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)
{
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);
}
void track_through_ztransverse(double **part, long np, ZTRANSVERSE *ztransverse, double Po,
RUN *run, long i_pass, CHARGE *charge
)
{
static double *posItime[2] = {NULL, NULL}; /* array for particle density times x, y*/
static double *posIfreq; /* array for FFT of particle density times x or y*/
static double *Vtime = NULL; /* array for voltage acting on each bin */
static long max_n_bins = 0;
static long *pbin = NULL; /* array to record which bin each particle is in */
static double *time = NULL; /* array to record arrival time of each particle */
static double *pz = NULL;
static long max_np = 0;
double *Vfreq, *iZ;
#if USE_MPI
long i;
#endif
long ib, nb, n_binned, nfreq, iReal, iImag, plane, first;
double factor, tmin, tmax, tmean, dt, userFactor[2], rampFactor=1;
static long not_first_call = -1;
long ip, ip1, ip2, bunches, bunch, npb, i_pass0;
long bucketEnd[MAX_BUCKETS];
#if USE_MPI
float *buffer_send, *buffer_recv;
#endif
#if defined(DEBUG)
FILE *fp;
#endif
i_pass0 = i_pass;
if ((i_pass -= ztransverse->startOnPass)<0)
return;
if (i_pass>=(ztransverse->rampPasses-1))
rampFactor = 1;
else
rampFactor = (i_pass+1.0)/ztransverse->rampPasses;
not_first_call += 1;
#if (!USE_MPI)
if (np>max_np) {
pbin = trealloc(pbin, sizeof(*pbin)*(max_np=np));
time = trealloc(time, sizeof(*time)*max_np);
pz = trealloc(pz, sizeof(*pz)*max_np);
}
#else
if (USE_MPI) {
long np_total;
if (isSlave) {
MPI_Allreduce(&np, &np_total, 1, MPI_LONG, MPI_SUM, workers);
if (np_total>max_np) {
/* if the total number of particles is increased, we do reallocation for every CPU */
pbin = trealloc(pbin, sizeof(*pbin)*(max_np=np));
time = trealloc(time, sizeof(*time)*max_np);
pz = trealloc(pz, sizeof(*pz)*max_np);
max_np = np_total; /* max_np should be the sum across all the processors */
}
}
}
#endif
if ((part[0][6]-floor(part[0][6]))!=0) {
/* This is a kludgey way to determine that particles have been assigned to buckets */
printf("Bunched beam detected\n"); fflush(stdout);
#if USE_MPI
if (n_processors!=1) {
printf("Error (ZTRANSVERSE): must have bunch_frequency=0 for parallel mode.\n");
MPI_Barrier(MPI_COMM_WORLD); /* Make sure the information can be printed before aborting */
MPI_Abort(MPI_COMM_WORLD, 2);
}
#endif
/* Start by sorting in bucket order */
qsort(part[0], np, COORDINATES_PER_PARTICLE*sizeof(double), comp_BucketNumbers);
/* Find the end of the buckets in the particle list */
bunches = 0;
for (ip=1; ip<np; ip++) {
if ((part[ip-1][6]-floor(part[ip-1][6]))!=(part[ip][6]-floor(part[ip][6]))) {
/* printf("Bucket %ld ends with ip=%ld\n", bunches, ip-1); fflush(stdout); */
bucketEnd[bunches++] = ip-1;
if (bunches>=MAX_BUCKETS) {
bombElegant("Error (wake): maximum number of buckets was exceeded", NULL);
}
}
}
bucketEnd[bunches++] = np-1;
} else {
bunches = 1;
bucketEnd[0] = np-1;
}
/* printf("Bucket %ld ends with ip=%ld\n", bunches, bucketEnd[bunches-1]); fflush(stdout); */
ip2 = -1;
for (bunch=0; bunch<bunches; bunch++) {
ip1 = ip2+1;
ip2 = bucketEnd[bunch];
npb = ip2-ip1+1;
/* printf("Processing bunch %ld with %ld particles\n", bunch, npb); fflush(stdout); */
/* Compute time coordinate of each particle */
tmean = computeTimeCoordinates(time+ip1, Po, part+ip1, npb);
find_min_max(&tmin, &tmax, time+ip1, npb);
#if USE_MPI
find_global_min_max(&tmin, &tmax, np, workers);
#endif
if (bunch==0) {
/* use np here since we need to compute the macroparticle charge */
set_up_ztransverse(ztransverse, run, i_pass, np, charge, tmax-tmin);
}
nb = ztransverse->n_bins;
dt = ztransverse->bin_size;
tmin -= dt;
tmax -= dt;
if ((tmax-tmin)*2>nb*dt) {
