int main(int argc, char **argv)
{
SDDS_DATASET SDDS_orig, SDDS_out;
int32_t i, j, k, i_arg, rows, xfilter_provided, yfilter_provided, zfilter_provided, row;
long power=1;
SCANNED_ARG *s_arg;
char *inputFile, *outputRoot, output[1024], tmpcol[256];
double xmin, xmax, ymin, ymax, zmin, zmax, xinterval, yinterval, zinterval;
int32_t xdim, ydim, zdim, columnNames, outputColumns, page=0;
char **columnName, **outputColumn;
double ***Rho, ***Jz, rhoSum, rhoSum1, yRho, zRho, jzRho;
double x_min, x_max, y_min, y_max, z_min, z_max, x, y, z;
unsigned long dummyFlags = 0;
x_min = x_max = y_min = y_max = z_min = z_max = 0;
xfilter_provided = yfilter_provided = zfilter_provided = 0;
inputFile = outputRoot = NULL;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2)
bomb(NULL, USAGE);
columnNames = outputColumns = 0;
columnName = outputColumn = NULL;
Rho = Jz = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
delete_chars(s_arg[i_arg].list[0], "_");
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_POWER:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("Invalid -power syntax.");
if (!get_long(&power, s_arg[i_arg].list[1]))
SDDS_Bomb("Invalid -power value provided.");
break;
case SET_XFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -xfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &x_min, 1, 0,
"maximum", SDDS_DOUBLE, &x_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -xfilter syntax");
s_arg[i_arg].n_items++;
if (x_max<=x_min) {
fprintf(stderr, "Invalid -xfilter provided, x_max <= x_min\n");
exit(1);
}
xfilter_provided =1;
break;
case SET_YFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -yfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &y_min, 1, 0,
"maximum", SDDS_DOUBLE, &y_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -yfilter syntax");
s_arg[i_arg].n_items++;
if (y_max<=y_min) {
fprintf(stderr, "Invalid -yfilter provided, y_max <= y_min\n");
exit(1);
}
yfilter_provided =1;
break;
case SET_ZFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -zfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &z_min, 1, 0,
"maximum", SDDS_DOUBLE, &z_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -zfilter syntax");
s_arg[i_arg].n_items++;
if (z_max<=z_min) {
fprintf(stderr, "Invalid -yfilter provided, z_max <= z_min\n");
exit(1);
}
zfilter_provided =1;
break;
default:
fprintf(stderr, "Unknown option - %s provided.\n", s_arg[i_arg].list[0]);
exit(1);
}
} else {
if (!inputFile)
inputFile = s_arg[i_arg].list[0];
else if (!outputRoot)
outputRoot = s_arg[i_arg].list[0];
else
SDDS_Bomb("Too many file names provided.");
}
}
if (!outputRoot)
outputRoot = inputFile;
sprintf(output, "%s.ave", outputRoot);
if (!SDDS_InitializeInput(&SDDS_orig, inputFile)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
xdim = ydim = zdim = 1;
zmin = zmax = zinterval = 0;
while (SDDS_ReadPage(&SDDS_orig)>0) {
if (page==0) {
if (!SDDS_GetParameterAsDouble(&SDDS_orig, "origin1", &xmin) || !SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext1", &xmax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta1", &xinterval) || !SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells1", &xdim) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "origin2", &ymin) || !SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext2", &ymax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta2", &yinterval) || !SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells2", &ydim)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (SDDS_CheckParameter(&SDDS_orig, "origin3", NULL, SDDS_ANY_NUMERIC_TYPE, NULL)==SDDS_CHECK_OK) {
if (!SDDS_GetParameterAsDouble(&SDDS_orig, "origin3", &zmin) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext3", &zmax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta3", &zinterval) ||
!SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells3", &zdim)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (xfilter_provided) {
if (x_min>xmax || x_max<xmin) {
fprintf(stderr, "Invalid xfilter provided, it should be between %le and %le\n", xmin, xmax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
x_min = xmin;
x_max = xmax;
}
if (yfilter_provided) {
if (y_min>ymax || y_max<ymin) {
fprintf(stderr, "Invalid yfilter provided, it should be between %le and %le\n", ymin, ymax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
y_min = ymin;
y_max = ymax;
}
if (zfilter_provided && zmin!=0 && zmax!=0) {
if (z_min>zmax || z_max<zmin) {
fprintf(stderr, "Invalid zfilter provided, it should be between %le and %le\n", zmin, zmax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
z_min = zmin;
z_max = zmax;
}
Rho = malloc(sizeof(*Rho)*zdim);
Jz = malloc(sizeof(*Rho)*zdim);
for (i=0; i<zdim; i++) {
Rho[i] = malloc(sizeof(**Rho)*ydim);
Jz[i] = malloc(sizeof(**Jz)*ydim);
}
SetupOutputFile(&SDDS_out, output, zdim);
}
rows = SDDS_CountRowsOfInterest(&SDDS_orig);
if (rows!=xdim) {
fprintf(stderr, "Row number does not equal xdim size.\n");
exit(1);
}
for (j=1; j<=ydim; j++) {
sprintf(tmpcol, "Rho_%d",j);
Rho[page][j-1] = NULL;
if (!(Rho[page][j-1]=SDDS_GetColumnInDoubles(&SDDS_orig, tmpcol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
sprintf(tmpcol, "Jz_%d",j);
Jz[page][j-1] = NULL;
if (!(Jz[page][j-1]=SDDS_GetColumnInDoubles(&SDDS_orig, tmpcol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
page ++;
}
if (!SDDS_Terminate(&SDDS_orig)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (page!=zdim) {
free_data_memory(Rho, zdim, ydim);
free_data_memory(Jz, zdim, ydim);
fprintf(stderr, "Error, the page number does not equal to zdim size.\n");
exit(1);
}
if (!SDDS_StartPage(&SDDS_out, xdim) ||
!SDDS_SetParameters(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin1", xmin, "origin2", ymin, "origin3", zmin, "max_ext1", xmax, "max_ext2", ymax,
"delta1", xinterval, "delta2", yinterval, "numPhysCells1", xdim,
"numPhysCells2", ydim, "xstart", x_min, "xend", x_max, "ystart", y_min, "yend", y_max, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (zdim>1) {
