long get_material_property(char *label, char *property, char **str_value, long *int_value, double *double_value) {
long rows=0, index, col_index=-1;
SDDS_DATASET table;
int32_t *intValue = NULL;
char **formula, **name;
double *doubleValue = NULL;
formula = name = NULL;
if ((col_index=match_string(property, table_column, TABLE_COLS, 0))<0) {
if (verbose)
fprintf(stderr, "Property - %s does not exist in the property table.\n", property);
return -1;
}
if (!SDDS_InitializeInput(&table, matTable))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_ReadPage(&table) || !(rows=SDDS_CountRowsOfInterest(&table)) ||
!(formula=(char**)SDDS_GetColumn(&table, "Formula")) ||
!(name=(char**)SDDS_GetColumn(&table, "Name")))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
index = match_string(label, formula, rows, EXACT_MATCH);
if (index<0)
index = match_string(label, name, rows, 0);
if (index<0) {
fprintf(stdout, "%s not found.\n", label);
return -1;
}
switch (col_index) {
case FORMULA_COL:
SDDS_CopyString(str_value, formula[index]);
break;
case NAME_COL:
SDDS_CopyString(str_value, name[index]);
break;
case Z_COL:
case GROUP_COL:
case PERIOD_COL:
intValue = (int32_t*)SDDS_GetColumn(&table, table_column[col_index]);
*int_value = intValue[index];
free(intValue);
break;
default:
doubleValue = (double*)SDDS_GetColumn(&table, table_column[col_index]);
*double_value = doubleValue[index];
free(doubleValue);
break;
}
if (!SDDS_Terminate(&table))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_FreeStringArray(formula, rows);
SDDS_FreeStringArray(name, rows);
free(formula);
free(name);
return index;
}
void addFileFilterOutput(double *outputRI, double *inputRI, long frequencies, double dfrequency, FILE_FILTER *filter)
{
long i, code;
double factor, ifactor, rfactor, rdata, idata, f;
if (!filter->freqData) {
SDDS_DATASET SDDSin;
long readCode = 0;
if (!SDDS_InitializeInput(&SDDSin, filter->file) ||
(readCode=SDDS_ReadPage(&SDDSin))==0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (readCode<0) {
fprintf(stderr, "error: unable to read filter file %s (sddsfdfilter)\n",
filter->file);
exit(1);
}
if ((filter->points = SDDS_CountRowsOfInterest(&SDDSin))<=0) {
fprintf(stderr, "error: file %s has no data on first page (sddsfdfilter)\n",
filter->file);
exit(1);
}
if (!(filter->freqData=SDDS_GetColumnInDoubles(&SDDSin, filter->freqName)) ||
(filter->magName && !(filter->magData=SDDS_GetColumnInDoubles(&SDDSin, filter->magName))) ||
(filter->imagName && !(filter->imagData=SDDS_GetColumnInDoubles(&SDDSin, filter->imagName))) ||
(filter->realName && !(filter->realData=SDDS_GetColumnInDoubles(&SDDSin, filter->realName))) ||
!SDDS_Terminate(&SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=1; i<filter->points; i++)
if (filter->freqData[i-1]>=filter->freqData[i]) {
fprintf(stderr, "error: frequency data not monotonically increasing for %s (sddsfdfilter)\n",
filter->file);
exit(1);
}
}
for (i=0; i<frequencies; i++) {
f = i*dfrequency;
if (filter->freqData[0]>f || filter->freqData[filter->points-1]<f)
continue;
if (filter->magName) {
factor = interp(filter->magData, filter->freqData, filter->points, f, 0, 1, &code);
outputRI[2*i ] += factor*inputRI[2*i ];
outputRI[2*i+1] += factor*inputRI[2*i+1];
}
else {
rfactor = interp(filter->realData, filter->freqData, filter->points, f, 0, 1, &code);
ifactor = interp(filter->imagData, filter->freqData, filter->points, f, 0, 1, &code);
rdata = inputRI[2*i ];
idata = inputRI[2*i+1];
outputRI[2*i ] += rdata*rfactor - idata*ifactor;
outputRI[2*i+1] += rdata*ifactor + idata*rfactor;
}
}
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDS_1, SDDS_2, SDDS_output;
long i, j, i_arg, rows1, rows2, reuse, reusePage, i1, i2;
SCANNED_ARG *s_arg;
char s[200], *ptr;
char **match_column, **equate_column;
long match_columns, equate_columns;
char *input1, *input2, *output;
long tmpfile_used, retval1, retval2;
long warnings, invert;
unsigned long pipeFlags;
KEYED_EQUIVALENT **keyGroup=NULL;
long keyGroups=0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<3)
bomb(NULL, USAGE);
input1 = input2 = output = NULL;
match_column = equate_column = NULL;
match_columns = equate_columns = reuse = reusePage = 0;
tmpfile_used = invert = 0;
warnings = 1;
pipeFlags = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
delete_chars(s_arg[i_arg].list[0], "_");
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_MATCH_COLUMN:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -match syntax");
if (match_columns!=0)
SDDS_Bomb("only one -match option may be given");
match_column = tmalloc(sizeof(*match_column)*2);
if ((ptr=strchr(s_arg[i_arg].list[1], '=')))
*ptr++ = 0;
else
ptr = s_arg[i_arg].list[1];
match_column[0] = s_arg[i_arg].list[1];
match_column[1] = ptr;
match_columns = 1;
break;
case SET_EQUATE_COLUMN:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -equate syntax");
if (equate_columns!=0)
SDDS_Bomb("only one -equate option may be given");
equate_column = tmalloc(sizeof(*equate_column)*2);
if ((ptr=strchr(s_arg[i_arg].list[1], '=')))
*ptr++ = 0;
else
ptr = s_arg[i_arg].list[1];
equate_column[0] = s_arg[i_arg].list[1];
equate_column[1] = ptr;
equate_columns = 1;
break;
case SET_REUSE:
if (s_arg[i_arg].n_items==1)
reuse = 1;
else {
char *reuseOptions[2] = {"rows", "page"};
for (i=1; i<s_arg[i_arg].n_items; i++) {
switch (match_string(s_arg[i_arg].list[i], reuseOptions, 2, 0)) {
case 0:
reuse = 1;
break;
case 1:
reusePage = 1;
break;
default:
SDDS_Bomb("unknown reuse keyword");
break;
}
}
}
break;
case SET_INVERT:
invert = 1;
break;
case SET_NOWARNINGS:
warnings = 0;
break;
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
default:
fprintf(stderr, "error: unknown switch: %s\n", s_arg[i_arg].list[0]);
SDDS_Bomb(NULL);
break;
}
}
else {
if (input1==NULL)
input1 = s_arg[i_arg].list[0];
else if (input2==NULL)
input2 = s_arg[i_arg].list[0];
else if (output==NULL)
output = s_arg[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
if (pipeFlags&USE_STDIN && input1) {
if (output)
SDDS_Bomb("too many filenames (sddsxref)");
output = input2;
input2 = input1;
input1 = NULL;
}
processFilenames("sddsselect", &input1, &output, pipeFlags, !warnings, &tmpfile_used);
if (!input2)
SDDS_Bomb("second input file not specified (sddsxref)");
if (equate_columns && match_columns)
SDDS_Bomb("only one of -equate or -match may be given");
if (!equate_columns && !match_columns)
SDDS_Bomb("one of -equate or -match must be given");
if (!SDDS_InitializeInput(&SDDS_1, input1)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_InitializeInput(&SDDS_2, input2)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (match_columns) {
if ((j=SDDS_GetColumnIndex(&SDDS_1, match_column[0]))<0 || SDDS_GetColumnType(&SDDS_1, j)!=SDDS_STRING) {
sprintf(s, "error: column %s not found or not string type in file %s", match_column[0], input1?input1:"stdin");
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ((j=SDDS_GetColumnIndex(&SDDS_2, match_column[1]))<0 || SDDS_GetColumnType(&SDDS_2, j)!=SDDS_STRING) {
sprintf(s, "error: column %s not found or not string type in file %s", match_column[1], input2);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (equate_columns) {
if ((j=SDDS_GetColumnIndex(&SDDS_1, equate_column[0]))<0 || !SDDS_NUMERIC_TYPE(SDDS_GetColumnType(&SDDS_1, j))) {
sprintf(s, "error: column %s not found or not numeric type in file %s", equate_column[0], input1?input1:"stdin");
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ((j=SDDS_GetColumnIndex(&SDDS_2, equate_column[1]))<0 || !SDDS_NUMERIC_TYPE(SDDS_GetColumnType(&SDDS_2, j))) {
sprintf(s, "error: column %s not found or not numeric type in file %s", equate_column[1], input2);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (output && pipeFlags&USE_STDOUT)
SDDS_Bomb("too many filenames with -pipe option");
if (!output && !(pipeFlags&USE_STDOUT)) {
if (warnings)
fprintf(stderr, "warning: existing file %s will be replaced (sddsselect)\n", input1?input1:"stdin");
tmpfile_used = 1;
cp_str(&output, tmpname(NULL));
}
if (!SDDS_InitializeCopy(&SDDS_output, &SDDS_1, output, "w")) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_WriteLayout(&SDDS_output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
while ((retval1=SDDS_ReadPage(&SDDS_1))>0) {
if (!reusePage) {
if ((retval2=SDDS_ReadPage(&SDDS_2))<=0) {
if (warnings)
fprintf(stderr, "warning: <input2> ends before <input1>\n");
if (invert) {
/* nothing to match, so everything would normally be thrown out */
if (!SDDS_CopyPage(&SDDS_output, &SDDS_1) || !SDDS_WritePage(&SDDS_output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
continue;
}
else
/* nothing to match, so everything thrown out */
break;
}
}
else {
if (retval1==1 && (retval2=SDDS_ReadPage(&SDDS_2))<=0)
SDDS_Bomb("<input2> has no data");
SDDS_SetRowFlags(&SDDS_2, 1);
}
rows1 = SDDS_CountRowsOfInterest(&SDDS_1);
rows2 = SDDS_CountRowsOfInterest(&SDDS_2);
if (!SDDS_StartPage(&SDDS_output, rows1)) {
SDDS_SetError("Problem starting output page");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_CopyParameters(&SDDS_output, &SDDS_2) || !SDDS_CopyArrays(&SDDS_output, &SDDS_2)) {
SDDS_SetError("Problem copying parameter or array data from second input file");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_CopyParameters(&SDDS_output, &SDDS_1) || !SDDS_CopyArrays(&SDDS_output, &SDDS_1)) {
SDDS_SetError("Problem copying parameter or array data from first input file");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (match_columns) {
char **string1, **string2;
long matched;
string2 = NULL;
if (!(string1 = SDDS_GetColumn(&SDDS_1, match_column[0]))) {
fprintf(stderr, "Error: problem getting column %s from file %s\n",
match_column[0], input1?input1:"stdin");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (rows2 && !(string2 = SDDS_GetColumn(&SDDS_2, match_column[1]))) {
fprintf(stderr, "Error: problem getting column %s from file %s\n",
match_column[1], input2);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (rows2)
keyGroup = MakeSortedKeyGroups(&keyGroups, SDDS_STRING, string2, rows2);
for (i1=0; i1<rows1; i1++) {
if (!SDDS_CopyRowDirect(&SDDS_output, i1, &SDDS_1, i1)) {
sprintf(s, "Problem copying row %ld of first data set", i1);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
matched = 0;
if (rows2 &&(i2 = FindMatchingKeyGroup(keyGroup, keyGroups, SDDS_STRING, string1+i1, reuse))>=0) {
matched = 1;
}
if ((!matched && !invert) || (matched && invert)) {
if (!SDDS_AssertRowFlags(&SDDS_output, SDDS_INDEX_LIMITS, i1, i1, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (string1) {
for (i=0;i<rows1;i++)
free(string1[i]);
free(string1);
string1 = NULL;
}
if (string2) {
for (i=0;i<rows2;i++)
free(string2[i]);
free(string2);
string2 = NULL;
}
for (i=0;i<keyGroups;i++) {
if (keyGroup[i]) {
if (keyGroup[i]->equivalent)
free(keyGroup[i]->equivalent);
free(keyGroup[i]);
keyGroup[i] = NULL;
}
}
if (keyGroups) {
free(keyGroup);
keyGroup = NULL;
keyGroups = 0;
}
}
else if (equate_columns) {
double *value1, *value2;
long equated;
value2 = NULL;
if (!(value1 = SDDS_GetColumnInDoubles(&SDDS_1, equate_column[0]))) {
fprintf(stderr, "Error: problem getting column %s from file %s\n",
equate_column[0], input1?input1:"stdin");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (rows2 && !(value2 = SDDS_GetColumnInDoubles(&SDDS_2, equate_column[1]))) {
fprintf(stderr, "Error: problem getting column %s from file %s\n",
equate_column[1], input2);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (rows2)
keyGroup = MakeSortedKeyGroups(&keyGroups, SDDS_DOUBLE, value2, rows2);
for (i1=0; i1<rows1; i1++) {
if (!SDDS_CopyRowDirect(&SDDS_output, i1, &SDDS_1, i1)) {
sprintf(s, "Problem copying row %ld of first data set", i1);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
equated = 0;
if (rows2 && (i2 = FindMatchingKeyGroup(keyGroup, keyGroups, SDDS_DOUBLE, value1+i1, reuse))>=0) {
equated = 1;
}
if ((!equated && !invert) || (equated && invert)) {
if (!SDDS_AssertRowFlags(&SDDS_output, SDDS_INDEX_LIMITS, i1, i1, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (value1)
free(value1);
value1 = NULL;
if (rows2 && value2)
free(value2);
value2 = NULL;
for (i=0;i<keyGroups;i++) {
if (keyGroup[i]) {
if (keyGroup[i]->equivalent)
free(keyGroup[i]->equivalent);
free(keyGroup[i]);
keyGroup[i] = NULL;
}
}
if (keyGroups) {
free(keyGroup);
keyGroup = NULL;
keyGroups = 0;
}
}
if (!SDDS_WritePage(&SDDS_output)) {
SDDS_SetError("Problem writing data to output file");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_Terminate(&SDDS_1) || !SDDS_Terminate(&SDDS_2) || !SDDS_Terminate(&SDDS_output)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (tmpfile_used && !replaceFileAndBackUp(input1, output))
exit(1);
free_scanargs(&s_arg,argc);
if (match_columns)
free(match_column);
return(0);
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDS_orig, SDDS_out;
int32_t i, j, k, i_arg, rows, xfilter_provided, yfilter_provided, zfilter_provided, row;
long power=1;
SCANNED_ARG *s_arg;
char *inputFile, *outputRoot, output[1024], tmpcol[256];
double xmin, xmax, ymin, ymax, zmin, zmax, xinterval, yinterval, zinterval;
int32_t xdim, ydim, zdim, columnNames, outputColumns, page=0;
char **columnName, **outputColumn;
double ***Rho, ***Jz, rhoSum, rhoSum1, yRho, zRho, jzRho;
double x_min, x_max, y_min, y_max, z_min, z_max, x, y, z;
unsigned long dummyFlags = 0;
x_min = x_max = y_min = y_max = z_min = z_max = 0;
xfilter_provided = yfilter_provided = zfilter_provided = 0;
inputFile = outputRoot = NULL;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2)
bomb(NULL, USAGE);
columnNames = outputColumns = 0;
columnName = outputColumn = NULL;
Rho = Jz = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
delete_chars(s_arg[i_arg].list[0], "_");
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_POWER:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("Invalid -power syntax.");
if (!get_long(&power, s_arg[i_arg].list[1]))
SDDS_Bomb("Invalid -power value provided.");
break;
case SET_XFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -xfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &x_min, 1, 0,
"maximum", SDDS_DOUBLE, &x_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -xfilter syntax");
s_arg[i_arg].n_items++;
if (x_max<=x_min) {
fprintf(stderr, "Invalid -xfilter provided, x_max <= x_min\n");
exit(1);
}
xfilter_provided =1;
break;
case SET_YFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -yfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &y_min, 1, 0,
"maximum", SDDS_DOUBLE, &y_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -yfilter syntax");
s_arg[i_arg].n_items++;
if (y_max<=y_min) {
fprintf(stderr, "Invalid -yfilter provided, y_max <= y_min\n");
exit(1);
}
yfilter_provided =1;
break;
case SET_ZFILTER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -zfilter syntax.");
s_arg[i_arg].n_items--;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"minimum", SDDS_DOUBLE, &z_min, 1, 0,
"maximum", SDDS_DOUBLE, &z_max, 1, 0,
NULL))
SDDS_Bomb("Invalid -zfilter syntax");
s_arg[i_arg].n_items++;
if (z_max<=z_min) {
fprintf(stderr, "Invalid -yfilter provided, z_max <= z_min\n");
exit(1);
}
zfilter_provided =1;
break;
default:
fprintf(stderr, "Unknown option - %s provided.\n", s_arg[i_arg].list[0]);
exit(1);
}
} else {
if (!inputFile)
inputFile = s_arg[i_arg].list[0];
else if (!outputRoot)
outputRoot = s_arg[i_arg].list[0];
else
SDDS_Bomb("Too many file names provided.");
}
}
if (!outputRoot)
outputRoot = inputFile;
sprintf(output, "%s.ave", outputRoot);
if (!SDDS_InitializeInput(&SDDS_orig, inputFile)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
xdim = ydim = zdim = 1;
zmin = zmax = zinterval = 0;
while (SDDS_ReadPage(&SDDS_orig)>0) {
if (page==0) {
if (!SDDS_GetParameterAsDouble(&SDDS_orig, "origin1", &xmin) || !SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext1", &xmax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta1", &xinterval) || !SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells1", &xdim) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "origin2", &ymin) || !SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext2", &ymax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta2", &yinterval) || !SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells2", &ydim)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (SDDS_CheckParameter(&SDDS_orig, "origin3", NULL, SDDS_ANY_NUMERIC_TYPE, NULL)==SDDS_CHECK_OK) {
if (!SDDS_GetParameterAsDouble(&SDDS_orig, "origin3", &zmin) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "max_ext3", &zmax) ||
!SDDS_GetParameterAsDouble(&SDDS_orig, "delta3", &zinterval) ||
!SDDS_GetParameterAsLong(&SDDS_orig, "numPhysCells3", &zdim)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (xfilter_provided) {
if (x_min>xmax || x_max<xmin) {
fprintf(stderr, "Invalid xfilter provided, it should be between %le and %le\n", xmin, xmax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
x_min = xmin;
x_max = xmax;
}
if (yfilter_provided) {
if (y_min>ymax || y_max<ymin) {
fprintf(stderr, "Invalid yfilter provided, it should be between %le and %le\n", ymin, ymax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
y_min = ymin;
y_max = ymax;
}
if (zfilter_provided && zmin!=0 && zmax!=0) {
if (z_min>zmax || z_max<zmin) {
fprintf(stderr, "Invalid zfilter provided, it should be between %le and %le\n", zmin, zmax);
if (!SDDS_Terminate(&SDDS_orig))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
} else {
z_min = zmin;
z_max = zmax;
}
Rho = malloc(sizeof(*Rho)*zdim);
Jz = malloc(sizeof(*Rho)*zdim);
for (i=0; i<zdim; i++) {
Rho[i] = malloc(sizeof(**Rho)*ydim);
Jz[i] = malloc(sizeof(**Jz)*ydim);
}
SetupOutputFile(&SDDS_out, output, zdim);
}
rows = SDDS_CountRowsOfInterest(&SDDS_orig);
if (rows!=xdim) {
fprintf(stderr, "Row number does not equal xdim size.\n");
exit(1);
}
for (j=1; j<=ydim; j++) {
sprintf(tmpcol, "Rho_%d",j);
Rho[page][j-1] = NULL;
if (!(Rho[page][j-1]=SDDS_GetColumnInDoubles(&SDDS_orig, tmpcol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
sprintf(tmpcol, "Jz_%d",j);
Jz[page][j-1] = NULL;
if (!(Jz[page][j-1]=SDDS_GetColumnInDoubles(&SDDS_orig, tmpcol)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
page ++;
}
if (!SDDS_Terminate(&SDDS_orig)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (page!=zdim) {
free_data_memory(Rho, zdim, ydim);
free_data_memory(Jz, zdim, ydim);
fprintf(stderr, "Error, the page number does not equal to zdim size.\n");
exit(1);
}
if (!SDDS_StartPage(&SDDS_out, xdim) ||
!SDDS_SetParameters(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin1", xmin, "origin2", ymin, "origin3", zmin, "max_ext1", xmax, "max_ext2", ymax,
"delta1", xinterval, "delta2", yinterval, "numPhysCells1", xdim,
"numPhysCells2", ydim, "xstart", x_min, "xend", x_max, "ystart", y_min, "yend", y_max, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (zdim>1) {
if (!SDDS_SetParameters(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"origin3", zmin, "max_ext3", zmax,
"delta3", zinterval, "numPhysCells3", zdim,
"zstart", z_min, "zend", z_max, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
row = 0;
x = y = z = 0;
for (i=0; i<xdim; i++) {
rhoSum = rhoSum1 = 0;
yRho = zRho = jzRho = 0;
x = i * xinterval + xmin;
if (xfilter_provided && (x<x_min || x>x_max))
continue;
for (j=0; j<ydim; j++) {
y = j * yinterval + ymin;
if (yfilter_provided && (y<y_min || y>y_max))
continue;
for (k=0; k<zdim; k++) {
z = k * zinterval + zmin;
if (zfilter_provided && zdim>1 && (z<z_min || z>z_max))
continue;
if (power==1) {
yRho += fabs(Rho[k][j][i]) * y;
zRho += fabs(Rho[k][j][i]) * z;
jzRho += Rho[k][j][i] * Jz[k][j][i];
rhoSum += fabs(Rho[k][j][i]);
rhoSum1 += Rho[k][j][i];
} else {
yRho += pow(fabs(Rho[k][j][i]), power) * y;
zRho += pow(fabs(Rho[k][j][i]), power) * z;
jzRho += pow(Rho[k][j][i] * Jz[k][j][i], power);
