long CreatePoissonDistributionTable(double **x, double **pos_CDF, double mean)
{
long i, npoints=20, count=0;
double *pos=NULL;
SDDS_DATASET pos_out;
*x = *pos_CDF = NULL;
if (!(*x=malloc(sizeof(**x)*npoints)) ||
!(pos=malloc(sizeof(*pos)*npoints)) || !(*pos_CDF=malloc(sizeof(**pos_CDF)*npoints)))
SDDS_Bomb("memeroy allocation failure.");
i = count = 0;
while (1) {
if (count+2>=npoints) {
npoints += 20;
*x = SDDS_Realloc(*x, sizeof(**x)*npoints);
*pos_CDF = SDDS_Realloc(*pos_CDF, sizeof(**pos_CDF)*npoints);
pos = SDDS_Realloc(pos, sizeof(*pos)*npoints);
}
(*x)[count] = i;
if (!i) {
pos[i] = exp(-mean);
(*pos_CDF)[count] = pos[i];
count ++;
}
else {
pos[i] = pos[i-1]*mean/i;
(*pos_CDF)[count] = (*pos_CDF)[count-1];
(*pos_CDF)[count+1] = (*pos_CDF)[count-1] + pos[i];
(*x)[count+1] = i;
if (1.0-(*pos_CDF)[count+1]<=1.0e-15)
break;
count +=2;
}
i++;
}
/* fprintf(stderr,"lamda=%f\n", mean);
if (!SDDS_InitializeOutput(&pos_out, SDDS_BINARY, 0, NULL, NULL, "pos_dist.sdds"))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_DefineSimpleColumn(&pos_out, "Count", NULL, SDDS_DOUBLE) ||
!SDDS_DefineSimpleColumn(&pos_out, "P", NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_SaveLayout(&pos_out) || !SDDS_WriteLayout(&pos_out))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_StartPage(&pos_out, count) ||
!SDDS_SetColumnFromDoubles(&pos_out, SDDS_SET_BY_NAME, *x, count, "Count") ||
!SDDS_SetColumnFromDoubles(&pos_out, SDDS_SET_BY_NAME, *pos_CDF, count, "P"))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_WritePage(&pos_out) || !SDDS_Terminate(&pos_out))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
*/
free(pos);
return count;
}
void *AllocateColumnData(long type, void *values, int32_t rows)
{
switch (type) {
case SDDS_SHORT:
return SDDS_Realloc(values,rows*(sizeof(short)));
case SDDS_LONG:
return SDDS_Realloc(values,rows*(sizeof(int32_t)));
case SDDS_FLOAT:
return SDDS_Realloc(values,rows*(sizeof(float)));
case SDDS_DOUBLE:
return SDDS_Realloc(values,rows*(sizeof(double)));
case SDDS_CHARACTER:
return SDDS_Realloc(values,rows*2*(sizeof(char)));
}
return values;
}
int32_t SDDS_CopyArrays(SDDS_DATASET *SDDS_target, SDDS_DATASET *SDDS_source)
{
int32_t i, j, target_index;
char messageBuffer[1024];
for (i=0; i<SDDS_source->layout.n_arrays; i++) {
if ((target_index=SDDS_GetArrayIndex(SDDS_target, SDDS_source->layout.array_definition[i].name))<0)
continue;
SDDS_target->array[target_index].definition = SDDS_target->layout.array_definition+target_index;
SDDS_target->array[target_index].elements = SDDS_source->array[i].elements;
if (!(SDDS_target->array[target_index].dimension
= (int32_t*)SDDS_Malloc(sizeof(*SDDS_target->array[i].dimension)*SDDS_target->array[target_index].definition->dimensions)) ||
!(SDDS_target->array[target_index].data
= SDDS_Realloc(SDDS_target->array[target_index].data,
SDDS_type_size[SDDS_target->array[target_index].definition->type-1]*
SDDS_target->array[target_index].elements))) {
SDDS_SetError("Unable to copy arrays--allocation failure (SDDS_CopyArrays)");
return(0);
}
for (j=0; j<SDDS_target->array[target_index].definition->dimensions; j++)
SDDS_target->array[target_index].dimension[j] = SDDS_source->array[i].dimension[j];
if (!SDDS_source->array[i].data) {
SDDS_target->array[target_index].data=NULL;
continue;
}
if (SDDS_source->layout.array_definition[i].type!=SDDS_target->layout.array_definition[target_index].type) {
if (!SDDS_NUMERIC_TYPE(SDDS_source->layout.array_definition[i].type) ||
!SDDS_NUMERIC_TYPE(SDDS_target->layout.array_definition[target_index].type)) {
sprintf(messageBuffer,
"Can't cast between nonnumeric types for parameters %s and %s (SDDS_CopyArrays)",
SDDS_source->layout.array_definition[i].name,
SDDS_target->layout.array_definition[target_index].name);
SDDS_SetError(messageBuffer);
return 0;
}
for (j=0;j<SDDS_source->array[i].elements;j++) {
if (!SDDS_CastValue(SDDS_source->array[i].data, j,
SDDS_source->layout.array_definition[i].type,
SDDS_target->layout.array_definition[target_index].type,
(char*)(SDDS_target->array[target_index].data)
+j*SDDS_type_size[SDDS_target->layout.array_definition[target_index].type-1])) {
SDDS_SetError("Problem with cast (SDDS_CopyArrays)");
return 0;
}
}
} else {
if (SDDS_target->array[target_index].definition->type!=SDDS_STRING)
memcpy(SDDS_target->array[target_index].data, SDDS_source->array[i].data,
SDDS_type_size[SDDS_target->array[target_index].definition->type-1]*SDDS_target->array[target_index].elements);
else if (!SDDS_CopyStringArray(SDDS_target->array[target_index].data, SDDS_source->array[i].data,
SDDS_target->array[target_index].elements)) {
SDDS_SetError("Unable to copy arrays (SDDS_CopyArrays)");
return(0);
}
}
}
return(1);
}
long appendToStringArray(char ***item, long items, char *newItem)
{
if (!(*item = SDDS_Realloc(*item, sizeof(**item)*(items+1))))
SDDS_Bomb("allocation failure in appendToStringArray");
if (!SDDS_CopyString((*item)+items, newItem)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return items+1;
}
void moveToStringArray(char ***target, long *targets, char **source, long sources)
{
long i, j;
if (!sources)
return;
*target = SDDS_Realloc(*target, sizeof(**target)*(*targets+sources));
for (i=0; i<sources; i++) {
for (j=0; j<*targets; j++)
if (strcmp(source[i], (*target)[j])==0)
break;
if (j==*targets) {
(*target)[j] = source[i];
*targets += 1;
}
}
}
long addStatRequests(STAT_REQUEST **statRequest, long requests, char **item,
long items, long code, unsigned long flags)
{
long i;
if (!(*statRequest = SDDS_Realloc(*statRequest, sizeof(**statRequest)*(requests+1))) ||
!((*statRequest)[requests].sourceColumn = (char**)malloc(sizeof(*(*statRequest)[requests].sourceColumn)*
(items-1))))
SDDS_Bomb("memory allocation failure");
for (i=0; i<items-1; i++)
SDDS_CopyString(&((*statRequest)[requests].sourceColumn[i]), item[i+1]);
(*statRequest)[requests].resultColumn = item[0];
(*statRequest)[requests].sourceColumns = items-1;
(*statRequest)[requests].optionCode = code;
(*statRequest)[requests].sumPower = 1;
(*statRequest)[requests].flags = flags;
(*statRequest)[requests].positionColumn = NULL;
return requests+1;
}
void addTransmutationSpec(char *name, char *type, char *exclude,
long newType)
{
if (!(transmutationSpec
= SDDS_Realloc(transmutationSpec,
sizeof(*transmutationSpec)*(transmutationSpecs+1))))
bombElegant("memory allocation failure", NULL);
transmutationSpec[transmutationSpecs].name = NULL;
transmutationSpec[transmutationSpecs].type = NULL;
transmutationSpec[transmutationSpecs].exclude = NULL;
transmutationSpec[transmutationSpecs].newType = newType;
if ((name &&
!SDDS_CopyString(&transmutationSpec[transmutationSpecs].name, name)) ||
(type &&
!SDDS_CopyString(&transmutationSpec[transmutationSpecs].type, type)) ||
(exclude &&
!SDDS_CopyString(&transmutationSpec[transmutationSpecs].exclude, exclude)))
bombElegant("memory allocation failure", NULL);
transmutationSpecs++;
}
void replaceWithRank(double *data, long n)
{
static DATAnINDEX *indexedData = NULL;
long i, j, iStart, iEnd;
indexedData = SDDS_Realloc(indexedData, sizeof(*indexedData)*n);
for (i=0; i<n; i++) {
indexedData[i].data = data[i];
indexedData[i].originalIndex = i;
}
qsort((void*)indexedData, n, sizeof(*indexedData), compareData);
for (i=0; i<n; i++)
data[indexedData[i].originalIndex] = i;
for (i=0; i<n-1; i++) {
if (data[i]==data[i+1]) {
iStart = i;
for (j=i+2; j<n-1; j++)
if (data[i]!=data[j])
break;
iEnd = j-1;
for (j=iStart; j<=iEnd; j++)
data[i] = (iStart+iEnd)/2.0;
}
}
}
long perform_sddsplot_time_filtering(SDDS_TABLE *table, TIME_FILTER_DEFINITION **time_filter, long time_filters)
{
long i, j, accept, skip_table;
long n_left, row_deletion, n_rows;
TIME_FILTER_DEFINITION *time_filter_ptr;
PARAMETER_DEFINITION *pardefptr;
double result;
static int32_t *rowFlag1 = NULL, *rowFlag2 = NULL;
static long rowFlags = 0;
skip_table = 0;
#if DEBUG
fprintf(stderr, "%ld time filters being applied\n", time_filters);
#endif
if (time_filters==0)
return !skip_table;
n_rows = SDDS_RowCount(table);
row_deletion = 1;
for (i=0;i<time_filters;i++) {
time_filter_ptr=time_filter[i];
if (time_filter_ptr->is_parameter) {
if (!(pardefptr=SDDS_GetParameterDefinition(table, time_filter_ptr->name)) ||
(pardefptr->type==SDDS_STRING || pardefptr->type==SDDS_CHARACTER)) {
fprintf(stderr, "error: unknown or non-numeric parameter %s given for time filter\n",
time_filter_ptr->name);
exit(1);
}
accept=SDDS_ItemInsideWindow(SDDS_GetParameter(table, time_filter_ptr->name, &result),
0, pardefptr->type, time_filter_ptr->after,time_filter_ptr->before);
if (!accept)
skip_table=1;
if (time_filter_ptr->flags&TIMEFILTER_INVERT_GIVEN)
skip_table=!skip_table;
if (skip_table)
break;
}
else if (n_rows) {
if (!rowFlag1 || !rowFlag2 || n_rows>rowFlags) {
if (!(rowFlag1 = SDDS_Realloc(rowFlag1, sizeof(*rowFlag1)*n_rows)) ||
!(rowFlag2 = SDDS_Realloc(rowFlag2, sizeof(*rowFlag2)*n_rows))) {
fprintf(stderr, "Problem reallocating row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_GetRowFlags(table, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#if DEBUG
fprintf(stderr, " * applying time filter (column %s)", time_filter_ptr->name);
#endif
if ((n_left=SDDS_FilterRowsOfInterest(table, time_filter_ptr->name, time_filter_ptr->after,
time_filter_ptr->before,
time_filter_ptr->flags&TIMEFILTER_INVERT_GIVEN? SDDS_NEGATE_EXPRESSION:SDDS_AND ))<0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_GetRowFlags(table, rowFlag2, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
n_left=0;
for (j=0; j<n_rows; j++) {
rowFlag1[j] = rowFlag1[j]&rowFlag2[j];
if (rowFlag1[j])
n_left++;
}
if (!SDDS_AssertRowFlags(table, SDDS_FLAG_ARRAY, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to assert row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/* fprintf(stderr,"total_rows=%d,left rows=%d\n",n_rows,n_left); */
/* fprintf(stderr,"total_rows=%d, time filtered left=%d\n",n_rows,n_left); */
if (!n_left)
skip_table=1;
if (skip_table)
break;
row_deletion = 1;
}
}
return !skip_table;
}
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);
}
void ReadPointFile(char *inputFile, char *xCol, char *yCol,
long *pages, OUT_POINT **out_point)
{
SDDS_DATASET SDDS_in;
int32_t rows1=0;
long pages0=0, std_exist=0;
double *x, *y, dx, dy, xmin, xmax, firstx, firsty, ymin, ymax;
int nx, ny, i;
if (!SDDS_InitializeInput(&SDDS_in, inputFile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_CheckColumn(&SDDS_in, xCol, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
fprintf(stderr,"x column - %s does not exist!\n", xCol);
exit(1);
}
if (SDDS_CheckColumn(&SDDS_in, yCol, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
fprintf(stderr,"y column - %s does not exist!\n", yCol);
exit(1);
}
while (SDDS_ReadPage(&SDDS_in)>0) {
rows1 = 0;
rows1=SDDS_CountRowsOfInterest(&SDDS_in);
if (!rows1)
continue;
*out_point = SDDS_Realloc(*out_point, sizeof(**out_point)*(pages0+1));
x = y = NULL;
(*out_point)[pages0].pout = malloc(sizeof(point)*rows1);
(*out_point)[pages0].nout = rows1;
if (!(x=(double*)SDDS_GetColumnInDoubles(&SDDS_in, xCol)) ||
!(y=(double*)SDDS_GetColumnInDoubles(&SDDS_in, yCol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
xmin = xmax = firstx = x[0];
ymin = ymax = firsty = y[0];
nx = ny = 0;
for (i=0; i<rows1; i++) {
(*out_point)[pages0].pout[i].x = x[i];
(*out_point)[pages0].pout[i].y = y[i];
if (x[i]<xmin)
xmin = x[i];
else if (x[i]>xmax)
xmax = x[i];
if (x[i]==firstx)
ny ++;
if (y[i]<ymin)
ymin = y[i];
else if (y[i]>ymax)
ymax = y[i];
if (y[i]==firsty)
nx ++;
}
free(x);
free(y);
(*out_point)[pages0].xmin = xmin;
(*out_point)[pages0].xmax = xmax;
(*out_point)[pages0].ymin = ymin;
(*out_point)[pages0].ymax = ymax;
(*out_point)[pages0].nx = nx;
(*out_point)[pages0].ny = ny;
if (nx>1)
(*out_point)[pages0].dx = (xmax - xmin)/(nx-1);
else
(*out_point)[pages0].dx = 0;
if (ny>1)
(*out_point)[pages0].dx = (ymax - ymin)/(ny-1);
else
(*out_point)[pages0].dy = 0;
pages0 ++;
}
if (!SDDS_Terminate(&SDDS_in))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!pages0) {