if (!SDDS_SetParameters(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin3", zmin, "max_ext3", zmax,
"delta3", zinterval, "numPhysCells3", zdim,
"zstart", z_min, "zend", z_max, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
row = 0;
x = y = z = 0;
for (i=0; i<xdim; i++) {
rhoSum = rhoSum1 = 0;
yRho = zRho = jzRho = 0;
x = i * xinterval + xmin;
if (xfilter_provided && (x<x_min || x>x_max))
continue;
for (j=0; j<ydim; j++) {
y = j * yinterval + ymin;
if (yfilter_provided && (y<y_min || y>y_max))
continue;
for (k=0; k<zdim; k++) {
z = k * zinterval + zmin;
if (zfilter_provided && zdim>1 && (z<z_min || z>z_max))
continue;
if (power==1) {
yRho += fabs(Rho[k][j][i]) * y;
zRho += fabs(Rho[k][j][i]) * z;
jzRho += Rho[k][j][i] * Jz[k][j][i];
rhoSum += fabs(Rho[k][j][i]);
rhoSum1 += Rho[k][j][i];
} else {
yRho += pow(fabs(Rho[k][j][i]), power) * y;
zRho += pow(fabs(Rho[k][j][i]), power) * z;
jzRho += pow(Rho[k][j][i] * Jz[k][j][i], power);
rhoSum += pow(fabs(Rho[k][j][i]), power);
rhoSum1 += pow(Rho[k][j][i], power);
}
}
}
/*set row values */
if (!SDDS_SetRowValues(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
"x", x, "YAve", yRho/(rhoSum+1.0e-20), "JzAve", jzRho/(rhoSum1 + 1.0e-20), NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (zdim>1 && !SDDS_SetRowValues(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
"ZAve",zRho/(rhoSum+1.0e-20), NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row++;
}
if (!SDDS_WritePage(&SDDS_out) || !SDDS_Terminate(&SDDS_out))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free_data_memory(Rho, zdim, ydim);
free_data_memory(Jz, zdim, ydim);
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);
}
int main( int argc, char **argv)
{
SCANNED_ARG *scanned;
char *inputfile, *outputfile;
SDDS_DATASET twissPage, resultsPage;
double particles, charge, length;
long verbosity, noWarning, i, elements, superperiods, growthRatesOnly, force;
double pCentral0, I1, I2, I3, I4, I5, taux, tauy, taudelta;
double EMeV;
double emitx0, emitx, emitxInput, emityInput, emity, coupling, sigmaz0, sigmaz;
double sigmaDelta0, sigmaDelta, sigmaDeltaInput, xGrowthRate, yGrowthRate, zGrowthRate;
double xGrowthRateInitial, yGrowthRateInitial, zGrowthRateInitial;
double emitxOld, sigmaDeltaOld;
long method, converged;
/* used in simplex minimization */
double yReturn, *xGuess, *dxGuess, *xLowerLimit, *xUpperLimit;
short *disable;
long dimensions = 15, maxEvaluations = 500, maxPasses = 2;
double target = 1e-6;
int32_t integrationTurns, integrationStepSize;
long integrationPoints = 0;
double *exInteg=NULL, *eyInteg=NULL, *elInteg=NULL, *xRateInteg=NULL, *yRateInteg=NULL, *zRateInteg=NULL;
double *SdeltaInteg=NULL, *SzInteg=NULL;
int32_t *passInteg=NULL;
unsigned long dummyFlags;
double rfVoltage, rfHarmonic;
double alphac, U0, circumference, energy;
double *xRateVsS, *yRateVsS, *zRateVsS;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
xRateVsS = yRateVsS = zRateVsS = NULL;
inputfile = NULL;
outputfile = NULL;
energy = 0;
verbosity = 0;
isRing = 1;
particles = 0;
charge = 0;
coupling = emityInput = 0;
force = 1;
length = 0;
superperiods=1;
method = 0;
emitxInput = 0;
sigmaDeltaInput = 0;
growthRatesOnly = 0;
integrationTurns = 0;
rfVoltage = rfHarmonic = 0;
noWarning = 0;
for (i = 1; i<argc; i++) {
if (scanned[i].arg_type == OPTION) {
delete_chars(scanned[i].list[0], "_");
switch(match_string(scanned[i].list[0], option, N_OPTIONS, UNIQUE_MATCH)) {
case VERBOSE:
if(scanned[i].n_items > 1 ) {
get_long(&verbosity, scanned[i].list[1]);
} else {
verbosity=1;
}
break;
case ISRING:
if(scanned[i].n_items > 1 ) {
get_long(&isRing, scanned[i].list[1]);
} else {
isRing=1;
}
break;
case CHARGE:
get_double(&charge, scanned[i].list[1]);
break;
case EMITXINPUT:
/* This is really the emitx+emity, not emitx */
get_double(&emitxInput, scanned[i].list[1]);
break;
case EMITINPUT:
get_double(&emitxInput, scanned[i].list[1]);
break;
case DELTAINPUT:
get_double(&sigmaDeltaInput, scanned[i].list[1]);
break;
case LENGTH:
get_double(&length, scanned[i].list[1]);
length /= 1000; /* convert input length from mm to m */
break;
case COUPLING:
get_double(&coupling, scanned[i].list[1]);
break;
case EMITYINPUT:
get_double(&emityInput, scanned[i].list[1]);
break;
case FORCECOUPLING:
get_long(&force, scanned[i].list[1]);
break;
case PARTICLES:
get_double(&particles, scanned[i].list[1]);
break;
case SUPERPERIOD:
get_long(&superperiods, scanned[i].list[1]);
break;
case METHOD:
get_long(&method, scanned[i].list[1]);
break;
case GROWTHRATESONLY:
growthRatesOnly = 1;
break;
case SET_TARGET:
if (scanned[i].n_items!=2 ||
!get_double(&target, scanned[i].list[1]) ||
target<0)
bomb("invalid -target syntax", NULL);
break;
case RF:
if (scanned[i].n_items<2)
bomb("invalid -rf syntax", NULL);
scanned[i].n_items--;
rfVoltage = rfHarmonic = 0;
if (!scanItemList(&dummyFlags, scanned[i].list+1, &scanned[i].n_items, 0,
"voltage", SDDS_DOUBLE, &rfVoltage, 1, 0,
"harmonic", SDDS_DOUBLE, &rfHarmonic, 1, 0,
NULL) ||
rfVoltage<=0 || rfHarmonic<=0)
bomb("invalid -rf syntax/values", "-rf=voltage=MV,harmonic=<value>");
break;
case SET_ENERGY:
if (scanned[i].n_items!=2)
bomb("invalid -energy syntax", NULL);
if (!sscanf(scanned[i].list[1], "%lf", &energy) || energy<=0)
bomb("invalid -energy syntax/values", "-energy=<MeV>");
break;
case SET_INTEGRATE:
if (scanned[i].n_items<2)
bomb("invalid -integrate syntax", NULL);
integrationTurns = 0;
integrationStepSize = 1;
scanned[i].n_items--;
if (!scanItemList(&dummyFlags, scanned[i].list+1, &scanned[i].n_items, 0,
"turns", SDDS_LONG, &integrationTurns, 1, 0,
"stepsize", SDDS_LONG, &integrationStepSize, 1, 0,
NULL) ||
integrationTurns<=0 || integrationStepSize<1)
bomb("invalid -integrate syntax", NULL);
break;
case NO_WARNING:
noWarning = 1;
break;
default:
fprintf(stderr, "Unknown option %s given", scanned[i].list[0]);
exit(1);
break;
}
}
else {
if (!inputfile)
inputfile = scanned[i].list[0];
else if (!outputfile)
outputfile = scanned[i].list[0];