rhoSum += pow(fabs(Rho[k][j][i]), power);
rhoSum1 += pow(Rho[k][j][i], power);
}
}
}
/*set row values */
if (!SDDS_SetRowValues(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
"x", x, "YAve", yRho/(rhoSum+1.0e-20), "JzAve", jzRho/(rhoSum1 + 1.0e-20), NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (zdim>1 && !SDDS_SetRowValues(&SDDS_out, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, row,
"ZAve",zRho/(rhoSum+1.0e-20), NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row++;
}
if (!SDDS_WritePage(&SDDS_out) || !SDDS_Terminate(&SDDS_out))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free_data_memory(Rho, zdim, ydim);
free_data_memory(Jz, zdim, ydim);
return 0;
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDSnew, SDDSold;
long i, j, iArg;
SCANNED_ARG *scArg;
char *input, *output, *columnName;
long mode, matchCode, rows, rowsMinus1, tmpfile_used;
double gapAmount, *columnData, gapFactor;
char *matchPattern;
long matchPatternAfter = 0;
double changeAmount, changeBase;
long retval, newStart, rowLimit, breakNext;
int32_t dataType, overlap=0;
unsigned long flags, pipeFlags, changeFlags;
char **stringData;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scArg, argc, argv);
if (argc<2) {
fprintf(stderr, "%s", USAGE);
return(1);
}
columnData = NULL;
stringData = NULL;
input = output = columnName = NULL;
mode = -1;
pipeFlags = flags = 0;
gapAmount = changeAmount = rowLimit = gapFactor = 0;
matchPattern = NULL;
for (iArg=1; iArg<argc; iArg++) {
if (scArg[iArg].arg_type==OPTION) {
switch (matchCode=match_string(scArg[iArg].list[0], option, N_OPTIONS, 0)) {
case SET_GAPIN:
if ((scArg[iArg].n_items-=2)<0 ||
!scanItemList(&flags, scArg[iArg].list+2, &scArg[iArg].n_items, 0,
"amount", SDDS_DOUBLE, &gapAmount, 1, GAPIN_AMOUNT,
"factor", SDDS_DOUBLE, &gapFactor, 1, GAPIN_FACTOR,
NULL) ||
(flags&GAPIN_AMOUNT && gapAmount<=0) ||
(flags&GAPIN_FACTOR && gapFactor<=0)) {
fprintf(stderr, "Error: invalid -gapin syntax/values\n");
return(1);
}
columnName = scArg[iArg].list[1];
mode = matchCode;
break;
case SET_INCREASEOF: case SET_DECREASEOF:
if (scArg[iArg].n_items!=2) {
fprintf(stderr, "Error: invalid option syntax---specify column-name with -increaseof and -decreaseof\n");
return(1);
}
columnName = scArg[iArg].list[1];
mode = matchCode;
break;
case SET_CHANGEOF:
if ((scArg[iArg].n_items-=2)<0 ||
!scanItemList(&changeFlags, scArg[iArg].list+2, &scArg[iArg].n_items, 0,
"amount", SDDS_DOUBLE, &changeAmount, 1, CHANGEOF_AMOUNT,
"base", SDDS_DOUBLE, &changeBase, 1, CHANGEOF_BASE,
NULL) ||
(changeFlags&CHANGEOF_AMOUNT && changeAmount<=0)) {
fprintf(stderr, "Error: invalid -changeof syntax/values\n");
return(1);
}
columnName = scArg[iArg].list[1];
mode = matchCode;
break;
case SET_ROWLIMIT:
if (scArg[iArg].n_items<2) {
fprintf(stderr, "Error: invalid -rowlimit syntax\n");
return(1);
}
if (sscanf(scArg[iArg].list[1], "%ld", &rowLimit)!=1 ||
rowLimit<=0) {
fprintf(stderr, "Error: invalid -rowlimit syntax\n");
return(1);
}
if (scArg[iArg].n_items>2) {
scArg[iArg].n_items-=2;
if (!scanItemList(&flags, scArg[iArg].list+2, &scArg[iArg].n_items, 0,
"overlap", SDDS_LONG, &overlap, NULL) ||
overlap<0) {
fprintf(stderr, "Error: invalid overlap given in -rowlimit syntax\n");
return(1);
}
}
mode = matchCode;
break;
case SET_PIPE:
if (!processPipeOption(scArg[iArg].list+1, scArg[iArg].n_items-1, &pipeFlags)) {
fprintf(stderr, "Error: invalid -pipe syntax\n");
return(1);
}
break;
case SET_MATCHTO:
if ((scArg[iArg].n_items!=3 && scArg[iArg].n_items!=4) ||
strlen(columnName=scArg[iArg].list[1])==0 ||
strlen(matchPattern=scArg[iArg].list[2])==0) {
fprintf(stderr, "Error: invalid -matchTo syntax\n");
return(1);
}
if (scArg[iArg].n_items==4) {
if (strncmp(scArg[iArg].list[3], "after", strlen(scArg[iArg].list[3]))==0)
matchPatternAfter = 1;
else {
fprintf(stderr, "Error: invalid -matchTo syntax\n");
return(1);
}
}
mode = matchCode;
break;
default:
fprintf(stderr, "Error: unknown switch: %s\n", scArg[iArg].list[0]);
fprintf(stderr, "%s", USAGE);
return(1);
}
}
else {
if (input==NULL)
input = scArg[iArg].list[0];
else if (output==NULL)
output = scArg[iArg].list[0];
else {
fprintf(stderr, "Error: too many filenames given\n");
return(1);
}
}
}
processFilenames("sddsbreak", &input, &output, pipeFlags, 0, &tmpfile_used);
if (mode==-1) {
fprintf(stderr, "Error: no break mode specified\n");
return(1);
}
if (!SDDS_InitializeInput(&SDDSold, input) ||
!SDDS_InitializeCopy(&SDDSnew, &SDDSold, output, "w")) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
SDDSnew.layout.data_mode.no_row_counts = 0;
if (!SDDS_WriteLayout(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (mode!=SET_ROWLIMIT) {
if (SDDS_GetColumnInformation(&SDDSold, "type", &dataType, SDDS_BY_NAME, columnName)!=SDDS_LONG) {
SDDS_SetError("problem getting type information on given column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (mode==SET_MATCHTO) {
if (!(dataType==SDDS_STRING)) {
fprintf(stderr, "Error: given column does not contain string data\n");
return(1);
}
} else if (!SDDS_NUMERIC_TYPE(dataType)) {
if (!(mode==SET_CHANGEOF && !(changeFlags&CHANGEOF_AMOUNT) && !(changeFlags&CHANGEOF_BASE))) {
fprintf(stderr, "Error: given column does not contain numeric data\n");
return(1);
}
}
}
while ((retval=SDDS_ReadPage(&SDDSold))>0) {
if ((rows = SDDS_CountRowsOfInterest(&SDDSold))<0) {
SDDS_SetError("Problem getting number of rows of tabular data");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
rowsMinus1 = rows-1;
if (!SDDS_StartPage(&SDDSnew, rows) ||
!SDDS_CopyParameters(&SDDSnew, &SDDSold) ||
!SDDS_CopyArrays(&SDDSnew, &SDDSold)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (rows==0) {
if (!SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
continue;
}
switch (mode) {
case SET_GAPIN:
if (!(columnData=SDDS_GetColumnInDoubles(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (!gapAmount && rows>1) {
double *gap;
gap = tmalloc(sizeof(*gap)*rows);
for (i=1; i<rows; i++)
gap[i-1] = fabs(columnData[i]-columnData[i-1]);
if (!compute_average(&gapAmount, gap, rows-1)) {
fprintf(stderr, "Error: unable to determine default gap amount--couldn't find median gap\n");
return(1);
}
gapAmount *= (gapFactor?gapFactor:2);
free(gap);
}
newStart = 0;
for (i=1; i<=rows; i++) {
if (i!=rows && fabs(columnData[i]-columnData[i-1])<gapAmount)
continue;
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = i;
}
free(columnData);
break;
case SET_INCREASEOF:
if (!(columnData=SDDS_GetColumnInDoubles(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = 0;
for (i=1; i<=rows; i++) {
if (i!=rows && columnData[i]<=columnData[i-1])
continue;
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = i;
}
free(columnData);
break;
case SET_DECREASEOF:
if (!(columnData=SDDS_GetColumnInDoubles(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = 0;
for (i=1; i<=rows; i++) {
if (i!=rows && columnData[i]>=columnData[i-1])
continue;
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = i;
}
free(columnData);
break;
case SET_CHANGEOF:
if (dataType!=SDDS_STRING) {
if (!(columnData=SDDS_GetColumnInDoubles(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
} else {
if (!(stringData=SDDS_GetColumn(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
}
newStart = 0;
if (dataType==SDDS_STRING || !changeAmount) {
for (i=1; i<=rows; i++) {
if (i!=rows &&
((dataType==SDDS_STRING && strcmp(stringData[i], stringData[i-1])==0) ||
(dataType!=SDDS_STRING && columnData[i]==columnData[i-1])))
continue;
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = i;
}
}
else {
long region, lastRegion;
region = lastRegion = 0;
if (!(changeFlags&CHANGEOF_BASE) && rows>=1)
changeBase = columnData[0];
if (rows>1)
lastRegion = (columnData[0]-changeBase)/changeAmount;
#ifdef DEBUG
fprintf(stderr, "change base=%e, lastRegion=%ld\n", changeBase, lastRegion);
fprintf(stderr, "start value = %e\n", columnData[0]);
#endif
newStart = 0;
for (i=1; i<=rows; i++) {
if (i!=rows)
region = (columnData[i]-changeBase)/changeAmount;
if (i!=rows && region==lastRegion)
continue;
#ifdef DEBUG
fprintf(stderr, "split after %e, before %e, region = %d\n",
columnData[i-1], columnData[i], region);
#endif
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = i;
lastRegion = region;
#ifdef DEBUG
fprintf(stderr, "start value = %e\n", columnData[i]);
#endif
}
}
if (dataType!=SDDS_STRING)
free(columnData);
else
SDDS_FreeStringArray(stringData, rows);
break;
case SET_MATCHTO:
if (!(stringData=SDDS_GetColumn(&SDDSold, columnName))) {
SDDS_SetError("unable to read specified column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
newStart = 0;
breakNext = 0;
for (i=1; i<=rows; i++) {
if (i!=rows && !breakNext) {
if (wild_match(stringData[i], matchPattern)) {
if (matchPatternAfter) {
breakNext = 1;
continue;
}
} else
continue;
}
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, newStart, i-1, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
breakNext = 0;
newStart = i;
}
SDDS_FreeStringArray(stringData, rows);
break;
case SET_ROWLIMIT:
for (i=0; i<rows; i+=rowLimit-overlap) {
if ((j=i+rowLimit-1)>=rows)
j = rows-1;
if (!SDDS_SetRowFlags(&SDDSold, 0) ||
!SDDS_AssertRowFlags(&SDDSold, SDDS_INDEX_LIMITS, i, j, 1) ||
!SDDS_CopyRowsOfInterest(&SDDSnew, &SDDSold) || !SDDS_WritePage(&SDDSnew)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (j==rows-1)
break;
}
break;
default:
fprintf(stderr, "Error: unknown break mode code seen---this can't happen\n");
return(1);
}
}
if (retval==0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (!SDDS_Terminate(&SDDSold)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
return(1);
}
if (tmpfile_used && !replaceFileAndBackUp(input, output)) {
return(1);
}
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)
{
SCANNED_ARG *scanned;
SDDS_TABLE inputPage, *copiedPage, outputPage;
long copiedPages;
char *inputfile, *outputfile;
char **column, **excludeColumn=NULL;
int32_t columns;
long excludeColumns;
char *indParameterName;
char **copyColumn;
int32_t copyColumns;
long verbose;
long slopeErrors;
long iArg,i;
double *indVar;
char *indVarUnits;
char **intColumn,**slopeColumn,**slopeSigmaColumn;
char *Units,*slopeUnits;
double *depVar;
long order;
double *coef,*coefsigma,*weight,*diff,chi;
long iCol,iRow,iPage;
long rows;
double *slope, slope2, slopeAve, slopeSigma;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long generateIndex;
short columnMajorOrder=-1;
copiedPage = NULL;
slopeSigmaColumn = NULL;
slopeUnits = Units = indVarUnits = NULL;
rows = 0;
slope = NULL;
slope2 = 0;
coef = coefsigma = weight = diff = slope = NULL;
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
indParameterName = NULL;
verbose = 0;
slopeErrors = 0;
pipeFlags = 0;
tmpfile_used=0;
noWarnings=0;
for (iArg = 1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type == OPTION) {
delete_chars(scanned[iArg].list[0], "_");
switch (match_string(scanned[iArg].list[0], commandline_option, COMMANDLINE_OPTIONS, UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
scanned[iArg].n_items--;
if (scanned[iArg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_INDEPENDENT_PARAMETER:
if (!(indParameterName = scanned[iArg].list[1]))
SDDS_Bomb("no string given for option -independentVariable");
break;
case CLO_COLUMNS:
if (columns)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
column = tmalloc(sizeof(*column)*(columns = scanned[iArg].n_items-1));
for (i = 0; i<columns; i++)
column[i] = scanned[iArg].list[i+1];
break;
case CLO_EXCLUDE:
if (excludeColumns)
SDDS_Bomb("only one -excludecolumns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -excludecolumns syntax");
excludeColumn = tmalloc(sizeof(*excludeColumn)*(excludeColumns = scanned[iArg].n_items-1));
for (i = 0; i<excludeColumns; i++)
excludeColumn[i] = scanned[iArg].list[i+1];
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_SLOPE_ERRORS:
slopeErrors = 1;
break;
default:
SDDS_Bomb("unrecognized option given");
break;
}
}
else {
if (!inputfile)
inputfile = scanned[iArg].list[0];
else if (!outputfile)
outputfile = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames given");
}
}
processFilenames("sddsvslopes", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (!indParameterName)
SDDS_Bomb("independentVariable not given");
if (!excludeColumns) {
excludeColumn = defaultExcludedColumn;
excludeColumns = DEFAULT_EXCLUDED_COLUMNS;
}
if (verbose)
fprintf(stderr,"Reading file %s.\n",inputfile);
SDDS_InitializeInput(&inputPage, inputfile);
copiedPages = 0;
while (SDDS_ReadTable(&inputPage)>0) {
if (!copiedPages) {
copiedPage = (SDDS_TABLE*)malloc(sizeof(SDDS_TABLE));
rows = SDDS_CountRowsOfInterest(&inputPage);
}
else {
copiedPage = (SDDS_TABLE*)realloc(copiedPage, (copiedPages+1)*sizeof(SDDS_TABLE));
}
if (!SDDS_InitializeCopy(&copiedPage[copiedPages], &inputPage, NULL, "m"))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (!SDDS_CopyTable(&copiedPage[copiedPages], &inputPage))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
copiedPages++;
}
if (copiedPages<2) {
fprintf(stderr,"Insufficient data (i.e. number of data pages) to fit a straight line.\n");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Rootname", NULL, SDDS_STRING, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Index", NULL, SDDS_LONG, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
generateIndex = 0;
break;
case SDDS_CHECK_NONEXISTENT:
generateIndex = 1;
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
/****************\
* make array of independent variable
\**************/
indVar = (double*)malloc(sizeof(*indVar)*copiedPages);
switch(SDDS_CheckParameter(&inputPage, indParameterName, NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with parameter %s.\n", indParameterName);
exit(1);
}
for (iPage = 0; iPage<copiedPages; iPage++) {
if (!SDDS_GetParameter(&copiedPage[iPage],indParameterName,&indVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!SDDS_GetParameterInformation(&inputPage, "units", &indVarUnits, SDDS_GET_BY_NAME, indParameterName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!indVarUnits) {
indVarUnits = (char *) malloc(sizeof(*indVarUnits));
indVarUnits[0] = 0;
}
/************************************\
* get columns of interest. use set_multicolumn_flags to simply
* return new values for array column.
\*************************************/
if (!set_multicolumn_flags(&inputPage, &column, &columns, excludeColumn, excludeColumns)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/************************************\
* make column names for the output
\*************************************/
intColumn = (char**)malloc((sizeof(char*)*columns));
slopeColumn = (char**)malloc((sizeof(char*)*columns));
if (slopeErrors)
slopeSigmaColumn = (char**)malloc((sizeof(char*)*columns));
for (i=0; i<columns; i++) {
intColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Intercept")+1)));
strcat(strcpy(intColumn[i], column[i]), "Intercept");
slopeColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Slope")+1)));
strcat(strcpy(slopeColumn[i], column[i]), "Slope");
if (slopeErrors) {
slopeSigmaColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("SlopeSigma")+1)));
strcat(strcpy(slopeSigmaColumn[i], column[i]), "SlopeSigma");
}
}
/************************************\
* Write layout for output file
\*************************************/
if (verbose)
fprintf(stderr,"Opening file %s.\n",outputfile);
if(!SDDS_InitializeOutput(&outputPage,SDDS_BINARY,1,
"lsf of sddsvexperiment",NULL,outputfile) ||
0>SDDS_DefineParameter(&outputPage, "InputFile", "InputFile", NULL,
"InputFile", NULL, SDDS_STRING, 0) ||
0>SDDS_DefineParameter(&outputPage, "IndependentVariable", "IndependentVariable", NULL,
"IndependentVariable", NULL, SDDS_STRING, 0) ||
(0>SDDS_DefineColumn(&outputPage,"Index",NULL,NULL,"Rootname index",NULL,SDDS_LONG,0))||
(0>SDDS_DefineColumn(&outputPage,"Rootname",NULL,NULL,NULL,NULL,SDDS_STRING,0)))
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (columnMajorOrder!=-1)
outputPage.layout.data_mode.column_major = columnMajorOrder;
else
outputPage.layout.data_mode.column_major = inputPage.layout.data_mode.column_major;
for (iCol=0; iCol<columns; iCol++) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &Units, SDDS_GET_BY_NAME,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!Units) {
Units = (char*) malloc(sizeof(*Units));
Units[0] = 0;
}
if (0>SDDS_DefineColumn(&outputPage, intColumn[iCol], NULL, Units, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* units for slopes columns */
if (strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+strlen(indVarUnits)+2));
strcat( strcat( strcpy(slopeUnits, Units), "/"), indVarUnits);
}
if (strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(indVarUnits)+2));
strcat( strcpy( slopeUnits, "1/"), indVarUnits);
}
if (!strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+2));
strcpy( slopeUnits, indVarUnits);
}
if (!strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits));
strcpy( slopeUnits, "");
}
if (0>SDDS_DefineColumn(&outputPage, slopeColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (slopeErrors) {
if (0>SDDS_DefineColumn(&outputPage, slopeSigmaColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(slopeUnits);
}
if(!SDDS_WriteLayout(&outputPage) ||
!SDDS_StartTable(&outputPage,rows) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile",inputfile?inputfile:"pipe",NULL) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
"IndependentVariable", indParameterName, NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/************************************\
* Copy columns to output file (usually columns Index and Rootname)
\*************************************/
copyColumns = DEFAULT_COPY_COLUMNS;
copyColumn = defaultCopyColumn;
if (!set_multicolumn_flags(&inputPage, ©Column, ©Columns, NULL, 0)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
if(!SDDS_CopyColumns(&outputPage, &inputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
depVar = (double*)malloc(sizeof(*depVar)*copiedPages);
weight = (double*)malloc(sizeof(*weight)*copiedPages);
diff = (double*)malloc(sizeof(*weight)*copiedPages);
order=1;
coef = (double*)malloc(sizeof(*coef)*(order+1));
coefsigma = (double*)malloc(sizeof(*coefsigma)*(order+1));
if(slopeErrors)
slope = (double*)malloc(sizeof(*slope)*copiedPages);
for (iCol=0; iCol<columns; iCol++) {
for (iPage=0; iPage<copiedPages; iPage++)
weight[iPage]=1;
if (verbose)
fprintf(stderr,"Doing column %s.\n", column[iCol]);
for (iRow=0; iRow<rows; iRow++) {
for (iPage=0; iPage<copiedPages; iPage++) {
if (!SDDS_GetValue(&copiedPage[iPage], column[iCol], iRow, &depVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
if (generateIndex) {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
"Index",iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if(slopeErrors){
/* recalculate the slope with a subset of points */
slopeAve= slope2 = 0;
for (iPage=0; iPage<copiedPages; iPage++) {
weight[iPage] = 1e10;
if(iPage)
weight[iPage-1] = 1;
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
slope[iPage] = coef[1];
slopeAve += slope[iPage];
slope2 += sqr(slope[iPage]);
}
slopeSigma = sqrt(slope2/copiedPages - sqr(slopeAve/copiedPages));
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
slopeSigmaColumn[iCol], slopeSigma, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
if( !SDDS_WriteTable(&outputPage)|| SDDS_Terminate(&inputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (iPage=0; iPage<copiedPages; iPage++) {
if( !SDDS_Terminate(&copiedPage[iPage]) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if( SDDS_Terminate(&outputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
SDDS_FreeStringArray(column, columns);
free(column);
SDDS_FreeStringArray(intColumn, columns);
SDDS_FreeStringArray(slopeColumn, columns);
free(intColumn);
free(slopeColumn);