TRACKING_CONTEXT tcontext;
getTrackingContext(&tcontext);
fprintf(stderr, "%s %s: Time span of bunch (%le s) is more than half the total time span (%le s).\n",
entity_name[tcontext.elementType],
tcontext.elementName,
tmax-tmin, nb*dt);
fprintf(stderr, "If using broad-band impedance, you should increase the number of bins and rerun.\n");
fprintf(stderr, "If using file-based impedance, you should increase the number of data points or decrease the frequency resolution.\n");
exitElegant(1);
}
if (nb>max_n_bins) {
posItime[0] = trealloc(posItime[0], 2*sizeof(**posItime)*(max_n_bins=nb));
posItime[1] = trealloc(posItime[1], 2*sizeof(**posItime)*(max_n_bins=nb));
posIfreq = trealloc(posIfreq, 2*sizeof(*posIfreq)*(max_n_bins=nb));
Vtime = trealloc(Vtime, 2*sizeof(*Vtime)*(max_n_bins+1));
}
for (ib=0; ib<nb; ib++)
posItime[0][2*ib] = posItime[0][2*ib+1] =
posItime[1][2*ib] = posItime[1][2*ib+1] = 0;
/* make arrays of I(t)*x and I(t)*y */
n_binned = binTransverseTimeDistribution(posItime, pz, pbin, tmin, dt, nb,
time+ip1, part+ip1, Po, npb,
ztransverse->dx, ztransverse->dy,
ztransverse->xDriveExponent, ztransverse->yDriveExponent);
#if (!USE_MPI)
if (n_binned!=npb) {
fprintf(stdout, "Warning: only %ld of %ld particles were binned (ZTRANSVERSE)!\n", n_binned, npb);
if (!not_first_call) {
fprintf(stdout, "*** This may produce unphysical results. Your wake needs smaller frequency\n");
fprintf(stdout, " spacing to cover a longer time span.\n");
}
fflush(stdout);
}
#else
if (USE_MPI) {
int all_binned, result = 1;
if (isSlave)
result = ((n_binned==np) ? 1 : 0);
MPI_Allreduce(&result, &all_binned, 1, MPI_INT, MPI_LAND, workers);
if (!all_binned) {
if (myid==1) {
/* This warning will be given only if the flag MPI_DEBUG is defined for the Pelegant */
fprintf(stdout, "warning: Not all of %ld particles were binned (WAKE)\n", np);
fprintf(stdout, "consider setting n_bins=0 in WAKE definition to invoke autoscaling\n");
fflush(stdout);
}
}
}
#endif
userFactor[0] = ztransverse->factor*ztransverse->xfactor*rampFactor;
userFactor[1] = ztransverse->factor*ztransverse->yfactor*rampFactor;
first = 1;
for (plane=0; plane<2; plane++) {
#if USE_MPI
/* This could be good for some advanced network structures */
/*
if (isSlave) {
double buffer[nb];
MPI_Allreduce(posItime[plane], buffer, nb, MPI_DOUBLE, MPI_SUM, workers);
memcpy(posItime[plane], buffer, sizeof(double)*nb);
}
*/
if (isSlave) {
buffer_send = malloc(sizeof(float) * nb);
buffer_recv = malloc(sizeof(float) * nb);
for (i=0; i<nb; i++)
buffer_send[i] = posItime[plane][i];
MPI_Reduce(buffer_send, buffer_recv, nb, MPI_FLOAT, MPI_SUM, 1, workers);
MPI_Bcast(buffer_recv, nb, MPI_FLOAT, 1, workers);
for (i=0; i<nb; i++)
posItime[plane][i] = buffer_recv[i];
free(buffer_send);
free(buffer_recv);
}
#endif
if (userFactor[plane]==0) {
for (ib=0; ib<nb; ib++)
Vtime[ib] = 0;
} else {
if (ztransverse->smoothing)
SavitzyGolaySmooth(posItime[plane], nb, ztransverse->SGOrder,
ztransverse->SGHalfWidth, ztransverse->SGHalfWidth, 0);
/* Take the FFT of (x*I)(t) to get (x*I)(f) */
memcpy(posIfreq, posItime[plane], 2*nb*sizeof(*posIfreq));
realFFT(posIfreq, nb, 0);
/* Compute V(f) = i*Z(f)*(x*I)(f), putting in a factor
* to normalize the current waveform
*/
Vfreq = Vtime;
factor = ztransverse->macroParticleCharge*particleRelSign/dt*userFactor[plane];
iZ = ztransverse->iZ[plane];
Vfreq[0] = posIfreq[0]*iZ[0]*factor;
nfreq = nb/2 + 1;
if (nb%2==0)
/* Nyquist term */
Vfreq[nb-1] = posIfreq[nb-1]*iZ[nb-1]*factor;
for (ib=1; ib<nfreq-1; ib++) {
iImag = (iReal = 2*ib-1)+1;
/* The signs are chosen here to get agreement with TRFMODE.
In particular, test particles following closely behind the
drive particle get defocused.