fprintf(stderr, "No data found in the points file.\n");
exit(1);
}
*pages = pages0;
return;
}
long SetupNAFFOutput(SDDS_DATASET *SDDSout, char *output, SDDS_DATASET *SDDSin,
char *indepQuantity,
long depenQuantities, char **depenQuantity,
long **frequencyIndex, long **amplitudeIndex, long **phaseIndex,
long **significanceIndex, char **depenQuantityPair,
long **amplitudeIndex1, long **phaseIndex1,
long **significanceIndex1)
{
char *freqUnits, *buffer, *ampUnits;
long i, maxBuffer, bufferNeeded;
if (!(*frequencyIndex = SDDS_Malloc(sizeof(**frequencyIndex)*depenQuantities)) ||
!(*amplitudeIndex = SDDS_Malloc(sizeof(**amplitudeIndex)*depenQuantities)) ||
!(*phaseIndex = SDDS_Malloc(sizeof(**phaseIndex)*depenQuantities)) ||
!(*significanceIndex = SDDS_Malloc(sizeof(**significanceIndex)*depenQuantities)) ||
!(buffer = SDDS_Malloc(sizeof(*buffer)*(maxBuffer=1024)))) {
SDDS_SetError("memory allocation failure");
return 0;
}
if (!(freqUnits = makeFrequencyUnits(SDDSin, indepQuantity)) ||
!SDDS_InitializeOutput(SDDSout, SDDS_BINARY, 0, NULL, "sddsnaff output", output))
return 0;
for (i=0; i<depenQuantities; i++) {
if ((bufferNeeded=strlen(depenQuantity[i])+12)>maxBuffer &&
!(buffer = SDDS_Realloc(buffer, sizeof(*buffer)*bufferNeeded)))
SDDS_Bomb("memory allocation failure");
sprintf(buffer, "%sFrequency", depenQuantity[i]);
if (((*frequencyIndex)[i]=
SDDS_DefineColumn(SDDSout, buffer, NULL, freqUnits, NULL, NULL, SDDS_DOUBLE, 0))<0 ||
SDDS_GetColumnInformation(SDDSin, "units", &Units, SDDS_GET_BY_NAME,
depenQuantity[i])!=SDDS_STRING)
return 0;
sprintf(buffer, "%sAmplitude", depenQuantity[i]);
if (((*amplitudeIndex)[i]=
SDDS_DefineColumn(SDDSout, buffer, NULL, ampUnits, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
sprintf(buffer, "%sPhase", depenQuantity[i]);
if (((*phaseIndex)[i] =
SDDS_DefineColumn(SDDSout, buffer, NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
sprintf(buffer, "%sSignificance", depenQuantity[i]);
if (((*significanceIndex)[i] =
SDDS_DefineColumn(SDDSout, buffer, NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
}
if (depenQuantityPair) {
if (!(*amplitudeIndex1 = SDDS_Malloc(sizeof(**amplitudeIndex1)*depenQuantities)) ||
!(*phaseIndex1 = SDDS_Malloc(sizeof(**phaseIndex1)*depenQuantities)) ||
!(*significanceIndex1 = SDDS_Malloc(sizeof(**significanceIndex1)*depenQuantities))) {
SDDS_SetError("memory allocation failure");
return 0;
}
for (i=0; i<depenQuantities; i++) {
if ((bufferNeeded=strlen(depenQuantityPair[i])+12)>maxBuffer &&
!(buffer = SDDS_Realloc(buffer, sizeof(*buffer)*bufferNeeded)))
SDDS_Bomb("memory allocation failure");
sprintf(buffer, "%sAmplitude", depenQuantityPair[i]);
if (((*amplitudeIndex1)[i]=
SDDS_DefineColumn(SDDSout, buffer, NULL, ampUnits, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
sprintf(buffer, "%sPhase", depenQuantityPair[i]);
if (((*phaseIndex1)[i] =
SDDS_DefineColumn(SDDSout, buffer, NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
sprintf(buffer, "%sSignificance", depenQuantityPair[i]);
if (((*significanceIndex1)[i] =
SDDS_DefineColumn(SDDSout, buffer, NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0))<0)
return 0;
}
}
free(ampUnits);
free(freqUnits);
if (!SDDS_TransferAllParameterDefinitions(SDDSout, SDDSin, SDDS_TRANSFER_KEEPOLD) ||
!SDDS_WriteLayout(SDDSout))
return 0;
free(buffer);
return 1;
}
void determine_dataset_labels(PLOT_SPEC *plspec, SDDS_TABLE *table, PLOT_DATA *dataset)
{
PLOT_REQUEST *request;
long i;
DATA_INFO *info;
char printBuffer[SDDS_MAXLINE];
request = plspec->plot_request+dataset->request_index;
for (i=0; i<4; i++) {
dataset->label[i] = NULL;
if (request->label[i].flags&LABEL_STRING_GIVEN) {
if (!SDDS_CopyString(&dataset->label[i], request->label[i].label))
SDDS_Bomb("String copy error (determine_dataset_labels)");
}
else if (request->label[i].flags&LABEL_PARAMETER_GIVEN) {
long type;
char *dataBuffer = NULL;
char *format =NULL;
if ( !(dataBuffer = malloc(sizeof(double)*4)))
SDDS_Bomb("Allocation failure in determin_dataset_labels");
if (!SDDS_GetParameter(table,request->label[i].label, dataBuffer))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if(!(type=SDDS_GetParameterType(table,SDDS_GetParameterIndex(table,request->label[i].label))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if(SDDS_GetParameterInformation(table,"format_string",&format,SDDS_GET_BY_NAME,request->label[i].label) !=SDDS_STRING)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if ( request->label[i].flags&LABEL_FORMAT_GIVEN) {
if(!SDDS_VerifyPrintfFormat(request->label[i].format,type)) {
fprintf(stderr, "error: given format (\"%s\") for parameter %s is invalid\n",
request->label[i].format, request->label[i].label);
exit(1);
}
if(!(SDDS_SprintTypedValue((void*)dataBuffer,0,type,request->label[i].format,printBuffer,SDDS_PRINT_NOQUOTES)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_CopyString(&dataset->label[i],printBuffer);
} else {
if(!SDDS_StringIsBlank(format)) {
if(!(SDDS_SprintTypedValue((void*)dataBuffer,0,type,format,printBuffer,SDDS_PRINT_NOQUOTES)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_CopyString(&dataset->label[i],printBuffer);
} else {
if (!(dataset->label[i]=SDDS_GetParameterAsString(table,request->label[i].label,NULL)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
free(format);
free(dataBuffer);
/*if (SDDS_GetParameterType(table, SDDS_GetParameterIndex(table, request->label[i].label)) != SDDS_STRING) {
fprintf(stderr, "labels taken from parameters must be strings\n");
exit(1);
}
if (!SDDS_GetParameter(table, request->label[i].label, &s))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
dataset->label[i] = s; */
}
else if (request->label[i].flags&(LABEL_USE_NAME+LABEL_USE_SYMBOL+LABEL_USE_DESCRIPTION)) {
if (i==0)
info = &dataset->info[0];
else
info = &dataset->info[1];
if (request->label[i].flags&LABEL_USE_NAME)
SDDS_CopyString(&dataset->label[i],
i==0?request->xname[dataset->dataname_index]:request->yname[dataset->dataname_index]);
else if (request->label[i].flags&LABEL_USE_SYMBOL && info->symbol)
SDDS_CopyString(&dataset->label[i], info->symbol);
else if (request->label[i].flags&LABEL_USE_DESCRIPTION && info->description)
SDDS_CopyString(&dataset->label[i], info->description);
if (dataset->label[i] && request->label[i].flags&LABEL_INCLUDE_UNITS && info->units &&
!SDDS_StringIsBlank(info->units)) {
if (!(dataset->label[i] = SDDS_Realloc(dataset->label[i],
sizeof(*dataset->label[i])*(strlen(dataset->label[i])+strlen(info->units)+4))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
strcat(dataset->label[i], " (");
strcat(dataset->label[i], info->units);
strcat(dataset->label[i], ")");
}
}
}
}
void run_rpn_load(NAMELIST_TEXT *nltext, RUN *run)
{
SDDS_DATASET SDDSin;
long code, foundPage, iColumn, matchRow, rows, iParameter;
int32_t columns, parameters;
char *parameterValue = NULL;
double *data, data1;
char **columnName, **matchColumnData, *memName = NULL;
char **parameterName;
/* process the namelist text */
set_namelist_processing_flags(STICKY_NAMELIST_DEFAULTS);
set_print_namelist_flags(0);
if (processNamelist(&rpn_load, nltext)==NAMELIST_ERROR)
bombElegant(NULL, NULL);
if (echoNamelists) print_namelist(stdout, &rpn_load);
if (match_column && strlen(match_column)) {
if (use_row!=-1) {
fprintf(stdout, "Error: you asked to match a column and also gave use_row.\n");
exitElegant(1);
}
if (!match_column_value || !strlen(match_column_value)) {
fprintf(stdout, "Error: you must give match_column_value with match_column\n");
exitElegant(1);
}
}
if (match_parameter && strlen(match_parameter)) {
if (use_page!=-1) {
fprintf(stdout, "Error: you asked to match a parameter and also gave use_page.\n");
exitElegant(1);
}
if (!match_parameter_value || !strlen(match_parameter_value)) {
fprintf(stdout, "Error: you must give match_parameter_value with match_parameter\n");
exitElegant(1);
}
}
if (!filename || !strlen(filename)) {
fprintf(stdout, "Error: no filename given for rpn_load.\n");
exitElegant(1);
}
filename = compose_filename(filename, run->rootname);
if (!SDDS_InitializeInputFromSearchPath(&SDDSin, filename)) {
fprintf(stdout, "Error: couldn't initialize SDDS input for %s\n",
filename);
exitElegant(1);
}
foundPage = 0;
while ((code=SDDS_ReadPage(&SDDSin))>0) {
if (use_page>0) {
if (code==use_page) {
foundPage = 1;
break;
}
continue;
}
if (match_parameter && strlen(match_parameter)) {
if (!(parameterValue=SDDS_GetParameterAsString(&SDDSin, match_parameter, NULL)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!wild_match(parameterValue, match_parameter_value))
continue;
foundPage = 1;
break;
}
if (use_page==-1 && SDDS_CheckEndOfFile(&SDDSin)==1) {
foundPage = 1;
break;
}
}
if (!foundPage) {
fprintf(stdout, "Error: no appropriate page found\n");
exitElegant(1);
}
if (!load_parameters) {
if ((columnName = SDDS_GetColumnNames(&SDDSin, &columns))==NULL) {
fprintf(stdout, "Warning: No columns in file!\n");
return;
}
rows = SDDS_RowCount(&SDDSin);
matchRow = rows-1;
if (use_row!=-1) {
if (use_row>=rows) {
fprintf(stdout, "Error: number of rows in file (%ld) less than needed for use_row=%ld\n",
rows, use_row);
exitElegant(1);
}
matchRow = use_row;
}
if (match_column) {
if (SDDS_GetNamedColumnType(&SDDSin, match_column)!=SDDS_STRING) {
fprintf(stdout, "Error: column %s nonexistent or not string type.\n",
match_column);
exitElegant(1);
}
if (!(matchColumnData=SDDS_GetColumn(&SDDSin, match_column))) {
fprintf(stdout, "Error: unable to get data for column %s\n", match_column);
exitElegant(1);
}
if (matching_row_number<0) {
/* use last match */
for (matchRow=rows-1; matchRow>=0; matchRow--)
if (wild_match(matchColumnData[matchRow], match_column_value))
break;
} else {
/* use nth match */
for (matchRow=0; matchRow<rows; matchRow++)
if (wild_match(matchColumnData[matchRow], match_column_value) &&
matching_row_number-- == 0)
break;
}
if (matchRow<0 || matchRow>=rows) {
fprintf(stdout, "Error: unable to find match for %s in column %s\n",
match_column_value, match_column);
exitElegant(1);
}
SDDS_FreeStringArray(matchColumnData, rows);
}
for (iColumn=0; iColumn<columns; iColumn++) {
switch (SDDS_GetNamedColumnType(&SDDSin, columnName[iColumn])) {
case SDDS_CHARACTER:
case SDDS_STRING:
break;
default:
if (!(data=SDDS_GetColumnInDoubles(&SDDSin, columnName[iColumn]))) {
fprintf(stdout, "Error: unable to get data for column %s as numerical data.\n",
columnName[iColumn]);
exitElegant(1);
}
if (!(memName=SDDS_Realloc(memName, sizeof(*memName)*((tag?strlen(tag):0)+strlen(columnName[iColumn])+2)))) {
fprintf(stdout, "Memory allocation failure trying to create memory name for loaded data\n");
exitElegant(1);
}
if (tag && strlen(tag))
sprintf(memName, "%s.%s", tag, columnName[iColumn]);
else
sprintf(memName, "%s", columnName[iColumn]);
rpn_store(data[matchRow], NULL, rpn_create_mem(memName, 0));
fprintf(stdout, "%le --> %s\n", data[matchRow], memName);
free(columnName[iColumn]);
free(data);
}
}
if (memName)
free(memName);
if (columnName)
free(columnName);
} else {
/* load data from parameters */
if ((parameterName = SDDS_GetParameterNames(&SDDSin, ¶meters))==NULL) {
fprintf(stdout, "Warning: No parameters in file!\n");
return;
}
for (iParameter=0; iParameter<parameters; iParameter++) {
switch (SDDS_GetNamedParameterType(&SDDSin, parameterName[iParameter])) {
case SDDS_CHARACTER:
case SDDS_STRING:
break;
default:
if (!SDDS_GetParameterAsDouble(&SDDSin, parameterName[iParameter], &data1)) {
fprintf(stdout, "Error: unable to get data for parameter %s as numerical data.\n",
parameterName[iParameter]);
exitElegant(1);
}
if (!(memName=SDDS_Realloc(memName, sizeof(*memName)*((tag?strlen(tag):0)+strlen(parameterName[iParameter])+2)))) {
fprintf(stdout, "Memory allocation failure trying to create memory name for loaded data\n");
exitElegant(1);
}
if (tag && strlen(tag))
sprintf(memName, "%s.%s", tag, parameterName[iParameter]);
else
sprintf(memName, "%s", parameterName[iParameter]);
rpn_store(data1, NULL, rpn_create_mem(memName, 0));