else
bomb("too many filenames given", NULL);
}
}
if (charge && particles) {
bomb("Options charge and particles cannot be both specified.",NULL);
}
if (!charge)
charge = particles * e_mks;
if (!particles) {
/* command line input value is in units of nC */
charge /= 1e9;
particles = charge/ e_mks;
}
if ((!coupling && !emityInput) || (coupling && emityInput))
bomb("Give -coupling or -emityInput (but not both)", NULL);
if (!length && !rfVoltage)
bomb("Specify either the bunch length or the rf voltage.", NULL);
if (growthRatesOnly && integrationTurns) {
growthRatesOnly = 0;
if (!noWarning)
fprintf( stdout, "*Warning* -growthRatesOnly option is incompatiable with -integrate option. The -growthRatesOnly will be disabled.\n");
}
if (!growthRatesOnly && !integrationTurns && !noWarning)
fprintf( stdout, "*Warning* The growth rate contribution columns in the results file will be those calculated from the equilibrium (or final) condition.\n");
if (integrationTurns && !isRing) {
integrationTurns = 0;
fprintf( stdout, "*Warning* -isRing=0 is incompatiable with -integrate option. The -integrate will be disabled.\n");
}
if (energy && !isRing) {
energy = 0;
fprintf( stdout, "*Warning* you can not scale energy for linac beam. Scaling will be disabled.\n");
}
/***************************************************\
* get parameter information from first input file *
\***************************************************/
if (verbosity)
fprintf( stdout, "Opening \"%s\" for checking presence of parameters.\n", inputfile);
if (!SDDS_InitializeInput(&twissPage, inputfile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* read first page of input file to get parameters
I1 I2 I3 I4 I5.
Check presence of first radiation integral.
*/
SDDS_ReadPage(&twissPage);
/* parameter Type */
switch(SDDS_CheckParameter(&twissPage, "I1", NULL, SDDS_DOUBLE, verbosity?stdout:NULL)) {
case SDDS_CHECK_NONEXISTENT:
if (verbosity)
fprintf( stdout, "\tParameter I1 not found in input file.\n");
break;
case SDDS_CHECK_WRONGTYPE:
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exitElegant(1);
break;
case SDDS_CHECK_OKAY:
break;
default:
fprintf( stdout, "Unexpected result from SDDS_CheckParameter routine while checking parameter Type.\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exitElegant(1);
break;
}
if (verbosity)
fprintf( stdout, "Opening \"%s\" for writing...\n", outputfile);
if (!SDDS_InitializeOutput(&resultsPage, SDDS_BINARY, 1, "Intra-beam scattering rates",
"Intra-beam scattering rates", outputfile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "I1", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "I2", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "I3", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "I4", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "I5", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "pCentral", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "taux", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "tauy", NULL) ||
!SDDS_TransferParameterDefinition(&resultsPage, &twissPage, "taudelta", NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (0>SDDS_DefineParameter(&resultsPage, "Superperiods", NULL, NULL, "Superperiods", NULL, SDDS_LONG, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "Energy", "E", "MeV", "Total Energy", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "Particles", NULL, NULL, "Particles", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "Charge", NULL, "nC", "Charge", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "PeakCurrent", "I$bp$n", "A", "Peak Current", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "RfVoltage", NULL, "MV", "Rf Voltage", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "xGrowthRateInitial", "g$bIBS,x$n", "1/s", "Initial IBS emittance growth rate in the horizontal plane", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "yGrowthRateInitial", "g$bIBS,y$n", "1/s", "Initial IBS emittance growth rate in the vertical plane", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "zGrowthRateInitial", "g$bIBS,z$n", "1/s", "Initial IBS emittance growth rate in the longitudinal plane", NULL, SDDS_DOUBLE, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (0>SDDS_DefineParameter(&resultsPage, "Convergence", NULL, NULL, "Convergence state of emittance calculations", NULL, SDDS_STRING, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "emitx0", "$ge$r$bx,0$n", "$gp$rm", "Equilibrium horizontal emittance with no coupling and no IBS", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "emitxInput", "$ge$r$bx,Input$n", "$gp$rm", "Initial horizontal emittance with coupling", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "emityInput", "$ge$r$by,Input$n", "$gp$rm", "Initial vertical emittance with coupling", NULL, SDDS_DOUBLE, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* requested equilibrium emittances or integrate emittances turn-by-turn*/
if (!growthRatesOnly) {
if (0>SDDS_DefineParameter(&resultsPage, "xGrowthRate", "g$bIBS,x$n", "1/s", "IBS emittance growth rate in the horizontal plane", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "yGrowthRate", "g$bIBS,y$n", "1/s", "IBS emittance growth rate in the vertical plane", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "zGrowthRate", "g$bIBS,z$n", "1/s", "IBS emittance growth rate in the longitudinal plane", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "emitx", "$ge$r$bx$n", "$gp$rm", "Horizontal emittance with coupling and with IBS", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "emity", "$ge$r$by$n", "$gp$rm", "Vertical emittance with coupling and with IBS", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "sigmaDelta", "$gs$r$bd$n", NULL, "Relative momentum spread with IBS", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "sigmaz", "$gs$r$bz$n", "m", "Bunch length with IBS", NULL, SDDS_DOUBLE, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (0>SDDS_DefineParameter(&resultsPage, "sigmaDelta0", "$gs$r$bd,0$n", NULL, "Equilibrium relative momentum spread without IBS", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "sigmaDeltaInput", "$gs$r$bd,0$n", NULL, "Initial relative momentum spread", NULL, SDDS_DOUBLE, NULL) ||