*/
Vfreq[iReal] = (posIfreq[iReal]*iZ[iImag] + posIfreq[iImag]*iZ[iReal])*factor;
Vfreq[iImag] = -(posIfreq[iReal]*iZ[iReal] - posIfreq[iImag]*iZ[iImag])*factor;
}
/* Compute inverse FFT of V(f) to get V(t) */
realFFT(Vfreq, nb, INVERSE_FFT);
Vtime = Vfreq;
/* change particle transverse momenta to reflect voltage in relevant bin */
applyTransverseWakeKicks(part+ip1, time+ip1, pz, pbin, npb,
Po, plane,
Vtime, nb, tmin, dt, ztransverse->interpolate,
plane==0?ztransverse->xProbeExponent:ztransverse->yProbeExponent);
}
if (ztransverse->SDDS_wake_initialized && ztransverse->wakes) {
/* wake potential output */
factor = ztransverse->macroParticleCharge*particleRelSign/dt;
if ((ztransverse->wake_interval<=0 || ((i_pass0-ztransverse->wake_start)%ztransverse->wake_interval)==0) &&
i_pass0>=ztransverse->wake_start && i_pass0<=ztransverse->wake_end) {
if (first && !SDDS_StartTable(&ztransverse->SDDS_wake, nb)) {
SDDS_SetError("Problem starting SDDS table for wake output (track_through_ztransverse)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (ib=0; ib<nb; ib++) {
if (!SDDS_SetRowValues(&ztransverse->SDDS_wake, SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE, ib,
0, ib*dt,
1+plane*2, posItime[plane][ib]*factor,
2+plane*2, Vtime[ib], -1)) {
SDDS_SetError("Problem setting rows of SDDS table for wake output (track_through_ztransverse)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_SetParameters(&ztransverse->SDDS_wake, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"Pass", i_pass0, "q", ztransverse->macroParticleCharge*particleRelSign*np, NULL)) {
SDDS_SetError("Problem setting parameters of SDDS table for wake output (track_through_ztransverse)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (ztransverse->broad_band) {
if (!SDDS_SetParameters(&ztransverse->SDDS_wake, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"Rs", ztransverse->Rs, "fo", ztransverse->freq,
"Deltaf", ztransverse->bin_size, NULL)) {
SDDS_SetError("Problem setting parameters of SDDS table for wake output (track_through_ztransverse)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!first) {
if (!SDDS_WriteTable(&ztransverse->SDDS_wake)) {
SDDS_SetError("Problem writing SDDS table for wake output (track_through_ztransverse)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!inhibitFileSync)
SDDS_DoFSync(&ztransverse->SDDS_wake);
}
}
}
first = 0;
}
}
#if defined(MIMIMIZE_MEMORY)
free(posItime[0]);
free(posItime[1]);
free(posIfreq);
free(Vtime);
free(pbin);
free(time);
free(pz);
posItime[0] = posItime[1] = Vtime = time = pz = posIfreq = NULL;
pbin = NULL;
max_n_bins = max_np = 0 ;
#endif
}
int main(int argc, char **argv)
{
SDDS_TABLE SDDS_table;
SCANNED_ARG *scanned;
long i, i_arg, points;
char *input, *output, *name, *indep_var, *var_list_format;
char *mpl_title, *mpl_topline, *descrip_text, *descrip_contents;
FILE *fpi;
char buffer[BUFSIZE], buffer0[BUFSIZE], buffer1[BUFSIZE];
char *ptr, *ptr1, *ptr2;
char **data_name, *package_name, *data_format;
long data_names, data_sets_seen, data_sets_expected, realIndex, imagIndex;
double **real_data, **imag_data, *var_list;
argc = scanargs(&scanned, argc, argv);
if (argc<3)
bomb(NULL, USAGE);
input = output = package_name = data_format = indep_var = var_list_format = ptr = NULL;
mpl_title = mpl_topline = descrip_text = descrip_contents = NULL;
data_names = realIndex = imagIndex = 0;
data_name = NULL;
real_data = imag_data = NULL;
var_list = NULL;
data_sets_expected = data_sets_seen = 0;
points = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (scanned[i_arg].arg_type==OPTION) {
delete_chars(scanned[i_arg].list[0], "_");
/* process options here */
switch (match_string(scanned[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_DESCRIPTION:
if (scanned[i_arg].n_items!=3)
SDDS_Bomb("invalid -description syntax");
descrip_text = scanned[i_arg].list[1];
descrip_contents = scanned[i_arg].list[2];
break;
case SET_MPL_LABELS:
if (scanned[i_arg].n_items!=3)
SDDS_Bomb("invalid -mpllabels syntax");
mpl_title = scanned[i_arg].list[1];
mpl_topline = scanned[i_arg].list[2];
break;
default:
SDDS_Bomb("invalid option seen");
break;
}
}
else {
if (!input)
input = scanned[i_arg].list[0];
else if (!output)
output = scanned[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
if (!input)
SDDS_Bomb("input file not seen");
if (!output)
SDDS_Bomb("output file not seen");
fpi = fopen_e(input, "r", 0);
if (!fgets(buffer, BUFSIZE, fpi) || strncmp(buffer, CITIFILE_TAG, strlen(CITIFILE_TAG))!=0 ||
!(ptr=strchr(buffer, ' ')))
SDDS_Bomb("valid CITIFILE version line not found");
*ptr++ = 0;
ptr[strlen(ptr)-1] = 0;
if (strncmp(ptr, CITIFILE_VERSION, strlen(CITIFILE_VERSION))!=0)