fprintf(stdout, "%le --> %s\n", data1, memName);
free(parameterName[iParameter]);
}
}
if (memName)
free(memName);
if (parameterName)
free(parameterName);
}
}
void addFilter(FILTER_STAGE *filterStage, long optionCode, SCANNED_ARG *scanned)
{
THRESHOLD_FILTER *thresholdFilter;
HILO_FILTER *hiloFilter;
NHBP_FILTER *nhbpFilter;
FILE_FILTER *fileFilter;
CLIP_FILTER *clipFilter;
FILTER *filter;
long items, filters;
char **item;
if (!(filterStage->filter
= SDDS_Realloc(filterStage->filter, sizeof(*filterStage->filter)*(filterStage->filters+1))))
SDDS_Bomb("allocation failure adding filter slot");
filter = filterStage->filter;
filters = filterStage->filters;
filterStage->filters ++;
items = scanned->n_items - 1;
item = scanned->list + 1;
switch (filter[filters].filterType = optionCode) {
case SET_THRESHOLD:
if (!(thresholdFilter = filter[filters].filter = calloc(1, sizeof(THRESHOLD_FILTER))))
SDDS_Bomb("allocation failure allocating threshold filter");
if (items<1)
SDDS_Bomb("invalid -threshold syntax");
if (!scanItemList(&thresholdFilter->flags, item, &items, 0,
"level", SDDS_DOUBLE, &thresholdFilter->level, 1, FILT_LEVEL_GIVEN,
"fractional", -1, NULL, 0, FILT_FRACTHRES_GIVEN,
"start", SDDS_DOUBLE, &thresholdFilter->start, 1, FILT_START_GIVEN,
"end", SDDS_DOUBLE, &thresholdFilter->end, 1, FILT_START_GIVEN,
NULL))
SDDS_Bomb("invalid -threshold syntax/values");
if (!(thresholdFilter->flags&FILT_LEVEL_GIVEN))
SDDS_Bomb("supply level=<value> qualifier for -threshold");
if ((thresholdFilter->flags&FILT_START_GIVEN && thresholdFilter->flags&FILT_END_GIVEN)
&& thresholdFilter->start>thresholdFilter->end)
SDDS_Bomb("start>end for -threshold filter");
break;
case SET_HIGHPASS:
case SET_LOWPASS:
if (!(hiloFilter = filter[filters].filter = calloc(1, sizeof(HILO_FILTER))))
SDDS_Bomb("allocation failure allocating low-pass or high-pass filter");
if (!scanItemList(&hiloFilter->flags, item, &items, 0,
"start", SDDS_DOUBLE, &hiloFilter->start, 1, FILT_START_GIVEN,
"end", SDDS_DOUBLE, &hiloFilter->end, 1, FILT_END_GIVEN,
NULL))
SDDS_Bomb("invalid -highpass or -lowpass syntax");
if (!(hiloFilter->flags&FILT_START_GIVEN) ||
!(hiloFilter->flags&FILT_END_GIVEN))
SDDS_Bomb("supply start=<value> and end=<value> qualifiers with -highpass and -lowpass");
break;
case SET_NOTCH:
case SET_BANDPASS:
if (!(nhbpFilter = filter[filters].filter = calloc(1, sizeof(NHBP_FILTER))))
SDDS_Bomb("allocation failure allocating notch or bandpass filter");
if (!scanItemList(&nhbpFilter->flags, item, &items, 0,
"center", SDDS_DOUBLE, &nhbpFilter->center, 1, FILT_CENTER_GIVEN,
"fullwidth", SDDS_DOUBLE, &nhbpFilter->fullwidth, 1, FILT_FULLWIDTH_GIVEN,
"flatwidth", SDDS_DOUBLE, &nhbpFilter->flatwidth, 1, FILT_FLATWIDTH_GIVEN,
NULL))
SDDS_Bomb("invalid -notch or -bandpass syntax");
if (!(nhbpFilter->flags&FILT_CENTER_GIVEN) || !(nhbpFilter->flags&FILT_FLATWIDTH_GIVEN) )
SDDS_Bomb("supply center=<value> and flatWidth=<value> qualifiers with -notch and -bandpass");
if (!(nhbpFilter->flags&FILT_FULLWIDTH_GIVEN))
nhbpFilter->fullwidth = nhbpFilter->flatwidth;
if (nhbpFilter->fullwidth<nhbpFilter->flatwidth)
SDDS_Bomb("full width may not be less that flat width for notch/bandpass filter");
break;
case SET_FILTERFILE:
if (!(fileFilter = filter[filters].filter = calloc(1, sizeof(FILE_FILTER))))
SDDS_Bomb("allocation failure allocating file filter");
if (!scanItemList(&fileFilter->flags, item, &items, 0,
"filename", SDDS_STRING, &fileFilter->file, 1, FILT_FILENAME_GIVEN,
"frequency", SDDS_STRING, &fileFilter->freqName, 1, FILT_FREQNAME_GIVEN,
"real", SDDS_STRING, &fileFilter->realName, 1, FILT_REALNAME_GIVEN,
"imaginary", SDDS_STRING, &fileFilter->imagName, 1, FILT_IMAGNAME_GIVEN,
"magnitude", SDDS_STRING, &fileFilter->magName, 1, FILT_MAGNAME_GIVEN,
NULL))
SDDS_Bomb("invalid -fileFilter syntax");
if (!(fileFilter->flags&FILT_FILENAME_GIVEN))
SDDS_Bomb("supply filename=<string> with -fileFilter");
if (!(fileFilter->flags&FILT_FREQNAME_GIVEN))
SDDS_Bomb("supply frequency=<columnName> with -fileFilter");
if (!(fileFilter->flags&FILT_MAGNAME_GIVEN) &&
!(fileFilter->flags&FILT_REALNAME_GIVEN && fileFilter->flags&FILT_IMAGNAME_GIVEN))
SDDS_Bomb("supply either magnitude=<columnName>, or real=<columnName> and imag=<columnName>, with -fileFilter");
if (fileFilter->flags&FILT_MAGNAME_GIVEN &&
(fileFilter->flags&FILT_REALNAME_GIVEN || fileFilter->flags&FILT_IMAGNAME_GIVEN))
SDDS_Bomb("magnitude=<columnName> is incompatible with real=<columnName> and imag=<columnName> for -fileFilter");
fileFilter->freqData = NULL; /* indicates no data present */
break;
case SET_CLIPFREQ:
if (!(clipFilter = filter[filters].filter = calloc(1, sizeof(CLIP_FILTER))))
SDDS_Bomb("allocation failure allocating clip filter");
if (!scanItemList(&clipFilter->flags, item, &items, 0,
"high", SDDS_LONG, &clipFilter->high, 1, FILT_HIGH_GIVEN,
"low", SDDS_LONG, &clipFilter->low, 1, FILT_LOW_GIVEN,
NULL))
SDDS_Bomb("invalid -clipFrequencies syntax");
if (!(clipFilter->flags&FILT_HIGH_GIVEN) && !(clipFilter->flags&FILT_LOW_GIVEN))
SDDS_Bomb("supply at least one of high=<number> or low=<number> with -clipFrequencies");
break;
default:
SDDS_Bomb("invalid filter code---this shouldn't happen");
break;
}
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDS_orig, SDDS_out1, SDDS_out2;
int32_t i, j, k, row, str_len;
SCANNED_ARG *s_arg;
char *inputFile, *outputRoot, output1[1024], output2[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 ****data;
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;
inputFile = s_arg[1].list[0];
if (argc==3)
outputRoot = s_arg[2].list[0];
else
outputRoot = inputFile;
sprintf(output1, "%s.yz", outputRoot);
sprintf(output2, "%s.xz", outputRoot);
data = NULL;
if (!SDDS_InitializeInput(&SDDS_orig, inputFile)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
columnName = (char**)SDDS_GetColumnNames(&SDDS_orig, &columnNames);
for (i=0; i<columnNames; i++) {
if (wild_match(columnName[i], "*_1")) {
outputColumn = SDDS_Realloc(outputColumn, (outputColumns+1)*sizeof(*outputColumn));
outputColumn[outputColumns] = malloc(sizeof(**outputColumn)*strlen(columnName[i]));
str_len = strlen(columnName[i]);
strncpy(outputColumn[outputColumns], columnName[i], str_len-2);
outputColumn[outputColumns][str_len-2]=0;
outputColumns ++;
}
}
data = malloc(sizeof(*data)*outputColumns);
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_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);
}
SetupOutputFile(&SDDS_out1, output1, 1, outputColumns, outputColumn);
SetupOutputFile(&SDDS_out2, output2, 0, outputColumns, outputColumn);
for (i=0; i<outputColumns; i++) {
data[i] = malloc(sizeof(**data)*zdim);
for (j=0; j<zdim; j++)
data[i][j] = malloc(sizeof(***data)*ydim);
}
}
for (i=0; i<outputColumns; i++) {
for (j=1; j<=ydim; j++) {
sprintf(tmpcol, "%s_%d", outputColumn[i], j);
data[i][page][j-1] = NULL;
if (!(data[i][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(data, outputColumns, zdim, ydim);
fprintf(stderr, "Error, the page number does not equal to zdim size.\n");
exit(1);
}
/* write to yz output, each page has the same x */
for (page=0; page<xdim; page++) {
if (!SDDS_StartPage(&SDDS_out1, ydim*zdim) ||
!SDDS_SetParameters(&SDDS_out1,SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin1", xmin, "origin2", ymin, "origin3", zmin, "max_ext1", xmax, "max_ext2", ymax, "max_ext3", zmax,
"delta1", xinterval, "delta2", yinterval, "delta3", zinterval, "numPhysCells1", xdim,
"numPhysCells2", ydim, "numPhysCells3", zdim, "Variable1Name", "Y", "Variable2Name", "Z",
"ZMinimum", zmin, "ZMaximum", zmax, "ZInterval", zinterval, "ZDimension", zdim,
"YMinimum", ymin, "YMaximum", ymax, "YInterval", yinterval, "YDimension", ydim, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<outputColumns; i++) {
row = 0;
for (j=0; j<ydim; j++) {
for (k=0; k<zdim; k++) {
if (!SDDS_SetRowValues(&SDDS_out1, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
outputColumn[i], data[i][k][j][page],
"z", k*zinterval + zmin,
"y", j*yinterval + ymin, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row ++;
}
}
}
if (!SDDS_WritePage(&SDDS_out1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_Terminate(&SDDS_out1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* write to xz output, each page has the same y */
for (page=0; page<ydim; page++) {
if (!SDDS_StartPage(&SDDS_out2, xdim*zdim) ||
!SDDS_SetParameters(&SDDS_out2, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin1", xmin, "origin2", ymin, "origin3", zmin, "max_ext1", xmax, "max_ext2", ymax, "max_ext3", zmax,
"delta1", xinterval, "delta2", yinterval, "delta3", zinterval, "numPhysCells1", xdim,
"numPhysCells2", ydim, "numPhysCells3", zdim, "Variable1Name", "X", "Variable2Name", "Z",
"ZMinimum", zmin, "ZMaximum", zmax, "ZInterval", zinterval, "ZDimension", zdim,
"XMinimum", xmin, "XMaximum", xmax, "XInterval", xinterval, "XDimension", xdim, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<outputColumns; i++) {
row = 0;
for (j=0; j<xdim; j++) {
for (k=0; k<zdim; k++) {
if (!SDDS_SetRowValues(&SDDS_out2, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
outputColumn[i], data[i][k][page][j],
"z", k*zinterval + zmin,
"x", j*xinterval+xmin, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row ++;
}
}
}
if (!SDDS_WritePage(&SDDS_out2))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free_data_memory(data, outputColumns, zdim, ydim);
if (!SDDS_Terminate(&SDDS_out2))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
return 0;
}
int main(int argc, char **argv)
{
POLYNOMIAL *poly;
long nPoly, iPoly, row, rows, iInput;
int iArg;
char *input, *output;
unsigned long pipeFlags;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout;
double *outputData ;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<3)
bomb(NULL, USAGE);
outputData = NULL;
input = output = NULL;
pipeFlags = 0;
poly = NULL;
nPoly = 0;
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_EVALUATE:
if (!(poly = SDDS_Realloc(poly, sizeof(*poly)*(nPoly+1))) ||
!(poly[nPoly].inputColumn
=SDDS_Malloc(sizeof(*(poly[nPoly].inputColumn))*5)) ||
!(poly[nPoly].powerColumn
=SDDS_Malloc(sizeof(*(poly[nPoly].powerColumn))*5)))
SDDS_Bomb("memory allocation failure");
scanned[iArg].n_items -= 1;
if (!scanItemList(&poly[nPoly].flags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"filename", SDDS_STRING, &(poly[nPoly].filename), 1, POLY_FILE_SEEN,
"output", SDDS_STRING, &(poly[nPoly].outputColumn), 1, POLY_OUTPUT_SEEN,
"coefficients", SDDS_STRING, &(poly[nPoly].coefColumn), 1, POLY_COEF_SEEN,
"input0", SDDS_STRING, poly[nPoly].inputColumn+0, 1, POLY_IN0_SEEN,
"power0", SDDS_STRING, poly[nPoly].powerColumn+0, 1, POLY_OUT0_SEEN,
"input1", SDDS_STRING, poly[nPoly].inputColumn+1, 1, POLY_IN1_SEEN,
"power1", SDDS_STRING, poly[nPoly].powerColumn+1, 1, POLY_OUT1_SEEN,
"input2", SDDS_STRING, poly[nPoly].inputColumn+2, 1, POLY_IN2_SEEN,
"power2", SDDS_STRING, poly[nPoly].powerColumn+2, 1, POLY_OUT2_SEEN,
"input3", SDDS_STRING, poly[nPoly].inputColumn+3, 1, POLY_IN3_SEEN,
"power3", SDDS_STRING, poly[nPoly].powerColumn+3, 1, POLY_OUT3_SEEN,
"input4", SDDS_STRING, poly[nPoly].inputColumn+4, 1, POLY_IN4_SEEN,
"power4", SDDS_STRING, poly[nPoly].powerColumn+4, 1, POLY_OUT4_SEEN,
NULL) ||
!(poly[nPoly].flags&POLY_FILE_SEEN) || !(poly[nPoly].flags&POLY_OUTPUT_SEEN) ||
!(poly[nPoly].flags&POLY_COEF_SEEN) || !(poly[nPoly].flags&POLY_IN0_SEEN) ||
!(poly[nPoly].flags&POLY_OUT0_SEEN))
SDDS_Bomb("invalid -evaluate syntax");
nPoly++;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
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");
}
}
processFilenames("sddspoly", &input, &output, pipeFlags, 0, NULL);
if (nPoly==0)
SDDS_Bomb("give at least one -evaluate option");
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_InitializeCopy(&SDDSout, &SDDSin, output, "w"))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (iPoly=0; iPoly<nPoly; iPoly++)
initializePolynomial(&poly[iPoly], &SDDSin, &SDDSout);