0>SDDS_DefineParameter(&resultsPage, "sigmaz0", "$gs$r$bz,0$n", "m", "Bunch length without IBS", NULL, SDDS_DOUBLE, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbosity)
fprintf( stdout, "Opening for reading \"%s\"\n", inputfile);
if (!SDDS_InitializeInput(&twissPage, inputfile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (integrationTurns) {
if (SDDS_DefineColumn(&resultsPage, "ex", "$ge$r$bx$n", "$gp$rm", "Horizontal Emittance", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "ey", "$ge$r$by$n", "$gp$rm", "Vertical Emittance", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "el", "$ge$r$bl$n", "s", "Longitudinal Emittance", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "Sdelta", "$gs$bd$n$r", "", "Fractional RMS Energy Spread", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "Sz", "$gs$r$bz$n", "m", "RMS Bunch Length", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "IBSRatex", NULL, "1/s", "Horizontal IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "IBSRatey", NULL, "1/s", "Vertical IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "IBSRatel", NULL, "1/s", "Longitudinal IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "Pass", NULL, NULL, NULL, NULL, SDDS_LONG, 0)<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
integrationPoints = integrationTurns/integrationStepSize+1;
if (!(exInteg = SDDS_Malloc(sizeof(*exInteg)*integrationPoints)) ||
!(eyInteg = SDDS_Malloc(sizeof(*eyInteg)*integrationPoints)) ||
!(elInteg = SDDS_Malloc(sizeof(*elInteg)*integrationPoints)) ||
!(SdeltaInteg = SDDS_Malloc(sizeof(*SdeltaInteg)*integrationPoints)) ||
!(SzInteg = SDDS_Malloc(sizeof(*SzInteg)*integrationPoints)) ||
!(xRateInteg = SDDS_Malloc(sizeof(*xRateInteg)*integrationPoints)) ||
!(yRateInteg = SDDS_Malloc(sizeof(*yRateInteg)*integrationPoints)) ||
!(zRateInteg = SDDS_Malloc(sizeof(*zRateInteg)*integrationPoints)) ||
!(passInteg = SDDS_Malloc(sizeof(*passInteg)*integrationPoints)))
bomb("memory allocation failure (integration arrays)", NULL);
} else {
if (SDDS_DefineColumn(&resultsPage, "s", NULL, "m", "Position", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "dIBSRatex", NULL, "1/s", "Local Horizontal IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "dIBSRatey", NULL, "1/s", "Local Vertical IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&resultsPage, "dIBSRatel", NULL, "1/s", "Local Longitudinal IBS Emittance Growth Rate", NULL, SDDS_DOUBLE, 0)<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteLayout(&resultsPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
while(SDDS_ReadPage(&twissPage)>0) {
if (!SDDS_GetParameters(&twissPage,
"pCentral", &pCentral0,
"I1", &I1,
"I2", &I2,
"I3", &I3,
"I4", &I4,
"I5", &I5,
"taux", &taux,
"tauy", &tauy,
"taudelta", &taudelta,
"alphac", &alphac,
"U0", &U0,
NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
EMeV = sqrt(sqr(pCentral0) + 1) * me_mev;
elements = SDDS_CountRowsOfInterest(&twissPage);
s = SDDS_GetColumnInDoubles(&twissPage, "s");
pCentral = SDDS_GetColumnInDoubles(&twissPage, "pCentral0");
circumference = s[elements-1]*superperiods;
U0 *= superperiods;
if (energy!=0) {
/* scale to new energy */
pCentral0 = sqrt(sqr(energy/me_mev)-1);
taux /= ipow(energy/EMeV, 3);
tauy /= ipow(energy/EMeV, 3);
taudelta /= ipow(energy/EMeV, 3);
U0 *= ipow(energy/EMeV, 4);
for (i=0; i<elements; i++) pCentral[i] = pCentral0;
EMeV = energy;
}
if (!length && U0>rfVoltage)
bomb("energy loss per turn is greater than rf voltage", NULL);
betax = SDDS_GetColumnInDoubles(&twissPage, "betax");
betay = SDDS_GetColumnInDoubles(&twissPage, "betay");
alphax = SDDS_GetColumnInDoubles(&twissPage, "alphax");
alphay = SDDS_GetColumnInDoubles(&twissPage, "alphay");
etax = SDDS_GetColumnInDoubles(&twissPage, "etax");
etaxp = SDDS_GetColumnInDoubles(&twissPage, "etaxp");
etay = SDDS_GetColumnInDoubles(&twissPage, "etay");
etayp = SDDS_GetColumnInDoubles(&twissPage, "etayp");
/* emitx0 and sigmaDelta0 are unperturbed quantities
(i.e. no coupling and no IBS) that
zibs requires to internally calculate the quantum excitation.
(zibs doesn't use the radiation integrals but should!)
*/
emitx0 = 55.0/ (32.*sqrt(3.)) * hbar_mks * sqr(pCentral0)/ (me_mks * c_mks)
* I5 / (I2 - I4);
sigmaDelta0 = sqrt(55.0/ (32.*sqrt(3.)) * hbar_mks * sqr(pCentral0)/ (me_mks * c_mks)
* I3 / (2 * I2 + I4));
/* use unperturbed quantities in no input supplied. */
if (!sigmaDeltaInput)
sigmaDeltaInput = sigmaDelta0;
if (!emitxInput)
emitxInput = emitx0/ ( 1 + coupling);
else
/* The emitxInput value is really emit=emitx+emity */
emitxInput = emitxInput/ ( 1 + coupling);
if (!emityInput)
emityInput = emitxInput * coupling;
else
coupling = emityInput/emityInput;
sigmaDelta = sigmaDeltaInput;
if (length)
sigmaz0 = length;
else {
/* compute length in m from rf voltage, energy spread, etc */
sigmaz0 =
circumference*sigmaDelta*
sqrt(alphac*EMeV/(PIx2*rfHarmonic*sqrt(sqr(rfVoltage)-sqr(U0))));
}
sigmaz = sigmaz0;
emity = emityInput;
emitx = emitxInput;
if (integrationPoints) {
IBSIntegrate(exInteg, eyInteg, elInteg, passInteg,
SdeltaInteg, SzInteg,
xRateInteg, yRateInteg, zRateInteg,
integrationTurns, integrationStepSize,
pCentral0, emitx, emity, sigmaDelta, sigmaz, particles,
emitx0, sigmaDelta0, 2./taux, 2./tauy, 2./taudelta, coupling,
s, pCentral, betax, alphax, betay, alphay, etax, etaxp, etay, etayp, elements,
superperiods, verbosity, isRing, force);
} else {
if (!(xRateVsS = SDDS_Realloc(xRateVsS, sizeof(*xRateVsS)*elements)) ||
!(yRateVsS = SDDS_Realloc(yRateVsS, sizeof(*yRateVsS)*elements)) ||
!(zRateVsS = SDDS_Realloc(zRateVsS, sizeof(*zRateVsS)*elements)) )
bomb("memory allocation failure", NULL);
}
/* This call is to get the initial growth rates for writing to results file.