fprintf(stderr, "warning: the CITIFILE version is %s--this program is only designed for version %s\n",
ptr, CITIFILE_VERSION);
if (!SDDS_InitializeOutput(&SDDS_table, SDDS_BINARY, 0, descrip_text, descrip_contents,
output))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if ((mpl_title &&
SDDS_DefineParameter(&SDDS_table, "mplTitle", NULL, NULL, NULL, NULL, SDDS_STRING, mpl_title)<0) ||
(mpl_topline &&
SDDS_DefineParameter(&SDDS_table, "mplTopline", NULL, NULL, NULL, NULL, SDDS_STRING, mpl_topline)<0))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
while (fgets(buffer, BUFSIZE, fpi)) {
#if DEBUG
fputs(buffer, stderr);
#endif
buffer[strlen(buffer)-1] = 0;
strcpy(buffer0, buffer);
ptr1 = NULL;
if ((ptr1=strchr(buffer, ' ')))
*ptr1++ = 0;
switch (match_string(buffer, citi_keyword, N_CITI_KEYWORDS, EXACT_MATCH)) {
case CITI_NA_KEYWORD:
name = buffer+1;
if (!*ptr1 || !(ptr2=strchr(ptr1, ' '))) {
fprintf(stderr, "The following line contains an apparently invalid #NA keyword:\n%s\n",
buffer0);
exit(1);
}
*(ptr1-1) = '_';
*ptr2++ = 0;
if (SDDS_DefineParameter(&SDDS_table, name, NULL, NULL, NULL, NULL, SDDS_STRING, ptr2)<0) {
SDDS_SetError(buffer0);
SDDS_SetError("Problem creating parameter for #NA keyword in the following line:");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
break;
case CITI_NAME_KEYWORD:
if (!ptr1 || SDDS_StringIsBlank(ptr1)) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
#if DEBUG
fprintf(stderr, "NAME: %s\n", ptr1);
#endif
cp_str(&package_name, ptr1);
if (SDDS_DefineParameter(&SDDS_table, "CITIPackageName", NULL, NULL, NULL, NULL, SDDS_STRING,
package_name)<0) {
SDDS_SetError(buffer0);
SDDS_SetError("Problem creating parameter for NAME keyword in the following line:");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
break;
case CITI_VAR_KEYWORD:
if (!ptr1 || SDDS_StringIsBlank(ptr1)) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
#if DEBUG
fprintf(stderr, "VAR: %s\n", ptr1);
#endif
if (!(indep_var=get_token(ptr1)) || !(var_list_format=get_token(ptr1)) || !get_long(&points, ptr1) ||
points<=0) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
if (SDDS_DefineColumn(&SDDS_table, indep_var, NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0)<0) {
SDDS_SetError(buffer0);
SDDS_SetError("Problem creating column for data element in the following line:");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
break;
case CITI_CONSTANT_KEYWORD:
if (!ptr1 || !(ptr2=strchr(ptr1, ' '))) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
#if DEBUG
fprintf(stderr, "CONSTANT: %s\n", ptr1);
#endif
*ptr2++ = 0;
if (SDDS_DefineParameter(&SDDS_table, ptr1, NULL, NULL, NULL, NULL, SDDS_STRING, ptr2)<0) {
SDDS_SetError(buffer0);
SDDS_SetError("Problem creating parameter for CONSTANT keyword in the following line:");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
break;
case CITI_COMMENT_KEYWORD:
if (!ptr1 || SDDS_StringIsBlank(ptr1)) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
#if DEBUG
fprintf(stderr, "COMMENT: %s\n", ptr1);
#endif
break;
case CITI_DATA_KEYWORD:
if (!ptr1 || !(ptr2 = strchr(ptr1, ' '))) {
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
exit(1);
}
#if DEBUG
fprintf(stderr, "DATA: %s\n", ptr1);
#endif
*ptr2++ = 0;
cp_str(&data_format, ptr2);
data_name = trealloc(data_name, sizeof(*data_name)*(data_names+1));
cp_str(data_name+data_names, ptr1);
alter_data_name(data_name[data_names]);
real_data = trealloc(real_data, sizeof(*real_data)*(data_names+1));
imag_data = trealloc(imag_data, sizeof(*imag_data)*(data_names+1));
sprintf(buffer, "%sReal", data_name[data_names]);
sprintf(buffer1, "%sImag", data_name[data_names]);
if ((realIndex=SDDS_DefineColumn(&SDDS_table, buffer,
NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0 ||
(imagIndex=SDDS_DefineColumn(&SDDS_table, buffer1,
NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0 ) {
SDDS_SetError(buffer0);
SDDS_SetError("Problem creating column for data element in the following line:");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
data_names++;
break;
case CITI_VAR_LIST_KEYWORD:
if (ptr1 && !SDDS_StringIsBlank(ptr1))
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
#if DEBUG
fprintf(stderr, "VAR_LIST_BEGIN seen\n");
#endif
if (points==0)
SDDS_Bomb("VAR_LIST_BEGIN statement seen without prior VAR statement");
var_list = tmalloc(sizeof(*var_list)*points);
if (!read_CITI_var_list(fpi, var_list, points))
SDDS_Bomb("unable to read VAR_LIST");
break;
case CITI_BEGIN_KEYWORD:
if (ptr1 && !SDDS_StringIsBlank(ptr1))
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
#if DEBUG
fprintf(stderr, "BEGIN seen\n");
#endif
if (points==0)
SDDS_Bomb("BEGIN statement seen without prior VAR statement");