if (!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
while (SDDS_ReadPage(&SDDSin)>0) {
rows = SDDS_CountRowsOfInterest(&SDDSin);
if (!SDDS_CopyPage(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(outputData = SDDS_Realloc(outputData, sizeof(*outputData)*rows)))
SDDS_Bomb("memory allocation failure");
for (iPoly=0; iPoly<nPoly; iPoly++) {
for (iInput=0; iInput<poly[iPoly].nInputs; iInput++) {
if (!(poly[iPoly].inputData[iInput]=
SDDS_GetColumnInDoubles(&SDDSin, poly[iPoly].inputColumn[iInput])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (row=0; row<rows; row++) {
for (iInput=0; iInput<poly[iPoly].nInputs; iInput++)
poly[iPoly].input[iInput] = poly[iPoly].inputData[iInput][row];
outputData[row] = evaluatePoly(poly[iPoly].coef, poly[iPoly].power,
poly[iPoly].nTerms,
poly[iPoly].input, poly[iPoly].nInputs);
}
if (!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_NAME,
outputData, rows, poly[iPoly].outputColumn))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(outputData);
if (!SDDS_Terminate(&SDDSin)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
free_scanargs(&scanned,argc);
FreePolynormialMemory(poly,nPoly);
free(poly);
return 0;
}
int32_t SDDS_RestoreLayout(SDDS_DATASET *SDDS_dataset)
{
SDDS_LAYOUT *source, *target;
if (!SDDS_CheckDataset(SDDS_dataset, "SDDS_RestoreLayout"))
return(0);
source = &SDDS_dataset->original_layout;
target = &SDDS_dataset->layout;
/* copy pointer elements of structure into new memory */
if (source->n_columns) {
if (target->column_definition==source->column_definition) {
SDDS_SetError("Unable to restore layout--column definition pointers are the same (SDDS_RestoreLayout)");
return(0);
}
if (!(target->column_definition =
(COLUMN_DEFINITION*)SDDS_Realloc((void*)target->column_definition,
sizeof(COLUMN_DEFINITION)*source->n_columns))) {
SDDS_SetError("Unable to restore layout--allocation failure (SDDS_RestoreLayout)");
return(0);
}
memcpy((char*)target->column_definition, (char*)source->column_definition, sizeof(COLUMN_DEFINITION)*source->n_columns);
}
if (source->n_parameters) {
if (target->parameter_definition==source->parameter_definition) {
SDDS_SetError("Unable to restore layout--parameter definition pointers are the same (SDDS_RestoreLayout)");
return(0);
}
if (!(target->parameter_definition =
(PARAMETER_DEFINITION*)SDDS_Realloc((void*)target->parameter_definition,
sizeof(PARAMETER_DEFINITION)*source->n_parameters))) {
SDDS_SetError("Unable to restore layout--allocation failure (SDDS_RestoreLayout)");
return(0);
}
memcpy((char*)target->parameter_definition, (char*)source->parameter_definition,
sizeof(PARAMETER_DEFINITION)*source->n_parameters);
}
if (source->n_arrays) {
if (target->array_definition==source->array_definition) {
SDDS_SetError("Unable to restore layout--array definition pointers are the same (SDDS_RestoreLayout)");
return(0);
}
if (!(target->array_definition =
(ARRAY_DEFINITION*)SDDS_Realloc((void*)target->array_definition,
sizeof(ARRAY_DEFINITION)*source->n_arrays))) {
SDDS_SetError("Unable to restore layout--allocation failure (SDDS_RestoreLayout)");
return(0);
}
memcpy((char*)target->array_definition, (char*)source->array_definition, sizeof(ARRAY_DEFINITION)*source->n_arrays);
}
if (source->n_associates) {
if (target->associate_definition==source->associate_definition) {
SDDS_SetError("Unable to restore layout--associate definition pointers are the same (SDDS_RestoreLayout)");
return(0);
}
if (!(target->associate_definition =
(ASSOCIATE_DEFINITION*)SDDS_Realloc((void*)target->associate_definition,
sizeof(ASSOCIATE_DEFINITION)*source->n_associates))) {
SDDS_SetError("Unable to restore layout--allocation failure (SDDS_RestoreLayout)");
return(0);
}
memcpy((char*)target->associate_definition, (char*)source->associate_definition,
sizeof(ASSOCIATE_DEFINITION)*source->n_associates);
}
target->n_columns = source->n_columns;
target->n_parameters = source->n_parameters;
target->n_associates = source->n_associates;
target->n_arrays = source->n_arrays;
target->description = source->description;
target->contents = source->contents;
target->version = source->version;
target->data_mode = source->data_mode;
target->filename = source->filename;
target->fp = source->fp;
return(1);
}
int32_t SDDS_SaveLayout(SDDS_DATASET *SDDS_dataset)
{
SDDS_LAYOUT *source, *target;
if (deferSavingLayout)
return 1;
if (!SDDS_CheckDataset(SDDS_dataset, "SDDS_SaveLayout"))
return(0);
if ((source = &SDDS_dataset->layout)==(target = &SDDS_dataset->original_layout)) {
SDDS_SetError("\"original\" and working page layouts share memory!");
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
/* copy pointer elements of structure into new memory */
if (source->n_columns) {
if (!(target->column_definition =
(COLUMN_DEFINITION*)SDDS_Realloc((void*)target->column_definition,
sizeof(COLUMN_DEFINITION)*source->n_columns)) ||
!(target->column_index =
(SORTED_INDEX**)SDDS_Realloc((void*)target->column_index,
sizeof(SORTED_INDEX*)*source->n_columns))) {
SDDS_SetError("Unable to save layout--allocation failure (SDDS_SaveLayout)");
return(0);
}
memcpy((char*)target->column_definition, (char*)source->column_definition,
sizeof(COLUMN_DEFINITION)*source->n_columns);
memcpy((char*)target->column_index, (char*)source->column_index,
sizeof(SORTED_INDEX*)*source->n_columns);
}
if (source->n_parameters) {
if (!(target->parameter_definition =
(PARAMETER_DEFINITION*)SDDS_Realloc((void*)target->parameter_definition,
sizeof(PARAMETER_DEFINITION)*source->n_parameters)) ||
!(target->parameter_index =
(SORTED_INDEX**)SDDS_Realloc((void*)target->parameter_index,
sizeof(SORTED_INDEX*)*source->n_parameters))) {
SDDS_SetError("Unable to save layout--allocation failure (SDDS_SaveLayout)");
return(0);
}
memcpy((char*)target->parameter_definition, (char*)source->parameter_definition,
sizeof(PARAMETER_DEFINITION)*source->n_parameters);
memcpy((char*)target->parameter_index, (char*)source->parameter_index,
sizeof(SORTED_INDEX*)*source->n_parameters);
}
if (source->n_arrays) {
if (!(target->array_definition =
(ARRAY_DEFINITION*)SDDS_Realloc((void*)target->array_definition,
sizeof(ARRAY_DEFINITION)*source->n_arrays)) ||
!(target->array_index =
(SORTED_INDEX**)SDDS_Realloc((void*)target->array_index,
sizeof(SORTED_INDEX*)*source->n_arrays))) {
SDDS_SetError("Unable to save layout--allocation failure (SDDS_SaveLayout)");
return(0);
}
memcpy((char*)target->array_definition, (char*)source->array_definition, sizeof(ARRAY_DEFINITION)*source->n_arrays);
memcpy((char*)target->array_index, (char*)source->array_index, sizeof(SORTED_INDEX*)*source->n_arrays);
}
if (source->n_associates) {
if (!(target->associate_definition =
(ASSOCIATE_DEFINITION*)SDDS_Realloc((void*)target->associate_definition,
sizeof(ASSOCIATE_DEFINITION)*source->n_associates))) {
SDDS_SetError("Unable to save layout--allocation failure (SDDS_SaveLayout)");
return(0);
}
memcpy((char*)target->associate_definition, (char*)source->associate_definition,
sizeof(ASSOCIATE_DEFINITION)*source->n_associates);
}
target->n_columns = source->n_columns;
target->n_parameters = source->n_parameters;
target->n_associates = source->n_associates;
target->n_arrays = source->n_arrays;
target->description = source->description;
target->contents = source->contents;
target->version = source->version;
target->data_mode = source->data_mode;
target->filename = source->filename;
target->fp = source->fp;
target->popenUsed = source->popenUsed;
return(1);
}
long perform_sddsplot_filtering(SDDS_TABLE *table, FILTER_DEFINITION **filter, long filters)
{
long i, j, accept, skip_table;
long n_left, row_deletion, n_rows;
FILTER_TERM *filter_term;
FILTER_DEFINITION *filter_ptr;
PARAMETER_DEFINITION *pardefptr;
double result;
static int32_t *rowFlag1 = NULL, *rowFlag2 = NULL;
static long rowFlags = 0;
skip_table = 0;
#if DEBUG
fprintf(stderr, "%ld filters being applied\n", filters);
#endif
if (filters==0)
return !skip_table;
n_rows = SDDS_RowCount(table);
row_deletion = 1;
for (i=0; i<filters; i++) {
filter_ptr = filter[i];
if (filter_ptr->is_parameter) {
accept = 1;
filter_term = filter_ptr->filter_term;
for (j=0; j<filter_ptr->filter_terms; j++) {
if (!(pardefptr=SDDS_GetParameterDefinition(table, filter_term[j].name)) ||
(pardefptr->type==SDDS_STRING || pardefptr->type==SDDS_CHARACTER)) {
fprintf(stderr, "error: unknown or non-numeric parameter %s given for filter\n",
filter_term[j].name);
exit(1);
}
accept =
SDDS_Logic(accept,
SDDS_ItemInsideWindow(SDDS_GetParameter(table, filter_term[j].name,
&result),
0, pardefptr->type, filter_term[j].lower,
filter_term[j].upper),
filter_term[j].logic);
}
if (!accept) {
skip_table = 1;
break;
}
}
else if (n_rows) {
if (!rowFlag1 || !rowFlag2 || n_rows>rowFlags) {
if (!(rowFlag1 = SDDS_Realloc(rowFlag1, sizeof(*rowFlag1)*n_rows)) ||
!(rowFlag2 = SDDS_Realloc(rowFlag2, sizeof(*rowFlag2)*n_rows))) {
fprintf(stderr, "Problem reallocating row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_GetRowFlags(table, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
filter_term = filter_ptr->filter_term;
for (j=0; j<filter_ptr->filter_terms; j++) {
#if defined(DEBUG)
fprintf(stderr, "Filtering by %s on [%e, %e] with logic %x\n",
filter_term[j].name, filter_term[j].lower,
filter_term[j].upper, filter_term[j].logic);
#endif
if ((n_left=SDDS_FilterRowsOfInterest(table, filter_term[j].name, filter_term[j].lower,
filter_term[j].upper, filter_term[j].logic))<0) {
fprintf(stderr, "error: unable to filter by column %s\n",
filter_term[j].name);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/* fprintf(stderr,"total_rows=%d, filtered left=%d\n",n_rows,n_left);*/
#if defined(DEBUG)
fprintf(stderr, "%ld rows of %ld left after filter %ld of set %ld\n",
n_left, n_rows, j, i);
#endif
}
if (i) {
if (!SDDS_GetRowFlags(table, rowFlag2, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
for (j=0; j<n_rows; j++) {
rowFlag1[j] = rowFlag1[j]&rowFlag2[j];
}
if (!SDDS_AssertRowFlags(table, SDDS_FLAG_ARRAY, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to assert row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
} else {
if (!SDDS_GetRowFlags(table, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_filtering)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
row_deletion = 1;
}
}
return !skip_table;
}
int main(int argc, char **argv)
{
double *xData, *yData, *xError, *yError, *derivative, *derivativeError, *derivativePosition;
char *input, *output, *xName, *xErrorName, **yName, **yErrorName, **yOutputName, **yOutputErrorName, *ptr;
char **yOutputUnits, **yExcludeName;
char *mainTemplate[3] = {NULL, NULL, NULL};
char *errorTemplate[3] = {NULL, NULL, NULL};
long i, iArg, yNames, yExcludeNames, rows;
int32_t interval;
SDDS_DATASET SDDSin, SDDSout;
SCANNED_ARG *scanned;
unsigned long flags, pipeFlags;
long SGLeft, SGRight, SGOrder, SGDerivOrder, intervalGiven, yErrorsSeen;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
input = output = xName = xErrorName = NULL;
yName = yErrorName = yExcludeName = NULL;
derivative = derivativeError = derivativePosition = yError = yData = xData = xError = NULL;
yNames = yExcludeNames = 0;
pipeFlags = 0;
interval = 2;
SGOrder = -1;
SGDerivOrder = 1;
intervalGiven = 0;
yErrorsSeen = 0;
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_DIFFERENTIATE:
if (scanned[iArg].n_items!=2 && scanned[iArg].n_items!=3)
SDDS_Bomb("invalid -differentiate syntax");
yName = SDDS_Realloc(yName, sizeof(*yName)*(yNames+1));
yErrorName = SDDS_Realloc(yErrorName, sizeof(*yErrorName)*(yNames+1));
yName[yNames] = scanned[iArg].list[1];
if (scanned[iArg].n_items==3) {
yErrorsSeen = 1;
yErrorName[yNames] = scanned[iArg].list[2];
} else
yErrorName[yNames] = NULL;
yNames++;
break;
case CLO_EXCLUDE:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -exclude syntax");
moveToStringArray(&yExcludeName, &yExcludeNames, scanned[iArg].list+1, scanned[iArg].n_items-1);
break;
case CLO_VERSUS:
if (xName)
SDDS_Bomb("give -versus only once");
if (scanned[iArg].n_items!=2)
SDDS_Bomb("invalid -versus syntax");