if (slopeErrors) {
SDDS_FreeStringArray(slopeSigmaColumn, columns);
free(slopeSigmaColumn);
}
free(copiedPage);
free(indVar);
free(depVar);
if (weight)
free(weight);
if (diff)
free(diff);
if (slope)
free(slope);
if (coef) free(coef);
if (coefsigma) free(coefsigma);
if (Units) free(Units);
if (indVarUnits) free(indVarUnits);
free_scanargs(&scanned, argc);
return(0);
}
int main(int argc, char **argv)
{
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)
{
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);
}
void initializePolynomial(POLYNOMIAL *poly, SDDS_DATASET *SDDSin, SDDS_DATASET *SDDSout)
{
long i;
SDDS_DATASET SDDSpoly;
char buffer[1024];
for (i=1; i<5; i++) {
if ((poly->flags&(POLY_IN0_SEEN<<(2*i))) &&
!(poly->flags&(POLY_OUT0_SEEN<<(2*i))))
SDDS_Bomb("input qualifier seen without matching output qualifier");
if (!(poly->flags&(POLY_IN0_SEEN<<(2*i))) &&
(poly->flags&(POLY_OUT0_SEEN<<(2*i))))
SDDS_Bomb("output qualifier seen without matching input qualifier");
if (!(poly->flags&(POLY_IN0_SEEN<<(2*i))) &&
!(poly->flags&(POLY_OUT0_SEEN<<(2*i))))
break;
}
poly->nInputs = i;
for (i++; i<5; i++) {
if ((poly->flags&(POLY_IN0_SEEN<<(2*i))) ||
(poly->flags&(POLY_OUT0_SEEN<<(2*i))))
SDDS_Bomb("input<n> or output<n> qualifiers skipped");
}
if (!SDDS_InitializeInput(&SDDSpoly, poly->filename))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_GetColumnIndex(&SDDSpoly,poly->outputColumn)==-1) {
if (!SDDS_DefineSimpleColumn(SDDSout, poly->outputColumn, NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
if (SDDS_CheckColumn(&SDDSpoly, poly->outputColumn, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OKAY)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (SDDS_CheckColumn(&SDDSpoly, poly->coefColumn, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OKAY)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<poly->nInputs; i++) {
if (SDDS_CheckColumn(SDDSin, poly->inputColumn[i], NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OKAY)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (SDDS_CheckColumn(&SDDSpoly, poly->powerColumn[i], NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OKAY)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (SDDS_ReadPage(&SDDSpoly)<=0) {
sprintf(buffer, "problem with file %s\n", poly->filename);
SDDS_SetError(buffer);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ((poly->nTerms=SDDS_RowCount(&SDDSpoly))<=0) {
sprintf(buffer, "problem with file %s: no rows\n", poly->filename);
SDDS_SetError(buffer);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!(poly->coef=SDDS_GetColumnInDoubles(&SDDSpoly, poly->coefColumn)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(poly->power=SDDS_Malloc(sizeof(*(poly->power))*poly->nInputs)))
SDDS_Bomb("memory allocation failure");
for (i=0; i<poly->nInputs; i++) {
if (!(poly->power[i]=
SDDS_GetColumnInLong(&SDDSpoly, poly->powerColumn[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_Terminate(&SDDSpoly))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(poly->input = SDDS_Malloc(sizeof(*(poly->input))*poly->nInputs)))
SDDS_Bomb("memory allocation failure");
if (!(poly->inputData = SDDS_Malloc(sizeof(*(poly->inputData))*poly->nInputs)))
SDDS_Bomb("memory allocation failure");
}
/**************************** main ****************************************/
int main(int argc, char **argv)
{
FILE *outfile;
SDDS_TABLE SDDS_table;
SDDS_LAYOUT *layout;
COLUMN_DEFINITION *coldef;
PARAMETER_DEFINITION *pardef;
ARRAY_DEFINITION *arraydef;
long list_request;
char s[256];
char *input, *output;
long i, j, i_arg, append_units, nrows, ntable, len;
SCANNED_ARG *s_arg;
char *text, *contents, *ss, *ptr, *iformat=FORMAT, *format, *rformat;
long verbose=0, comments=0, addquotes=1;
short nexp;
double dd, ddred;
float ff, ffred;
void *data;
unsigned long pipeFlags;
SDDS_RegisterProgramName(argv[0]);
list_request = -1;
input = output = NULL;
append_units = 0;
pipeFlags = 0;
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_COMMENTS:
comments = 1;
break;
case SET_FORMAT:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -format syntax");
iformat = s_arg[i_arg].list[1]; /* Input format */
break;
case SET_VERBOSE:
verbose = 1;
break;
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1,
s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
default:
SDDS_Bomb(strcat("Unknown option: ", s_arg[i_arg].list[0]));
break;
}
}
else {
if (input==NULL)
input = s_arg[i_arg].list[0];
else if (output==NULL)
output = s_arg[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
processFilenames("sdds2math", &input, &output, pipeFlags, 0, NULL);
if (output) {
outfile=fopen(output,"w");
if(!outfile)
SDDS_Bomb(strcat("Can't open output file ", output));
}
else {
outfile = stdout;
}
/* Calculate formats for converting to Mathematica convention */
len=strlen(iformat); /* Inputformat */
format=(char *)calloc(256,sizeof(char)); /* Whole format */
rformat=(char *)calloc(256,sizeof(char)); /* Part before e */
strcpy(format,iformat);
if((ptr=strchr(format,'E'))) *ptr='e'; /* Aren't going to use E or G anyway */
if((ptr=strchr(format,'G'))) *ptr='g';
strcpy(rformat,format);
if((ptr=strpbrk(rformat,"eg"))) *ptr='f';
/* fprintf(outfile,"Created from SDDS file: %s\n",filename[file]); */
if (!SDDS_InitializeInput(&SDDS_table, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
layout = &SDDS_table.layout;
/* Start top level */
fprintf(outfile,"{");
/* Description */
fprintf(outfile,"{");
if(verbose) printf("\nfile %s is in SDDS protocol version %" PRId32 "\n", input, layout->version);
if (!SDDS_GetDescription(&SDDS_table, &text, &contents))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (text)
if(verbose) printf("description: %s\n", text);
if (text)
fprintf(outfile,"\"%s\",",text?text:"No description\t");
if (contents)
if(verbose) printf("contents: %s\n", contents);
fprintf(outfile,"\"%s\"",contents?contents:"No description\t");
if (layout->data_mode.mode==SDDS_ASCII) {
if(verbose) printf("\ndata is ASCII with %" PRId32 " lines per row and %" PRId32 " additional header lines expected.\n",
layout->data_mode.lines_per_row, layout->data_mode.additional_header_lines);
if(verbose) printf("row counts: %s \n",
layout->data_mode.no_row_counts?"no":"yes");
}
else
if(verbose) printf("\ndata is binary\n");
fprintf(outfile,"},\n");
/* Columns */
fprintf(outfile," {");
if (layout->n_columns) {
if(verbose) printf("\n%" PRId32 " columns of data:\n", layout->n_columns);
if(verbose) printf("NAME UNITS SYMBOL FORMAT TYPE FIELD DESCRIPTION\n");
if(verbose) printf(" LENGTH\n");
for (i=0; i<layout->n_columns; i++) {
if(i > 0) fprintf(outfile,",\n ");
coldef = layout->column_definition+i;
if(verbose) printf("%-15s %-15s %-15s %-15s %-7s %-7" PRId32 " %s\n",
coldef->name, coldef->units, coldef->symbol,
coldef->format_string, SDDS_type_name[coldef->type-1], coldef->field_length, coldef->description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\",%" PRId32 ",\"%s\"}",
coldef->name?coldef->name:"No name",
coldef->units?coldef->units:"",
coldef->symbol?coldef->symbol:"",
coldef->format_string?coldef->format_string:"",
SDDS_type_name[coldef->type-1],
coldef->field_length,
coldef->description?coldef->description:"No description");
}
}
fprintf(outfile,"},\n");
/* Parameters */
fprintf(outfile," {");
if (layout->n_parameters) {
if(verbose) printf("\n%" PRId32 " parameters:\n", layout->n_parameters);
if(verbose) printf("NAME UNITS SYMBOL TYPE DESCRIPTION\n");
for (i=0; i < layout->n_parameters; i++) {
if(i > 0) fprintf(outfile,",\n ");
pardef = layout->parameter_definition+i;
if(verbose) printf("%-19s %-19s %-19s %-19s %s\n",
pardef->name, pardef->units, pardef->symbol,
SDDS_type_name[pardef->type-1], pardef->description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
pardef->name?pardef->name:"No name",
pardef->fixed_value?pardef->units:"",
pardef->units?pardef->units:"",
pardef->symbol?pardef->symbol:"",
SDDS_type_name[pardef->type-1],
pardef->description?pardef->description:"No description");
}
}
fprintf(outfile,"},\n");
/* Arrays */
fprintf(outfile," {");
if (layout->n_arrays) {
if(verbose) printf("\n%" PRId32 " arrays of data:\n", layout->n_arrays);
if(verbose) printf("NAME UNITS SYMBOL"
" FORMAT TYPE FIELD GROUP DESCRIPTION\n");
if(verbose) printf(" LENGTH NAME\n");
for (i=0; i<layout->n_arrays; i++) {
if(i > 0) fprintf(outfile,",\n ");
arraydef = layout->array_definition+i;
if(verbose) printf("%-15s %-15s %-15s %-7s %-8s*^%-5" PRId32 " %-7" PRId32 " %-15s %s\n",
arraydef->name, arraydef->units, arraydef->symbol,
arraydef->format_string, SDDS_type_name[arraydef->type-1], arraydef->dimensions,
arraydef->field_length, arraydef->group_name, arraydef->description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s*^%" PRId32 "\",%-7" PRId32 ",\"%s\",\"%s\"}",
arraydef->name?arraydef->name:"No name",
arraydef->units?arraydef->units:"",
arraydef->symbol?arraydef->symbol:"",
arraydef->format_string?arraydef->format_string:"",
SDDS_type_name[arraydef->type-1], arraydef->dimensions,
arraydef->field_length,
arraydef->group_name,
arraydef->description);
}
}
fprintf(outfile,"},\n");
/* Associates */
fprintf(outfile," {");
if (layout->n_associates) {
if(verbose) printf("\n%" PRId32 " associates:\n", layout->n_associates);
if(verbose) printf("SDDS FILENAME PATH CONTENTS DESCRIPTION\n");
for (i=0; i<layout->n_associates; i++)
if(i > 0) fprintf(outfile,",\n ");
if(verbose) printf("%-5s %-19s %-29s %-19s %s\n",
layout->associate_definition[i].sdds?"SDDS":"Non-SDDS",
layout->associate_definition[i].filename, layout->associate_definition[i].path,
layout->associate_definition[i].contents, layout->associate_definition[i].description);
fprintf(outfile,"{\"%s\",\"%s\",\"%s\",\"%s\",\"%s\"}",
layout->associate_definition[i].sdds?"True":"False",
layout->associate_definition[i].filename,
layout->associate_definition[i].path,
layout->associate_definition[i].contents,
layout->associate_definition[i].description);
}
fprintf(outfile,"},\n");
/* Process tables */
fprintf(outfile," {"); /* Start of array of tables */
while ((ntable=SDDS_ReadTable(&SDDS_table))>0) {
if(ntable > 1) fprintf(outfile,",\n ");
if(comments) fprintf(outfile,"(*Table %ld*)",ntable);
fprintf(outfile,"{\n"); /* Start of this table */
/* Variable parameters */
fprintf(outfile," {"); /* Start of parameters */
for (i=0; i<layout->n_parameters; i++) {
if(i > 0) fprintf(outfile,",\n ");
pardef = layout->parameter_definition+i;
if (!(data=SDDS_GetParameter(&SDDS_table, pardef->name, NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/* This parameter */
if(comments) fprintf(outfile,"(*%s*)",pardef->name);
addquotes=1;
switch(pardef->type) {
case SDDS_DOUBLE:
dd=*(double *)data;
sprintf(s,format,dd);
if((ptr=strchr(s,'e'))) {
*ptr=' ';
sscanf(s,"%lf %hd",&ddred,&nexp);
fprintf(outfile,rformat,ddred);
fprintf(outfile,"*10^%d",nexp);
}
else {
fprintf(outfile,s);
}
break;
case SDDS_FLOAT:
ff=*(float *)data;
sprintf(s,format,ff);
if((ptr=strchr(s,'e'))) {
*ptr=' ';
sscanf(s,"%f %hd",&ffred,&nexp);
fprintf(outfile,rformat,ffred);
fprintf(outfile,"*10^%d",nexp);
}
else {
fprintf(outfile,s);
}
break;
case SDDS_STRING:
ss=*(char **)data;
if(*ss == '"') addquotes=0;
else if(SDDS_StringIsBlank(ss) || SDDS_HasWhitespace(ss)) addquotes=0;
case SDDS_CHARACTER:
if(addquotes) fprintf(outfile,"\"");
SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
if(addquotes) fprintf(outfile,"\"");
break;
default:
SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
break;
}
}
fprintf(outfile,"},\n"); /* End of parameters */
/* Columns */
fprintf(outfile," {"); /* Start of data array */
if (layout->n_columns) {
SDDS_SetColumnFlags(&SDDS_table, 1);
SDDS_SetRowFlags(&SDDS_table, 1);
if ((nrows=SDDS_CountRowsOfInterest(&SDDS_table))<0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/* for (i=0; i<layout->n_columns; i++) { */
/* coldef = layout->column_definition+i; */
/* fprintf(outfile,"%s%s",coldef->name,delimiter); */
/* } */
/* fprintf(outfile,"\n"); */
if (nrows) {
for (j=0; j<nrows; j++) {
if(j > 0) fprintf(outfile,",\n ");
fprintf(outfile,"{"); /* Start of row */
for (i=0; i<layout->n_columns; i++) {
if( i > 0) fprintf(outfile,",");
coldef = layout->column_definition+i;
if (!(data=SDDS_GetValue(&SDDS_table, coldef->name,j,NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
addquotes=1;
switch(coldef->type) {
case SDDS_DOUBLE:
dd=*(double *)data;
sprintf(s,format,dd);
if((ptr=strchr(s,'e'))) {
*ptr=' ';
sscanf(s,"%lf %hd",&ddred,&nexp);
fprintf(outfile,rformat,ddred);
fprintf(outfile,"*10^%d",nexp);
}
else {
fprintf(outfile,s);
}
break;
case SDDS_FLOAT:
ff=*(float *)data;
sprintf(s,format,ff);
if((ptr=strchr(s,'e'))) {
*ptr=' ';
sscanf(s,"%f %hd",&ffred,&nexp);
fprintf(outfile,rformat,ffred);
fprintf(outfile,"*10^%d",nexp);
}
else {
fprintf(outfile,s);
}
break;
case SDDS_STRING:
ss=*(char **)data;
if(*ss == '"') addquotes=0;
else if(SDDS_StringIsBlank(ss) || SDDS_HasWhitespace(ss)) addquotes=0;
case SDDS_CHARACTER:
if(addquotes) fprintf(outfile,"\"");
SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
if(addquotes) fprintf(outfile,"\"");
break;
default:
SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
break;
}
}
fprintf(outfile,"}"); /* End of row */
}
}
}
fprintf(outfile,"}"); /* End of data array */
fprintf(outfile,"}"); /* End of this table */
}
fprintf(outfile,"\n }\n"); /* End of array of tables, last major component */
/* End top level */
fprintf(outfile,"}\n"); /* End of top level */
/*
QUIT:
*/
fflush(stdout);
if (!SDDS_Terminate(&SDDS_table)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return(0);
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDSin, SDDSout;
long i_arg, tmpfileUsed;
SCANNED_ARG *s_arg;
char *input, *output, *description_text, *description_contents;
unsigned long pipeFlags;
long pageNumber, nonNative = 0;
char *outputEndianess = NULL;
char buffer[40];
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2)
bomb(NULL, USAGE);
input = output = description_text = description_contents = NULL;
pipeFlags = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
delete_chars(s_arg[i_arg].list[0], "_");
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case NONNATIVE:
nonNative = 1;
break;
default:
fprintf(stderr, "Error (%s): unknown switch: %s\n", argv[0], 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("sddsendian", &input, &output, pipeFlags, 0, &tmpfileUsed);
outputEndianess = getenv("SDDS_OUTPUT_ENDIANESS");
if (outputEndianess) {
putenv("SDDS_OUTPUT_ENDIANESS=");
}
if (!SDDS_InitializeInput(&SDDSin, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!description_text)
SDDS_GetDescription(&SDDSin, &description_text, &description_contents);
if (!SDDS_InitializeCopy(&SDDSout, &SDDSin, output, "w") ||
!SDDS_SetDataMode(&SDDSout, nonNative?SDDS_BINARY:-SDDS_BINARY) ||
!SDDS_WriteLayout(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (nonNative) {
while ((pageNumber=SDDS_ReadNonNativePage(&SDDSin))>=0) {
if (!SDDS_CopyPage(&SDDSout, &SDDSin) ||
!SDDS_WritePage(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
} else {
while ((pageNumber=SDDS_ReadPage(&SDDSin))>=0) {
if (!SDDS_CopyPage(&SDDSout, &SDDSin) ||
!SDDS_WriteNonNativeBinaryPage(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
}
if (!SDDS_Terminate(&SDDSin) || !SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (tmpfileUsed && !replaceFileAndBackUp(input, output))
exit(1);
if (outputEndianess) {
sprintf(buffer, "SDDS_OUTPUT_ENDIANESS=%s", outputEndianess);
putenv(buffer);
}
return(0);
}
int main(int argc, char **argv)
{
int iArg;
char **column, **excludeColumn, *withOnly;
long columns, excludeColumns;
char *input, *output;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout;
long i, j, row, rows, count, readCode, rankOrder, iName1, iName2;
int32_t outlierStDevPasses;
double **data, correlation, significance, outlierStDevLimit;
double **rank;
short **accept;
char s[SDDS_MAXLINE];
unsigned long pipeFlags, dummyFlags, majorOrderFlag;
short columnMajorOrder=-1;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<2)
bomb(NULL, USAGE);
output = input = withOnly = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
pipeFlags = 0;
rankOrder = 0;
outlierStDevPasses = 0;
outlierStDevLimit = 1.;
rank = NULL;
accept = NULL;
for (iArg=1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type==OPTION) {
/* process options here */
switch (match_string(scanned[iArg].list[0], option, N_OPTIONS, 0)) {
case SET_MAJOR_ORDER:
majorOrderFlag=0;
scanned[iArg].n_items--;
if (scanned[iArg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case SET_COLUMNS:
if (columns)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
column = tmalloc(sizeof(*column)*(columns=scanned[iArg].n_items-1));
for (i=0; i<columns; i++)
column[i] = scanned[iArg].list[i+1];
break;
case SET_EXCLUDE:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -excludeColumns syntax");
moveToStringArray(&excludeColumn, &excludeColumns, scanned[iArg].list+1, scanned[iArg].n_items-1);
break;
case SET_WITHONLY:
if (withOnly)
SDDS_Bomb("only one -withOnly option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -withOnly syntax");
withOnly = scanned[iArg].list[1];
break;
case SET_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_RANKORDER:
rankOrder = 1;
break;
case SET_STDEVOUTLIER:
scanned[iArg].n_items--;
outlierStDevPasses = 1;
outlierStDevLimit = 1;
if (!scanItemList(&dummyFlags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"limit", SDDS_DOUBLE, &outlierStDevLimit, 1, 0,
"passes", SDDS_LONG, &outlierStDevPasses, 1, 0,
NULL) ||
outlierStDevPasses<=0 || outlierStDevLimit<=0)
SDDS_Bomb("invalid -stdevOutlier syntax/values");
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("sddscorrelate", &input, &output, pipeFlags, 0, NULL);
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!columns)
columns = appendToStringArray(&column, columns, "*");
if (withOnly)
columns = appendToStringArray(&column, columns, withOnly);
if ((columns=expandColumnPairNames(&SDDSin, &column, NULL, columns,
excludeColumn, excludeColumns, FIND_NUMERIC_TYPE, 0))<=0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_Bomb("no columns selected for correlation analysis");
}
if (!SDDS_InitializeOutput(&SDDSout, SDDS_BINARY, 0, NULL, "sddscorrelate output", output) ||
SDDS_DefineColumn(&SDDSout, "Correlate1Name", NULL, NULL, "Name of correlated quantity 1", NULL, SDDS_STRING, 0)<0 ||
SDDS_DefineColumn(&SDDSout, "Correlate2Name", NULL, NULL, "Name of correlated quantity 2", NULL, SDDS_STRING, 0)<0 ||
SDDS_DefineColumn(&SDDSout, "CorrelatePair", NULL, NULL, "Names of correlated quantities", NULL, SDDS_STRING, 0)<0 ||
SDDS_DefineColumn(&SDDSout, "CorrelationCoefficient", "r", NULL, "Linear correlation coefficient",
NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&SDDSout, "CorrelationSignificance", "P$br$n", NULL, "Linear correlation coefficient significance",
NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(&SDDSout, "CorrelationPoints", NULL, NULL, "Number of points used for correlation",
NULL, SDDS_LONG, 0)<0 ||
SDDS_DefineParameter(&SDDSout, "CorrelatedRows", NULL, NULL, "Number of data rows in correlation analysis",
NULL, SDDS_LONG, NULL)<0 ||
SDDS_DefineParameter(&SDDSout, "sddscorrelateInputFile", NULL, NULL, "Data file processed by sddscorrelate",
NULL, SDDS_STRING, input?input:"stdin")<0 ||
SDDS_DefineParameter(&SDDSout, "sddscorrelateMode", NULL, NULL, NULL, NULL, SDDS_STRING,
rankOrder?"Rank-Order (Spearman)":"Linear (Pearson)")<0 ||
SDDS_DefineParameter1(&SDDSout, "sddscorrelateStDevOutlierPasses", NULL, NULL,
"Number of passes of standard-deviation outlier elimination applied",
NULL, SDDS_LONG, &outlierStDevPasses)<0 ||
SDDS_DefineParameter1(&SDDSout, "sddscorrelateStDevOutlierLimit", NULL, NULL,
"Standard-deviation outlier limit applied",