real_data[data_sets_seen] = tmalloc(sizeof(**real_data)*points);
imag_data[data_sets_seen] = tmalloc(sizeof(**imag_data)*points);
if (!read_CITI_data(fpi, real_data[data_sets_seen], imag_data[data_sets_seen], points))
SDDS_Bomb("problem reading data section");
data_sets_seen++;
break;
case CITI_SEG_LIST_BEGIN:
if (ptr1 && !SDDS_StringIsBlank(ptr1))
fprintf(stderr, "The following line contains erroneous input:\n%s\n", buffer0);
#if DEBUG
fprintf(stderr, "SEG_LIST_BEGIN seen\n");
#endif
if (points==0)
SDDS_Bomb("SEG_LIST_BEGIN statement seen without prior SEG statement");
var_list = tmalloc(sizeof(*var_list)*points);
if (!read_CITI_seg_list(fpi, var_list, points))
SDDS_Bomb("unable to read SEG_LIST");
break;
default:
fprintf(stderr, "unidentifiable line in file--not CITI format:\n\"%s\"\n",
buffer0);
exit(1);
break;
}
}
if (!points)
SDDS_Bomb("no data in file");
if (data_sets_seen!=(data_sets_expected=data_names))
SDDS_Bomb("fewer data sets than expected were actually present");
if (!var_list) {
fprintf(stderr, "warning: no independent variable data---supplying index\n");
var_list = tmalloc(sizeof(*var_list)*points);
for (i=0; i<points; i++)
var_list[i] = i;
}
if (!SDDS_WriteLayout(&SDDS_table) || !SDDS_StartTable(&SDDS_table, points))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_NAME, (void*)var_list, points, indep_var))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
for (i=0; i<data_sets_expected; i++) {
if (!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_INDEX, (void*)real_data[i], points,
realIndex) ||
!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_INDEX, (void*)imag_data[i], points,
imagIndex)) {
fprintf(stderr, "problem setting data for column(s) %s\n", data_name[i]);
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
}
if (!SDDS_WriteTable(&SDDS_table) || !SDDS_Terminate(&SDDS_table))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
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);
}
void dump_IBScatter(SDDS_TABLE *SDDS_table, IBSCATTER *IBS, long pass)
{
long i, islice;
double gamma;
log_entry("dump_IBScatter");
if (!IBS->elements)
return;
gamma = sqrt(ipow(IBS->pCentral[IBS->elements-1], 2)+1.);
for (islice=0; islice<IBS->nslice; islice++) {
if (!SDDS_StartTable(SDDS_table, IBS->elements)) {
SDDS_SetError("Problem starting SDDS table (dump_IBScatter)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (i=0; i<IBS->elements; i++) {
if (!SDDS_SetRowValues(SDDS_table, SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE, i,
0, IBS->name[i], 1, IBS->s[i],
2, IBS->xRateVsS[islice][i], 3, IBS->yRateVsS[islice][i], 4, IBS->zRateVsS[islice][i],
5, IBS->betax[islice][i], 6, IBS->alphax[islice][i], 7, IBS->etax[i], 8, IBS->etaxp[i],
9, IBS->betay[islice][i], 10, IBS->alphay[islice][i], 11, IBS->etay[i], 12, IBS->etayp[i], -1)) {
SDDS_SetError("Problem setting SDDS row values (dump_IBScatter)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if ((!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "Particles", fabs(IBS->icharge[islice]/particleCharge), NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "Charge", IBS->icharge[islice]*1e9, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "TotalSlice", IBS->nslice, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "NSlice", islice+1, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "s", IBS->s[IBS->elements-1], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "Pass", pass, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "StartPoint", IBS->offset, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "Elements", IBS->elements, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "ds", IBS->revolutionLength, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "dt", IBS->dT, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "xGrowthRate", IBS->xGrowthRate[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "yGrowthRate", IBS->yGrowthRate[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "zGrowthRate", IBS->zGrowthRate[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "enx0", IBS->emitx0[islice]*gamma, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "eny0", IBS->emity0[islice]*gamma, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "emitx0", IBS->emitx0[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "emity0", IBS->emity0[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "sigmaDelta0", IBS->sigmaDelta0[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "sigmaz0", IBS->sigmaz0[islice], NULL))){
SDDS_SetError("Problem setting SDDS parameters (dump_IBScatter)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!IBS->isRing) {