xName = scanned[iArg].list[1];
xErrorName = NULL;
break;
case CLO_MAINTEMPLATE:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -mainTemplate syntax");
scanned[iArg].n_items--;
if (!scanItemList(&flags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"name", SDDS_STRING, mainTemplate+0, 1, 0,
"description", SDDS_STRING, mainTemplate+1, 1, 0,
"symbol", SDDS_STRING, mainTemplate+2, 1, 0,
NULL))
SDDS_Bomb("invalid -mainTemplate syntax");
break;
case CLO_ERRORTEMPLATE:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -errorTemplate syntax");
scanned[iArg].n_items--;
if (!scanItemList(&flags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"name", SDDS_STRING, errorTemplate+0, 1, 0,
"description", SDDS_STRING, errorTemplate+1, 1, 0,
"symbol", SDDS_STRING, errorTemplate+2, 1, 0,
NULL))
SDDS_Bomb("invalid -errorTemplate 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_INTERVAL:
if (scanned[iArg].n_items!=2 || sscanf(scanned[iArg].list[1], "%" SCNd32, &interval)!=1 ||
interval<=0)
SDDS_Bomb("invalid -interval syntax/value");
intervalGiven = 1;
break;
case CLO_SAVITZKYGOLAY:
if ((scanned[iArg].n_items!=4 && scanned[iArg].n_items!=5) ||
sscanf(scanned[iArg].list[1], "%ld", &SGLeft)!=1 ||
sscanf(scanned[iArg].list[2], "%ld", &SGRight)!=1 ||
sscanf(scanned[iArg].list[3], "%ld", &SGOrder)!=1 ||
(scanned[iArg].n_items==5 &&
sscanf(scanned[iArg].list[4], "%ld", &SGDerivOrder)!=1) ||
SGLeft<0 || SGRight<0 || (SGLeft+SGRight)<SGOrder ||
SGOrder<0 || SGDerivOrder<0)
SDDS_Bomb("invalid -SavitzkyGolay syntax/values");
break;
default:
fprintf(stderr, "invalid option seen: %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");
}
}
if (intervalGiven && SGOrder>=0)
SDDS_Bomb("-interval and -SavitzkyGolay options are incompatible");
if (SGOrder>=0 && (xErrorName || yErrorsSeen))
SDDS_Bomb("Savitzky-Golay method does not support errors in data");
processFilenames("sddsderiv", &input, &output, pipeFlags, 0, NULL);
if (!yNames)
SDDS_Bomb("-differentiate option must be given at least once");
if (!checkErrorNames(yErrorName, yNames))
SDDS_Bomb("either all -differentiate quantities must have errors, or none");
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(ptr=SDDS_FindColumn(&SDDSin, FIND_NUMERIC_TYPE, xName, NULL))) {
fprintf(stderr, "error: column %s doesn't exist\n", xName);
exit(1);
}
free(xName);
xName = ptr;
if (xErrorName) {
if (!(ptr=SDDS_FindColumn(&SDDSin, FIND_NUMERIC_TYPE, xErrorName, NULL))) {
fprintf(stderr, "error: column %s doesn't exist\n", xErrorName);
exit(1);
}
else {
free(xErrorName);
xErrorName = ptr;
}
}
if (!(yNames=expandColumnPairNames(&SDDSin, &yName, &yErrorName, yNames,
yExcludeName, yExcludeNames, FIND_NUMERIC_TYPE, 0))) {
fprintf(stderr, "error: no quantities to differentiate found in file\n");
exit(1);
}
setupOutputFile(&SDDSout, &SDDSin, output, &yOutputName, &yOutputErrorName, &yOutputUnits,
xName, xErrorName, yName, yErrorName, yNames, mainTemplate, errorTemplate,
interval, SGOrder>=0?SGDerivOrder:1);
while (SDDS_ReadPage(&SDDSin)>0) {
if ((rows = SDDS_CountRowsOfInterest(&SDDSin))<2)
SDDS_Bomb("Can't compute derivatives: too little data.");
derivative = SDDS_Realloc(derivative, sizeof(*derivative)*rows);
derivativeError = SDDS_Realloc(derivativeError, sizeof(*derivativeError)*rows);
derivativePosition = SDDS_Realloc(derivativePosition, sizeof(*derivativePosition)*rows);
if (!SDDS_StartPage(&SDDSout, rows) || !SDDS_CopyParameters(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
xError = NULL;
if (!(xData = SDDS_GetColumnInDoubles(&SDDSin, xName)) ||
(xErrorName && !(xError=SDDS_GetColumnInDoubles(&SDDSin, xErrorName))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<yNames; i++) {
yError = NULL;
if (!(yData = SDDS_GetColumnInDoubles(&SDDSin, yName[i])) ||
(yErrorName && yErrorName[i] && !(yError=SDDS_GetColumnInDoubles(&SDDSin, yErrorName[i]))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SGOrder>=0)
takeSGDerivative(xData, yData, rows, derivative, derivativePosition,
SGLeft, SGRight, SGOrder, SGDerivOrder);
else
takeDerivative(xData, yData, yError, rows, derivative, derivativeError,
derivativePosition, interval);
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, derivative, rows, yOutputName[i]) ||
(yOutputErrorName && yOutputErrorName[i] &&
!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, derivativeError, rows, yOutputErrorName[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (yData) free(yData);
if (yError) free(yError);
yData = yError = NULL;
}
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, derivativePosition, rows, xName) ||
(xErrorName && !SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, xError, rows, xErrorName)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (xData) free(xData);
if (xError) free(xError);
xData = xError = NULL;
}
if (!SDDS_Terminate(&SDDSin) || !SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (derivative) free(derivative);
if (derivativeError) free(derivativeError);
if (derivativePosition) free(derivativePosition);
return(0);
}
long perform_sddsplot_matching(SDDS_TABLE *table, MATCH_DEFINITION **match, long matches)
{
long i, j, accept, skip_table;
long n_rows, row_deletion;
MATCH_TERM *match_term;
MATCH_DEFINITION *match_ptr;
PARAMETER_DEFINITION *pardefptr;
static char s[SDDS_MAXLINE];
static int32_t *rowFlag1 = NULL, *rowFlag2 = NULL;
static long rowFlags = 0;
skip_table = 0;
if (matches==0)
return !skip_table;
n_rows = SDDS_RowCount(table);
for (i=0; i<matches; i++) {
match_ptr = match[i];
if (match_ptr->is_parameter) {
accept = 1;
match_term = match_ptr->match_term;
for (j=0; j<match_ptr->match_terms; j++) {
if (!(pardefptr=SDDS_GetParameterDefinition(table, match_term[j].name)) ||
!(pardefptr->type==SDDS_STRING || pardefptr->type==SDDS_CHARACTER)) {
fprintf(stderr, "error: unknown or numeric parameter %s given for match\n",
match_term[j].name);
exit(1);
}
if (pardefptr->type==SDDS_STRING) {
char **ppc;
ppc = SDDS_GetParameter(table, match_term[j].name, NULL);
strcpy_ss(s, *ppc);
}
else {
char *pc;
pc = SDDS_GetParameter(table, match_term[j].name, NULL);
sprintf(s, "%c", *pc);
}
accept = SDDS_Logic(accept, wild_match(s, match_term[j].string), match_term[j].logic);
}
if (!accept) {
skip_table = 1;
break;
}
}
else if (n_rows) {
if (!rowFlag1 || !rowFlag2 || n_rows>rowFlags) {
if (!(rowFlag1 = SDDS_Realloc(rowFlag1, sizeof(*rowFlag1)*n_rows)) ||
!(rowFlag2 = SDDS_Realloc(rowFlag2, sizeof(*rowFlag2)*n_rows))) {
fprintf(stderr, "Unable to reallocate row flag arrays (perform_sddsplot_matching)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_GetRowFlags(table, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_matching-1)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
match_term = match_ptr->match_term;
for (j=0; j<match_ptr->match_terms; j++) {
#if defined(DEBUG)
fprintf(stderr, "Matching %s to %s on with logic %x\n",
match_term[j].name,
match_term[j].string, match_term[j].logic);
#endif
if (SDDS_MatchRowsOfInterest(table, match_term[j].name,
match_term[j].string, match_term[j].logic)<0) {
fprintf(stderr, "Error matching rows (perform_sddsplot_matching)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#if defined(DEBUG)
fprintf(stderr, "%ld rows left after match %ld of set %ld\n",
SDDS_CountRowsOfInterest(table), j, i);
#endif
}
if (i) {
if (!SDDS_GetRowFlags(table, rowFlag2, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_matching-2)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
for (j=0; j<n_rows; j++) {
rowFlag1[j] = rowFlag1[j]&rowFlag2[j];
}
if (!SDDS_AssertRowFlags(table, SDDS_FLAG_ARRAY, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to assert row flags (perform_sddsplot_matching)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
} else {
if (!SDDS_GetRowFlags(table, rowFlag1, n_rows)) {
fprintf(stderr, "Unable to get row flags (perform_sddsplot_matching-3)\n");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
row_deletion = 1;
}
}
return !skip_table;
}
int main(int argc, char **argv)
{
int iArg;
char **outputColumn, **difColumn;
char *indepColumn, **depenColumn, **exclude;
long depenColumns, excludes;
char *input, *output;
long i, rows, readCode, optionCode;
unsigned long flags, pipeFlags;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout;
double *timeData, *inputData, *outputData;
FILTER_STAGE *filterStage;
long filterStages, totalFilters;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<3 || argc>(3+N_OPTIONS))
bomb(NULL, USAGE);
output = input = NULL;
flags = pipeFlags = 0;
indepColumn = NULL;
depenColumn = exclude = NULL;
depenColumns = excludes = 0;
if (!(filterStage = (FILTER_STAGE*)calloc(1, sizeof(*filterStage))))
SDDS_Bomb("allocation failure");
filterStage->filter = NULL;
filterStage->filters = 0;
filterStages = 1;
totalFilters = 0;
for (iArg=1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type==OPTION) {
/* process options here */
switch (optionCode=match_string(scanned[iArg].list[0], option, N_OPTIONS, 0)) {
case SET_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_COLUMNS:
if (indepColumn)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
indepColumn = scanned[iArg].list[1];
if (scanned[iArg].n_items>=2) {
depenColumn = tmalloc(sizeof(*depenColumn)*(depenColumns=scanned[iArg].n_items-2));
for (i=0; i<depenColumns; i++)
depenColumn[i] = scanned[iArg].list[i+2];
}
break;
case SET_THRESHOLD:
case SET_HIGHPASS:
case SET_LOWPASS:
case SET_NOTCH:
case SET_BANDPASS:
case SET_FILTERFILE:
case SET_CLIPFREQ:
addFilter(filterStage+filterStages-1, optionCode, scanned+iArg);
totalFilters++;
break;
case SET_CASCADE:
if (filterStages==0)
SDDS_Bomb("-cascade option precedes all filter definitions");
if (!(filterStage = SDDS_Realloc(filterStage, (filterStages+1)*sizeof(*filterStage))))
SDDS_Bomb("allocation failure");
filterStage[filterStages].filter = NULL;
filterStage[filterStages].filters = 0;
filterStages++;
break;
case SET_NEWCOLUMNS:
flags |= FL_NEWCOLUMNS;
break;
case SET_DIFFERENCECOLUMNS:
flags |= FL_DIFCOLUMNS;
break;
case SET_EXCLUDE:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -exclude syntax");
moveToStringArray(&exclude, &excludes, scanned[iArg].list+1, scanned[iArg].n_items-1);
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s (%s)\n",
scanned[iArg].list[0], argv[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");
}
}
processFilenames("sddsfdfilter", &input, &output, pipeFlags, 0, NULL);
if (!totalFilters)
fputs("warning: no filters specified (sddsfdfilter)\n", stderr);
if (!indepColumn)
SDDS_Bomb("supply the independent column name with the -columns option");
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_CheckColumn(&SDDSin, indepColumn, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OKAY)
exit(1);
excludes = appendToStringArray(&exclude, excludes, indepColumn);
if (!depenColumns)
depenColumns = appendToStringArray(&depenColumn, depenColumns, "*");
if ((depenColumns=expandColumnPairNames(&SDDSin, &depenColumn, NULL, depenColumns, exclude, excludes,
FIND_NUMERIC_TYPE, 0))<=0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_Bomb("No quantities selected to filter");
}
if (!SDDS_InitializeCopy(&SDDSout, &SDDSin, output, "w"))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (flags&FL_NEWCOLUMNS) {
outputColumn = tmalloc(sizeof(*outputColumn)*depenColumns);
for (i=0; i<depenColumns; i++) {
outputColumn[i] = tmalloc(sizeof(**outputColumn)*(strlen(depenColumn[i])+1+strlen("Filtered")));
sprintf(outputColumn[i], "%sFiltered", depenColumn[i]);
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, depenColumn[i], outputColumn[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
else
outputColumn=depenColumn;
difColumn = NULL;
if (flags&FL_DIFCOLUMNS) {
difColumn = tmalloc(sizeof(*difColumn)*depenColumns);
for (i=0; i<depenColumns; i++) {
difColumn[i] = tmalloc(sizeof(**difColumn)*(strlen(depenColumn[i])+1+strlen("Difference")));
sprintf(difColumn[i], "%sDifference", depenColumn[i]);