NULL, SDDS_DOUBLE, &outlierStDevLimit)<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (columnMajorOrder!=-1)
SDDSout.layout.data_mode.column_major = columnMajorOrder;
else
SDDSout.layout.data_mode.column_major = SDDSin.layout.data_mode.column_major;
if (!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(data = (double**)malloc(sizeof(*data)*columns)) ||
(rankOrder && !(rank = (double**)malloc(sizeof(*rank)*columns))) ||
!(accept = (short**)malloc(sizeof(*accept)*columns)))
SDDS_Bomb("allocation failure");
while ((readCode=SDDS_ReadPage(&SDDSin))>0) {
if ((rows = SDDS_CountRowsOfInterest(&SDDSin))<3)
continue;
if (!SDDS_StartPage(&SDDSout, columns*(columns-1)/2) ||
!SDDS_SetParameters(&SDDSout, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"CorrelatedRows", rows, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<columns; i++) {
if (!(data[i] = SDDS_GetColumnInDoubles(&SDDSin, column[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (rankOrder)
rank[i] = findRank(data[i], rows);
if (outlierStDevPasses) {
if (!(accept[i] = (short*)malloc(sizeof(**accept)*rows)))
SDDS_Bomb("allocation failure");
markStDevOutliers(data[i], outlierStDevLimit, outlierStDevPasses,
accept[i], rows);
}
else
accept[i] = NULL;
}
for (i=row=0; i<columns; i++) {
for (j=i+1; j<columns; j++) {
iName1 = i;
iName2 = j;
if (withOnly) {
if (strcmp(withOnly, column[i])==0) {
iName1 = j;
iName2 = i;
}
else if (strcmp(withOnly, column[j])==0) {
iName1 = i;
iName2 = j;
}
else
continue;
}
correlation
= linearCorrelationCoefficient(rankOrder?rank[i]:data[i],
rankOrder?rank[j]:data[j],
accept[i], accept[j], rows, &count);
significance = linearCorrelationSignificance(correlation, count);
sprintf(s, "%s.%s", column[iName1], column[iName2]);
if (!SDDS_SetRowValues(&SDDSout, SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE, row++,
0, column[iName1],
1, column[iName2],
2, s, 3, correlation, 4, significance,
5, count, -1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
for (i=0; i<columns; i++) {
free(data[i]);
if (rankOrder)
free(rank[i]);
if (accept[i])
free(accept[i]);
}
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;
}
int main(int argc, char **argv)
{
double tolerance, result;
long nEval;
int32_t nEvalMax = 5000, nPassMax = 25;
double a[4], da[4];
double alo[4], ahi[4];
long n_dimen = 4, zeroes;
SDDS_DATASET InputTable, OutputTable;
SCANNED_ARG *s_arg;
long i_arg, i, clue, fullOutput;
char *input, *output, *xName, *yName;
int32_t xIndex, yIndex, fitIndex, residualIndex;
long retval;
double *fitData, *residualData, rmsResidual;
unsigned long guessFlags, dummyFlags, pipeFlags;
double constantGuess, factorGuess, freqGuess, phaseGuess;
double firstZero, lastZero;
unsigned long simplexFlags = 0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2 || argc>(2+N_OPTIONS))
bomb(NULL, USAGE);
input = output = NULL;
tolerance = 1e-6;
verbosity = fullOutput = 0;
clue = -1;
xName = yName = NULL;
guessFlags = 0;
pipeFlags = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_TOLERANCE:
if (s_arg[i_arg].n_items!=2 || sscanf(s_arg[i_arg].list[1], "%lf", &tolerance)!=1)
SDDS_Bomb("incorrect -tolerance syntax");
break;
case SET_VERBOSITY:
if (s_arg[i_arg].n_items!=2 || sscanf(s_arg[i_arg].list[1], "%ld", &verbosity)!=1)
SDDS_Bomb("incorrect -verbosity syntax");
break;
case SET_GUESS:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("incorrect -guess syntax");
s_arg[i_arg].n_items -= 1;
if (!scanItemList(&guessFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"constant", SDDS_DOUBLE, &constantGuess, 1, GUESS_CONSTANT_GIVEN,
"factor", SDDS_DOUBLE, &factorGuess, 1, GUESS_FACTOR_GIVEN,
"frequency", SDDS_DOUBLE, &freqGuess, 1, GUESS_FREQ_GIVEN,
"phase", SDDS_DOUBLE, &phaseGuess, 1, GUESS_PHASE_GIVEN,
NULL))
SDDS_Bomb("invalid -guess syntax");
break;
case SET_COLUMNS:
if (s_arg[i_arg].n_items!=3)
SDDS_Bomb("invalid -columns syntax");
xName = s_arg[i_arg].list[1];
yName = s_arg[i_arg].list[2];
break;
case SET_FULLOUTPUT:
fullOutput = 1;
break;
case SET_LIMITS:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("incorrect -limits syntax");
s_arg[i_arg].n_items -= 1;
if (!scanItemList(&dummyFlags, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"evaluations", SDDS_LONG, &nEvalMax, 1, 0,
"passes", SDDS_LONG, &nPassMax, 1, 0,
NULL) ||
nEvalMax<=0 || nPassMax<=0)
SDDS_Bomb("invalid -limits syntax");
break;
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
default:
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("sddssinefit", &input, &output, pipeFlags, 0, NULL);
if (!xName || !yName)
SDDS_Bomb("-columns option must be given");
if (!SDDS_InitializeInput(&InputTable, input) ||
SDDS_GetColumnIndex(&InputTable, xName)<0 || SDDS_GetColumnIndex(&InputTable, yName)<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
setupOutputFile(&OutputTable, &xIndex, &yIndex, &fitIndex, &residualIndex, output, fullOutput,
&InputTable, xName, yName);
fitData = residualData = NULL;
alo[0] = - (ahi[0] = DBL_MAX);
alo[1] = alo[2] = 0;
ahi[1] = ahi[2] = DBL_MAX;
alo[3] = - (ahi[3] = PIx2);
firstZero = lastZero = 0;
while ((retval=SDDS_ReadPage(&InputTable))>0) {
if (!(xData = SDDS_GetColumnInDoubles(&InputTable, xName)) ||
!(yData = SDDS_GetColumnInDoubles(&InputTable, yName)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if ((nData = SDDS_CountRowsOfInterest(&InputTable))<4)
continue;
find_min_max(&yMin, &yMax, yData, nData);
find_min_max(&xMin, &xMax, xData, nData);
zeroes = 0;
for (i=1; i<nData; i++)
if (yData[i]*yData[i-1]<=0) {
i++;
if (!zeroes)
firstZero = (xData[i]+xData[i-1])/2;
else
lastZero = (xData[i]+xData[i-1])/2;
zeroes ++;
}
a[0] = (yMin+yMax)/2;
a[1] = (yMax-yMin)/2;
if (!zeroes)
a[2] = 2/fabs(xMax-xMin);
else
a[2] = zeroes/(2*fabs(lastZero-firstZero));
a[3] = 0;
if (guessFlags&GUESS_CONSTANT_GIVEN)
a[0] = constantGuess;
if (guessFlags&GUESS_FACTOR_GIVEN)
a[1] = factorGuess;
if (guessFlags&GUESS_FREQ_GIVEN)
a[2] = freqGuess;
if (guessFlags&GUESS_PHASE_GIVEN)
a[3] = phaseGuess;
alo[1] = a[1]/2;
if (!(da[0] = a[0]*0.1))
da[0] = 0.01;
if (!(da[1] = a[1]*0.1))
da[1] = 0.01;
da[2] = a[2]*0.25;
da[3] = 0.01;
nEval = simplexMin(&result, a, da, alo, ahi, NULL, n_dimen, -DBL_MAX, tolerance, fitFunction,
(verbosity>0?report:NULL), nEvalMax, nPassMax,
12, 3, 1.0, simplexFlags);
fitData = trealloc(fitData, sizeof(*fitData)*nData);
residualData = trealloc(residualData, sizeof(*residualData)*nData);
for (i=result=0; i<nData; i++)
result += sqr(residualData[i] = yData[i]-(fitData[i]=a[0]+a[1]*sin(PIx2*a[2]*xData[i]+a[3])));
rmsResidual = sqrt(result/nData);
if (verbosity>1) {
fprintf(stderr, "RMS deviation: %.15e\n", rmsResidual);
fprintf(stderr, "(RMS deviation)/(largest value): %.15e\n", rmsResidual/MAX(fabs(yMin), fabs(yMax)));
}
if (verbosity>0) {
fprintf(stderr, "coefficients of fit to the form y = a0 + a1*sin(2*PI*a2*x+a3), a = \n");
for (i=0; i<4; i++)
fprintf(stderr, "%.8e ", a[i]);
fprintf(stderr, "\n");
}
if (!SDDS_StartPage(&OutputTable, nData) ||
!SDDS_SetColumn(&OutputTable, SDDS_SET_BY_INDEX, xData, nData, xIndex) ||
!SDDS_SetColumn(&OutputTable, SDDS_SET_BY_INDEX, fitData, nData, fitIndex) ||
!SDDS_SetParameters(&OutputTable, SDDS_PASS_BY_VALUE|SDDS_SET_BY_NAME,
"sinefitConstant", a[0], "sinefitFactor", a[1], "sinefitFrequency", a[2],
"sinefitPhase", a[3], "sinefitRmsResidual", rmsResidual, NULL) ||
(fullOutput &&
(!SDDS_SetColumn(&OutputTable, SDDS_SET_BY_INDEX, yData, nData, yIndex) ||
!SDDS_SetColumn(&OutputTable, SDDS_SET_BY_INDEX, residualData, nData, residualIndex) )) ||
!SDDS_WritePage(&OutputTable))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
return 0;
}
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;
}
int main(int argc, char **argv)
{
FILE *fileID;
SDDS_LAYOUT *layout=NULL;
SDDS_FILEBUFFER *fBuffer=NULL;
SDDS_DATASET SDDS_dataset, SDDS_dummy;
SCANNED_ARG *s_arg;
long i, j, i_arg, retval, page_number=0, size, columnOrder=0;
int32_t rows=0;
char *input, *output;
unsigned long pipeFlags=0, flags=0;
long noWarnings=0, tmpfile_used=0;
long *columnType, *columnIndex;
void **columnData;
char *buffer;
char **column, **column_match;
long columns=0, column_matches;
input = output = NULL;
columnType = columnIndex = NULL;
columnData = NULL;
column_match = NULL;
column_matches = 0;
buffer = tmalloc(sizeof(char)*16);
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<3)
bomb(NULL, USAGE);
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_ORDER:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -order syntax");
switch (match_string(s_arg[i_arg].list[1], order_names, ORDERS, 0)) {
case ROW_ORDER:
columnOrder = 0;
break;
case COLUMN_ORDER:
columnOrder = 1;
break;
default:
SDDS_Bomb("invalid -order syntax");
break;
}
break;
case SET_COLUMN:
if ((s_arg[i_arg].n_items<2))
SDDS_Bomb("invalid -column syntax");
column_matches = s_arg[i_arg].n_items - 1;
column_match = tmalloc(sizeof(*column_match)*column_matches);
for (i=0; i<column_matches; i++)
column_match[i] = s_arg[i_arg].list[i+1];
break;
default:
fprintf(stderr, "error: unknown switch: %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 {
fprintf(stderr, "too many filenames");
exit(1);
}
}
}
processFilenames("sdds2headlessdata", &input, &output, pipeFlags, noWarnings, &tmpfile_used);
if (!column_matches)
SDDS_Bomb("you must specify -column options");
if (!SDDS_InitializeInput(&SDDS_dataset, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
column = getMatchingSDDSNames(&SDDS_dataset, column_match, column_matches, &columns, SDDS_MATCH_COLUMN);
if (!columns)
SDDS_Bomb("No columns found in the input file.");
columnType = tmalloc(sizeof(*columnType)*columns);
columnIndex = tmalloc(sizeof(*columnIndex)*columns);
columnData = tmalloc(sizeof(*columnData)*columns);
for (i=0; i<columns; i++) {
if ((columnIndex[i]=SDDS_GetColumnIndex(&SDDS_dataset, column[i]))<0) {
fprintf(stderr, "error: column %s does not exist\n", column[i]);
exit(1);
}
if ((columnType[i]=SDDS_GetColumnType(&SDDS_dataset, columnIndex[i]))<=0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!output) {
#if defined(_WIN32)
if (_setmode(_fileno(stdout), _O_BINARY) == -1) {
fprintf(stderr, "error: unable to set stdout to binary mode\n");
exit(1);
}
#endif
fileID = stdout;
} else {
fileID = fopen(output, "wb");
}
if (fileID == NULL) {
fprintf(stderr, "unable to open output file for writing\n");
exit(1);
}
layout = &SDDS_dataset.layout;
fBuffer = &SDDS_dummy.fBuffer;
fBuffer->buffer = NULL;
if (!fBuffer->buffer) {
if (!(fBuffer->buffer = fBuffer->data = SDDS_Malloc(sizeof(char)*SDDS_FILEBUFFER_SIZE))) {
fprintf(stderr, "Unable to do buffered read--allocation failure\n");
exit(1);
}
fBuffer->bufferSize = SDDS_FILEBUFFER_SIZE;
fBuffer->bytesLeft = SDDS_FILEBUFFER_SIZE;
}
retval = -1;
while (retval!=page_number && (retval=SDDS_ReadPage(&SDDS_dataset))>0) {
if (page_number && retval!=page_number)
continue;
if ((rows=SDDS_CountRowsOfInterest(&SDDS_dataset))<0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (rows) {
if (columnOrder) {
for (j=0; j<columns; j++) {
if (columnType[j]==SDDS_STRING) {
for (i=0; i<rows; i++) {
if (!SDDS_WriteBinaryString(*((char**)SDDS_dataset.data[columnIndex[j]]+i), fileID, fBuffer)) {
fprintf(stderr, "Unable to write rows--failure writing string\n");
exit(1);
}
}
} else {
size = SDDS_type_size[columnType[j]-1];
for (i=0; i<rows; i++) {
if (!SDDS_BufferedWrite((char*)SDDS_dataset.data[columnIndex[j]]+i*size, size, fileID, fBuffer)) {
fprintf(stderr, "Unable to write rows--failure writing string\n");
exit(1);
}
}
}
}
} else {
for (i=0; i<rows; i++) {
for (j=0; j<columns; j++) {
if (columnType[j]==SDDS_STRING) {
if (!SDDS_WriteBinaryString(*((char**)SDDS_dataset.data[columnIndex[j]]+i), fileID, fBuffer)) {
fprintf(stderr, "Unable to write rows--failure writing string\n");
exit(1);
}
} else {
size = SDDS_type_size[columnType[j]-1];
if (!SDDS_BufferedWrite((char*)SDDS_dataset.data[columnIndex[j]]+i*size, size, fileID, fBuffer)) {
fprintf(stderr, "Unable to write rows--failure writing string\n");
exit(1);
}
}
}
}
}
}
if (retval==0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_FlushBuffer(fileID, fBuffer)) {
SDDS_SetError("Unable to write page--buffer flushing problem (SDDS_WriteBinaryPage)");
return 0;
}
fclose(fileID);
if (!SDDS_Terminate(&SDDS_dataset)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
exit(0);
}
int main(int argc, char **argv)
{
int iArg;
char *input, *output,*meanPar, *sigmaPar, *maxPar, *minPar;
long i, j, mainInputOpened, haltonID=0, requireInput=0;
unsigned long pipeFlags;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout, *SDDSptr;
long randomNumberSeed = 0;
SEQ_REQUEST *seqRequest;
long samples, values, seqRequests, randomizationGroups=0;
double *sample, *IVValue, *CDFValue;
char msgBuffer[1000];
RANDOMIZED_ORDER *randomizationData = NULL;
long verbose, optimalHalton=0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<2) {
fprintf(stderr, "%s%s%s\n", USAGE1, USAGE2, USAGE3);
return(1);
}
seqRequest = NULL;
seqRequests = 0;
output = input = NULL;
pipeFlags = 0;
samples = values = 0;
sample = IVValue = CDFValue = NULL;
verbose = 0;
maxPar = minPar = meanPar = sigmaPar = NULL;
for (iArg=1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type==OPTION) {
/* process options here */
switch (match_string(scanned[iArg].list[0], option, CLO_OPTIONS, 0)) {
case CLO_COLUMNS:
if (scanned[iArg].n_items<3)
SDDS_Bomb("invalid -columns syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
/*remove following pointer initialization because memset already initialize them */
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].factor = 1;
seqRequest[seqRequests].offset = 0;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"datafile", SDDS_STRING,
&seqRequest[seqRequests].dataFileName, 1, SEQ_DATAFILE,
"independentvariable", SDDS_STRING,
&seqRequest[seqRequests].indepName, 1, SEQ_INDEPNAME,
"cdf", SDDS_STRING,
&seqRequest[seqRequests].CDFName, 1, SEQ_CDFNAME,
"df", SDDS_STRING,
&seqRequest[seqRequests].DFName, 1, SEQ_DFNAME,
"output", SDDS_STRING,
&seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"units", SDDS_STRING,
&seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
"haltonradix", SDDS_LONG,
&seqRequest[seqRequests].haltonRadix, 1, SEQ_HALTONRADIX,
"haltonoffset", SDDS_LONG,
&seqRequest[seqRequests].haltonOffset, 1, SEQ_HALTONOFFSET,
"randomize", -1, NULL, 0, SEQ_RANDOMIZE,
"group", SDDS_LONG,
&seqRequest[seqRequests].randomizationGroup, 1, SEQ_RANDOMGROUP,
"factor", SDDS_DOUBLE,
&seqRequest[seqRequests].factor, 1, 0,
"offset", SDDS_DOUBLE,
&seqRequest[seqRequests].offset, 1, 0,
NULL) ||
bitsSet(seqRequest[seqRequests].flags&(SEQ_INDEPNAME+SEQ_CDFNAME+SEQ_DFNAME))!=2)
SDDS_Bomb("invalid -columns syntax");
if (seqRequest[seqRequests].flags&SEQ_RANDOMGROUP &&
seqRequest[seqRequests].randomizationGroup<=0)
SDDS_Bomb("use a positive integer for the randomization group ID");
if (seqRequest[seqRequests].flags&SEQ_CDFNAME &&
seqRequest[seqRequests].flags&SEQ_DFNAME)
SDDS_Bomb("give df or cdf for -columns, not both");
if (seqRequest[seqRequests].flags&SEQ_HALTONRADIX &&
!is_prime(seqRequest[seqRequests].haltonRadix))
SDDS_Bomb("halton radix must be a prime number");
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_GAUSSIAN:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -gaussian syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].mean = 0;
seqRequest[seqRequests].sigma = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"meanValue", SDDS_STRING, &meanPar, 1, 0,
"sigmaValue", SDDS_STRING, &sigmaPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -gaussian syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_GAUSSIAN;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for gaussian distribution/");
if (meanPar) {
if (wild_match(meanPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].meanPar, meanPar+1);
else if (!get_double(&seqRequest[seqRequests].mean, meanPar))
SDDS_Bomb("Invalid value given for mean value of -gaussian distribution.");
free(meanPar);
meanPar = NULL;
}
if (sigmaPar) {
if (wild_match(sigmaPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].sigmaPar, sigmaPar+1);
else if (!get_double(&seqRequest[seqRequests].sigma, sigmaPar))
SDDS_Bomb("Invalid value given for sigma value of -gaussian distribution.");
free(sigmaPar);
sigmaPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_UNIFORM:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -uniform syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].min = 0;
seqRequest[seqRequests].max = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"minimumValue", SDDS_STRING, &minPar, 1, 0,
"maximumValue", SDDS_STRING, &maxPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -uniform syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_UNIFORM;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for uniform distribution/");
if (minPar) {
if (wild_match(minPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].minPar, minPar+1);
else if (!get_double(&seqRequest[seqRequests].min, minPar))
SDDS_Bomb("Invalid value given for minimum value of -uniform distribution.");
free(minPar);
minPar = NULL;
}
if (maxPar) {
if (wild_match(maxPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].maxPar, maxPar+1);
else if (!get_double(&seqRequest[seqRequests].max, maxPar))
SDDS_Bomb("Invalid value given for maximum value of -uniform distribution.");
free(maxPar);
maxPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_POISSON:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -poisson syntax");
if (!(seqRequest = SDDS_Realloc(seqRequest, sizeof(*seqRequest)*(seqRequests+1))))
SDDS_Bomb("memory allocation failure");
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
scanned[iArg].n_items -= 1;
memset(seqRequest+seqRequests, 0, sizeof(*seqRequest));
seqRequest[seqRequests].randomizationGroup = -1;
seqRequest[seqRequests].mean = 1;
if (!scanItemList(&seqRequest[seqRequests].flags,
scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"columnName", SDDS_STRING, &seqRequest[seqRequests].outputName, 1, SEQ_OUTPUTNAME,
"meanValue", SDDS_STRING, &meanPar, 1, 0,
"units", SDDS_STRING, &seqRequest[seqRequests].units, 1, SEQ_UNITSGIVEN,
NULL))
SDDS_Bomb("invalid -poisson syntax");
seqRequest[seqRequests].flags |= SEQ_DIRECT_POISSON;
if (!(seqRequest[seqRequests].flags&SEQ_OUTPUTNAME) || !(seqRequest[seqRequests].outputName))
SDDS_Bomb("columnName is not provided for uniform distribution/");
if (meanPar) {
if (wild_match(meanPar, "@*"))
SDDS_CopyString(&seqRequest[seqRequests].meanPar, meanPar+1);
else if (!get_double(&seqRequest[seqRequests].mean, meanPar))
SDDS_Bomb("Invalid value given for mean value of -poisson distribution.");
free(meanPar);
meanPar = NULL;
}
seqRequests ++;
scanned[iArg].n_items += 1;
break;
case CLO_SAMPLES:
if (scanned[iArg].n_items!=2 ||
sscanf(scanned[iArg].list[1], "%ld", &samples)!=1 ||
samples<=0)
SDDS_Bomb("invalid -samples syntax");
break;
case CLO_SEED:
if (scanned[iArg].n_items!=2 ||
sscanf(scanned[iArg].list[1], "%ld", &randomNumberSeed)!=1 ||
randomNumberSeed<=0)
SDDS_Bomb("invalid -seed syntax");
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_OPTIMAL_HALTON:
optimalHalton = 1;
break;
default:
fprintf(stderr, "error: unknown/ambiguous option: %s\n",
scanned[iArg].list[0]);
exit(1);
break;
}
}
else {
if (!input)
input = scanned[iArg].list[0];
else if (!output)
output = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames seen");
}
}
if (!seqRequests)
SDDS_Bomb("give one or more -columns options");
if (samples<1)
SDDS_Bomb("-samples option not given");
for (i=0; i<seqRequests; i++) {
if (!(seqRequest[i].flags&
(SEQ_DATAFILE|SEQ_DIRECT_GAUSSIAN|SEQ_DIRECT_UNIFORM|SEQ_DIRECT_POISSON)))
break;
}
if (i==seqRequests) {
/* all columns options have either their own input files or else use
* one of the "direct" distributions. Hence, we don't expect an input
* file.
