file.");
}
}
#if defined(DEBUG)
fprintf(stderr, "row flags set\n");
#endif
if (inputDoubleColumns == 0)
SDDS_Bomb("No numerical columns in file.");
if ((ipage==1) && verbose) {
fprintf(stderr, "No. of double/float/integer columns: %ld.\n", inputDoubleColumns);
fprintf(stderr, "No. of string columns: %ld.\n", inputStringColumns);
fprintf(stderr, "No. of rows: %ld.\n", inputRows);
}
/****************\
* transpose data *
\****************/
if (inputDoubleColumns) {
if (ipage == 1) {
m_alloc(&RInv, inputRows, inputDoubleColumns);
m_alloc(&R, inputDoubleColumns, inputRows);
}
for (col=0;col<inputDoubleColumns;col++){
if (!(R->a[col]=(double*)SDDS_GetColumnInDoubles(&inputPage, inputDoubleColumnName[col]))) {
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (verbose) {
m_show(R, "%9.6le ", "Transpose of input matrix:\n", stdout);
}
m_trans(RInv, R);
}
/***************************\
* determine existence of *
* transposed string columns *
\***************************/
if (ipage == 1) {
OldStringColumnsDefined=0;
switch(SDDS_CheckParameter(&inputPage, OLD_STRING_COLUMN_NAMES, NULL, SDDS_STRING, NULL)){
case SDDS_CHECK_OKAY:
OldStringColumnsDefined=1;
break;
case SDDS_CHECK_NONEXISTENT:
break;
case SDDS_CHECK_WRONGTYPE:
case SDDS_CHECK_WRONGUNITS:
fprintf(stderr, "Something wrong with parameter OldStringColumns.\n");
exit(1);
break;
}
if (OldStringColumnsDefined){
/* decompose OldStringColumns into names of string columns for the output file */
if (!SDDS_GetParameter(&inputPage, OLD_STRING_COLUMN_NAMES, &inputStringRows))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Parameter OldStringColumns: %s.\n", inputStringRows);
}
outputStringColumnName=(char**)malloc(sizeof(char*));
outputStringColumns=0;
buffer_size=BUFFER_SIZE_INCREMENT;
buffer=(char*)malloc(sizeof(char)*buffer_size);
while ( 0 <= (token_length = SDDS_GetToken(inputStringRows, buffer, BUFFER_SIZE_INCREMENT))){
if (!token_length)
SDDS_Bomb("A null string was detected in parameter OldStringColumns.\n");
if (!SDDS_CopyString(&outputStringColumnName[outputStringColumns], buffer))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Output string column: %s\n", outputStringColumnName[outputStringColumns]);
}
outputStringColumns++;
}
}
}
/*********************\
* define output page *
\*********************/
if ( ipage == 1 ) {
outputRows = inputDoubleColumns;
outputDoubleColumns = inputRows;
if (inputDescription){
outputDescription = (char*) malloc( sizeof(char) * (strlen("Transpose of ") + strlen(inputDescription) + 1));
strcat(strcpy(outputDescription, "Transpose of "), inputDescription);
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, outputDescription, inputContents, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, NULL, NULL, outputfile))
SDDS_PrintErrors(stdout, 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;
/***********************************\
* define names for double columns *
\***********************************/
if (!Root && inputStringColumns ) {
/* use specified string column, or first string column encountered */
if (!newColumnNamesColumn)
/* first string column encountered */
outputDoubleColumnName = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[0]);
else {
/* use specified string column */
if (SDDS_CheckColumn(&inputPage, newColumnNamesColumn, NULL, SDDS_STRING, stderr)!=SDDS_CHECK_OKAY)
SDDS_Bomb("column named with -newColumnNames does not exist in input");
outputDoubleColumnName = (char**)SDDS_GetColumn(&inputPage, newColumnNamesColumn);
}
for (i=1; i<inputRows; i++) {
if (match_string(outputDoubleColumnName[i-1], outputDoubleColumnName+i, inputRows-i, EXACT_MATCH)>=0) {
fprintf(stderr, "Error, duplicate %s found in input file string column %s, can not be used as output column names\n", outputDoubleColumnName[i-1], newColumnNamesColumn ? newColumnNamesColumn : inputStringColumnName[0]);
exit(1);
}
}
}
else {
/* use command line options to produce column names in the output file */
outputDoubleColumnName = (char**) malloc( outputDoubleColumns * sizeof(char*) );
digits = MAX(digits, log10(inputRows) + 1);
if (!Root){
Root = (char*) malloc( sizeof(char) * (strlen("Column")+1) );
strcpy(Root, "Column");
}
if (outputDoubleColumns!=1) {
for ( i=0; i < outputDoubleColumns; i++){
outputDoubleColumnName[i] = (char*) malloc( sizeof(char) * (strlen(Root)+digits+1));
sprintf(format, "%s%%0%ldld", Root, digits);
sprintf(outputDoubleColumnName[i], format, i);
}
}
else {/* only one row to transpose */
outputDoubleColumnName[0] = (char*) malloc( sizeof(char) * (strlen(Root)+1));
strcpy( outputDoubleColumnName[0], Root);
}
}
/*************************\
* define string columns *
\*************************/
if (OldStringColumnsDefined) {
if (!SDDS_DefineSimpleColumns(&outputPage, outputStringColumns,
outputStringColumnName, NULL, SDDS_STRING))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
/* by default there should be at least one string column, that of the old column names. */
if (!noOldColumnNamesColumn) {
outputStringColumns = 1;
outputStringColumnName = (char**) malloc( sizeof(char*));
if (oldColumnNames) {
/* commanline option specification */
outputStringColumnName[0] = oldColumnNames;
}
else {
outputStringColumnName[0] = (char*) malloc( sizeof(char) * (strlen("OldColumnNames") + 1));
strcpy(outputStringColumnName[0], "OldColumnNames");
}
if ( 0 > SDDS_DefineColumn(&outputPage, outputStringColumnName[0], NULL, NULL, NULL, NULL, SDDS_STRING, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (indexColumn && !SDDS_DefineSimpleColumn(&outputPage, "Index", NULL, SDDS_LONG))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/*************************\
* define double columns *
\*************************/