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, depenColumn[i], difColumn[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
outputData = NULL;
while ((readCode=SDDS_ReadPage(&SDDSin))>0) {
if (!SDDS_CopyPage(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if ((rows = SDDS_CountRowsOfInterest(&SDDSin))<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (rows) {
if (!(timeData = SDDS_GetColumnInDoubles(&SDDSin, indepColumn)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(outputData = SDDS_Realloc(outputData, sizeof(*outputData)*rows)))
SDDS_Bomb("allocation failure");
for (i=0; i<depenColumns; i++) {
if (!(inputData = SDDS_GetColumnInDoubles(&SDDSin, depenColumn[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!applyFilters(outputData, inputData, timeData, rows, filterStage, filterStages))
exit(1);
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, outputData, rows, outputColumn[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (flags&FL_DIFCOLUMNS) {
long j;
for (j=0; j<rows; j++)
outputData[j] = inputData[j] - outputData[j];
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_BY_NAME, outputData, rows, difColumn[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(inputData);
}
free(timeData);
}
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(outputData);
for(i=0;i<depenColumns;i++) {
free(depenColumn[i]);
if (flags&FL_NEWCOLUMNS)
free(outputColumn[i]);
if (flags&FL_DIFCOLUMNS)
free(difColumn[i]);
}
for(i=0;i<excludes;i++)
free(exclude[i]);
free(indepColumn);
if (flags&FL_NEWCOLUMNS)
free(outputColumn);
free(depenColumn);
if (flags&FL_DIFCOLUMNS)
free(difColumn);
free(exclude);
for(i=0;i<filterStages;i++) {
long j;
for(j=0;j<filterStage[i].filters;j++) {
switch (filterStage[i].filter[j].filterType) {
case SET_FILTERFILE :
free( ((FILE_FILTER*) (filterStage[i].filter[j].filter))->freqData);
free( ((FILE_FILTER*) (filterStage[i].filter[j].filter))->magData);
free( ((FILE_FILTER*) (filterStage[i].filter[j].filter))->imagData);
free( ((FILE_FILTER*) (filterStage[i].filter[j].filter))->realData);
break;
default :
break;
}
}
}
if (!SDDS_Terminate(&SDDSout) || !SDDS_Terminate(&SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
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)
{
SDDS_DATASET inSet, outSet;
SCANNED_ARG *s_arg;
long i_arg, pageReturned, rows, row;
int32_t *rowFlag;
char *input, *output, *columnName, *par_thresholdName;
double *data;
unsigned long pipeFlags, flags;
double threshold, ezoneFraction, changeThreshold;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2 || argc>(2+N_OPTIONS))
bomb(NULL, USAGE);
flags = pipeFlags = 0;
input = output = NULL;
columnName = NULL;
ezoneFraction = changeThreshold = 0;
rowFlag = NULL;
par_thresholdName=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], option, N_OPTIONS, 0)) {
case CLO_THRESHOLD:
if (s_arg[i_arg].n_items==2) {
if (s_arg[i_arg].list[1][0]=='@' ) {
SDDS_CopyString(&par_thresholdName, s_arg[i_arg].list[1]+1);
flags |= PAR_THRESHOLD;
} else {
if (sscanf(s_arg[i_arg].list[1], "%lf", &threshold)!=1)
SDDS_Bomb("incorrect -threshold syntax");
flags |= THRESHOLD;
}
} else
SDDS_Bomb("incorrect -threshold syntax");
break;
case CLO_FIVEPOINT:
flags |= FIVEPOINT;
break;
case CLO_CHANGETHRESHOLD:
if (s_arg[i_arg].n_items!=2 ||
sscanf(s_arg[i_arg].list[1], "%lf", &changeThreshold)!=1 || changeThreshold<=0)
SDDS_Bomb("incorrect -changeThreshold syntax or values");
flags |= CHANGETHRES;
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_COLUMN:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -column syntax");
columnName = s_arg[i_arg].list[1];
break;
case CLO_EXCLUSIONZONE:
if (s_arg[i_arg].n_items!=2 || sscanf(s_arg[i_arg].list[1], "%lf", &ezoneFraction)!=1 ||
ezoneFraction<=0)
SDDS_Bomb("invalid -exclusionZone syntax or value");
flags |= EZONEFRAC;
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s\n", s_arg[i_arg].list[0]);
exit(1);
break;
}
}
else {
if (input==NULL)
input = s_arg[i_arg].list[0];
else if (output==NULL)
output = s_arg[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
processFilenames("sddspeakfind", &input, &output, pipeFlags, 0, NULL);
if (!columnName)
SDDS_Bomb("-column option must be given");
if (!SDDS_InitializeInput(&inSet, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_FindColumn(&inSet, FIND_NUMERIC_TYPE, columnName, NULL))
SDDS_Bomb("the given column is nonexistent or nonnumeric");
if (!SDDS_InitializeCopy(&outSet, &inSet, output, "w") || !SDDS_WriteLayout(&outSet))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
while ((pageReturned=SDDS_ReadPage(&inSet))>0) {
if (!SDDS_CopyPage(&outSet, &inSet)) {
SDDS_SetError("Problem copying data for output file");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ((rows=SDDS_CountRowsOfInterest(&outSet))>1) {
if (!(data = SDDS_GetColumnInDoubles(&inSet, columnName)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
rowFlag = SDDS_Realloc(rowFlag, sizeof(*rowFlag)*rows);
for (row=0; row<rows; row++)
rowFlag[row] = 0;
markPeaks(data, rowFlag, rows, flags&FIVEPOINT);
if (flags&PAR_THRESHOLD) {
if (!SDDS_GetParameter(&inSet,par_thresholdName,&threshold))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (flags&THRESHOLD || flags&PAR_THRESHOLD ) {
for (row=0; row<rows; row++)
if (rowFlag[row] && data[row]<threshold)
rowFlag[row] = 0;
}
if (flags&CHANGETHRES)
unmarkFlatPeaks(data, rowFlag, rows, changeThreshold, flags&FIVEPOINT);
if (flags&EZONEFRAC)
unmarkExcludedPeaks(data, rowFlag, rows, ezoneFraction);
if (!SDDS_AssertRowFlags(&outSet, SDDS_FLAG_ARRAY, rowFlag, rows))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(data);
}
if (!SDDS_WritePage(&outSet))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_Terminate(&inSet) || !SDDS_Terminate(&outSet)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
free_scanargs(&s_arg,argc);
if (par_thresholdName) free(par_thresholdName);
if (rowFlag) free(rowFlag);
return(0);
}
int main(int argc, char **argv)
{
char *input, *output;
char **copyColumnName, **usersCopyColumnName;
GROUPS *group;
int32_t copyColumns;
long usersCopyColumns, groups;
long iArg, i, rows, readCode, items;
unsigned long flags, pipeFlags;
SCANNED_ARG *scArg;
SDDS_DATASET SDDSin, SDDSout;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scArg, argc, argv);
if (argc<2)
bomb(USAGE, NULL);
output = input = NULL;
flags = pipeFlags = 0;
group = NULL;
copyColumnName = usersCopyColumnName = NULL;
usersCopyColumns = copyColumns = groups = 0;
for (iArg=1; iArg<argc; iArg++) {
if (scArg[iArg].arg_type==OPTION) {
/* process options here */
switch (match_string(scArg[iArg].list[0], option, N_OPTIONS, 0)) {
case SET_PIPE:
if (!processPipeOption(scArg[iArg].list+1, scArg[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_GROUP:
if ((items = scArg[iArg].n_items-1)<2)
SDDS_Bomb("invalid -group syntax");
if (!(group = SDDS_Realloc(group, sizeof(*group)*(groups+1))) ||
!SDDS_CopyString(&group[groups].newName, scArg[iArg].list[1]) ||
!(group[groups].usersOldName = SDDS_Malloc(sizeof(*group[groups].usersOldName)*
(group[groups].usersOldNames=items-1))) ||
!SDDS_CopyStringArray(group[groups].usersOldName, scArg[iArg].list+2,
group[groups].usersOldNames))
SDDS_Bomb("memory allocation failure");
group[groups].oldName = NULL;
group[groups].oldNames = 0;
groups++;
break;
case SET_COPY:
if (usersCopyColumns)
SDDS_Bomb("give -copy only once");
if ((usersCopyColumns=scArg[iArg].n_items-1)<1)
SDDS_Bomb("invalid -copy syntax");
if (!(usersCopyColumnName = SDDS_Malloc(sizeof(*usersCopyColumnName)*usersCopyColumns)) ||
!SDDS_CopyStringArray(usersCopyColumnName, scArg[iArg].list+1, usersCopyColumns))
SDDS_Bomb("memory allocation failure");
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s\n", scArg[iArg].list[0]);
exit(1);
break;
}
}
else {
if (!input)
input = scArg[iArg].list[0];
else if (!output)
output = scArg[iArg].list[0];
else
SDDS_Bomb("too many filenames seen");
}
}
if (groups==0)
SDDS_Bomb("no groups defined");
processFilenames("sddsseparate", &input, &output, pipeFlags, 0, NULL);
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (usersCopyColumns) {
SDDS_SetColumnFlags(&SDDSin, 0);
for (i=0; i<usersCopyColumns; i++)
SDDS_SetColumnsOfInterest(&SDDSin, SDDS_MATCH_STRING, usersCopyColumnName[i], SDDS_OR);
if (!(copyColumnName = SDDS_GetColumnNames(&SDDSin, ©Columns)) || copyColumns==0)
SDDS_Bomb("no match for copy columns");
}
for (i=0; i<groups; i++) {
long j, type=0;
SDDS_SetColumnFlags(&SDDSin, 0);
for (j=0; j<group[i].usersOldNames; j++)
SDDS_SetColumnsOfInterest(&SDDSin, SDDS_MATCH_STRING, group[i].usersOldName[j], SDDS_OR);
if (!(group[i].oldName = SDDS_GetColumnNames(&SDDSin, &group[i].oldNames))) {
fprintf(stderr, "No match for group %s (sddsseparate)\n",
group[i].newName);
exit(1);
}
if (i && group[i-1].oldNames!=group[i].oldNames) {
fprintf(stderr, "Group %s comprises %" PRId32 " columns, whereas the last group comprises %" PRId32 " (sddsseparate)\n",
group[i].newName, group[i].oldNames, group[i-1].oldNames);
exit(1);
}
type = SDDS_GetColumnType(&SDDSin, SDDS_GetColumnIndex(&SDDSin, group[i].oldName[0]));
for (j=1; j<group[i].oldNames; j++) {
if (type != SDDS_GetColumnType(&SDDSin, SDDS_GetColumnIndex(&SDDSin, group[i].oldName[j]))) {
fprintf(stderr, "Inconsistent data types in group %s (sddsseparate)\n", group[i].newName);
fprintf(stderr, "First inconsistent column is %s\n", group[i].oldName[j]);
exit(1);
}
}
}
if (!SDDS_InitializeOutput(&SDDSout, SDDS_BINARY, 0, NULL, NULL, output) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_Bomb("problem initializing output file");
for (i=0; i<copyColumns; i++)
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, copyColumnName[i], NULL))
SDDS_Bomb("problem transferring copy column definitions to output file");
for (i=0; i<groups; i++) {
char *name;
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, group[i].oldName[0], group[i].newName)) {
fprintf(stderr, "Problem transferring column %s as %s to output file (sddsseparate)\n",
group[i].oldName[0], group[i].newName);
exit(1);
}
if (!(group[i].parameterName = SDDS_Malloc(sizeof(*name)*(strlen(group[i].newName)+100))))
SDDS_Bomb("memory allocation failure");
sprintf(group[i].parameterName, "%sSourceColumn", group[i].newName);
if (!SDDS_DefineSimpleParameter(&SDDSout, group[i].parameterName, NULL, SDDS_STRING))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteLayout(&SDDSout))
SDDS_Bomb("problem writing layout to output file");
while ((readCode=SDDS_ReadPage(&SDDSin))>0) {
if ((rows = SDDS_CountRowsOfInterest(&SDDSin))<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!rows)
continue;
for (i=0; i<group[0].oldNames; i++) {
long ic, ig;
if (!SDDS_StartPage(&SDDSout, rows) || !SDDS_CopyParameters(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (ic=0; ic<copyColumns; ic++) {
void *data;
if (!(data = SDDS_GetInternalColumn(&SDDSin, copyColumnName[ic])) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_NAME, data, rows, copyColumnName[ic]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (ig=0; ig<groups; ig++) {
void *data;
if (!SDDS_SetParameters(&SDDSout, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
group[ig].parameterName,
group[ig].oldName[i], NULL) ||
!(data = SDDS_GetInternalColumn(&SDDSin, group[ig].oldName[i])) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_NAME, data, rows, group[ig].newName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_Terminate(&SDDSin)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return 0;
}
char *makeNameUnitsLabel(PLOT_SPEC *plspec, long panel, long plane, long group)
{
long set, datasets;
PLOT_DATA **dataset;
char **symbolUsed, buffer[LABEL_BUFLEN], *ptr;
long symbolsUsed, first, maxLabel, unitsIndex, request, unitsDataSet, addUnits;
static long warned[2] = { 0,0 } ;
long labelLimit = LABEL_BUFLEN-10;
dataset = plspec->panel[panel].dataset;
datasets = plspec->panel[panel].datasets;
symbolsUsed = maxLabel = 0;
symbolUsed = NULL;
first = addUnits = 1;
buffer[0] = 0;
unitsDataSet = -1;