This applies for any running option selected in the commandline */
IBSRate(particles, elements, superperiods, verbosity, isRing,
emitx, emity, sigmaDelta, sigmaz,
s, pCentral, betax, alphax, betay, alphay, etax, etaxp, etay, etayp,
NULL, NULL, NULL,
&xGrowthRateInitial, &yGrowthRateInitial, &zGrowthRateInitial, 0);
/* iterating for equilibrium emittances and final growth rates */
if (!integrationTurns && !growthRatesOnly && isRing) {
if (verbosity > 1) {
fprintf (stdout, "Starting values:\nemitx: %10.5g sigmaDelta %10.5g.\n", emitx, sigmaDelta);
}
emitxOld = emitx;
sigmaDeltaOld = sigmaDelta;
xGuess = (double*) malloc(sizeof(double)*dimensions);
dxGuess = (double*) malloc(sizeof(double)*dimensions);
xLowerLimit = (double*) malloc(sizeof(double)*dimensions);
xUpperLimit = (double*) malloc(sizeof(double)*dimensions);
disable = (short*) malloc(sizeof(short)*dimensions);
xGuess[0] = MAX(emitx, emitx0/ (1 + coupling));
xGuess[1] = MAX(sigmaDelta, sigmaDelta0);
dxGuess[0] = emitx * 0.1;
dxGuess[1] = sigmaDelta * 0.1;
xLowerLimit[0] = emitx0/ (1 + coupling);
xLowerLimit[1] = sigmaDelta0;
xUpperLimit[0] = emitx0/ (1 + coupling) * 200;
xUpperLimit[1] = MIN(sigmaDelta0 * 100, 1.0);
/* assign other variables to array which are not supoosed
to be varied by simplex minimization
*/
xGuess[2] = pCentral0;
xGuess[3] = emity;
xGuess[4] = sigmaz0;
xGuess[5] = particles;
xGuess[6] = emitx0;
xGuess[7] = sigmaDelta0;
xGuess[8] = taux;
xGuess[9] = tauy;
xGuess[10] = taudelta;
xGuess[11] = coupling;
xGuess[12] = elements;
xGuess[13] = superperiods;
xGuess[14] = verbosity;
xLowerLimit[2] = pCentral0;
xLowerLimit[3] = emity;
xLowerLimit[4] = sigmaz0;
xLowerLimit[5] = particles;
xLowerLimit[6] = emitx0;
xLowerLimit[7] = sigmaDelta0;
xLowerLimit[8] = taux;
xLowerLimit[9] = tauy;
xLowerLimit[10] = taudelta;
xLowerLimit[11] = coupling;
xLowerLimit[12] = elements;
xLowerLimit[13] = superperiods;
xLowerLimit[14] = verbosity;
xUpperLimit[2] = pCentral0;
xUpperLimit[3] = emity;
xUpperLimit[4] = sigmaz0;
xUpperLimit[5] = particles;
xUpperLimit[6] = emitx0;
xUpperLimit[7] = sigmaDelta0;
xUpperLimit[8] = taux;
xUpperLimit[9] = tauy;
xUpperLimit[10] = taudelta;
xUpperLimit[11] = coupling;
xUpperLimit[12] = elements;
xUpperLimit[13] = superperiods;
xUpperLimit[14] = verbosity;
disable[0] = 0;
disable[1] = 0;
for (i=2 ; i<dimensions ; i++) {
dxGuess[i] = 0.0;
disable[i] = 1;
}
if (verbosity) {
fprintf( stdout, "Doing simplex minimization...\n");
}
simplexMin( &yReturn, xGuess, dxGuess, xLowerLimit, xUpperLimit, disable, dimensions,
target, target/100.0, IBSequations, verbosity?IBSsimplexReport:NULL,
maxEvaluations, maxPasses, 12, 3.0, 1.0, 0);
/* final answers */
emitx = xGuess[0];
sigmaDelta = xGuess[1];
emity = emitx * coupling;
sigmaz = sigmaz0 * (sigmaDelta/ sigmaDelta0);
}
/* calculate growth rates contributions at equilibrium or
just one time (-growthRateOnly option) */
if (!integrationPoints) {
IBSRate(particles, elements, superperiods, verbosity, isRing,
emitx, emity, sigmaDelta, sigmaz,
s, pCentral, betax, alphax, betay, alphay, etax, etaxp, etay, etayp,
xRateVsS, yRateVsS, zRateVsS,
&xGrowthRate, &yGrowthRate, &zGrowthRate, 0);
} else {
/* final growth rates and emittances after integration */
xGrowthRate = xRateInteg[integrationPoints - 1] ;
yGrowthRate = yRateInteg[integrationPoints - 1] ;
zGrowthRate = zRateInteg[integrationPoints - 1] ;
emitx = exInteg[integrationPoints - 1] ;
emity = eyInteg[integrationPoints - 1] ;
sigmaDelta = SdeltaInteg[integrationPoints - 1] ;
sigmaz = SzInteg[integrationPoints - 1] ;
}
converged = 1;
if (0>SDDS_StartPage(&resultsPage, integrationPoints?integrationPoints:elements) ||
!SDDS_SetParameters(&resultsPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"Convergence", converged?"Emittance converged":"Emittance did not converge",
"pCentral", pCentral0, "RfVoltage", rfVoltage,
"I1", I1,
"I2", I2,
"I3", I3,
"I4", I4,
"I5", I5,
"taux", taux,
"tauy", tauy,
"taudelta", taudelta,
"Energy", EMeV,
"Particles", particles,
"Charge", (1e9 * charge),
"PeakCurrent", (charge*c_mks/(sqrt(2*PI)*sigmaz)),
"Superperiods", superperiods,
"emitx0", emitx0,
"emitxInput", emitxInput,
"emityInput", emityInput,
"xGrowthRateInitial", xGrowthRateInitial,
"yGrowthRateInitial", yGrowthRateInitial,
"zGrowthRateInitial", zGrowthRateInitial,
"sigmaDeltaInput", sigmaDeltaInput,
"sigmaDelta0", sigmaDelta0,
"sigmaz0", sigmaz0, NULL) ||
(!growthRatesOnly &&
!SDDS_SetParameters(&resultsPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"xGrowthRate", xGrowthRate,
"yGrowthRate", yGrowthRate,
"zGrowthRate", zGrowthRate,
"emitx", emitx,
"emity", emity,
"sigmaDelta", sigmaDelta,
"sigmaz", sigmaz, NULL)) ||
(integrationPoints &&
(!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, exInteg, integrationPoints, "ex") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, eyInteg, integrationPoints, "ey") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, elInteg, integrationPoints, "el") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, SdeltaInteg, integrationPoints, "Sdelta") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, SzInteg, integrationPoints, "Sz") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, xRateInteg, integrationPoints, "IBSRatex") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, yRateInteg, integrationPoints, "IBSRatey") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, zRateInteg, integrationPoints, "IBSRatel") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, passInteg, integrationPoints, "Pass"))) ||
(!integrationPoints &&
(!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, s, elements, "s") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, xRateVsS, elements, "dIBSRatex") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, yRateVsS, elements, "dIBSRatey") ||
!SDDS_SetColumn(&resultsPage, SDDS_SET_BY_NAME, zRateVsS, elements, "dIBSRatel"))) ||
!SDDS_WritePage(&resultsPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_Terminate(&twissPage) || !SDDS_Terminate(&resultsPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
return(0);
}
int main(int argc, char **argv)
{
int iArg;
char *input, *output,*meanPar, *sigmaPar, *maxPar, *minPar;
long i, j, mainInputOpened, haltonID=0, requireInput=0;
unsigned long pipeFlags;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout, *SDDSptr;
long randomNumberSeed = 0;
SEQ_REQUEST *seqRequest;
long samples, values, seqRequests, randomizationGroups=0;
double *sample, *IVValue, *CDFValue;
char msgBuffer[1000];