if ((!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "emitx", IBS->emitx[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "emity", IBS->emity[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "enx", IBS->emitx[islice]*gamma, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "eny", IBS->emity[islice]*gamma, NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "sigmaDelta", IBS->sigmaDelta[islice], NULL))||
(!SDDS_SetParameters(SDDS_table, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, "sigmaz", IBS->sigmaz[islice], NULL))){
SDDS_SetError("Problem setting SDDS parameters (dump_IBScatter)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_WriteTable(SDDS_table)) {
SDDS_SetError("Problem writing SDDS table (dump_IBScatter)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
SDDS_UpdatePage(SDDS_table, 0);
if (!inhibitFileSync)
SDDS_DoFSync(SDDS_table);
}
log_exit("dump_IBScatter");
}
int main(int argc, char **argv)
{
SDDS_TABLE SDDS_table;
SCANNED_ARG *scanned;
unsigned long majorOrderFlag;
long i_arg;
char *input, *output, *definition;
long hsize, vsize;
char *data, *data_name;
char ts1[100], ts2[100];
FILE *fpi;
short columnMajorOrder=0;
argc = scanargs(&scanned, argc, argv);
if (argc<4)
bomb(NULL, USAGE);
input = output = data_name = NULL;
hsize = DEFAULT_HSIZE;
vsize = DEFAULT_VSIZE;
definition = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
if (scanned[i_arg].arg_type==OPTION) {
/* process options here */
switch (match_string(scanned[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_MAJOR_ORDER:
majorOrderFlag=0;
scanned[i_arg].n_items--;
if (scanned[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[i_arg].list+1, &scanned[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 SET_DEFINITION:
data_name = scanned[i_arg].list[1];
definition = process_column_definition(scanned[i_arg].list+1,
scanned[i_arg].n_items-1);
if (!strstr(definition, "type=character"))
SDDS_Bomb("data type must be character for now");
break;
case SET_SIZE:
if (scanned[i_arg].n_items!=3 ||
sscanf(scanned[i_arg].list[1], "%ld", &hsize)!=1 || hsize<=0 ||
sscanf(scanned[i_arg].list[2], "%ld", &vsize)!=1 || vsize<=0)
bomb("invalid -size syntax", USAGE);
break;
default:
bomb("invalid option seen", USAGE);
break;
}
}
else {
if (!input)
input = scanned[i_arg].list[0];
else if (!output)
output = scanned[i_arg].list[0];
else
bomb("too many filenames", USAGE);
}
}
if (!input)
SDDS_Bomb("input file not seen");
if (!output)
SDDS_Bomb("output file not seen");
if (!definition)
SDDS_Bomb("definition not seen");
sprintf(ts1, "%ld", hsize);
sprintf(ts2, "%ld", vsize);
if (!SDDS_InitializeOutput(&SDDS_table, SDDS_BINARY, 0,
"screen image from raw file", "screen image",
output) ||
SDDS_ProcessColumnString(&SDDS_table, definition, 0)<0 ||
SDDS_DefineParameter(&SDDS_table, "NumberOfRows", NULL, NULL, "number of rows",
NULL, SDDS_LONG, ts1)<0 ||
!SDDS_DefineParameter(&SDDS_table, "NumberOfColumns", NULL, NULL,
"number of columns", NULL, SDDS_LONG, ts2)<0)
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
SDDS_table.layout.data_mode.column_major = columnMajorOrder;
if (!SDDS_WriteLayout(&SDDS_table) || !SDDS_StartTable(&SDDS_table, hsize*vsize))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
data = tmalloc(sizeof(*data)*hsize*vsize);
fpi = fopen_e(input, "r", 0);
if (fread(data, sizeof(*data), hsize*vsize, fpi)!=hsize*vsize)
SDDS_Bomb("unable to read (all) data from input file");
fclose(fpi);
if (!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_NAME, data, hsize*vsize,
data_name) ||
!SDDS_WriteTable(&SDDS_table) || !SDDS_Terminate(&SDDS_table))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
return(0);
}
void dump_cormon_stats(long verbose, long plane, double **kick, long n_kicks,
double **position, long n_positions, double *Cdp, long n_iterations, long cycle,
long final_cycle, long sim_step, long textOnly)
{
long i, j;
static double **data = NULL;
static char **stage = NULL;
static long n_iter = 0;
if (!verbose && !SDDS_cormon_initialized)
return;
log_entry("dump_cormon_stats");
if (!data || n_iterations>n_iter) {
if (data)
free_czarray_2d((void**)data, n_iter+1, N_COLUMNS);
if (stage)
free(stage);
data = (double**)czarray_2d(sizeof(**data), n_iterations+1, N_COLUMNS);
stage = tmalloc(sizeof(*stage)*(n_iterations+1));
n_iter = n_iterations;
}
for (j=0; j<=n_iterations; j++) {
if (j==0)
stage[j] = "uncorrected";
else if (j==n_iterations)
stage[j] = "corrected";
else
stage[j] = "intermediate";
data[j][IC_ITERATION] = j;
data[j][IC_CYCLE] = cycle;
data[j][IC_KRMS] = data[j][IC_KMAX] = data[j][IC_PRMS] =
data[j][IC_PMAX] = 0;
for (i=0; i<n_kicks; i++) {
if (FABS(kick[j][i]) > data[j][IC_KMAX])
data[j][IC_KMAX] = FABS(kick[j][i]);
data[j][IC_KRMS] += sqr(kick[j][i]);
}