for (set=0; set<datasets; set++) {
if (dataset[set]->scalesGroupIndex[plane]!=group)
continue;
if (unitsDataSet<0)
unitsDataSet = set;
request = dataset[set]->request_index;
if (plspec->plot_request[request].overlay.flags)
continue;
if (!first &&
((!dataset[set]->info[plane].units && dataset[set-1]->info[plane].units) ||
(dataset[set]->info[plane].units && !dataset[set-1]->info[plane].units) ||
(dataset[set]->info[plane].units && dataset[set-1]->info[plane].units &&
strcmp(dataset[set]->info[plane].units, dataset[set-1]->info[plane].units)!=0))) {
if (!warned[plane]) {
fprintf(stderr, "Warning: not all %lc quantities have the same units\n",
'x'+plane);
warned[plane] = 1;
}
addUnits = 0;
}
if (!dataset[set]->info[plane].symbol) {
fprintf(stderr, "internal error: info[%ld] symbol is NULL for dataset %ld (panel %ld)\n",
plane, set, panel);
exit(1);
}
unitsIndex = set;
if (!maxLabel &&
(first || !symbolsUsed ||
match_string(dataset[set]->info[plane].symbol, symbolUsed, symbolsUsed, EXACT_MATCH)<0)) {
if (!(symbolUsed=
SDDS_Realloc(symbolUsed, sizeof(*symbolUsed)*(symbolsUsed+1))))
SDDS_Bomb("Memory allocation failure (makeNameUnitsLabel)");
symbolUsed[symbolsUsed] = dataset[set]->info[plane].symbol;
if ((long)(strlen(buffer)+strlen(symbolUsed[symbolsUsed]))<labelLimit) {
if (!first)
strcat(buffer, ", ");
strcat(buffer, symbolUsed[symbolsUsed]);
}
else {
if (first)
strncpy(buffer, symbolUsed[symbolsUsed], labelLimit);
buffer[labelLimit] = 0;
maxLabel = 1;
}
symbolsUsed++;
}
first = 0;
}
if (symbolUsed)
free(symbolUsed);
if (maxLabel)
strcat(buffer, "...");
if (addUnits && unitsDataSet>=0 &&
dataset[unitsDataSet]->info[plane].units &&
strlen(dataset[unitsDataSet]->info[plane].units)) {
strcat(buffer, " (");
strcat(buffer, dataset[unitsDataSet]->info[plane].units);
strcat(buffer, ")");
}
if (strlen(buffer)) {
if (!SDDS_CopyString(&ptr, buffer))
SDDS_Bomb("String copying problem (makeNameUnitsLabel)");
return ptr;
}
return NULL;
}
void ReadInputFile(char *inputFile, char *xCol, char *yCol, char *zCol, char *stdCol,
long *pages, long **rows, double ***x, double ***y, double ***z, double ***std, SDDS_DATASET *SDDS_in)
{
int32_t rows1=0;
long pages0=0, std_exist=0;
*rows = NULL;
if (!SDDS_InitializeInput(SDDS_in, inputFile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_CheckColumn(SDDS_in, xCol, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
fprintf(stderr,"x column - %s does not exist!\n", xCol);
exit(1);
}
if (SDDS_CheckColumn(SDDS_in, yCol, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
fprintf(stderr,"y column - %s does not exist!\n", yCol);
exit(1);
}
if (SDDS_CheckColumn(SDDS_in, zCol, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
fprintf(stderr,"z column - %s does not exist!\n", zCol);
exit(1);
}
if (SDDS_CheckColumn(SDDS_in, stdCol, NULL, SDDS_ANY_NUMERIC_TYPE, NULL)==SDDS_CHECK_OK)
std_exist = 1;
while (SDDS_ReadPage(SDDS_in)>0) {
rows1 = 0;
rows1=SDDS_CountRowsOfInterest(SDDS_in);
if (!rows1)
continue;
*rows = SDDS_Realloc(*rows, sizeof(**rows)*(pages0+1));
(*rows)[pages0] = rows1;
if (!(*x = SDDS_Realloc(*x, sizeof(**x)*(pages0+1))) ||
!(*y = SDDS_Realloc(*y, sizeof(**y)*(pages0+1))) ||
!(*z = SDDS_Realloc(*z, sizeof(**z)*(pages0+1)))) {
fprintf(stderr, "Memory allocation error.\n");
exit(1);
}
if (std_exist) {
if (!(*std = SDDS_Realloc(*std, sizeof(**std)*(pages0+1)))) {
fprintf(stderr, "Memory allocation error.\n");
exit(1);
}
(*std)[pages0] = NULL;
}
(*x)[pages0] = (*y)[pages0] = (*z)[pages0] = NULL;
if (!((*x)[pages0]=(double*)SDDS_GetColumnInDoubles(SDDS_in, xCol)) ||
!((*y)[pages0]=(double*)SDDS_GetColumnInDoubles(SDDS_in, yCol)) ||
!((*z)[pages0]=(double*)SDDS_GetColumnInDoubles(SDDS_in, zCol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (std_exist && !((*std)[pages0]=(double*)SDDS_GetColumnInDoubles(SDDS_in, stdCol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
pages0 ++;
}
if (!pages0) {
fprintf(stderr, "No data found in the input file.\n");
exit(1);
}
*pages = pages0;
return;
}
void add_element_links(ELEMENT_LINKS *links, NAMELIST_TEXT *nltext, LINE_LIST *beamline)
{
long n_links, src_position_code=0, n_targets, n_sources, mode_code=0;
long targets, iTarget, j;
char **targetList;
ELEMENT_LIST *t_context, *s_context, **eptr, *eptr1;
double dz_min, dz;
#if DEBUG
long i;
#endif
log_entry("add_element_links");
/* set namelist variables to defaults */
target = item = source = equation = exclude = NULL;
/* must initialize these hear rather than in the .nl file
* to avoid problems with str_tolower() and other operations
*/
cp_str(&source_position, "before");
cp_str(&mode, "dynamic");
/* process namelist text */
if (processNamelist(&link_elements, nltext)==NAMELIST_ERROR)
bombElegant(NULL, NULL);
if (target) str_toupper(target);
if (exclude) str_toupper(exclude);
if (item) str_toupper(item);
if (source) str_toupper(source);
if (source_position)
str_tolower(source_position);
else
cp_str(&source_position, "nearest");
if (mode)
str_tolower(mode);
else
cp_str(&mode, "dynamic");
if (echoNamelists) print_namelist(stdout, &link_elements);
/* check for valid input */
if (!target)
bombElegant("link target not named", NULL);
if (!item)
bombElegant("link item not named", NULL);
if (!source)
bombElegant("link source not named", NULL);
if (!equation)
bombElegant("link equation not given", NULL);
if (!source_position || (src_position_code=match_string(source_position, src_position_name, N_SRC_POSITIONS, 0))<0)
bombElegant("source_position not given/unknown", NULL);
if (!mode || (mode_code=match_string(mode, link_mode, N_LINK_MODES, 0))<0)
bombElegant("link mode not known", NULL);
if (minimum>maximum)
bombElegant("minimum>maximum", NULL);
t_context = s_context = NULL;
if (has_wildcards(target) && strchr(target, '-'))
target = expand_ranges(target);
if (exclude && strlen(exclude) && has_wildcards(exclude) && strchr(exclude, '-'))
exclude = expand_ranges(exclude);
if (!(t_context=wfind_element(target, &t_context, &(beamline->elem)))) {
fprintf(stdout, "error: cannot make link with target element %s--not in beamline\n", target);
fflush(stdout);
exitElegant(1);
}
if (!(s_context=find_element(source, &s_context, &(beamline->elem)))) {
fprintf(stdout, "error: cannot make link with source element %s--not in beamline\n", source);
fflush(stdout);
exitElegant(1);
}
targets = 0;
targetList = NULL;
/* make a list of all the unique element names that match this (possibly wildcard) target */
do {
int32_t duplic;
if (!exclude || !strlen(exclude) || !wild_match(t_context->name, exclude)) {
targetList = SDDS_Realloc(targetList, sizeof(*targetList)*(targets+1));
binaryInsert((void**)targetList, targets, t_context->name, strcmp, &duplic);
if (!duplic)
targets++;
}
} while ((t_context=wfind_element(target, &t_context, &(beamline->elem))));
if (!targets)
bombElegant("cannot make link--no targets found\n", NULL);
/* note that targets==1 if all the targets have the same name ! */
for (iTarget=0; iTarget<targets; iTarget++) {
n_links = links->n_links;
target = targetList[iTarget];
t_context = NULL;
t_context = find_element(target, &t_context, &(beamline->elem));
/* expand the arrays */
links->target_name = trealloc(links->target_name, sizeof(*links->target_name)*(n_links+1));
links->target_elem = trealloc(links->target_elem, sizeof(*links->target_elem)*(n_links+1));
links->item = trealloc(links->item, sizeof(*links->item)*(n_links+1));
links->target_param = trealloc(links->target_param, sizeof(*links->target_param)*(n_links+1));
links->source_name = trealloc(links->source_name, sizeof(*links->source_name)*(n_links+1));
links->source_position = trealloc(links->source_position, sizeof(*links->source_position)*(n_links+1));
links->flags = trealloc(links->flags, sizeof(*links->flags)*(n_links+1));
links->source_elem = trealloc(links->source_elem, sizeof(*links->source_elem)*(n_links+1));
links->equation = trealloc(links->equation, sizeof(*links->equation)*(n_links+1));
links->n_targets = trealloc(links->n_targets, sizeof(*links->n_targets)*(n_links+1));
links->initial_value = trealloc(links->initial_value, sizeof(*links->initial_value)*(n_links+1));
links->baseline_value = trealloc(links->baseline_value, sizeof(*links->baseline_value)*(n_links+1));
links->minimum = trealloc(links->minimum, sizeof(*links->minimum)*(n_links+1));
links->maximum = trealloc(links->maximum, sizeof(*links->maximum)*(n_links+1));
/* copy the basic data */
cp_str(links->target_name+n_links, target);
cp_str(links->item+n_links, item);
cp_str(links->source_name+n_links, source);
cp_str(links->equation+n_links, equation);
links->source_position[n_links] = src_position_code;
links->flags[n_links] = link_mode_flag[mode_code];
links->minimum[n_links] = minimum;
links->maximum[n_links] = maximum;
/* make the list of pointers to targets */
eptr = tmalloc(sizeof(*eptr));
eptr[0] = t_context;
if ((links->target_param[n_links] = confirm_parameter(item, t_context->type))<0) {
fprintf(stdout, "error: element %s does not have a parameter %s\n", target, item);
fflush(stdout);
exitElegant(1);
}
n_targets = 1;
while ((t_context=find_element(target, &t_context, &(beamline->elem)))) {
eptr = trealloc(eptr, sizeof(*eptr)*(n_targets+1));
eptr[n_targets] = t_context;
n_targets++;
}
links->baseline_value[n_links] = tmalloc(sizeof(*links->baseline_value[n_links])*n_targets);
links->n_targets[n_links] = n_targets;
links->target_elem[n_links] = eptr;
t_context = links->target_elem[n_links][0];
switch (entity_description[eptr[0]->type].parameter[links->target_param[n_links]].type) {
case IS_DOUBLE:
links->initial_value[n_links] =
*((double*)(eptr[0]->p_elem+entity_description[eptr[0]->type].parameter[links->target_param[n_links]].offset));
break;
case IS_LONG:
links->initial_value[n_links] =
*((long*)(eptr[0]->p_elem+entity_description[eptr[0]->type].parameter[links->target_param[n_links]].offset));
break;
default:
bombElegant("invalid type of item for target of link", NULL);
break;
}
for (j=0; j<n_targets; j++)
links->baseline_value[n_links][j] = links->initial_value[n_links];
/* make the list of pointers to sources */
if (iTarget) {
s_context = NULL;
if (!(s_context=find_element(source, &s_context, &(beamline->elem)))) {
fprintf(stdout, "error: cannot make link with source element %s--not in beamline\n", source);
fflush(stdout);
exitElegant(1);
}
}
eptr = tmalloc(sizeof(*eptr)*(n_targets));
if (src_position_code==SRC_POSITION_SAME_OCCURENCE) {
n_sources = 0;
while (n_sources<n_targets) {
eptr1 = NULL;
s_context = NULL;
while (find_element(source, &s_context, &(beamline->elem))) {
if (s_context->occurence==links->target_elem[n_links][n_sources]->occurence) {
eptr1 = s_context;
break;
}
}
if (!eptr1) {
fprintf(stdout, "error: no %s element is found with the same occurence number as the %ld-th %s element--can't link as requested\n",
source, n_sources, target);
fflush(stdout);
exitElegant(1);
}
eptr[n_sources++] = eptr1;
}
}
else if (src_position_code==SRC_POSITION_NEAREST) {
n_sources = 0;
while (n_sources<n_targets) {
dz_min = DBL_MAX;
eptr1 = NULL;
s_context = NULL;
while (find_element(source, &s_context, &(beamline->elem))) {
if ((dz = fabs(s_context->end_pos-links->target_elem[n_links][n_sources]->end_pos))<dz_min) {
eptr1 = s_context;
dz_min = dz;
}
}
if (!eptr1) {
fprintf(stdout, "error: no %s element is found near the %ld-th %s element--can't link as requested\n",
source, n_sources, target);
fflush(stdout);
exitElegant(1);
}
eptr[n_sources++] = eptr1;
}
}
else if (src_position_code==SRC_POSITION_ADJACENT) {
n_sources = 0;
while (n_sources<n_targets) {
eptr1 = NULL;
if ((eptr1=links->target_elem[n_links][n_sources]->pred)) {
if (strcmp(eptr1->name, source)!=0)
eptr1 = NULL;
}
if (!eptr1 && (eptr1=links->target_elem[n_links][n_sources]->succ)) {
if (strcmp(eptr1->name, source)!=0)
eptr1 = NULL;
}
if (!eptr1) {
fprintf(stdout, "error: no %s element is found adjacent to the %ld-th %s element--can't link as requested\n",
source, n_sources, target);
fflush(stdout);
exitElegant(1);
}