*/
if (!input)
pipeFlags |= USE_STDIN; /* not really, but fakes out processFilenames */
if (input && !output) {
output = input;
input = NULL;
pipeFlags |= USE_STDIN;
if (fexists(output)) {
sprintf(msgBuffer, "%s exists already (sddssampledist)", output);
SDDS_Bomb(msgBuffer);
}
}
}
processFilenames("sddssampledist", &input, &output, pipeFlags, 0, NULL);
if (!SDDS_InitializeOutput(&SDDSout, SDDS_BINARY, 0, NULL, NULL, output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose)
fprintf(stderr, "Initialized output file %s\n", output);
/* open and check input files */
for (i=mainInputOpened=0; i<seqRequests; i++) {
if (seqRequest[i].flags&SEQ_DIRECT_GAUSSIAN) {
if (seqRequest[i].meanPar || seqRequest[i].sigmaPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ((seqRequest[i].meanPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].meanPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) ||
(seqRequest[i].sigmaPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].sigmaPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else if (seqRequest[i].flags&SEQ_DIRECT_UNIFORM) {
if (seqRequest[i].minPar || seqRequest[i].maxPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ((seqRequest[i].minPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].minPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) ||
(seqRequest[i].maxPar &&
SDDS_CheckParameter(SDDSptr, seqRequest[i].maxPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else if (seqRequest[i].flags&SEQ_DIRECT_POISSON) {
if (seqRequest[i].meanPar) {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
if ( SDDS_CheckParameter(SDDSptr, seqRequest[i].meanPar, NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OK) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_DefineSimpleColumn(&SDDSout, seqRequest[i].outputName, NULL, SDDS_LONG))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
if (seqRequest[i].flags&SEQ_RANDOMIZE) {
long newGroupID=0;
/* define randomization groups */
if (seqRequest[i].flags&SEQ_RANDOMGROUP) {
newGroupID = seqRequest[i].randomizationGroup;
for (j=0; j<randomizationGroups; j++)
if (randomizationData[j].group==newGroupID) {
newGroupID = 0;
break;
}
} else {
seqRequest[i].randomizationGroup = newGroupID = -(i+1);
}
if (newGroupID!=0) {
if (!(randomizationData =
SDDS_Realloc(randomizationData,
sizeof(*randomizationData)*(randomizationGroups+1))))
SDDS_Bomb("memory allocation failure");
randomizationData[randomizationGroups].group = newGroupID;
randomizationData[randomizationGroups].order = NULL;
randomizationGroups ++;
}
}
if (seqRequest[i].flags&SEQ_DATAFILE) {
if (!SDDS_InitializeInput(&seqRequest[i].SDDSin,
seqRequest[i].dataFileName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDSptr = &seqRequest[i].SDDSin;
} else {
if (!mainInputOpened) {
if (!SDDS_InitializeInput(&SDDSin, input) ||
!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
mainInputOpened = 1;
}
requireInput = 1;
SDDSptr = &SDDSin;
}
if (SDDS_CheckColumn(SDDSptr,
seqRequest[i].indepName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK ||
((seqRequest[i].flags&SEQ_CDFNAME) &&
SDDS_CheckColumn(SDDSptr, seqRequest[i].CDFName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK) ||
((seqRequest[i].flags&SEQ_DFNAME) &&
SDDS_CheckColumn(SDDSptr, seqRequest[i].DFName, NULL, SDDS_ANY_NUMERIC_TYPE,
stderr)!=SDDS_CHECK_OK) ||
!SDDS_TransferColumnDefinition(&SDDSout, SDDSptr,
seqRequest[i].indepName,
seqRequest[i].outputName)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (seqRequest[i].flags&SEQ_UNITSGIVEN &&
!SDDS_ChangeColumnInformation(&SDDSout, "units", seqRequest[i].units,
SDDS_SET_BY_NAME,
seqRequest[i].outputName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (verbose)
fprintf(stderr, "Initialized input files\n");
if (!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (randomNumberSeed==0) {
randomNumberSeed = (long)time((time_t *) NULL);
randomNumberSeed = 2*(randomNumberSeed/2) + 1;
#if defined(_WIN32)
random_1(-labs(randomNumberSeed));
#else
random_1(-FABS(randomNumberSeed));
#endif
} else
random_1(-randomNumberSeed);
if (!((sample = calloc(sizeof(*sample), samples))))
SDDS_Bomb("memory allocation failure");
while (1) {
if (verbose)
fprintf(stderr, "Beginning page loop\n");
if (input && SDDS_ReadPage(&SDDSin)<=0)
break;
for (i=0; i<seqRequests; i++) {
if (seqRequest[i].flags&SEQ_DATAFILE &&
SDDS_ReadPage(&seqRequest[i].SDDSin)<=0)
break;
}
if (i!=seqRequests)
break;
if (!SDDS_StartPage(&SDDSout, samples) ||
(input && !SDDS_CopyParameters(&SDDSout, &SDDSin)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose)
fprintf(stderr, "Defining randomization tables\n");
/* define randomization tables */
for (i=0; i<randomizationGroups; i++) {
if (!(randomizationData[i].order=
SDDS_Malloc(sizeof(*randomizationData[i].order)*samples)))
SDDS_Bomb("memory allocation failure");
for (j=0; j<samples; j++)
randomizationData[i].order[j] = j;
randomizeOrder((char*)randomizationData[i].order,
sizeof(*randomizationData[i].order), samples, 0,
random_1);
}
if (verbose)
fprintf(stderr, "Beginning loop over sequence requests\n");
for (i=0; i<seqRequests; i++) {
if (verbose)
fprintf(stderr, "Processing sequence request %ld\n", i);
if (seqRequest[i].flags&SEQ_DIRECT_GAUSSIAN) {
if ((seqRequest[i].meanPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].meanPar, &seqRequest[i].mean)) ||
(seqRequest[i].sigmaPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].sigmaPar, &seqRequest[i].sigma)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (j=0; j<samples; j++)
sample[j] = gauss_rn_lim(seqRequest[i].mean, seqRequest[i].sigma, -1, random_1);
} else if (seqRequest[i].flags&SEQ_DIRECT_UNIFORM) {
if ((seqRequest[i].minPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].minPar, &seqRequest[i].min)) ||
(seqRequest[i].maxPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].maxPar, &seqRequest[i].max)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (j=0; j<samples; j++)
sample[j] = seqRequest[i].min + (seqRequest[i].max - seqRequest[i].min) * random_1(1);
} else if (seqRequest[i].flags&SEQ_DIRECT_POISSON) {
double *pos_x, *pos_cdf, CDF;
long pos_points, code;
pos_x = pos_cdf = NULL;
if ((seqRequest[i].meanPar && !SDDS_GetParameterAsDouble(&SDDSin, seqRequest[i].meanPar, &seqRequest[i].mean)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
pos_points = CreatePoissonDistributionTable(&pos_x, &pos_cdf, seqRequest[i].mean);
for (j=0; j<samples; j++) {
CDF = random_1(1);
sample[j]= (int)(interp(pos_x, pos_cdf, pos_points, CDF, 0, 1, &code));
/* fprintf(stderr, "%d, cdf=%f, sample=%f\n", j, CDF, sample[j]);*/
}
free(pos_x);
free(pos_cdf);
} else {
if (input && !(seqRequest[i].flags&SEQ_DATAFILE))
SDDSptr = &SDDSin;
else
SDDSptr = &seqRequest[i].SDDSin;
if ((values = SDDS_CountRowsOfInterest(SDDSptr))) {
if (!(IVValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].indepName)) ||
(seqRequest[i].flags&SEQ_CDFNAME &&
!(CDFValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].CDFName))) ||
(seqRequest[i].flags&SEQ_DFNAME &&
!(CDFValue
= SDDS_GetColumnInDoubles(SDDSptr, seqRequest[i].DFName))))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
sprintf(msgBuffer, "empty page for file %s\n",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
if (verbose)
fprintf(stderr, "Checking and converting CDF/DF values\n");
/* check/convert CDF/DF values */
for (j=1; j<values; j++) {
if (IVValue[j-1]>IVValue[j]) {
sprintf(msgBuffer, "random variate values not monotonically increasing for %s",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
if (seqRequest[i].flags&SEQ_DFNAME)
/* convert DF to CDF */
CDFValue[j] += CDFValue[j-1];
if (CDFValue[j] < CDFValue[j-1]) {
sprintf(msgBuffer, "CDF values decreasing for %s",
seqRequest[i].flags&SEQ_DATAFILE?
seqRequest[i].dataFileName:input);
SDDS_Bomb(msgBuffer);
}
}
if (verbose)
fprintf(stderr, "Normalizing CDF\n");
/* normalize the CDF */
if (CDFValue[values-1]<=0) {
sprintf(msgBuffer, "CDF not valid for %s\n",
seqRequest[i].dataFileName);
SDDS_Bomb(msgBuffer);
}
for (j=0; j<values; j++)
CDFValue[j] /= CDFValue[values-1];
if (seqRequest[i].flags&SEQ_HALTONRADIX) {
if (verbose)
fprintf(stderr, "Starting halton sequence, offset=%" PRId32 "\n", seqRequest[i].haltonOffset);
if (!optimalHalton)
haltonID = startHaltonSequence(&seqRequest[i].haltonRadix, 0.5);
else
haltonID = startModHaltonSequence(&seqRequest[i].haltonRadix, 0);
while (seqRequest[i].haltonOffset-- >0) {
if (!optimalHalton)
nextHaltonSequencePoint(haltonID);
else
nextModHaltonSequencePoint(haltonID);
}
}
if (verbose)
fprintf(stderr, "Generating samples\n");
for (j=0; j<samples; j++) {
double CDF;
long code;
while (1) {
if (seqRequest[i].flags&SEQ_HALTONRADIX) {
if (!optimalHalton)
CDF = nextHaltonSequencePoint(haltonID);
else
CDF = nextModHaltonSequencePoint(haltonID);
}
else
CDF = random_1(1);
if (CDF<=CDFValue[values-1] && CDF>=CDFValue[0])
break;
}
sample[j]
= seqRequest[i].factor*interp(IVValue, CDFValue, values, CDF, 0, 1, &code)
+ seqRequest[i].offset;
}
if (seqRequest[i].flags&SEQ_RANDOMIZE) {
long k, l;
double *sample1;
if (verbose)
fprintf(stderr, "Randomizing order of values\n");
if (!(sample1 = malloc(sizeof(*sample1)*samples)))
SDDS_Bomb("memory allocation failure");
for (l=0; l<randomizationGroups; l++)
if (randomizationData[l].group==seqRequest[i].randomizationGroup)
break;
if (l==randomizationGroups)
SDDS_Bomb("problem with construction of randomization groups!");
for (k=0; k<samples; k++)
sample1[k] = sample[randomizationData[l].order[k]];
free(sample);
sample = sample1;
}
free(IVValue);
free(CDFValue);
}
if (verbose)
fprintf(stderr, "Setting SDDS column values\n");
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_SET_BY_NAME,
sample, samples,
seqRequest[i].outputName?
seqRequest[i].outputName:
seqRequest[i].indepName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (verbose)
fprintf(stderr, "Writing data page\n");
if (!SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!requireInput)
break;
}
if (verbose)
fprintf(stderr, "Exited read loop\n");
free(sample);
if ((input && !SDDS_Terminate(&SDDSin)) || !SDDS_Terminate(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<seqRequests; i++) {
if (seqRequest[i].dataFileName) free(seqRequest[i].dataFileName);
if (seqRequest[i].indepName) free(seqRequest[i].indepName);
if (seqRequest[i].outputName) free(seqRequest[i].outputName);
if (seqRequest[i].DFName) free(seqRequest[i].DFName);
if (seqRequest[i].CDFName) free(seqRequest[i].CDFName);
if (seqRequest[i].units) free(seqRequest[i].units);
if (seqRequest[i].meanPar) free(seqRequest[i].meanPar);
if (seqRequest[i].sigmaPar) free(seqRequest[i].sigmaPar);
if (seqRequest[i].minPar) free(seqRequest[i].minPar);
if (seqRequest[i].maxPar) free(seqRequest[i].maxPar);
if (seqRequest[i].flags&SEQ_DATAFILE && !SDDS_Terminate(&(seqRequest[i].SDDSin)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(seqRequest);
for (i=0; i<randomizationGroups; i++)
free(randomizationData[i].order);
if (randomizationData) free(randomizationData);
free_scanargs(&scanned, argc);
return(0);
}
int main(int argc, char **argv)
{
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;
}
int main(int argc, char **argv)
{
SDDS_DATASET SDDS_input, SDDS_output;
char *inputfile, *outputfile, **column;
long i, i_arg;
long page_number, allocated_rows, noWarnings, setPageNumber;
int32_t columns;
SCANNED_ARG *s_arg;
char s[SDDS_MAXLINE];
unsigned long pipeFlags, majorOrderFlag;
long buffer[16];
short columnMajorOrder = -1;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc<2)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
pipeFlags = noWarnings = 0;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_MAJOR_ORDER:
majorOrderFlag=0;
s_arg[i_arg].n_items -=1;
if (s_arg[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_NOWARNINGS:
noWarnings = 1;
break;
default:
fprintf(stderr, "error: unknown switch: %s\n", s_arg[i_arg].list[0]);
exit(1);
break;
}
}
else {
if (inputfile==NULL)
inputfile = s_arg[i_arg].list[0];
else if (outputfile==NULL)
outputfile = s_arg[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
#ifdef DEBUG
fprintf(stderr, "About to process filename arguments\n");
#endif
processFilenames("sddscollapse", &inputfile, &outputfile, pipeFlags, noWarnings, NULL);
#ifdef DEBUG
fprintf(stderr, "About to initialize input\n");
#endif
if (!SDDS_InitializeInput(&SDDS_input, inputfile)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef DEBUG
fprintf(stderr, "About to initialize output\n");
#endif
if (!SDDS_InitializeOutput(&SDDS_output, SDDS_input.layout.data_mode.mode, 1,
NULL, NULL, outputfile) ) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (columnMajorOrder!=-1)
SDDS_output.layout.data_mode.column_major = columnMajorOrder;
else
SDDS_output.layout.data_mode.column_major = SDDS_input.layout.data_mode.column_major;
#ifdef DEBUG
fprintf(stderr, "About to get parameter names\n");
#endif
if (!(column = SDDS_GetParameterNames(&SDDS_input, &columns))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef DEBUG
fprintf(stderr, "About to define parameters\n");
#endif
for (i=0; i<columns; i++) {
if (!SDDS_DefineColumnLikeParameter(&SDDS_output, &SDDS_input, column[i], NULL)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
sprintf(s, "corresponding page number of %s for this row", inputfile?inputfile:"stdin");
if (SDDS_GetColumnIndex(&SDDS_output, "PageNumber")<0) {
if (SDDS_DefineColumn(&SDDS_output, "PageNumber", NULL, NULL, s,
NULL, SDDS_LONG, 0)<0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
setPageNumber = 1;
} else {
setPageNumber = 0;
}
if (!SDDS_WriteLayout(&SDDS_output) || !SDDS_StartPage(&SDDS_output, allocated_rows=ROW_INCREMENT)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
while ((page_number=SDDS_ReadPageSparse(&SDDS_input, 0, LONG_MAX-1, 0))>0) {
#ifdef DEBUG
fprintf(stderr, "working on page %ld\n", page_number);
#endif
if (page_number>allocated_rows) {
if (!SDDS_LengthenTable(&SDDS_output, ROW_INCREMENT)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
allocated_rows += ROW_INCREMENT;
}
for (i=0; i<columns; i++) {
#ifdef DEBUG
fprintf(stderr, "Getting param %s\n", column[i]);
#endif
if (!SDDS_GetParameter(&SDDS_input, column[i], buffer)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef DEBUG
fprintf(stderr, "Setting column %s\n", column[i]);
#endif
if (!SDDS_SetRowValues(&SDDS_output, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE, page_number-1,
column[i], buffer, NULL)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef DEBUG
fprintf(stderr, "Done setting %s\n", column[i]);
#endif
}
#ifdef DEBUG
fprintf(stderr, "Setting page number\n");
#endif
if (setPageNumber &&
!SDDS_SetRowValues(&SDDS_output, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, page_number-1,
"PageNumber", page_number, NULL)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
if (!SDDS_WritePage(&SDDS_output)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (page_number==0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_Terminate(&SDDS_input) || !SDDS_Terminate(&SDDS_output)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return(0);
}
int main(int argc, char **argv)
{
SCANNED_ARG *s_arg;
SDDS_DATASET inputPage, outputPage;
char *inputfile, *outputfile;
char **inputColumnName, **inputStringColumnName, **inputDoubleColumnName;
char **outputStringColumnName, **outputDoubleColumnName, **matchColumn=NULL;
long inputRows, inputDoubleColumns, inputStringColumns, indexColumn=0, matchColumns=0, noOldColumnNamesColumn=0;
long outputRows, outputDoubleColumns, outputStringColumns;
char **inputParameterName;
int32_t inputParameters, inputColumns;
char *inputDescription, *inputContents;
char *outputDescription;
long i, i_arg, col;
char *buffer;
char **columnOfStrings;
long buffer_size;
#define BUFFER_SIZE_INCREMENT 16384
MATRIX *R, *RInv;
long OldStringColumnsDefined;
char *inputStringRows, *outputStringRows;
char **stringArray, *stringParameter;
long token_length;
long verbose;
char format[32];
long digits;
char *Symbol, *Root;
void *parameterPointer;
long ascii;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long ipage=0, columnType;
char *oldColumnNames, *newColumnNamesColumn;
short columnMajorOrder=-1;
inputColumnName = outputStringColumnName = outputDoubleColumnName = inputParameterName = NULL;
outputRows = outputDoubleColumns = outputStringColumns = OldStringColumnsDefined = 0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
verbose = 0;
Symbol = Root = NULL;
ascii = 0;
digits=3;
pipeFlags = 0;
tmpfile_used = 0;
noWarnings = 0;
oldColumnNames = NULL;
newColumnNamesColumn = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch(match_string(s_arg[i_arg].list[0], commandline_option, COMMANDLINE_OPTIONS,
UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
s_arg[i_arg].n_items--;
if (s_arg[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_MATCH_COLUMN:
matchColumns = s_arg[i_arg].n_items-1;
matchColumn = s_arg[i_arg].list+1;
break;
case CLO_INDEX_COLUMN:
indexColumn = 1;
break;
case CLO_NO_OLDCOLUMNNAMES:
noOldColumnNamesColumn = 1;
break;
case CLO_VERBOSE:
verbose=1;
break;
case CLO_ASCII:
ascii=1;
break;
case CLO_DIGITS:
if (!(get_long(&digits, s_arg[i_arg].list[1])))
bomb("no string given for option -digits", USAGE);
break;
case CLO_COLUMNROOT:
if (!(Root=s_arg[i_arg].list[1]))
SDDS_Bomb("No root string given");
break;
case CLO_SYMBOL:
if (!(Symbol=s_arg[i_arg].list[1]))
SDDS_Bomb("No symbol string given");
break;
case CLO_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_OLDCOLUMNNAMES:
if (!(oldColumnNames=s_arg[i_arg].list[1]))
SDDS_Bomb("No oldColumnNames string given");
break;
case CLO_NEWCOLUMNNAMES:
if (s_arg[i_arg].n_items!=2 ||
SDDS_StringIsBlank(newColumnNamesColumn = s_arg[i_arg].list[1]))
SDDS_Bomb("Invalid -newColumnNames syntax/value");
break;
default:
bomb("unrecognized option given", USAGE);
}
}
else {
if (!inputfile)
inputfile = s_arg[i_arg].list[0];
else if (!outputfile)
outputfile = s_arg[i_arg].list[0];
else
bomb("too many filenames given", USAGE);
}
}
processFilenames("sddstranpose", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (newColumnNamesColumn && Root)
SDDS_Bomb("-root and -newColumnNames are incompatible");
if (!SDDS_InitializeInput(&inputPage, inputfile) ||
!(inputParameterName=(char**)SDDS_GetParameterNames(&inputPage, &inputParameters)) ||
!SDDS_GetDescription(&inputPage, &inputDescription, &inputContents))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (matchColumns)
inputColumnName = getMatchingSDDSNames(&inputPage, matchColumn, matchColumns, &inputColumns, SDDS_MATCH_COLUMN);
else {
if (!(inputColumnName=(char**)SDDS_GetColumnNames(&inputPage, &inputColumns)))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
inputDoubleColumns=0;
inputStringColumns=0;
inputDoubleColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputStringColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputRows = 0;
/*********** \
* read data *
\***********/
while (0<SDDS_ReadTable(&inputPage)) {
ipage ++;
#if defined(DEBUG)
fprintf(stderr, "working on page %ld\n", ipage);
#endif
if (ipage==1) {
SDDS_DeferSavingLayout(1);
if( !SDDS_SetColumnFlags(&inputPage, 0))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
/* count the string and numerical columns in the input file */
for (i=0;i<inputColumns;i++) {
if ( SDDS_NUMERIC_TYPE( columnType = SDDS_GetColumnType( &inputPage, i))) {
inputDoubleColumnName[inputDoubleColumns]=inputColumnName[i];
inputDoubleColumns++;
}
}
for (i=0; i<inputPage.layout.n_columns; i++) {
if (inputPage.layout.column_definition[i].type == SDDS_STRING ) {
inputStringColumnName[inputStringColumns] = inputPage.layout.column_definition[i].name;
inputStringColumns++;
}
}
if( !(inputRows=SDDS_CountRowsOfInterest(&inputPage)))
SDDS_Bomb("No rows in dataset.");
}
else {
/* these statements are executed on the subsequent pages */
if (inputRows != SDDS_CountRowsOfInterest(&inputPage)) {
SDDS_Bomb("Datasets don't have the same number of rows.\nProcessing stopped before reaching the end of the input file.");
}
}
#if defined(DEBUG)
fprintf(stderr, "row flags set\n");
#endif
if (inputDoubleColumns == 0)
SDDS_Bomb("No numerical columns in file.");
if ((ipage==1) && verbose) {
fprintf(stderr, "No. of double/float/integer columns: %ld.\n", inputDoubleColumns);
fprintf(stderr, "No. of string columns: %ld.\n", inputStringColumns);
fprintf(stderr, "No. of rows: %ld.\n", inputRows);
}
/****************\
* transpose data *
\****************/
if (inputDoubleColumns) {
if (ipage == 1) {
m_alloc(&RInv, inputRows, inputDoubleColumns);
m_alloc(&R, inputDoubleColumns, inputRows);
}
for (col=0;col<inputDoubleColumns;col++){
if (!(R->a[col]=(double*)SDDS_GetColumnInDoubles(&inputPage, inputDoubleColumnName[col]))) {
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (verbose) {
m_show(R, "%9.6le ", "Transpose of input matrix:\n", stdout);
}
m_trans(RInv, R);
}
/***************************\
* determine existence of *
* transposed string columns *
\***************************/
if (ipage == 1) {
OldStringColumnsDefined=0;
switch(SDDS_CheckParameter(&inputPage, OLD_STRING_COLUMN_NAMES, NULL, SDDS_STRING, NULL)){
case SDDS_CHECK_OKAY:
OldStringColumnsDefined=1;
break;
case SDDS_CHECK_NONEXISTENT:
break;
case SDDS_CHECK_WRONGTYPE:
case SDDS_CHECK_WRONGUNITS:
fprintf(stderr, "Something wrong with parameter OldStringColumns.\n");
exit(1);
break;
}
if (OldStringColumnsDefined){
/* decompose OldStringColumns into names of string columns for the output file */
if (!SDDS_GetParameter(&inputPage, OLD_STRING_COLUMN_NAMES, &inputStringRows))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Parameter OldStringColumns: %s.\n", inputStringRows);
}
outputStringColumnName=(char**)malloc(sizeof(char*));
outputStringColumns=0;
buffer_size=BUFFER_SIZE_INCREMENT;