if (n_kicks)
data[j][IC_KRMS] = sqrt(data[j][IC_KRMS]/n_kicks);
for (i=0; i<n_positions; i++) {
if (FABS(position[j][i]) > data[j][IC_PMAX])
data[j][IC_PMAX] = FABS(position[j][i]);
data[j][IC_PRMS] += sqr(position[j][i]);
}
if (n_positions)
data[j][IC_PRMS] = sqrt(data[j][IC_PRMS]/n_positions);
data[j][IC_CDP] = (Cdp?Cdp[j]:0);
}
if (SDDS_cormon_initialized && !textOnly) {
if (!SDDS_StartTable(&SDDS_cormon, n_iterations+1)) {
SDDS_SetError("Unable to start SDDS table (dump_cormon_stats)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_cormon, SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,
IP_STEP, sim_step, IP_PLANE, plane?"vertical":"horizontal",
IP_FINAL, final_cycle?'y':'n', -1)) {
SDDS_SetError("Unable to set SDDS parameter values (dump_cormon_stats)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (j=0; j<=n_iterations; j++) {
if (!SDDS_SetRowValues(&SDDS_cormon, SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE, j,
IC_ITERATION, j,
IC_CYCLE, cycle,
IC_KRMS, data[j][IC_KRMS],
IC_PRMS, data[j][IC_PRMS],
IC_KMAX, data[j][IC_KMAX],
IC_PMAX, data[j][IC_PMAX],
IC_CDP, data[j][IC_CDP],
IC_STAGE, stage[j], -1)) {
fprintf(stdout, "Unable to set row %ld values (dump_cormon_stats)\n", j);
fflush(stdout);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exitElegant(1);
}
}
if (!SDDS_WriteTable(&SDDS_cormon)) {
SDDS_SetError("Unable to write corrector data (dump_cormon_stats)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!inhibitFileSync)
SDDS_DoFSync(&SDDS_cormon);
if (!SDDS_EraseData(&SDDS_cormon)) {
SDDS_SetError("Unable to erase corrector data (dump_cormon_stats)");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (verbose) {
for (j=0; j<=n_iterations; j++)
if (Cdp) {
fprintf(stdout, " %c %4ld %8.3f %8.3f %8.3f %8.3f %8.3f %s\n",
'x'+(plane?1:0), j,
1e3*data[j][IC_KRMS], 1e3*data[j][IC_PRMS],
1e3*data[j][IC_KMAX], 1e3*data[j][IC_PMAX],
1e2*data[j][IC_CDP],
(j==n_iterations?"**":"") );
fflush(stdout);
}
else {
fprintf(stdout, " %c %4ld %8.3f %8.3f %8.3f %8.3f %s\n",
'x'+(plane?1:0), j,
1e3*data[j][IC_KRMS], 1e3*data[j][IC_PRMS],
1e3*data[j][IC_KMAX], 1e3*data[j][IC_PMAX],
(j==n_iterations?"**":"") );
fflush(stdout);
}
}
log_exit("dump_cormon_stats");
}
int main(int argc, char **argv)
{
SDDS_TABLE SDDS_table;
SCANNED_ARG *scanned;
long i, i_arg, index, points, lsb_first, bytes_per_number;
char *input, *output, buffer[BUFSIZE];
char *signal_name, *ptr, *parameter_name;
char *mpl_title, *mpl_topline, *descrip_text, *descrip_contents;
FILE *fpi;
long code, binary;
double xIncrement, xZero, yMultiplier, yZero;
char *xUnits, *yUnits;
double *time, *data;
short columnMajorOrder=0;
unsigned long majorOrderFlag;
xUnits = yUnits = NULL;
argc = scanargs(&scanned, argc, argv);
if (argc<3)
bomb(NULL, USAGE);
input = output = signal_name = NULL;
mpl_title = mpl_topline = descrip_text = descrip_contents = NULL;
binary = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (scanned[i_arg].arg_type==OPTION) {
delete_chars(scanned[i_arg].list[0], "_");
/* process options here */
switch (match_string(scanned[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_MAJOR_ORDER:
majorOrderFlag=0;
scanned[i_arg].n_items--;
if (scanned[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[i_arg].list+1, &scanned[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 SET_SIGNAL_NAME:
if (scanned[i_arg].n_items!=2)
bomb("invalid -signal_name syntax", USAGE);
signal_name = scanned[i_arg].list[1];
break;
case SET_DESCRIPTION:
if (scanned[i_arg].n_items!=3)
bomb("invalid -description syntax", USAGE);
descrip_text = scanned[i_arg].list[1];
descrip_contents = scanned[i_arg].list[2];
break;
case SET_MPL_LABELS:
if (scanned[i_arg].n_items!=3)
bomb("invalid -mpl_labels syntax", USAGE);
mpl_title = scanned[i_arg].list[1];
mpl_topline = scanned[i_arg].list[2];
break;
default:
bomb("invalid option seen", USAGE);
break;
}
}
else {
if (!input)
input = scanned[i_arg].list[0];
else if (!output)
output = scanned[i_arg].list[0];
else
bomb("too many filenames", USAGE);
}
}
if (!input)
SDDS_Bomb("input file not seen");
if (!output)
SDDS_Bomb("output file not seen");
if (!signal_name)
signal_name = "V";
fpi = fopen_e(input, "r", 0);
if (fread(buffer, 1, strlen(TEK_PreambleString), fpi)!=strlen(TEK_PreambleString) ||
strncmp(TEK_PreambleString, buffer, strlen(TEK_PreambleString))!=0)
SDDS_Bomb("file does not appear to be in Tektronix format");
parameter_name = buffer;
while ((code=GetNextItem(buffer, BUFSIZE, fpi))<3) {
if (!(ptr=strchr(buffer, ':')))
SDDS_Bomb("error parsing input file--missing colon on parameter tag");
*ptr++ = 0;
if (strcmp(TEK_DataMarker, parameter_name)==0)
break;
index = 0;
while (TEK_parameter[index].TEK_name) {