eptr[n_sources++] = eptr1;
}
}
else if (src_position_code==SRC_POSITION_BEFORE) {
if (links->target_elem[n_links][0]->end_pos<s_context->end_pos) {
fprintf(stdout, "error: there is no %s element before the first %s element--can't link as requested\n",
source, target);
fflush(stdout);
exitElegant(1);
}
eptr[0] = s_context;
n_sources = 0;
while (n_sources<n_targets) {
eptr1 = NULL;
do {
if (s_context->end_pos<links->target_elem[n_links][n_sources]->end_pos)
eptr1 = s_context;
else if (s_context->end_pos==links->target_elem[n_links][n_sources]->end_pos) {
eptr1 = s_context;
break;
}
else
break;
} while (find_element(source, &s_context, &(beamline->elem)));
if (!eptr1) {
fprintf(stdout, "error: no %s element is found before the %ld-th %s element--can't link as requested\n",
source, n_sources, target);
fflush(stdout);
exitElegant(1);
}
eptr[n_sources++] = eptr1;
s_context = eptr[n_sources-1];
}
}
else if (src_position_code==SRC_POSITION_AFTER) {
if (links->target_elem[n_links][0]->end_pos>=s_context->end_pos) {
/* search for first source element after first target element */
while (find_element(source, &s_context, &(beamline->elem))) {
if (links->target_elem[n_links][0]->end_pos<s_context->end_pos)
break;
}
if (!s_context) {
fprintf(stdout, "error: no %s element after the first %s element--can't link as requested\n",
source, target);
fflush(stdout);
exitElegant(1);
}
}
eptr[0] = s_context;
n_sources = 1;
while (n_sources<n_targets) {
s_context = links->target_elem[n_links][n_sources-1];
while (find_element(source, &s_context, &(beamline->elem))) {
if (s_context->end_pos>links->target_elem[n_links][n_sources]->end_pos)
break;
}
if (!s_context) {
fprintf(stdout, "error: no %s element is found after the %ld-th %s element--can't link as requested\n",
source, n_sources, target);
fflush(stdout);
exitElegant(1);
}
eptr[n_sources++] = s_context;
}
}
links->source_elem[n_links] = eptr;
#if DEBUG
fprintf(stdout, "list of targets and sources:\n");
fflush(stdout);
for (i=0; i<n_targets; i++)
fprintf(stdout, "%s at z=%em linked to %s at z=%em\n",
links->target_elem[n_links][i]->name, links->target_elem[n_links][i]->end_pos,
links->source_elem[n_links][i]->name, links->source_elem[n_links][i]->end_pos);
fflush(stdout);
#endif
links->n_links += 1;
}
log_exit("add_element_links");
}
int main(int argc, char **argv)
{
char *indepQuantity, **depenQuantity, **exclude, **depenQuantityPair;
long depenQuantities, excludes;
char *input, *output;
long iArg, i, j, rows, readCode, noWarnings, items;
long rowsToUse;
unsigned long flags, pairFlags, tmpFlags, pipeFlags;
SCANNED_ARG *scArg;
SDDS_DATASET SDDSin, SDDSout;
double *tdata, *data, t0, dt;
double fracRMSChangeLimit, fracFreqAccuracyLimit;
int32_t frequenciesDesired, maxFrequencies, freqCycleLimit;
short truncate;
double *frequency, *amplitude=NULL, *phase=NULL, *significance=NULL, *phase1=NULL, *amplitude1=NULL, *significance1=NULL;
long frequenciesFound;
long *frequencyIndex, *amplitudeIndex, *phaseIndex, *significanceIndex, pairs;
long *amplitudeIndex1, *phaseIndex1, *significanceIndex1;
SDDS_RegisterProgramName(argv[0]);
#ifdef DEBUG
if (1) {
long code;
double x, y;
x = 1.1;
code = OneDFunctionOptimize(&y, &x, 0.07, -4, 4,
trialFn, 50, 1e-6, 0, 1);
fprintf(stderr, "code: %ld x=%e, y=%e\n", code, x, y);
x = .9;
code = OneDFunctionOptimize(&y, &x, 0.15, -4, 4,
trialFn, 50, 1e-6, 0, 1);
fprintf(stderr, "code: %ld x=%e, y=%e\n", code, x, y);
x = .999;
code = OneDFunctionOptimize(&y, &x, 0.11, -4, 4,
trialFn, 50, 1e-6, 0, 1);
fprintf(stderr, "code: %ld x=%e, y=%e\n", code, x, y);
exit(0);
}
#endif
argc = scanargs(&scArg, argc, argv);
if (argc<3) {
fprintf(stderr, "%s%s", USAGE1, USAGE2);
exit(1);
}
output = input = NULL;
flags = pipeFlags = excludes = truncate = pairFlags= 0;
indepQuantity = NULL;
depenQuantity = exclude = depenQuantityPair=NULL;
depenQuantities = 0;
noWarnings = 0;
fracRMSChangeLimit = 0.0;
fracFreqAccuracyLimit = 0.00001;
frequenciesDesired = 1;
maxFrequencies = 4;
freqCycleLimit = 100;
pairs=0;
for (iArg=1; iArg<argc; iArg++) {
if (scArg[iArg].arg_type==OPTION) {
/* process options here */
switch (match_string(scArg[iArg].list[0], option, N_OPTIONS, 0)) {
case SET_TRUNCATE:
truncate = 1;
break;
case SET_PAIR:
if (depenQuantities)
SDDS_Bomb("Invalid -pair option, the depent-quantity is provided by -column option already.");
if (scArg[iArg].n_items!=3)
SDDS_Bomb("invalid -pair syntax");
depenQuantity = SDDS_Realloc(depenQuantity, sizeof(*depenQuantity)*(pairs+1));
depenQuantityPair = SDDS_Realloc(depenQuantityPair, sizeof(*depenQuantityPair)*(pairs+1));
depenQuantity[pairs] = scArg[iArg].list[1];
depenQuantityPair[pairs] = scArg[iArg].list[2];
pairs++;
break;
case SET_COLUMN:
if (indepQuantity)
SDDS_Bomb("only one -column option may be given");
if (scArg[iArg].n_items<2)
SDDS_Bomb("invalid -column syntax");
indepQuantity = scArg[iArg].list[1];
if (scArg[iArg].n_items>=2) {
if (pairs)
SDDS_Bomb("Invalid -column syntax, the depent-quantity is provided by -pair option already.");
depenQuantity = tmalloc(sizeof(*depenQuantity)*(depenQuantities=scArg[iArg].n_items-2));
for (i=0; i<depenQuantities; i++)
depenQuantity[i] = scArg[iArg].list[i+2];
}
break;
case SET_PIPE:
if (!processPipeOption(scArg[iArg].list+1, scArg[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_EXCLUDE:
if (scArg[iArg].n_items<2)
SDDS_Bomb("invalid -exclude syntax");
moveToStringArray(&exclude, &excludes, scArg[iArg].list+1, scArg[iArg].n_items-1);
break;
case SET_NOWARNINGS:
noWarnings = 1;
break;
case SET_TERM_SEARCH:
items = scArg[iArg].n_items-1;
flags &= ~(NAFF_RMS_CHANGE_LIMIT|NAFF_FREQS_DESIRED|NAFF_MAX_FREQUENCIES);
fracRMSChangeLimit = 0;
frequenciesDesired = 0;
maxFrequencies = 10;
if (!scanItemList(&tmpFlags, scArg[iArg].list+1, &items, 0,
"changelimit", SDDS_DOUBLE, &fracRMSChangeLimit, 1,
NAFF_RMS_CHANGE_LIMIT,
"maxfrequencies", SDDS_LONG, &maxFrequencies, 1,
NAFF_MAX_FREQUENCIES,
"frequencies", SDDS_LONG, &frequenciesDesired, 1,
NAFF_FREQS_DESIRED,
NULL) ||
(tmpFlags&NAFF_RMS_CHANGE_LIMIT && tmpFlags&NAFF_FREQS_DESIRED) ||
maxFrequencies<1)
SDDS_Bomb("invalid -terminateSearch syntax");
flags |= tmpFlags;
if (frequenciesDesired)
maxFrequencies = frequenciesDesired;
break;
case SET_ITERATE_FREQ:
items = scArg[iArg].n_items - 1;
flags &= ~(NAFF_FREQ_CYCLE_LIMIT|NAFF_FREQ_ACCURACY_LIMIT);
if (!scanItemList(&tmpFlags, scArg[iArg].list+1, &items, 0,
"cyclelimit", SDDS_LONG, &freqCycleLimit, 1, NAFF_FREQ_CYCLE_LIMIT,
"accuracylimit", SDDS_DOUBLE, &fracFreqAccuracyLimit,
1, NAFF_FREQ_ACCURACY_LIMIT,
NULL) || !bitsSet(tmpFlags) || freqCycleLimit<2)
SDDS_Bomb("invalid -iterateFrequency syntax");
flags |= tmpFlags;
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s\n",
scArg[iArg].list[0]);
exit(1);
break;
}
}
else {
if (!input)
input = scArg[iArg].list[0];
else if (!output)
output = scArg[iArg].list[0];
else
SDDS_Bomb("too many filenames seen");
}
}
processFilenames("sddsnaff", &input, &output, pipeFlags, 0, NULL);
if (!indepQuantity)
SDDS_Bomb("supply the independent quantity name with the -columns option");
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_CheckColumn(&SDDSin, indepQuantity, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)
!=SDDS_CHECK_OKAY)
exit(1);
excludes = appendToStringArray(&exclude, excludes, indepQuantity);
if (pairs) {
pairFlags = flags | NAFF_FREQ_FOUND;
depenQuantities = pairs;
}
if (!depenQuantities)
depenQuantities = appendToStringArray(&depenQuantity, depenQuantities, "*");
if (!pairs) {
if ((depenQuantities=expandColumnPairNames(&SDDSin, &depenQuantity, NULL,
depenQuantities, exclude, excludes,
FIND_NUMERIC_TYPE, 0))<=0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_Bomb("No quantities selected to fft");
}
}
if (!SetupNAFFOutput(&SDDSout, output, &SDDSin, indepQuantity,
depenQuantities, depenQuantity,
&frequencyIndex, &litudeIndex, &phaseIndex,
&significanceIndex, depenQuantityPair,&litudeIndex1,
&phaseIndex1,&significanceIndex1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(frequency = SDDS_Malloc(sizeof(*frequency)*maxFrequencies)) ||
!(amplitude = SDDS_Malloc(sizeof(*amplitude)*maxFrequencies)) ||
!(phase = SDDS_Malloc(sizeof(*phase )*maxFrequencies)) ||
!(significance= SDDS_Malloc(sizeof(*significance)*maxFrequencies)))
SDDS_Bomb("memory allocation failure");
if (pairs) {
if (!(amplitude1 = SDDS_Malloc(sizeof(*amplitude1)*maxFrequencies)) ||
!(phase1 = SDDS_Malloc(sizeof(*phase1 )*maxFrequencies)) ||
!(significance1 = SDDS_Malloc(sizeof(*significance1)*maxFrequencies)))
SDDS_Bomb("memory allocation failure");
}
while ((readCode=SDDS_ReadPage(&SDDSin))>0) {
if ((rows = SDDS_CountRowsOfInterest(&SDDSin))<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (rows) {
long primeRows;
rowsToUse = rows;
primeRows = greatestProductOfSmallPrimes(rows);
if (rows!=primeRows) {
if (truncate)
rowsToUse = greatestProductOfSmallPrimes(rows);
else if (largest_prime_factor(rows)>100 && !noWarnings)
fputs("Warning: number of points has large prime factors.\nThis could take a very long time.\nConsider using the -truncate option.\n", stderr);
}
if (!SDDS_StartPage(&SDDSout, maxFrequencies) ||
!SDDS_CopyParameters(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(tdata = SDDS_GetColumnInDoubles(&SDDSin, indepQuantity)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=1; i<rowsToUse; i++)
if (tdata[i]<=tdata[i-1])
SDDS_Bomb("independent data is not monotonically increasing");
dt = (tdata[rowsToUse-1]-tdata[0])/(rowsToUse-1.0),
t0 = tdata[0];
free(tdata);
for (i=0; i<depenQuantities; i++) {
if (!(data = SDDS_GetColumnInDoubles(&SDDSin, depenQuantity[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (j=0; j<maxFrequencies; j++)
frequency[j] = amplitude[j] = phase[j] = significance[j] = -1;
frequenciesFound = PerformNAFF(frequency, amplitude, phase, significance,
t0, dt,
data, rowsToUse, flags,
fracRMSChangeLimit, maxFrequencies,
freqCycleLimit, fracFreqAccuracyLimit, 0, 0);
#ifdef DEBUG
fprintf(stderr, "Column %s: ", depenQuantity[i]);
fprintf(stderr, "f=%10.3e a=%10.3e p=%10.3e s=%10.3e\n",
frequency[0], amplitude[0], phase[0], significance[0]);
#endif
free(data);
data = NULL;
if (pairs) {
if (!(data = SDDS_GetColumnInDoubles(&SDDSin, depenQuantityPair[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
frequenciesFound = PerformNAFF(frequency, amplitude1, phase1, significance1,
t0, dt,
data, rowsToUse, pairFlags,
fracRMSChangeLimit, maxFrequencies,
freqCycleLimit, fracFreqAccuracyLimit, 0, 0);
for (j=0; j<maxFrequencies; j++)
if (frequency[j]!=-1)
frequency[j] = adjustFrequencyHalfPlane(frequency[j], phase[j], phase1[j], dt);
free(data);
data = NULL;
}
if (!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
frequency, maxFrequencies, frequencyIndex[i]) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
amplitude, maxFrequencies, amplitudeIndex[i]) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
phase, maxFrequencies, phaseIndex[i]) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
significance, maxFrequencies, significanceIndex[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (pairs) {
if (!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
amplitude1, maxFrequencies, amplitudeIndex1[i]) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
phase1, maxFrequencies, phaseIndex1[i]) ||
!SDDS_SetColumn(&SDDSout, SDDS_SET_BY_INDEX,
significance1, maxFrequencies, significanceIndex1[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
else {
if (!SDDS_StartPage(&SDDSout, 0) || !SDDS_CopyParameters(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_Terminate(&SDDSin)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
free(frequency);
free(amplitude);
free(phase);
free(significance);
if (pairs) {
free(amplitude1);
free(phase1);
free(significance1);
free(amplitudeIndex1);
free(phaseIndex1);
free(significanceIndex1);
free(depenQuantityPair);
}
free(depenQuantity);
free(frequencyIndex);
free(amplitudeIndex);
free(phaseIndex);
free(significanceIndex);
return 0;
}