buffer=(char*)malloc(sizeof(char)*buffer_size);
while ( 0 <= (token_length = SDDS_GetToken(inputStringRows, buffer, BUFFER_SIZE_INCREMENT))){
if (!token_length)
SDDS_Bomb("A null string was detected in parameter OldStringColumns.\n");
if (!SDDS_CopyString(&outputStringColumnName[outputStringColumns], buffer))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Output string column: %s\n", outputStringColumnName[outputStringColumns]);
}
outputStringColumns++;
}
}
}
/*********************\
* define output page *
\*********************/
if ( ipage == 1 ) {
outputRows = inputDoubleColumns;
outputDoubleColumns = inputRows;
if (inputDescription){
outputDescription = (char*) malloc( sizeof(char) * (strlen("Transpose of ") + strlen(inputDescription) + 1));
strcat(strcpy(outputDescription, "Transpose of "), inputDescription);
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, outputDescription, inputContents, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, NULL, NULL, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (columnMajorOrder!=-1)
outputPage.layout.data_mode.column_major = columnMajorOrder;
else
outputPage.layout.data_mode.column_major = inputPage.layout.data_mode.column_major;
/***********************************\
* define names for double columns *
\***********************************/
if (!Root && inputStringColumns ) {
/* use specified string column, or first string column encountered */
if (!newColumnNamesColumn)
/* first string column encountered */
outputDoubleColumnName = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[0]);
else {
/* use specified string column */
if (SDDS_CheckColumn(&inputPage, newColumnNamesColumn, NULL, SDDS_STRING, stderr)!=SDDS_CHECK_OKAY)
SDDS_Bomb("column named with -newColumnNames does not exist in input");
outputDoubleColumnName = (char**)SDDS_GetColumn(&inputPage, newColumnNamesColumn);
}
for (i=1; i<inputRows; i++) {
if (match_string(outputDoubleColumnName[i-1], outputDoubleColumnName+i, inputRows-i, EXACT_MATCH)>=0) {
fprintf(stderr, "Error, duplicate %s found in input file string column %s, can not be used as output column names\n", outputDoubleColumnName[i-1], newColumnNamesColumn ? newColumnNamesColumn : inputStringColumnName[0]);
exit(1);
}
}
}
else {
/* use command line options to produce column names in the output file */
outputDoubleColumnName = (char**) malloc( outputDoubleColumns * sizeof(char*) );
digits = MAX(digits, log10(inputRows) + 1);
if (!Root){
Root = (char*) malloc( sizeof(char) * (strlen("Column")+1) );
strcpy(Root, "Column");
}
if (outputDoubleColumns!=1) {
for ( i=0; i < outputDoubleColumns; i++){
outputDoubleColumnName[i] = (char*) malloc( sizeof(char) * (strlen(Root)+digits+1));
sprintf(format, "%s%%0%ldld", Root, digits);
sprintf(outputDoubleColumnName[i], format, i);
}
}
else {/* only one row to transpose */
outputDoubleColumnName[0] = (char*) malloc( sizeof(char) * (strlen(Root)+1));
strcpy( outputDoubleColumnName[0], Root);
}
}
/*************************\
* define string columns *
\*************************/
if (OldStringColumnsDefined) {
if (!SDDS_DefineSimpleColumns(&outputPage, outputStringColumns,
outputStringColumnName, NULL, SDDS_STRING))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
/* by default there should be at least one string column, that of the old column names. */
if (!noOldColumnNamesColumn) {
outputStringColumns = 1;
outputStringColumnName = (char**) malloc( sizeof(char*));
if (oldColumnNames) {
/* commanline option specification */
outputStringColumnName[0] = oldColumnNames;
}
else {
outputStringColumnName[0] = (char*) malloc( sizeof(char) * (strlen("OldColumnNames") + 1));
strcpy(outputStringColumnName[0], "OldColumnNames");
}
if ( 0 > SDDS_DefineColumn(&outputPage, outputStringColumnName[0], NULL, NULL, NULL, NULL, SDDS_STRING, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (indexColumn && !SDDS_DefineSimpleColumn(&outputPage, "Index", NULL, SDDS_LONG))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/*************************\
* define double columns *
\*************************/
for ( i=0; i < outputDoubleColumns; i++)
if (Symbol){
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], Symbol, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], NULL, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/********************************\
* define string parameters *
* i.e. transposed string columns *
\********************************/
if ( inputStringColumns>1 ) {
if (0>SDDS_DefineParameter(&outputPage, OLD_STRING_COLUMN_NAMES,
NULL, NULL, "Transposed string columns", NULL, SDDS_STRING,
NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for ( i=0; i < inputStringColumns; i++){
if (0>SDDS_DefineParameter(&outputPage, inputStringColumnName[i], NULL, NULL, "Transposed string column data", NULL,
SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/*************************\
* transfer parameters not *
* associated with old *
* string columns *
\*************************/
if (inputParameters) {
for ( i=0; i < inputParameters; i++) {
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES)))
if ( 0 > SDDS_TransferParameterDefinition(&outputPage, &inputPage, inputParameterName[i], NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/***************\
* write layout *
\***************/
SDDS_DeferSavingLayout(0);
/* if InputFile is not already transfered ot the output file, then create it. */
switch( SDDS_CheckParameter(&outputPage, "InputFile", NULL, SDDS_STRING, NULL) ) {
case SDDS_CHECK_NONEXISTENT:
if (0>SDDS_DefineParameter(&outputPage, "InputFile", NULL, NULL, "Original matrix file", NULL, SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
default:
break;
}
if (!SDDS_WriteLayout(&outputPage) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "table layout defined\n");
#endif
if (!SDDS_StartTable(&outputPage, outputRows) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (ipage == 1) {
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile", inputfile?inputfile:"pipe", NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/***************************************\
* assign string columns from input *
* to string parameters in output *
\**************************************/
if ( inputStringColumns > 1) {
for ( i=0; i < inputStringColumns; i++){
columnOfStrings = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[i]);
stringParameter = JoinStrings(columnOfStrings, inputRows, BUFFER_SIZE_INCREMENT);
if ( !SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
inputStringColumnName[i], stringParameter, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(columnOfStrings);
free(stringParameter);
}
outputStringRows = JoinStrings(inputStringColumnName, inputStringColumns, BUFFER_SIZE_INCREMENT);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
OLD_STRING_COLUMN_NAMES, outputStringRows, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string parameters assigned\n");
#endif
if (inputParameters){
for ( i=0; i < inputParameters; i++){
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES))) {
parameterPointer = (void*) SDDS_GetParameter(&inputPage, inputParameterName[i], NULL);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputParameterName[i], parameterPointer, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(parameterPointer);
}
}
}
#if defined(DEBUG)
fprintf(stderr, "input parameters assigned\n");
#endif
/**********************************\
* assign data to *
* output table part of data set *
\**********************************/
if (outputRows) {
/***************************\
* assign string column data *
\***************************/
if (OldStringColumnsDefined){
for ( i=0 ; i < outputStringColumns; i++){
if (!SDDS_GetParameter(&inputPage, outputStringColumnName[i], &stringParameter))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
stringArray=TokenizeString(stringParameter, outputRows);
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
stringArray, outputRows, outputStringColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
else {
if (!noOldColumnNamesColumn && !SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputDoubleColumnName, outputRows, outputStringColumnName[0]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string data columns assigned\n");
#endif
/***************************\
* assign double column data *
\***************************/
for ( i=0 ; i < outputDoubleColumns; i++) /* i is the row index */
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
RInv->a[i], outputRows, outputDoubleColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (indexColumn) {
for (i=0; i<outputRows; i++)
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, i, "Index", i, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "double data columns assigned\n");
#endif
}
#if defined(DEBUG)
fprintf(stderr, "data assigned\n");
#endif
if (!SDDS_WriteTable(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
#if defined(DEBUG)
fprintf(stderr, "data written out\n");
#endif
}
if (inputDoubleColumns) {
m_free(&RInv);
m_free(&R);
}
if (inputColumnName) {
SDDS_FreeStringArray(inputColumnName, inputColumns);
free(inputColumnName);
}
if (inputStringColumns)
free(inputStringColumnName);
if (inputDescription)
free(inputDescription);
if (inputParameterName) {
SDDS_FreeStringArray(inputParameterName, inputParameters);
free(inputParameterName);
}
if (outputDoubleColumns) {
SDDS_FreeStringArray(outputDoubleColumnName, outputDoubleColumns);
free(outputDoubleColumnName);
}
if (!SDDS_Terminate(&inputPage) || !SDDS_Terminate(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
return(0);
}
int main(int argc, char **argv)
{
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)
{
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)
{
SCANNED_ARG *scanned;
SDDS_TABLE inputPage, outputPage, residualPage;
char *inputfile, *outputfile;
char **column, **excludeColumn;
int32_t columns;
long excludeColumns;
char *indColumnName;
long verbose;
long iArg, i, j, ipage;
double *indVar, *indVarOrig;
char *indVarUnits;
char **intColumn, **slopeColumn, **slopeSigmaColumn, **interceptSigmaColumn;
char *Units,*slopeUnits;
double *depVar, *depVarOrig;
long order;
double *coef, *coefsigma, *weight, *diff, *diffOrig, chi;
long iCol, iRow;
long rows, rowsOrig;
double rmsResidual;
double slopeSigma, interceptSigma;
char **sigmaColumn, **chiSquaredColumn;
long *sigmaColumnExists;
long doSlopeSigma, generateSigma, doPreliminaryFit;
long validSigmas;
double sigmaSum, averageSigma;
long ascii;
char *residualFile;
unsigned long pipeFlags;
long tmpfile_used, noWarnings;
double xMin, xMax;
indVar = indVarOrig = depVar = depVarOrig = coef = coefsigma = weight = diff = NULL;
intColumn = slopeColumn = slopeSigmaColumn = interceptSigmaColumn = sigmaColumn = chiSquaredColumn = NULL;
slopeUnits = NULL;
sigmaColumnExists = NULL;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
indColumnName = NULL;
verbose = 0;
doSlopeSigma = 0;
generateSigma = 0;
doPreliminaryFit = 0;
ascii = 0;
pipeFlags = 0;
tmpfile_used=0;
noWarnings=0;
residualFile = NULL;
xMin = xMax = 0;
for (iArg = 1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type == OPTION) {
delete_chars(scanned[iArg].list[0], "_");
switch (match_string(scanned[iArg].list[0], commandline_option, COMMANDLINE_OPTIONS, UNIQUE_MATCH)) {
case CLO_INDEPENDENT_COLUMN:
if (!(indColumnName = scanned[iArg].list[1]))
SDDS_Bomb("no string given for option -independentVariable");
break;
case CLO_COLUMNS:
if (columns)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
column = tmalloc(sizeof(*column)*(columns = scanned[iArg].n_items-1));
for (i = 0; i<columns; i++)
column[i] = scanned[iArg].list[i+1];
break;
case CLO_EXCLUDE:
if (excludeColumns)
SDDS_Bomb("only one -excludecolumns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -excludecolumns syntax");
excludeColumn = tmalloc(sizeof(*excludeColumn)*(excludeColumns = scanned[iArg].n_items-1));
for (i = 0; i<excludeColumns; i++)
excludeColumn[i] = scanned[iArg].list[i+1];
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_ASCII:
ascii = 1;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_SIGMA:
doSlopeSigma = 1;
if (scanned[iArg].n_items > 1 ) {
switch (match_string(scanned[iArg].list[1], sigma_option, SIGMA_OPTIONS, UNIQUE_MATCH)) {
case SIGMA_GENERATE:
generateSigma = 1;
break;
default:
SDDS_Bomb("unrecognized sigma option given");
break;
}
}
break;
case CLO_RESIDUAL:
if (!(residualFile=scanned[iArg].list[1])){
fprintf(stderr,"No file specified in -residual option.\n");
exit(1);
}
break;
case CLO_RANGE:
if (scanned[iArg].n_items!=3 ||
1!=sscanf(scanned[iArg].list[1], "%lf", &xMin) ||
1!=sscanf(scanned[iArg].list[2], "%lf", &xMax) ||
xMin>=xMax)
SDDS_Bomb("incorrect -range syntax");
break;
default:
SDDS_Bomb("unrecognized option given");
break;
}
}
else {
if (!inputfile)
inputfile = scanned[iArg].list[0];
else if (!outputfile)
outputfile = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames given");
}
}
if (residualFile && outputfile) {
if (!strcmp( residualFile, outputfile)) {
fprintf( stderr, "Residual file can't be the same as the output file.\n");
exit(1);
}
}
processFilenames("sddsslopes", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (!indColumnName) {
fprintf( stderr, "independentVariable not given\n");
exit(1);
}
if (!excludeColumns) {
excludeColumn = defaultExcludedColumn;
excludeColumns = DEFAULT_EXCLUDED_COLUMNS;
}
if (verbose)
fprintf(stderr,"Reading file %s.\n",inputfile);
if ( !SDDS_InitializeInput( &inputPage, inputfile) )
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
while (0 < (ipage=SDDS_ReadTable( &inputPage))) {
if (verbose) {
fprintf(stderr, "working on page %ld\n", ipage);
}
rows = SDDS_CountRowsOfInterest(&inputPage);
rowsOrig = rows;
/*************************************\
* make array of independent variable
\*************************************/
if (ipage==1) {
indVar = (double*) malloc( sizeof(*indVar) * rows);
}
else {
indVar = (double*) realloc( indVar, sizeof(*indVar) * rows);
}
if (ipage==1) {
if (!SDDS_FindColumn(&inputPage, FIND_NUMERIC_TYPE, indColumnName, NULL)){
fprintf(stderr,"Something wrong with column %s.\n", indColumnName);
SDDS_CheckColumn(&inputPage, indColumnName, NULL, SDDS_ANY_NUMERIC_TYPE, stderr);
exit(1);
}
}
/* filter out the specified range in independent variable */
if (xMin!=xMax) {
if (!(indVarOrig = SDDS_GetColumnInDoubles( &inputPage, indColumnName)))
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
for (i=j=0; i<rowsOrig; i++) {
if (indVarOrig[i]<=xMax && indVarOrig[i]>=xMin) {
indVar[j] = indVarOrig[i];
j++;
}
}
rows = j;
}
else {
if (!(indVar = SDDS_GetColumnInDoubles( &inputPage, indColumnName)))
SDDS_PrintErrors( stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if ( ipage == 1 ) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &indVarUnits, SDDS_GET_BY_NAME, indColumnName))
SDDS_PrintErrors( stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!indVarUnits) {
indVarUnits = (char *) malloc(sizeof(*indVarUnits));
indVarUnits[0] = 0;
}
}
/************************************\
* initialize residual file
\************************************/
if (residualFile) {
if ( ipage == 1 ) {
if(!SDDS_InitializeOutput(&residualPage,ascii?SDDS_ASCII:SDDS_BINARY,1,
"Residual of 2-term fit",NULL,outputfile) ||
!SDDS_InitializeCopy(&residualPage, &inputPage, residualFile, "w") ||
!SDDS_WriteLayout(&residualPage) )
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_CopyPage(&residualPage,&inputPage))
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/************************************\
* get columns of interest. use set_multicolumn_flags to simply
* return new values for array column.
\*************************************/
if (!set_multicolumn_flags(&inputPage, &column, &columns, excludeColumn, excludeColumns)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/************************************\
* make column names for the output
\*************************************/
if (ipage==1) {
intColumn = (char**) malloc((sizeof(char*)*columns));
slopeColumn = (char**) malloc((sizeof(char*)*columns));
if (doSlopeSigma) {
slopeSigmaColumn = (char**) malloc((sizeof(char*)*columns));
interceptSigmaColumn = (char**) malloc((sizeof(char*)*columns));
chiSquaredColumn = (char**) malloc((sizeof(char*)*columns));
}
for (i=0; i<columns; i++) {
intColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("Intercept")+1)));
strcat(strcpy(intColumn[i], column[i]), "Intercept");
slopeColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("Slope")+1)));
strcat(strcpy(slopeColumn[i], column[i]), "Slope");
if (doSlopeSigma) {
slopeSigmaColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("SlopeSigma")+1)));
strcat(strcpy(slopeSigmaColumn[i], column[i]), "SlopeSigma");
interceptSigmaColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("InterceptSigma")+1)));
strcat(strcpy(interceptSigmaColumn[i], column[i]), "InterceptSigma");
chiSquaredColumn[i] = (char*) malloc((sizeof(char)*(strlen(column[i])+strlen("ChiSquared")+1)));
strcat(strcpy(chiSquaredColumn[i], column[i]), "ChiSquared");
}
}
}
/************************************\
* Write layout for output file
\*************************************/
if (ipage==1) {
if (verbose)
fprintf(stderr,"Opening file %s.\n",outputfile);
if(!SDDS_InitializeOutput(&outputPage,ascii?SDDS_ASCII:SDDS_BINARY,1,
"2-term fit",NULL,outputfile) ||
0>SDDS_DefineParameter(&outputPage, "InputFile", "InputFile", NULL,
"InputFile", NULL, SDDS_STRING, 0) ||
0>SDDS_DefineColumn(&outputPage, "IndependentVariable", NULL, NULL, NULL, NULL, SDDS_STRING,0) )
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (iCol=0; iCol<columns; iCol++) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &Units, SDDS_GET_BY_NAME, column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!Units) {
Units = (char*) malloc(sizeof(*Units));
Units[0] = 0;
}
if (0>SDDS_DefineColumn(&outputPage, intColumn[iCol], NULL, Units, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* units for slopes columns */
if (strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+strlen(indVarUnits)+2));
strcat( strcat( strcpy(slopeUnits, Units), "/"), indVarUnits);
}
if (strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(indVarUnits)+2));
strcat( strcpy( slopeUnits, "1/"), indVarUnits);
}
if (!strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+2));
strcpy( slopeUnits, indVarUnits);
}
if (!strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits));
strcpy( slopeUnits, "");
}
if (0>SDDS_DefineColumn(&outputPage, slopeColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (doSlopeSigma) {
if (0>SDDS_DefineColumn(&outputPage, interceptSigmaColumn[iCol], NULL, Units,
NULL, NULL, SDDS_DOUBLE,0) ||
0>SDDS_DefineColumn(&outputPage, slopeSigmaColumn[iCol], NULL, slopeUnits,
NULL, NULL, SDDS_DOUBLE,0) ||
0>SDDS_DefineColumn(&outputPage, chiSquaredColumn[iCol], NULL, NULL,
NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(slopeUnits);
}
if ( !SDDS_WriteLayout(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if ( !SDDS_StartTable(&outputPage,1) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile",inputfile?inputfile:"pipe",NULL) ||
!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
"IndependentVariable", indColumnName, NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* determine which included columns has a Sigma column defined in the input file */
if ( ipage == 1 ) {
sigmaColumn = (char **) malloc( sizeof(*sigmaColumn)*columns);
sigmaColumnExists = (long *) malloc(columns*sizeof(*sigmaColumnExists));
for (iCol=0; iCol<columns; iCol++) {
sigmaColumn[iCol] = (char *) malloc( sizeof(**sigmaColumn) *
(strlen(column[iCol]) + strlen("Sigma") + 1) );
strcat( strcpy(sigmaColumn[iCol], column[iCol]), "Sigma");
switch(SDDS_CheckColumn(&inputPage, sigmaColumn[iCol], NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
sigmaColumnExists[iCol] = 1;
break;
default:
/* try other possible spelling */
strcat( strcpy(sigmaColumn[iCol] ,"Sigma"), column[iCol]);
switch(SDDS_CheckColumn(&inputPage, sigmaColumn[iCol], NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
sigmaColumnExists[iCol] = 1;
break;
default:
sigmaColumnExists[iCol] = 0;
}
break;
}
}
}
if ( ipage == 1 ) {
weight = (double*)malloc(sizeof(*weight)*rows);
diff = (double*)malloc(sizeof(*diff)*rows);
order=1;
coef = (double*)malloc(sizeof(*coef)*(order+1));
coefsigma = (double*)malloc(sizeof(*coefsigma)*(order+1));
}
else {
weight = (double*)realloc( weight, sizeof(*weight)*rows);
diff = (double*)realloc( diff, sizeof(*diff)*rows);
order=1;
coef = (double*)realloc( coef, sizeof(*coef)*(order+1));
coefsigma = (double*)realloc( coefsigma, sizeof(*coefsigma)*(order+1));
}
if (ipage==1) {
depVar = (double*) malloc( sizeof(*depVar) * rows);
}
else {
depVar = (double*) realloc( depVar, sizeof(*depVar) * rows);
}
for (iCol=0; iCol<columns; iCol++) {
if (verbose)
fprintf(stderr,"Doing column %s.\n", column[iCol]);
/* filter out the specified range in independent variable */
if (xMin!=xMax) {
if (!(depVarOrig = (double*) SDDS_GetColumnInDoubles(&inputPage, column[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
for (i=j=0; i<rowsOrig; i++) {
if ( xMin <= indVarOrig[i] && indVarOrig[i] <= xMax ) {
depVar[j] = depVarOrig[i];
j++;
}
}
}
else {
if (!(depVar=SDDS_GetColumnInDoubles(&inputPage, column[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
/*********************
three possibilities:
1) don't do or write slope errors. (doSlopeSigma=0)
do one lsf call with all weights = 1
2) calculated slope errors from sigma columns in the input file.
(doSlopeSigma=1 && generateSigma=0 && sigmaColumnExists[iCol]=1 )
do one lsf call with weights from sigma columns
3) calculate slope errors from generated sigma from a preliminary fit.