RANDOMIZED_ORDER *randomizationData = NULL;
long verbose, optimalHalton=0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<2) {
fprintf(stderr, "%s%s%s\n", USAGE1, USAGE2, USAGE3);
return(1);
}
seqRequest = NULL;
seqRequests = 0;
output = input = NULL;
pipeFlags = 0;
samples = values = 0;
sample = IVValue = CDFValue = NULL;
verbose = 0;
maxPar = minPar = meanPar = sigmaPar = NULL;
for (iArg=1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type==OPTION) {
/* process options here */
switch (match_string(scanned[iArg].list[0], option, CLO_OPTIONS, 0)) {
case CLO_COLUMNS:
if (scanned[iArg].n_items<3)
SDDS_Bomb("invalid -columns syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
/*remove following pointer initialization because memset already initialize them */
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].factor = 1;
seqRequest[seqRequests].offset = 0;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"datafile", SDDS_STRING,
&seqRequest[seqRequests].dataFileName, 1, SEQ_DATAFILE,
"independentvariable", SDDS_STRING,
&seqRequest[seqRequests].indepName, 1, SEQ_INDEPNAME,
"cdf", SDDS_STRING,
&seqRequest[seqRequests].CDFName, 1, SEQ_CDFNAME,
"df", SDDS_STRING,
&seqRequest[seqRequests].DFName, 1, SEQ_DFNAME,
"output", SDDS_STRING,
&seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"units", SDDS_STRING,
&seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
"haltonradix", SDDS_LONG,
&seqRequest[seqRequests].haltonRadix, 1, SEQ_HALTONRADIX,
"haltonoffset", SDDS_LONG,
&seqRequest[seqRequests].haltonOffset, 1, SEQ_HALTONOFFSET,
"randomize", -1, NULL, 0, SEQ_RANDOMIZE,
"group", SDDS_LONG,
&seqRequest[seqRequests].randomizationGroup, 1, SEQ_RANDOMGROUP,
"factor", SDDS_DOUBLE,
&seqRequest[seqRequests].factor, 1, 0,
"offset", SDDS_DOUBLE,
&seqRequest[seqRequests].offset, 1, 0,
NULL) ||
bitsSet(seqRequest[seqRequests].flags&(SEQ_INDEPNAME+SEQ_CDFNAME+SEQ_DFNAME))!=2)
SDDS_Bomb("invalid -columns syntax");
if (seqRequest[seqRequests].flags&SEQ_RANDOMGROUP &&
seqRequest[seqRequests].randomizationGroup<=0)
SDDS_Bomb("use a positive integer for the randomization group ID");
if (seqRequest[seqRequests].flags&SEQ_CDFNAME &&
seqRequest[seqRequests].flags&SEQ_DFNAME)
SDDS_Bomb("give df or cdf for -columns, not both");
if (seqRequest[seqRequests].flags&SEQ_HALTONRADIX &&
!is_prime(seqRequest[seqRequests].haltonRadix))
SDDS_Bomb("halton radix must be a prime number");
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_GAUSSIAN:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -gaussian syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].mean = 0;
seqRequest[seqRequests].sigma = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"meanValue", SDDS_STRING, &meanPar, 1, 0,
"sigmaValue", SDDS_STRING, &sigmaPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -gaussian syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_GAUSSIAN;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for gaussian distribution/");
if (meanPar) {
if (wild_match(meanPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].meanPar, meanPar+1);
else if (!get_double(&seqRequest[seqRequests].mean, meanPar))
SDDS_Bomb("Invalid value given for mean value of -gaussian distribution.");
free(meanPar);
meanPar = NULL;
}
if (sigmaPar) {
if (wild_match(sigmaPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].sigmaPar, sigmaPar+1);
else if (!get_double(&seqRequest[seqRequests].sigma, sigmaPar))
SDDS_Bomb("Invalid value given for sigma value of -gaussian distribution.");
free(sigmaPar);
sigmaPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_UNIFORM:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -uniform syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].min = 0;
seqRequest[seqRequests].max = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"minimumValue", SDDS_STRING, &minPar, 1, 0,
"maximumValue", SDDS_STRING, &maxPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -uniform syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_UNIFORM;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for uniform distribution/");
if (minPar) {
if (wild_match(minPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].minPar, minPar+1);
else if (!get_double(&seqRequest[seqRequests].min, minPar))
SDDS_Bomb("Invalid value given for minimum value of -uniform distribution.");
free(minPar);
minPar = NULL;
}
if (maxPar) {
if (wild_match(maxPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].maxPar, maxPar+1);
else if (!get_double(&seqRequest[seqRequests].max, maxPar))
SDDS_Bomb("Invalid value given for maximum value of -uniform distribution.");
free(maxPar);
maxPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_POISSON:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -poisson syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].mean = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"meanValue", SDDS_STRING, &meanPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -poisson syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_POISSON;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for uniform distribution/");
if (meanPar) {
if (wild_match(meanPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].meanPar, meanPar+1);
else if (!get_double(&seqRequest[seqRequests].mean, meanPar))
SDDS_Bomb("Invalid value given for mean value of -poisson distribution.");
free(meanPar);
meanPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_SAMPLES:
if (scanned[iArg].n_items!=2 ||
sscanf(scanned[iArg].list[1], "%ld", &samples)!=1 ||
samples<=0)
SDDS_Bomb("invalid -samples syntax");
break;
case CLO_SEED:
if (scanned[iArg].n_items!=2 ||
sscanf(scanned[iArg].list[1], "%ld", &randomNumberSeed)!=1 ||
randomNumberSeed<=0)
SDDS_Bomb("invalid -seed syntax");
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_OPTIMAL_HALTON:
optimalHalton = 1;
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s\n",
scanned[iArg].list[0]);
exit(1);
break;
}
}
else {
if (!input)
input = scanned[iArg].list[0];
else if (!output)
output = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames seen");
}
}
if (!seqRequests)
SDDS_Bomb("give one or more -columns options");
if (samples<1)
SDDS_Bomb("-samples option not given");
for (i=0; i<seqRequests; i++) {
if (!(seqRequest[i].flags&
(SEQ_DATAFILE|SEQ_DIRECT_GAUSSIAN|SEQ_DIRECT_UNIFORM|SEQ_DIRECT_POISSON)))
break;
}
if (i==seqRequests) {
/* all columns options have either their own input files or else use
* one of the "direct" distributions. Hence, we don't expect an input
* file.