for ( i=0; i < outputDoubleColumns; i++)
if (Symbol){
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], Symbol, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], NULL, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/********************************\
* define string parameters *
* i.e. transposed string columns *
\********************************/
if ( inputStringColumns>1 ) {
if (0>SDDS_DefineParameter(&outputPage, OLD_STRING_COLUMN_NAMES,
NULL, NULL, "Transposed string columns", NULL, SDDS_STRING,
NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for ( i=0; i < inputStringColumns; i++){
if (0>SDDS_DefineParameter(&outputPage, inputStringColumnName[i], NULL, NULL, "Transposed string column data", NULL,
SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/*************************\
* transfer parameters not *
* associated with old *
* string columns *
\*************************/
if (inputParameters) {
for ( i=0; i < inputParameters; i++) {
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES)))
if ( 0 > SDDS_TransferParameterDefinition(&outputPage, &inputPage, inputParameterName[i], NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/***************\
* write layout *
\***************/
SDDS_DeferSavingLayout(0);
/* if InputFile is not already transfered ot the output file, then create it. */
switch( SDDS_CheckParameter(&outputPage, "InputFile", NULL, SDDS_STRING, NULL) ) {
case SDDS_CHECK_NONEXISTENT:
if (0>SDDS_DefineParameter(&outputPage, "InputFile", NULL, NULL, "Original matrix file", NULL, SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
default:
break;
}
if (!SDDS_WriteLayout(&outputPage) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "table layout defined\n");
#endif
if (!SDDS_StartTable(&outputPage, outputRows) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (ipage == 1) {
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile", inputfile?inputfile:"pipe", NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/***************************************\
* assign string columns from input *
* to string parameters in output *
\**************************************/
if ( inputStringColumns > 1) {
for ( i=0; i < inputStringColumns; i++){
columnOfStrings = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[i]);
stringParameter = JoinStrings(columnOfStrings, inputRows, BUFFER_SIZE_INCREMENT);
if ( !SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
inputStringColumnName[i], stringParameter, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(columnOfStrings);
free(stringParameter);
}
outputStringRows = JoinStrings(inputStringColumnName, inputStringColumns, BUFFER_SIZE_INCREMENT);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
OLD_STRING_COLUMN_NAMES, outputStringRows, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string parameters assigned\n");
#endif
if (inputParameters){
for ( i=0; i < inputParameters; i++){
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES))) {
parameterPointer = (void*) SDDS_GetParameter(&inputPage, inputParameterName[i], NULL);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputParameterName[i], parameterPointer, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(parameterPointer);
}
}
}
#if defined(DEBUG)
fprintf(stderr, "input parameters assigned\n");
#endif
/**********************************\
* assign data to *
* output table part of data set *
\**********************************/
if (outputRows) {
/***************************\
* assign string column data *
\***************************/
if (OldStringColumnsDefined){
for ( i=0 ; i < outputStringColumns; i++){
if (!SDDS_GetParameter(&inputPage, outputStringColumnName[i], &stringParameter))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
stringArray=TokenizeString(stringParameter, outputRows);
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
stringArray, outputRows, outputStringColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
else {
if (!noOldColumnNamesColumn && !SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputDoubleColumnName, outputRows, outputStringColumnName[0]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string data columns assigned\n");
#endif
/***************************\
* assign double column data *
\***************************/
for ( i=0 ; i < outputDoubleColumns; i++) /* i is the row index */
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
RInv->a[i], outputRows, outputDoubleColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (indexColumn) {
for (i=0; i<outputRows; i++)
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, i, "Index", i, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "double data columns assigned\n");
#endif
}
#if defined(DEBUG)
fprintf(stderr, "data assigned\n");
#endif
if (!SDDS_WriteTable(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
#if defined(DEBUG)
fprintf(stderr, "data written out\n");
#endif
}
if (inputDoubleColumns) {
m_free(&RInv);
m_free(&R);
}
if (inputColumnName) {
SDDS_FreeStringArray(inputColumnName, inputColumns);
free(inputColumnName);
}
if (inputStringColumns)
free(inputStringColumnName);
if (inputDescription)
free(inputDescription);
if (inputParameterName) {
SDDS_FreeStringArray(inputParameterName, inputParameters);
free(inputParameterName);
}
if (outputDoubleColumns) {
SDDS_FreeStringArray(outputDoubleColumnName, outputDoubleColumns);
free(outputDoubleColumnName);
}
if (!SDDS_Terminate(&inputPage) || !SDDS_Terminate(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
return(0);
}
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);
}
/**************************** 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);
}