(doSlopeSigma=1 && (generateSigma=1 || sigmaColumnExists[iCol]=NULL)
do preliminary fit to generate sigma
*********************/
for (iRow=0; iRow<rows; iRow++)
weight[iRow] = 1;
if (doSlopeSigma) {
/*********************
check validity of sigma column values
*********************/
if( !generateSigma && sigmaColumnExists[iCol]) {
if (verbose)
fprintf(stderr,"\tUsing column %s for sigma.\n",sigmaColumn[iCol]);
if(!(weight=SDDS_GetColumnInDoubles(&inputPage, sigmaColumn[iCol])))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
/* check for zero weight values which will give lsfn problems */
validSigmas = rows;
sigmaSum = 0;
for (iRow=0; iRow<rows; iRow++) {
sigmaSum += weight[iRow];
if(!weight[iRow]) {
validSigmas--;
/*
fprintf(stderr,"Warning: %s of row number %ld is zero. Using average sigma.\n",sigmaColumn[iCol],iRow); */
}
}
if (!validSigmas) {
fprintf(stderr,"Warning: All sigmas are zero.\n");
doPreliminaryFit = 1;
}
else if (validSigmas!=rows) {
/* fix some sigmas */
averageSigma = sigmaSum/ validSigmas;
fprintf(stderr, "Warning: replacing %ld invalid sigmas with average (%e)\n",
rows-validSigmas, averageSigma);
for (iRow=0; iRow<rows; iRow++) {
if(!weight[iRow]) {
weight[iRow] = averageSigma;
}
}
}
}
else {
doPreliminaryFit = 1;
}
}
if (doPreliminaryFit) {
if (verbose)
fprintf(stderr,"\tGenerating sigmas from rms residual of a preliminary fit.\n");
if (!(lsfn(indVar, depVar, weight, rows, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
rmsResidual = 0;
/* calculate rms residual */
for (iRow=0; iRow<rows; iRow++) {
rmsResidual += sqr(diff[iRow]);
}
rmsResidual = sqrt(rmsResidual/(rows));
for (iRow=0; iRow<rows; iRow++) {
weight[iRow] = rmsResidual;
}
}
if (!(lsfn(indVar, depVar, weight, rows, order, coef, coefsigma, &chi, diff))) {
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (doSlopeSigma) {
interceptSigma = coefsigma[0];
slopeSigma = coefsigma[1];
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
chiSquaredColumn[iCol], chi,
interceptSigmaColumn[iCol], interceptSigma,
slopeSigmaColumn[iCol], slopeSigma, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (residualFile) {
if (xMin!=xMax) {
/* calculate the residuals for the whole column explicitly since there
are points outside the range of which the lsf call did not calculate
the difference. */
diffOrig = (double*) malloc( rowsOrig * sizeof(double) );
for (i=0; i<rowsOrig; i++) {
diffOrig[i] = depVarOrig[i] - coef[0] - coef[1] * indVarOrig[i];
}
if( !SDDS_SetColumnFromDoubles(&residualPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
diffOrig,rowsOrig,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if( !SDDS_SetColumnFromDoubles(&residualPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
diff,rows,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
if (residualFile) {
if (!SDDS_WriteTable(&residualPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteTable(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (residualFile) {
if (!SDDS_Terminate(&residualPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if(!SDDS_Terminate(&inputPage) || !SDDS_Terminate(&outputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
return(0);
}
int main(int argc, char **argv)
{
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;
}
int main(int argc, char **argv)
{
int iArg;
char *indepQuantity, **depenQuantity, *fileValuesQuantity, *fileValuesFile, **exclude;
long depenQuantities, monotonicity, excludes;
char *input, *output;
long i, j, rows, readCode, order, valuesReadCode, fillIn, row;
long sequencePoints, combineDuplicates, branch;
int32_t *rowFlag;
double sequenceStart, sequenceEnd;
double sequenceSpacing;
unsigned long flags, interpCode, printFlags, forceMonotonic;
SCANNED_ARG *scanned;
SDDS_DATASET SDDSin, SDDSout, SDDSvalues;
OUTRANGE_CONTROL aboveRange, belowRange;
double *atValue;
long atValues, interpPoints, doNotRead, parallelPages;
double *indepValue, **depenValue, *interpPoint, **outputData;
unsigned long pipeFlags;
FILE *fpPrint;
short interpShort=0, interpShortOrder=-1, *shortValue=NULL;
long nextPos;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<3 || argc>(3+CLO_OPTIONS))
bomb(NULL, USAGE);
atValue = NULL;
atValues = fillIn = 0;
output = input = NULL;
combineDuplicates = branch = sequencePoints = parallelPages = 0;
indepQuantity = NULL;
depenQuantity = exclude = NULL;
depenQuantities = excludes = 0;
aboveRange.flags = belowRange.flags = OUTRANGE_SATURATE;
order = 1;
readCode = interpPoints = 0;
fileValuesFile = fileValuesQuantity = NULL;
sequenceStart = sequenceEnd = sequenceSpacing = 0;
printFlags = pipeFlags = 0;
forceMonotonic = 0;
indepValue = interpPoint = NULL;
depenValue = outputData = 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_ORDER:
if (scanned[iArg].n_items!=2 || sscanf(scanned[iArg].list[1], "%ld", &order)!=1 ||
order<1)
SDDS_Bomb("invalid -order syntax/value");
break;
case CLO_ATVALUES:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -atValues syntax");
if (atValue)
SDDS_Bomb("give -atValues only once");
atValue = tmalloc(sizeof(*atValue)*(atValues=scanned[iArg].n_items-1));
for (i=0; i<atValues; i++)
if (sscanf(scanned[iArg].list[i+1], "%lf", &atValue[i])!=1)
SDDS_Bomb("invalid -atValues value");
break;
case CLO_INTERP_SHORT:
if (scanned[iArg].n_items==2) {
if (sscanf(scanned[iArg].list[1], "%hd", &interpShortOrder)!=1)
SDDS_Bomb("invalid -interpShort value");
}
interpShort = 1;
break;
case CLO_SEQUENCE:
if ((scanned[iArg].n_items!=2 && scanned[iArg].n_items!=4) ||
sscanf(scanned[iArg].list[1], "%ld", &sequencePoints)!=1 || sequencePoints<2)
SDDS_Bomb("invalid -sequence syntax/value");
if (scanned[iArg].n_items==4 &&
(sscanf(scanned[iArg].list[2], "%lf", &sequenceStart)!=1 ||
sscanf(scanned[iArg].list[3], "%lf", &sequenceEnd)!=1))
SDDS_Bomb("invalid -sequence syntax/value");
if (sequenceSpacing)
SDDS_Bomb("give only one of -sequence and -equispaced");
break;
case CLO_EQUISPACED:
if ((scanned[iArg].n_items!=2 && scanned[iArg].n_items!=4) ||
sscanf(scanned[iArg].list[1], "%lf", &sequenceSpacing)!=1 || sequenceSpacing<=0)
SDDS_Bomb("invalid -equispaced syntax/value");
if (scanned[iArg].n_items==4 &&
(sscanf(scanned[iArg].list[2], "%lf", &sequenceStart)!=1 ||
sscanf(scanned[iArg].list[3], "%lf", &sequenceEnd)!=1))
SDDS_Bomb("invalid -equispaced syntax/values");
if (sequencePoints)
SDDS_Bomb("give only one of -sequence and -equispaced");
break;
case CLO_COLUMNS:
if (indepQuantity)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
indepQuantity = scanned[iArg].list[1];
if (scanned[iArg].n_items>=2) {
depenQuantity = tmalloc(sizeof(*depenQuantity)*(depenQuantities=scanned[iArg].n_items-2));
for (i=0; i<depenQuantities; i++)
depenQuantity[i] = scanned[iArg].list[i+2];
}
break;
case CLO_PRINTOUT:
if ((scanned[iArg].n_items-=1)>=1) {
if (!scanItemList(&printFlags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"bare", -1, NULL, 0, BARE_PRINTOUT,
"stdout", -1, NULL, 0, STDOUT_PRINTOUT,
NULL))
SDDS_Bomb("invalid -printout syntax");
}
if (!(printFlags&BARE_PRINTOUT))
printFlags |= NORMAL_PRINTOUT;
break;
case CLO_FILEVALUES:
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -fileValues syntax");
fileValuesFile = scanned[iArg].list[1];
scanned[iArg].n_items -= 2;
if (!scanItemList(&flags, scanned[iArg].list+2, &scanned[iArg].n_items, 0,
"column", SDDS_STRING, &fileValuesQuantity, 1, 0,
"parallelpages", -1, NULL, 0, FILEVALUES_PARALLEL_PAGES,
NULL))
SDDS_Bomb("invalid -fileValues syntax");
if (flags&FILEVALUES_PARALLEL_PAGES)
parallelPages = 1;
break;
case CLO_COMBINEDUPLICATES:
SDDS_Bomb("-combineDuplicates option not implemented yet--send email to [email protected]");
combineDuplicates = 1;
break;
case CLO_BRANCH:
SDDS_Bomb("-branch option not implemented yet--send email to [email protected]");
if (scanned[iArg].n_items!=2 || sscanf(scanned[iArg].list[1], "%ld", &branch)!=1 ||
branch<1)
SDDS_Bomb("invalid -branch syntax/value");
break;
case CLO_BELOWRANGE:
if ((scanned[iArg].n_items-=1)<1 ||
!scanItemList(&belowRange.flags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"value", SDDS_DOUBLE, &belowRange.value, 1, OUTRANGE_VALUE,
"skip", -1, NULL, 0, OUTRANGE_SKIP,
"saturate", -1, NULL, 0, OUTRANGE_SATURATE,
"extrapolate", -1, NULL, 0, OUTRANGE_EXTRAPOLATE,
"wrap", -1, NULL, 0, OUTRANGE_WRAP,
"abort", -1, NULL, 0, OUTRANGE_ABORT,
"warn", -1, NULL, 0, OUTRANGE_WARN,
NULL))
SDDS_Bomb("invalid -belowRange syntax/value");
if ((i=bitsSet(belowRange.flags&
(OUTRANGE_VALUE|OUTRANGE_SKIP|OUTRANGE_SATURATE|OUTRANGE_EXTRAPOLATE|OUTRANGE_WRAP|OUTRANGE_ABORT)))>1)
SDDS_Bomb("incompatible keywords given for -belowRange");
if (i!=1)
belowRange.flags |= OUTRANGE_SATURATE;
break;
case CLO_ABOVERANGE:
if ((scanned[iArg].n_items-=1)<1 ||
!scanItemList(&aboveRange.flags, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"value", SDDS_DOUBLE, &aboveRange.value, 1, OUTRANGE_VALUE,
"skip", -1, NULL, 0, OUTRANGE_SKIP,
"saturate", -1, NULL, 0, OUTRANGE_SATURATE,
"extrapolate", -1, NULL, 0, OUTRANGE_EXTRAPOLATE,
"wrap", -1, NULL, 0, OUTRANGE_WRAP,
"abort", -1, NULL, 0, OUTRANGE_ABORT,
"warn", -1, NULL, 0, OUTRANGE_WARN,
NULL))
SDDS_Bomb("invalid -aboveRange syntax/value");
if ((i=bitsSet(aboveRange.flags&
(OUTRANGE_VALUE|OUTRANGE_SKIP|OUTRANGE_SATURATE|OUTRANGE_EXTRAPOLATE|OUTRANGE_WRAP|OUTRANGE_ABORT)))>1)
SDDS_Bomb("incompatible keywords given for -aboveRange");
if (i!=1)
aboveRange.flags |= OUTRANGE_SATURATE;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_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;
case CLO_FORCEMONOTONIC:
if ((scanned[iArg].n_items-=1)>0) {
if (!scanItemList(&forceMonotonic, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"increasing", -1, NULL, 0, FORCE_INCREASING,
"decreasing", -1, NULL, 0, FORCE_DECREASING,
NULL) || bitsSet(forceMonotonic)!=1)
SDDS_Bomb("invalid -forceMonotonic syntax/value");
}
else
forceMonotonic = FORCE_MONOTONIC;
break;
case CLO_FILLIN:
fillIn = 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");
}
}
processFilenames("sddsinterp", &input, &output, pipeFlags, 0, NULL);
fpPrint = stderr;
if (printFlags&STDOUT_PRINTOUT)
fpPrint = stdout;
if (!indepQuantity)
SDDS_Bomb("supply the independent quantity name with the -columns option");
if ((atValues?1:0)+(fileValuesFile?1:0)+(sequencePoints?1:0)+fillIn+(sequenceSpacing>0?1:0) != 1)
SDDS_Bomb("you must give one and only one of -atValues, -fileValues, -sequence, -equispaced, and -fillIn");
if (!SDDS_InitializeInput(&SDDSin, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
excludes = appendToStringArray(&exclude, excludes, indepQuantity);
if (!depenQuantities)
depenQuantities = appendToStringArray(&depenQuantity, depenQuantities, "*");
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 dependent quantities selected for interpolation");
}
if (fileValuesFile && !SDDS_InitializeInput(&SDDSvalues, fileValuesFile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_InitializeOutput(&SDDSout, SDDS_BINARY, 0, NULL, "sddsinterp output", output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, indepQuantity, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/*
if (fileValuesQuantity && strcmp(fileValuesQuantity, indepQuantity)!=0 &&
!SDDS_TransferColumnDefinition(&SDDSout, &SDDSvalues, fileValuesQuantity, NULL)) {
fprintf(stderr, "problem creating -fileValues column %s\n", fileValuesQuantity);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
*/
if (SDDS_DefineParameter(&SDDSout, "InterpDataPage", NULL, NULL,
"Page of interpolation data file used to create this page",
NULL, SDDS_LONG, NULL)<0 ||
SDDS_DefineParameter(&SDDSout, "InterpPointsPage", NULL, NULL,
"Page of interpolation points file used to create this page",
NULL, SDDS_LONG, NULL)<0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<depenQuantities; i++)
if (!SDDS_TransferColumnDefinition(&SDDSout, &SDDSin, depenQuantity[i], NULL)) {
fprintf(stderr, "problem creating interpolated-output column %s\n", depenQuantity[i]);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_TransferAllParameterDefinitions(&SDDSout, &SDDSin, SDDS_TRANSFER_KEEPOLD) ||
!SDDS_WriteLayout(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
doNotRead = 0;
interpPoint = NULL;
outputData = tmalloc(sizeof(*outputData)*(depenQuantities));
depenValue = tmalloc(sizeof(*depenValue)*(depenQuantities));
rowFlag = NULL;
valuesReadCode = 0;
while (doNotRead || (readCode=SDDS_ReadPage(&SDDSin))>0) {
rows = SDDS_CountRowsOfInterest(&SDDSin);
if (!(indepValue = SDDS_GetColumnInDoubles(&SDDSin, indepQuantity)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (atValues) {
interpPoint = atValue;
interpPoints = atValues;
}
else if (fileValuesFile) {
if (interpPoint)
free(interpPoint);
if ((valuesReadCode=SDDS_ReadPage(&SDDSvalues))==0)
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
else if (valuesReadCode==-1) {
if (parallelPages) {
fprintf(stderr, "warning: file %s ends before file %s\n", fileValuesFile, input);
break;
}
else {
/* "rewind" the values file */
if (!SDDS_Terminate(&SDDSvalues) ||
!SDDS_InitializeInput(&SDDSvalues, fileValuesFile))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if ((valuesReadCode=SDDS_ReadPage(&SDDSvalues))<1) {
fprintf(stderr, "error: unable to (re)read file %s\n", fileValuesFile);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/* read the next page of the interpolation data file */
if ((readCode=SDDS_ReadPage(&SDDSin))<1) {
if (readCode==-1)
break;
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
rows = SDDS_CountRowsOfInterest(&SDDSin);
if (indepValue)
free(indepValue);
if (!(indepValue = SDDS_GetColumnInDoubles(&SDDSin, indepQuantity)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!parallelPages)
doNotRead = 1;
interpPoints = SDDS_CountRowsOfInterest(&SDDSvalues);
interpPoint = SDDS_GetColumnInDoubles(&SDDSvalues, fileValuesQuantity);
if (SDDS_NumberOfErrors())
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else if (sequencePoints || sequenceSpacing) {
if (interpPoint)
free(interpPoint);
interpPoints = sequencePoints;
if (!(interpPoint = makeSequence(&interpPoints, sequenceStart, sequenceEnd, sequenceSpacing,
indepValue, rows)))
exit(1);
} else {
/* fillIn interpolation */
if (interpPoint)
free(interpPoint);
if (!(interpPoint = makeFillInSequence(indepValue, rows, &interpPoints)))
exit(1);
}
for (i=0; i<depenQuantities; i++)
outputData[i] = tmalloc(sizeof(*outputData[i])*interpPoints);
rowFlag = trealloc(rowFlag, sizeof(*rowFlag)*interpPoints);
for (j=0; j<interpPoints; j++)
rowFlag[j] = 1;
for (i=0; i<depenQuantities; i++) {
if (!(depenValue[i] = SDDS_GetColumnInDoubles(&SDDSin, depenQuantity[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (forceMonotonic)
rows = forceMonotonicity(indepValue, depenValue, depenQuantities, rows, forceMonotonic);
else if (combineDuplicates)
rows = combineDuplicatePoints(indepValue, depenValue, depenQuantities, rows, 0.0);
if ((monotonicity=checkMonotonicity(indepValue, rows))==0)
SDDS_Bomb("independent data values do not change monotonically or repeated independent values exist");
if (interpShort)
shortValue = malloc(sizeof(*shortValue)*rows);
for (i=0; i<depenQuantities; i++) {
if (interpShort) {
for (row=0; row<rows; row++) {
shortValue[row] = (short)depenValue[i][row];
}
}
for (j=0; j<interpPoints; j++) {
if (!interpShort) {
outputData[i][j] = interpolate(depenValue[i], indepValue, rows, interpPoint[j], &belowRange,
&aboveRange, order, &interpCode, monotonicity);
} else {
outputData[i][j] = (double)interp_short(shortValue, indepValue, rows, interpPoint[j], 0, -1,
&interpCode, &nextPos);
}
if (interpCode) {
if (interpCode&OUTRANGE_ABORT) {
fprintf(stderr, "error: value %e is out of range for column %s\n",
interpPoint[j], depenQuantity[i]);
exit(1);
}
if (interpCode&OUTRANGE_WARN)
fprintf(stderr, "warning: value %e is out of range for column %s\n",
interpPoint[j], depenQuantity[i]);
if (interpCode&OUTRANGE_SKIP)
rowFlag[j] = 0;
}
}
}
if (interpShort)
free(shortValue);
if (!SDDS_StartPage(&SDDSout, interpPoints) ||
!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_SET_BY_NAME, interpPoint, interpPoints, indepQuantity))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_SetParameters(&SDDSout, SDDS_BY_NAME|SDDS_PASS_BY_VALUE,
"InterpDataPage", readCode,
"InterpPointsPage", valuesReadCode, NULL) ||
!SDDS_CopyParameters(&SDDSout, &SDDSin))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<depenQuantities; i++)
if (!SDDS_SetColumnFromDoubles(&SDDSout, SDDS_SET_BY_NAME, outputData[i], interpPoints, depenQuantity[i]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_AssertRowFlags(&SDDSout, SDDS_FLAG_ARRAY, rowFlag, rows) || !SDDS_WritePage(&SDDSout))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (printFlags&BARE_PRINTOUT) {
for (j=0; j<interpPoints; j++)
if (rowFlag[j]) {
fprintf(fpPrint, "%21.15e ", interpPoint[j]);
for (i=0; i<depenQuantities; i++)
fprintf(fpPrint, "%21.15e ", outputData[i][j]);
fputc('\n', fpPrint);
}
}
else if (printFlags&NORMAL_PRINTOUT) {
for (j=0; j<interpPoints; j++)
if (rowFlag[j]) {
fprintf(fpPrint, "%s=%21.15e ", indepQuantity, interpPoint[j]);
for (i=0; i<depenQuantities; i++)
fprintf(fpPrint, "%s=%21.15e ", depenQuantity[i], outputData[i][j]);
fputc('\n', fpPrint);
}
}
if (indepValue) free(indepValue);
indepValue = NULL;
for (i=0; i<depenQuantities; i++) {
if (outputData[i]) free(outputData[i]);
outputData[i] = NULL;
if (depenValue[i]) free(depenValue[i]);
depenValue[i] = NULL;
}
if (fileValuesFile) {
if (interpPoint) free(interpPoint);
interpPoint = NULL;
}
if (rowFlag) free(rowFlag);
rowFlag = NULL;
}
if (!SDDS_Terminate(&SDDSin)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (!SDDS_Terminate(&SDDSout)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (fileValuesFile) {
if (!SDDS_Terminate(&SDDSvalues)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
}
return 0;
}
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;
}
int main(int argc, char **argv)
{
FILE *outfile;
SDDS_TABLE SDDS_table;
SDDS_LAYOUT *layout;
COLUMN_DEFINITION *coldef;
PARAMETER_DEFINITION *pardef;
ARRAY_DEFINITION *arraydef;
long list_request;
char *input, *output;
long i, j, i_arg, append_units, nrows, ntable;
SCANNED_ARG *s_arg;
char *text, *contents, *delimiter;
long verbose=0, all=0, nvariableparms=0, excel=0, line=0;
void *data;
unsigned long pipeFlags;
#ifdef USE_XLS
workbook *w;
worksheet *ws;
#endif
int ret;
char sheet[256];
char buffer[5];
SDDS_RegisterProgramName(argv[0]);
list_request = -1;
input = output = NULL;
append_units = 0;
delimiter = DELIMITER;
pipeFlags = 0;
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch (match_string(s_arg[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_DELIMITER:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("Invalid -delimiter syntax");
delimiter = s_arg[i_arg].list[1];
break;
case SET_ALL:
all = 1;
break;
case SET_EXCEL:
#ifdef USE_XLS
excel = 1;
#else
SDDS_Bomb("-excel option is not available becuase sdds2spreadsheet was not compiled with xlslib support");
#endif
break;
case SET_VERBOSE:
verbose = 1;
break;
case SET_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1,
s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
default:
SDDS_Bomb(strcat("Unknown option: ", s_arg[i_arg].list[0]));
break;
}
}
else {
if (input==NULL)
input = s_arg[i_arg].list[0];
else if (output==NULL)
output = s_arg[i_arg].list[0];
else