*/
if (!input)
pipeFlags |= USE_STDIN; /* not really, but fakes out processFilenames */
if (input && !output) {
output = input;
input = NULL;
pipeFlags |= USE_STDIN;
if (fexists(output)) {
sprintf(msgBuffer, "%s exists already (sddssampledist)", output);
SDDS_Bomb(msgBuffer);
}
}
}
processFilenames("sddssampledist", &input, &output, pipeFlags, 0, NULL);
if (!SDDS_InitializeOutput(&SDDSout, SDDS_BINARY, 0, NULL, NULL, output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose)
fprintf(stderr, "Initialized output file %s\n", output);
/* open and check input files */
for (i=mainInputOpened=0; i<seqRequests; i++) {
if (seqRequest[i].flags&SEQ_DIRECT_GAUSSIAN) {
if (seqRequest[i].meanPar || seqRequest[i].sigmaPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ((seqRequest[i].meanPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].meanPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) ||
(seqRequest[i].sigmaPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].sigmaPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else if (seqRequest[i].flags&SEQ_DIRECT_UNIFORM) {
if (seqRequest[i].minPar || seqRequest[i].maxPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ((seqRequest[i].minPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].minPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) ||
(seqRequest[i].maxPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].maxPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else if (seqRequest[i].flags&SEQ_DIRECT_POISSON) {
if (seqRequest[i].meanPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ( SDDS_CheckParameter(SDDSptr, seqRequest[i].meanPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_LONG))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
if (seqRequest[i].flags&SEQ_RANDOMIZE) {
long newGroupID=0;
/* define randomization groups */
if (seqRequest[i].flags&SEQ_RANDOMGROUP) {
newGroupID = seqRequest[i].randomizationGroup;
for (j=0; j<randomizationGroups; j++)
if (randomizationData[j].group==newGroupID) {
newGroupID = 0;
break;
}
} else {
seqRequest[i].randomizationGroup = newGroupID = -(i+1);
}
if (newGroupID!=0) {
if (!(randomizationData =
SDDS_Realloc(randomizationData,
sizeof(*randomizationData)*(randomizationGroups+1))))
SDDS_Bomb("memory allocation failure");
randomizationData[randomizationGroups].group = newGroupID;
randomizationData[randomizationGroups].order = NULL;
randomizationGroups ++;
}
}
if (seqRequest[i].flags&SEQ_DATAFILE) {
if (!SDDS_InitializeInput(&seqRequest[i].SDDSin,
seqRequest[i].dataFileName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDSptr = &seqRequest[i].SDDSin;
} else {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
}
if (SDDS_CheckColumn(SDDSptr,
seqRequest[i].indepName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK ||
((seqRequest[i].flags&SEQ_CDFNAME) &&
SDDS_CheckColumn(SDDSptr, seqRequest[i].CDFName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK) ||
((seqRequest[i].flags&SEQ_DFNAME) &&
SDDS_CheckColumn(SDDSptr, seqRequest[i].DFName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK) ||
!SDDS_TransferColumnDefinition(&SDDSout, SDDSptr,
seqRequest[i].indepName,
seqRequest[i].outputName)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (seqRequest[i].flags&SEQ_UNITSGIVEN &&
!SDDS_ChangeColumnInformation(&SDDSout, "units", seqRequest[i].units,
SDDS_SET_BY_NAME,
seqRequest[i].outputName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (verbose)
fprintf(stderr, "Initialized input files\n");
if (!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (randomNumberSeed==0) {
randomNumberSeed = (long)time((time_t *) NULL);
randomNumberSeed = 2*(randomNumberSeed/2) + 1;
#if defined(_WIN32)
random_1(-labs(randomNumberSeed));
#else
random_1(-FABS(randomNumberSeed));
#endif
} else
random_1(-randomNumberSeed);
if (!((sample = calloc(sizeof(*sample), samples))))
SDDS_Bomb("memory allocation failure");
while (1) {
if (verbose)
fprintf(stderr, "Beginning page loop\n");
if (input && SDDS_ReadPage(&SDDSin)<=0)
break;
for (i=0; i<seqRequests; i++) {
if (seqRequest[i].flags&SEQ_DATAFILE &&
SDDS_ReadPage(&seqRequest[i].SDDSin)<=0)
break;
}
if (i!=seqRequests)
break;
if (!SDDS_StartPage(&SDDSout, samples) ||
(input && !SDDS_CopyParameters(&SDDSout, &SDDSin)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose)
fprintf(stderr, "Defining randomization tables\n");
/* define randomization tables */
for (i=0; i<randomizationGroups; i++) {
if (!(randomizationData[i].order=
SDDS_Malloc(sizeof(*randomizationData[i].order)*samples)))
SDDS_Bomb("memory allocation failure");
for (j=0; j<samples; j++)
randomizationData[i].order[j] = j;
randomizeOrder((char*)randomizationData[i].order,
sizeof(*randomizationData[i].order), samples, 0,
random_1);
}
if (verbose)
fprintf(stderr, "Beginning loop over sequence requests\n");
for (i=0; i<seqRequests; i++) {
if (verbose)
fprintf(stderr, "Processing sequence request %ld\n", i);
if (seqRequest[i].flags&SEQ_DIRECT_GAUSSIAN) {
if ((seqRequest[i].meanPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].meanPar, &seqRequest[i].mean)) ||
(seqRequest[i].sigmaPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].sigmaPar, &seqRequest[i].sigma)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (j=0; j<samples; j++)
sample[j] = gauss_rn_lim(seqRequest[i].mean, seqRequest[i].sigma, -1, random_1);
} else if (seqRequest[i].flags&SEQ_DIRECT_UNIFORM) {