if (strcmp(TEK_parameter[index].TEK_name, parameter_name)==0)
break;
index++;
}
if (!TEK_parameter[index].TEK_name) {
fprintf(stderr, "warning: parameter %s is not recognized\n",
parameter_name);
continue;
}
if (TEK_parameter[index].value_string) {
fprintf(stderr, "error: duplicate entries for parameter %s\n",
parameter_name);
exit(1);
}
SDDS_RemovePadding(ptr);
SDDS_CopyString(&TEK_parameter[index].value_string, ptr);
if (code==2 || code==3)
break;
}
if (code!=2)
SDDS_Bomb("unexpected end of file");
if (fread(buffer, 1, strlen(TEK_DataMarker), fpi)!=strlen(TEK_DataMarker) ||
strncmp(TEK_DataMarker, buffer, strlen(TEK_DataMarker))!=0)
SDDS_Bomb("CURVE item missing or not in right place");
if (!SDDS_InitializeOutput(&SDDS_table, SDDS_BINARY, 0, descrip_text, descrip_contents,
output))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
SDDS_table.layout.data_mode.column_major = columnMajorOrder;
index = 0;
while (TEK_parameter[index].TEK_name) {
if (!TEK_parameter[index].value_string) {
index++;
continue;
}
if (strcmp(TEK_parameter[index].TEK_name, TEK_XIncrementName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%lf", &xIncrement)!=1)
SDDS_Bomb("unable to scan value for x increment");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_XZeroName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%lf", &xZero)!=1)
SDDS_Bomb("unable to scan value for x zero");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_YZeroName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%lf", &yZero)!=1)
SDDS_Bomb("unable to scan value for y zero");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_YMultiplierName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%lf", &yMultiplier)!=1)
SDDS_Bomb("unable to scan value for y multiplier");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_XUnitsName)==0) {
xUnits = TEK_parameter[index].value_string;
str_tolower(xUnits);
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_YUnitsName)==0) {
yUnits = TEK_parameter[index].value_string;
str_tolower(yUnits);
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_PointsName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%ld", &points)!=1)
SDDS_Bomb("unable to scan value for number of points");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_EncodingName)==0) {
if (strcmp(TEK_parameter[index].value_string, "ASCII")==0)
binary = 0;
else if (strcmp(TEK_parameter[index].value_string, "BINARY")==0)
binary = 1;
else
SDDS_Bomb("data encoding is neither ASCII nor BINARY");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_BytesPerNumberName)==0) {
if (sscanf(TEK_parameter[index].value_string, "%ld", &bytes_per_number)!=1)
SDDS_Bomb("unable to scan value bytes per number");
}
else if (strcmp(TEK_parameter[index].TEK_name, TEK_ByteOrderName)==0) {
lsb_first = 1;
if (strcmp(TEK_parameter[index].value_string, "LSB")!=0)
lsb_first = 0;
}
if (SDDS_DefineParameter(&SDDS_table, TEK_parameter[index].SDDS_name,
NULL, NULL, TEK_parameter[index].TEK_name,
NULL, TEK_parameter[index].type,
TEK_parameter[index].value_string)<0)
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
index++;
}
if (mpl_title &&
(SDDS_DefineParameter(&SDDS_table, "mplTitle", NULL, NULL, NULL, NULL, SDDS_STRING, mpl_title)<0 ||
SDDS_DefineParameter(&SDDS_table, "mplTopline", NULL, NULL, NULL, NULL, SDDS_STRING, mpl_topline)<0))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (SDDS_DefineColumn(&SDDS_table, "t", NULL, xUnits, NULL, NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&SDDS_table, signal_name, NULL, yUnits, NULL, NULL, SDDS_DOUBLE, 0)<0 ||
!SDDS_WriteLayout(&SDDS_table) || !SDDS_StartTable(&SDDS_table, points))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
data = tmalloc(sizeof(*data)*points);
time = tmalloc(sizeof(*time)*points);
if (!binary) {
for (i=0; i<points; i++) {
if (!(code=GetNextItem(buffer, BUFSIZE, fpi)))
SDDS_Bomb("insufficient data in input file");
if (code==4) {
points = i;
break;
}
time[i] = xZero + i*xIncrement;
if (sscanf(buffer, "%lf", data+i)!=1)
SDDS_Bomb("invalid data in input file");
data[i] = yZero + data[i]*yMultiplier;
}
}
else {
short sdata;
fread(buffer, sizeof(char), 4, fpi);
for (i=0; i<points; i++) {
if (fread(&sdata, sizeof(sdata), 1, fpi)!=1) {
fprintf(stderr, "file ends unexpectedly\n");
points = i;
break;
}
time[i] = xZero + i*xIncrement;
data[i] = sdata;
data[i] = yZero + data[i]*yMultiplier;
}
}
if (!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_NAME, time, points, "t") ||
!SDDS_SetColumn(&SDDS_table, SDDS_SET_BY_NAME, data, points, signal_name) ||
!SDDS_WriteTable(&SDDS_table) || !SDDS_Terminate(&SDDS_table))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
return(0);
}