if ((seqRequest[i].minPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].minPar, &seqRequest[i].min)) ||
(seqRequest[i].maxPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].maxPar, &seqRequest[i].max)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (j=0; j<samples; j++)
sample[j] = seqRequest[i].min + (seqRequest[i].max - seqRequest[i].min) * random_1(1);
} else if (seqRequest[i].flags&SEQ_DIRECT_POISSON) {
double *pos_x, *pos_cdf, CDF;
long pos_points, code;
pos_x = pos_cdf = NULL;
if ((seqRequest[i].meanPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].meanPar, &seqRequest[i].mean)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
pos_points = CreatePoissonDistributionTable(&pos_x, &pos_cdf, seqRequest[i].mean);
for (j=0; j<samples; j++) {
CDF = random_1(1);
sample[j]= (int)(interp(pos_x, pos_cdf, pos_points, CDF, 0, 1, &code));
/* fprintf(stderr, "%d, cdf=%f, sample=%f\n", j, CDF, sample[j]);*/
}
free(pos_x);
free(pos_cdf);
} else {
if (input && !(seqRequest[i].flags&SEQ_DATAFILE))
SDDSptr = &SDDSin;
else
SDDSptr = &seqRequest[i].SDDSin;
if ((values = SDDS_CountRowsOfInterest(SDDSptr))) {
if (!(IVValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].indepName)) ||
(seqRequest[i].flags&SEQ_CDFNAME &&
!(CDFValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].CDFName))) ||
(seqRequest[i].flags&SEQ_DFNAME &&
!(CDFValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].DFName))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
sprintf(msgBuffer, "empty page for file %s\n",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
if (verbose)
fprintf(stderr, "Checking and converting CDF/DF values\n");
/* check/convert CDF/DF values */
for (j=1; j<values; j++) {
if (IVValue[j-1]>IVValue[j]) {
sprintf(msgBuffer, "random variate values not monotonically increasing for %s",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
if (seqRequest[i].flags&SEQ_DFNAME)
/* convert DF to CDF */
CDFValue[j] += CDFValue[j-1];
if (CDFValue[j] < CDFValue[j-1]) {
sprintf(msgBuffer, "CDF values decreasing for %s",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
}
if (verbose)
fprintf(stderr, "Normalizing CDF\n");
/* normalize the CDF */
if (CDFValue[values-1]<=0) {
sprintf(msgBuffer, "CDF not valid for %s\n",
seqRequest[i].dataFileName);
SDDS_Bomb(msgBuffer);
}
for (j=0; j<values; j++)
CDFValue[j] /= CDFValue[values-1];
if (seqRequest[i].flags&SEQ_HALTONRADIX) {
if (verbose)
fprintf(stderr, "Starting halton sequence, offset=%" PRId32 "\n", seqRequest[i].haltonOffset);
if (!optimalHalton)
haltonID = startHaltonSequence(&seqRequest[i].haltonRadix, 0.5);
else
haltonID = startModHaltonSequence(&seqRequest[i].haltonRadix, 0);
while (seqRequest[i].haltonOffset-- >0) {
if (!optimalHalton)
nextHaltonSequencePoint(haltonID);
else
nextModHaltonSequencePoint(haltonID);
}
}
if (verbose)
fprintf(stderr, "Generating samples\n");
for (j=0; j<samples; j++) {
double CDF;
long code;
while (1) {
if (seqRequest[i].flags&SEQ_HALTONRADIX) {
if (!optimalHalton)
CDF = nextHaltonSequencePoint(haltonID);
else
CDF = nextModHaltonSequencePoint(haltonID);
}
else
CDF = random_1(1);
if (CDF<=CDFValue[values-1] && CDF>=CDFValue[0])
break;
}
sample[j]
= seqRequest[i].factor*interp(IVValue, CDFValue, values, CDF, 0, 1, &code)
+ seqRequest[i].offset;
}
if (seqRequest[i].flags&SEQ_RANDOMIZE) {
long k, l;
double *sample1;
if (verbose)
fprintf(stderr, "Randomizing order of values\n");
if (!(sample1 = malloc(sizeof(*sample1)*samples)))
SDDS_Bomb("memory allocation failure");
for (l=0; l<randomizationGroups; l++)
if (randomizationData[l].group==seqRequest[i].randomizationGroup)
break;
if (l==randomizationGroups)
SDDS_Bomb("problem with construction of randomization groups!");
for (k=0; k<samples; k++)
sample1[k] = sample[randomizationData[l].order[k]];
free(sample);
sample = sample1;
}
free(IVValue);
free(CDFValue);
}
if (verbose)
fprintf(stderr, "Setting SDDS column values\n");
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_SET_BY_NAME,
sample, samples,
seqRequest[i].outputName?
seqRequest[i].outputName:
seqRequest[i].indepName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (verbose)
fprintf(stderr, "Writing data page\n");
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!requireInput)
break;
}
if (verbose)
fprintf(stderr, "Exited read loop\n");
free(sample);
if ((input && !SDDS_Terminate(&SDDSin)) || !SDDS_Terminate(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<seqRequests; i++) {
if (seqRequest[i].dataFileName) free(seqRequest[i].dataFileName);
if (seqRequest[i].indepName) free(seqRequest[i].indepName);
if (seqRequest[i].outputName) free(seqRequest[i].outputName);
if (seqRequest[i].DFName) free(seqRequest[i].DFName);
if (seqRequest[i].CDFName) free(seqRequest[i].CDFName);
if (seqRequest[i].units) free(seqRequest[i].units);
if (seqRequest[i].meanPar) free(seqRequest[i].meanPar);
if (seqRequest[i].sigmaPar) free(seqRequest[i].sigmaPar);
if (seqRequest[i].minPar) free(seqRequest[i].minPar);
if (seqRequest[i].maxPar) free(seqRequest[i].maxPar);
if (seqRequest[i].flags&SEQ_DATAFILE && !SDDS_Terminate(&(seqRequest[i].SDDSin)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(seqRequest);
for (i=0; i<randomizationGroups; i++)
free(randomizationData[i].order);
if (randomizationData) free(randomizationData);
free_scanargs(&scanned, argc);
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);
}