SDDS_Bomb("too many filenames");
}
}
processFilenames("sdds2spreadsheet", &input, &output, pipeFlags, 0, NULL);
if (output) {
if (!excel) {
outfile=fopen(output,"w");
if(!outfile)
SDDS_Bomb(strcat("Can't open output file ", output));
}
}
else {
if (excel) {
SDDS_Bomb("-pipe=out and -excel options cannot be used together");
}
outfile = stdout;
}
if (input && !excel)
fprintf(outfile,"Created from SDDS file: %s\n", input);
if (!SDDS_InitializeInput(&SDDS_table, input)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
layout = &SDDS_table.layout;
/* Description */
if(verbose && input)
fprintf(stderr, "\nfile %s is in SDDS protocol version %" PRId32 "\n",
input, layout->version);
if (!SDDS_GetDescription(&SDDS_table, &text, &contents))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (text)
if (verbose)
fprintf(stderr, "description: %s\n", text);
if (!excel)
fprintf(outfile,"%s%s\n",text?text:"No description",delimiter);
if (contents)
if (verbose)
fprintf(stderr, "contents: %s\n", contents);
if (!excel)
fprintf(outfile,"%s%s\n",contents?contents:"No description",delimiter);
if (layout->data_mode.mode==SDDS_ASCII) {
if (verbose) {
fprintf(stderr, "\ndata is ASCII with %" PRId32 " lines per row and %" PRId32 " additional header lines expected.\n",
layout->data_mode.lines_per_row, layout->data_mode.additional_header_lines);
fprintf(stderr, "row counts: %s \n",
layout->data_mode.no_row_counts?"no":"yes");
}
}
else if (verbose)
fprintf(stderr, "\ndata is binary\n");
/* Columns */
if (layout->n_columns) {
if(verbose) {
fprintf(stderr, "\n%" PRId32 " columns of data:\n", layout->n_columns);
fprintf(stderr, "NAME UNITS SYMBOL FORMAT TYPE FIELD DESCRIPTION\n");
fprintf(stderr, " LENGTH\n");
}
if (all && !excel)
fprintf(outfile,
"\nColumns%s\nName%sUnits%sSymbol%sFormat%sType%sField Length%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter,
delimiter);
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
if(verbose)
fprintf(stderr, "%-15s %-15s %-15s %-15s %-7s %-7" PRId32 " %s\n",
coldef->name, coldef->units?coldef->units:"",
coldef->symbol?coldef->symbol:"",
coldef->format_string?coldef->format_string:"",
SDDS_type_name[coldef->type-1],
coldef->field_length,
coldef->description?coldef->description:"");
if(all && !excel)
fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s%-7" PRId32 "%s%s%s\n",
coldef->name, delimiter,
coldef->units?coldef->units:"", delimiter,
coldef->symbol?coldef->symbol:"", delimiter,
coldef->format_string?coldef->format_string:"", delimiter,
SDDS_type_name[coldef->type-1], delimiter,
coldef->field_length, delimiter,
coldef->description?coldef->description:"", delimiter);
}
}
/* Parameters */
if (layout->n_parameters) {
if (verbose) {
fprintf(stderr, "\n%" PRId32 " parameters:\n", layout->n_parameters);
fprintf(stderr,
"NAME UNITS SYMBOL TYPE DESCRIPTION\n");
}
if(all && !excel)
fprintf(outfile,"\nParameters%s\nName%sFixedValue%sUnits%sSymbol%sType%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
for (i=0; i<layout->n_parameters; i++) {
pardef = layout->parameter_definition+i;
if(!pardef->fixed_value) {
nvariableparms++;
if(!all) continue;
}
if(verbose) fprintf(stderr, "%-19s %-19s %-19s %-19s %s\n",
pardef->name, pardef->units?pardef->units:"", pardef->symbol?pardef->symbol:"",
SDDS_type_name[pardef->type-1], pardef->description?pardef->description:"");
if (!excel) {
if(all) fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s%s%s\n",
pardef->name, delimiter,
pardef->fixed_value?pardef->fixed_value:"", delimiter,
pardef->units?pardef->units:"", delimiter,
pardef->symbol?pardef->symbol:"", delimiter,
SDDS_type_name[pardef->type-1], delimiter,
pardef->description?pardef->description:"", delimiter);
else fprintf(outfile,"%s%s%s%s%s\n",
pardef->name, delimiter, delimiter,
pardef->fixed_value?pardef->fixed_value:"", delimiter);
}
}
}
/* Arrays */
if (layout->n_arrays && all) {
if(verbose) {
fprintf(stderr, "\n%" PRId32 " arrays of data:\n", layout->n_arrays);
fprintf(stderr, "NAME UNITS SYMBOL"
" FORMAT TYPE FIELD GROUP DESCRIPTION\n");
fprintf(stderr, " LENGTH NAME\n");
}
if (!excel) {
fprintf(outfile,"\nArrays%s\nName%sUnits%sSymbol%sFormat%sType%sField Length%sGroup Name%sDescription%s\n", delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
}
for (i=0; i<layout->n_arrays; i++) {
arraydef = layout->array_definition+i;
if(verbose) fprintf(stderr, "%-15s %-15s %-15s %-7s %-8s*^%-5" PRId32 " %-7" PRId32 " %-15s %s\n",
arraydef->name, arraydef->units, arraydef->symbol,
arraydef->format_string, SDDS_type_name[arraydef->type-1], arraydef->dimensions,
arraydef->field_length, arraydef->group_name, arraydef->description);
if (!excel) {
fprintf(outfile,"%s%s%s%s%s%s%s%s%s*^%-5" PRId32 "%s%-7" PRId32 "%s%s%s%s%s\n",
arraydef->name, delimiter,
arraydef->units, delimiter,
arraydef->symbol, delimiter,
arraydef->format_string, delimiter,
SDDS_type_name[arraydef->type-1], arraydef->dimensions, delimiter,
arraydef->field_length, delimiter,
arraydef->group_name, delimiter,
arraydef->description, delimiter);
}
}
}
/* Associates */
/*
if (layout->n_associates && all) {
if(verbose) {
fprintf(stderr, "\n%ld associates:\n", layout->n_associates);
fprintf(stderr, "SDDS FILENAME PATH CONTENTS DESCRIPTION\n");
}
fprintf(outfile,"\nAssociates%s\nType%sFilename%sPath%sContents%sDescription%s\n",
delimiter, delimiter, delimiter, delimiter, delimiter, delimiter);
for (i=0; i<layout->n_associates; i++)
if(verbose) fprintf(stderr, "%-5s %-19s %-29s %-19s %s\n",
layout->associate_definition[i].sdds?"SDDS":"Non-SDDS",
layout->associate_definition[i].filename, layout->associate_definition[i].path,
layout->associate_definition[i].contents, layout->associate_definition[i].description);
fprintf(outfile,"%s%s%s%s%s%s%s%s%s%s\n",
layout->associate_definition[i].sdds?"yes":"no", delimiter,
layout->associate_definition[i].filename, delimiter,
layout->associate_definition[i].path, delimiter,
layout->associate_definition[i].contents, delimiter,
layout->associate_definition[i].description, delimiter);
}
*/
#ifdef USE_XLS
w = xlsNewWorkbook();
#ifdef __APPLE__
xlsWorkbookIconvInType(w, "UCS-4-INTERNAL");
#endif
#endif
/* Process tables */
while ((ntable=SDDS_ReadTable(&SDDS_table))>0) {
line=0;
#ifdef USE_XLS
if (excel) {
sprintf(sheet, "Sheet%d", ntable);
ws = xlsWorkbookSheet(w, sheet);
} else
fprintf(outfile,"\nTable %ld\n",ntable);
#else
fprintf(outfile,"\nTable %ld\n",ntable);
#endif
/* Variable parameters */
if (nvariableparms) {
for (i=0; i<layout->n_parameters; i++) {
pardef = layout->parameter_definition+i;
if(pardef->fixed_value) continue;
if (!(data=SDDS_GetParameter(&SDDS_table, pardef->name, NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef USE_XLS
if (excel) {
xlsWorksheetLabel(ws, line, 0, pardef->name, NULL);
switch(pardef->type) {
case SDDS_DOUBLE:
xlsWorksheetNumberDbl(ws, line, 1, *((double*)data), NULL);
break;
case SDDS_FLOAT:
xlsWorksheetNumberDbl(ws, line, 1, *((float*)data), NULL);
break;
case SDDS_ULONG:
xlsWorksheetNumberInt(ws, line, 1, *((uint32_t*)data), NULL);
break;
case SDDS_LONG:
xlsWorksheetNumberInt(ws, line, 1, *((int32_t*)data), NULL);
break;
case SDDS_USHORT:
xlsWorksheetNumberInt(ws, line, 1, *((unsigned short*)data), NULL);
break;
case SDDS_SHORT:
xlsWorksheetNumberInt(ws, line, 1, *((short*)data), NULL);
break;
case SDDS_STRING:
xlsWorksheetLabel(ws, line, 1, *((char**)data), NULL);
break;
case SDDS_CHARACTER:
sprintf(buffer, "%c", *((char*)data));
xlsWorksheetLabel(ws, line, 1, buffer, NULL);
break;
default:
break;
}
line++;
} else {
#endif
fprintf(outfile,"%s%s%s",pardef->name,delimiter,delimiter);
SDDS_PrintTypedValue(data, 0, pardef->type, NULL, outfile, 0);
fprintf(outfile,"%s\n",delimiter);
#ifdef USE_XLS
}
#endif
}
line++;
}
/* Columns */
if (layout->n_columns) {
SDDS_SetColumnFlags(&SDDS_table, 1);
SDDS_SetRowFlags(&SDDS_table, 1);
if ((nrows=SDDS_CountRowsOfInterest(&SDDS_table))<0) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
#ifdef USE_XLS
if (excel) {
xlsWorksheetLabel(ws, line, i, coldef->name, NULL);
}
else
fprintf(outfile,"%s%s",coldef->name,delimiter);
#else
fprintf(outfile,"%s%s",coldef->name,delimiter);
#endif
}
line++;
if (!excel)
fprintf(outfile,"\n");
if (nrows) {
for (j=0; j<nrows; j++) {
for (i=0; i<layout->n_columns; i++) {
coldef = layout->column_definition+i;
if (!(data=SDDS_GetValue(&SDDS_table, coldef->name,j,NULL))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
#ifdef USE_XLS
if (excel) {
switch(coldef->type) {
case SDDS_DOUBLE:
xlsWorksheetNumberDbl(ws, line, i, *((double*)data), NULL);
break;
case SDDS_FLOAT:
xlsWorksheetNumberDbl(ws, line, i, *((float*)data), NULL);
break;
case SDDS_ULONG:
xlsWorksheetNumberInt(ws, line, i, *((uint32_t*)data), NULL);
break;
case SDDS_LONG:
xlsWorksheetNumberInt(ws, line, i, *((int32_t*)data), NULL);
break;
case SDDS_USHORT:
xlsWorksheetNumberInt(ws, line, i, *((unsigned short*)data), NULL);
break;
case SDDS_SHORT:
xlsWorksheetNumberInt(ws, line, i, *((short*)data), NULL);
break;
case SDDS_STRING:
xlsWorksheetLabel(ws, line, i, *((char**)data), NULL);
break;
case SDDS_CHARACTER:
sprintf(buffer, "%c", *((char*)data));
xlsWorksheetLabel(ws, line, i, buffer, NULL);
break;
default:
break;
}
} else {
#endif
switch(coldef->type) {
case SDDS_DOUBLE:
fprintf(outfile, "%.*g", DBL_DIG, *((double*)data));
break;
case SDDS_FLOAT:
fprintf(outfile, "%.*g", FLT_DIG, *((float*)data));
break;
default:
SDDS_PrintTypedValue(data, 0, coldef->type, NULL, outfile, 0);
break;
}
fprintf(outfile,delimiter);
#ifdef USE_XLS
}
#endif
}
if (!excel)
fprintf(outfile,"\n");
line++;
}
}
}
}
#ifdef USE_XLS
ret = xlsWorkbookDump(w, output);
xlsDeleteWorkbook(w);
#endif
/*
QUIT:
*/
fflush(stdout);
if (!SDDS_Terminate(&SDDS_table)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
return(0);
}
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;
}
int main(int argc, char **argv)
{
SDDS_DATASET inSet, outSet;
SCANNED_ARG *s_arg;
char *input, *output, *zeroName, **columnName;
long i_arg, i, pageReturned, rows, row, zrow;
int32_t columnNames;
double **indepData, *depenData, **slopeData, slope, offset;
unsigned long pipeFlags, flags, majorOrderFlag;
char s[SDDS_MAXLINE];
short columnMajorOrder=-1;
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;
zeroName = NULL;
columnName = NULL;
columnNames = 0;
offset = 0;
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_MAJOR_ORDER:
majorOrderFlag=0;
s_arg[i_arg].n_items--;
if (s_arg[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_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_ZEROESOF:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -zeroesOf syntax");
zeroName = s_arg[i_arg].list[1];
break;
case CLO_COLUMNS:
if (s_arg[i_arg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
columnName = tmalloc(sizeof(*columnName)*(columnNames = s_arg[i_arg].n_items-1));
for (i=0; i<columnNames; i++)
columnName[i] = s_arg[i_arg].list[i+1];
break;
case CLO_SLOPEOUTPUT:
flags |= FL_SLOPEOUTPUT;
break;
case CLO_OFFSET:
if (s_arg[i_arg].n_items!=2 || sscanf(s_arg[i_arg].list[1], "%le", &offset)!=1)
SDDS_Bomb("invalid -offset syntax");
break;
default:
fprintf(stderr, "Error (%s): unknown/ambiguous option: %s\n", argv[0], 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("sddszerofind", &input, &output, pipeFlags, 0, NULL);
if (!zeroName)
SDDS_Bomb("-zeroesOf option must be given");
if (!SDDS_InitializeInput(&inSet, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!resolveColumnNames(&inSet, zeroName, &columnName, &columnNames) ||
!SDDS_InitializeOutput(&outSet, SDDS_BINARY, 0, NULL, "sddszerofind output", output) ||
!SDDS_TransferColumnDefinition(&outSet, &inSet, zeroName, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (columnMajorOrder!=-1)
outSet.layout.data_mode.column_major = columnMajorOrder;
else
outSet.layout.data_mode.column_major = inSet.layout.data_mode.column_major;
for (i=0; i<columnNames; i++) {
sprintf(s, "%sSlope", columnName[i]);
if (!SDDS_TransferColumnDefinition(&outSet, &inSet, columnName[i], NULL) ||
(flags&FL_SLOPEOUTPUT &&
!SDDS_TransferColumnDefinition(&outSet, &inSet, columnName[i], s)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteLayout(&outSet))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
indepData = tmalloc(sizeof(*indepData)*columnNames);
slopeData = tmalloc(sizeof(*slopeData)*columnNames);
while ((pageReturned=SDDS_ReadPage(&inSet))>0) {
if (!SDDS_StartPage(&outSet, 0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if ((rows=SDDS_CountRowsOfInterest(&inSet))>1) {
if (!(depenData = SDDS_GetColumnInDoubles(&inSet, zeroName)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<columnNames; i++) {
if (!(indepData[i] = SDDS_GetColumnInDoubles(&inSet, columnName[i])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (flags&FL_SLOPEOUTPUT)
slopeData[i] = tmalloc(sizeof(**slopeData)*rows);
}
if (offset)
for (row=0; row<rows; row++)
depenData[row] += offset;
for (zrow=row=0; row<rows-1; row++) {
if ((depenData[row]<=0 && depenData[row+1]>=0) ||
(depenData[row]>=0 && depenData[row+1]<=0)) {
for (i=0; i<columnNames; i++) {
if (indepData[i][row]==indepData[i][row+1]) {
if (flags&FL_SLOPEOUTPUT)
slopeData[i][zrow] = DBL_MAX;
indepData[i][zrow] = indepData[i][row];
}
else {
slope = (depenData[row+1]-depenData[row])/(indepData[i][row+1]-indepData[i][row]);
if (flags&FL_SLOPEOUTPUT)
slopeData[i][zrow] = slope;
if (slope)
indepData[i][zrow] = indepData[i][row] - depenData[row]/slope;
else
indepData[i][zrow] = (indepData[i][row] + indepData[i][row+1])/2;
}
}
depenData[zrow] = -offset;
zrow++;
}
}
if (zrow) {
if (!SDDS_LengthenTable(&outSet, zrow) ||
!SDDS_SetColumnFromDoubles(&outSet, SDDS_SET_BY_NAME, depenData, zrow, zeroName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (i=0; i<columnNames; i++) {
sprintf(s, "%sSlope", columnName[i]);
if (!SDDS_SetColumnFromDoubles(&outSet, SDDS_SET_BY_NAME, indepData[i], zrow, columnName[i]) ||
(flags&FL_SLOPEOUTPUT &&
!SDDS_SetColumnFromDoubles(&outSet, SDDS_SET_BY_NAME, slopeData[i], zrow, s)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
free(depenData);
for (i=0; i<columnNames; i++)
free(indepData[i]);
if (flags&FL_SLOPEOUTPUT)
for (i=0; i<columnNames; i++)
free(slopeData[i]);
}
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);
}
return(0);
}
int main(int argc, char **argv)
{
STAT_DEFINITION *stat;
long stats;
STAT_REQUEST *request;
long requests, count;
SCANNED_ARG *scanned;
SDDS_DATASET inData, outData;
int32_t power;
long i_arg, code, iStat, rows, tmpFileUsed, iColumn, row, posColIndex;
long noWarnings, maxSourceColumns;
char *input, *output, *positionColumn, **posColumnName;
double **inputData, *outputData, value1, value2, topLimit, bottomLimit;
unsigned long pipeFlags, scanFlags, majorOrderFlag;
char s[100];
double *statWorkArray;
double quartilePoint[2] = {25.0, 75.0 }, quartileResult[2];
double decilePoint[2] = {10.0, 90.0 }, decileResult[2];
double percent;
short columnMajorOrder=-1;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&scanned, argc, argv);
if (argc<2) {
bomb("too few arguments", USAGE);
}
posColumnName = NULL;
input = output = positionColumn = NULL;
stat = NULL;
request = NULL;
stats = requests = pipeFlags = 0;
noWarnings = 0;
outputData = NULL;
statWorkArray = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
scanFlags = 0;
if (scanned[i_arg].arg_type==OPTION) {
/* process options here */
switch (code=match_string(scanned[i_arg].list[0], option, N_OPTIONS, 0)) {
case SET_MAXIMUM:
case SET_MINIMUM:
case SET_MEAN:
case SET_MEDIAN:
case SET_STANDARDDEVIATION:
case SET_RMS:
case SET_SIGMA:
case SET_MAD:
case SET_COUNT:
case SET_DRANGE:
case SET_QRANGE:
case SET_SMALLEST:
case SET_LARGEST:
case SET_SPREAD:
if (scanned[i_arg].n_items<3) {
fprintf(stderr, "error: invalid -%s syntax\n", option[code]);
exit(1);
}
if (!scanItemList(&scanFlags, scanned[i_arg].list, &scanned[i_arg].n_items,
SCANITEMLIST_UNKNOWN_VALUE_OK|SCANITEMLIST_REMOVE_USED_ITEMS|
SCANITEMLIST_IGNORE_VALUELESS,
"positionColumn", SDDS_STRING, &positionColumn, 1, POSITIONCOLUMN_GIVEN,
"toplimit", SDDS_DOUBLE, &topLimit, 1, TOPLIMIT_GIVEN,
"bottomlimit", SDDS_DOUBLE, &bottomLimit, 1, BOTTOMLIMIT_GIVEN,
NULL)) {
sprintf(s, "invalid -%s syntax", scanned[i_arg].list[0]);
SDDS_Bomb(s);
}
requests = addStatRequests(&request, requests, scanned[i_arg].list+1, scanned[i_arg].n_items-1,
code, scanFlags);
request[requests-1].topLimit = topLimit;
request[requests-1].bottomLimit = bottomLimit;
if (positionColumn) {
if (code==SET_MAXIMUM || code==SET_MINIMUM || code==SET_LARGEST || code==SET_SMALLEST)
SDDS_CopyString(&request[requests-1].positionColumn, positionColumn);
free(positionColumn);
positionColumn = NULL;
}
break;
case SET_PERCENTILE:
if (scanned[i_arg].n_items<3) {
fprintf(stderr, "error: invalid -%s syntax\n", option[code]);
exit(1);
}
if (!scanItemList(&scanFlags, scanned[i_arg].list, &scanned[i_arg].n_items,
SCANITEMLIST_UNKNOWN_VALUE_OK|SCANITEMLIST_REMOVE_USED_ITEMS|
SCANITEMLIST_IGNORE_VALUELESS,
"value", SDDS_DOUBLE, &percent, 1, PERCENT_GIVEN,
"toplimit", SDDS_DOUBLE, &topLimit, 1, TOPLIMIT_GIVEN,
"bottomlimit", SDDS_DOUBLE, &bottomLimit, 1, BOTTOMLIMIT_GIVEN,
NULL) ||
!(scanFlags&PERCENT_GIVEN) || percent<=0 || percent>=100)
SDDS_Bomb("invalid -percentile syntax");
requests = addStatRequests(&request, requests, scanned[i_arg].list+1, scanned[i_arg].n_items-1,
code, scanFlags);
request[requests-1].percent = percent;
request[requests-1].topLimit = topLimit;
request[requests-1].bottomLimit = bottomLimit;
break;
case SET_SUM:
if (scanned[i_arg].n_items<3) {
fprintf(stderr, "error: invalid -%s syntax\n", option[code]);
exit(1);
}
power = 1;
if (!scanItemList(&scanFlags, scanned[i_arg].list, &scanned[i_arg].n_items,
SCANITEMLIST_UNKNOWN_VALUE_OK|SCANITEMLIST_REMOVE_USED_ITEMS|
SCANITEMLIST_IGNORE_VALUELESS,
"power", SDDS_LONG, &power, 1, 0,
"toplimit", SDDS_DOUBLE, &topLimit, 1, TOPLIMIT_GIVEN,
"bottomlimit", SDDS_DOUBLE, &bottomLimit, 1, BOTTOMLIMIT_GIVEN,
NULL))
SDDS_Bomb("invalid -sum syntax");
requests = addStatRequests(&request, requests, scanned[i_arg].list+1, scanned[i_arg].n_items-1,
code, scanFlags);
request[requests-1].sumPower = power;
request[requests-1].topLimit = topLimit;
request[requests-1].bottomLimit = bottomLimit;
break;
case SET_PIPE:
if (!processPipeOption(scanned[i_arg].list+1, scanned[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case SET_NOWARNINGS:
noWarnings = 1;
break;
case SET_MAJOR_ORDER:
majorOrderFlag=0;
scanned[i_arg].n_items --;
if (scanned[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[i_arg].list+1, &scanned[i_arg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
default:
fprintf(stderr, "error: unknown option '%s' given\n", scanned[i_arg].list[0]);
exit(1);
break;
}
}
else {
/* argument is filename */
if (!input)
input = scanned[i_arg].list[0];
else if (!output)
output = scanned[i_arg].list[0];
else
SDDS_Bomb("too many filenames seen");
}
}
processFilenames("sddsrowstats", &input, &output, pipeFlags, noWarnings, &tmpFileUsed);
if (!requests)
SDDS_Bomb("no statistics requested");
if (!SDDS_InitializeInput(&inData, input))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!(stat=compileStatDefinitions(&inData, request, requests, &stats, noWarnings))) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (stats<0)
SDDS_Bomb("No valid statistics requests.");
for (iStat=maxSourceColumns=0; iStat<stats; iStat++) {
if (stat[iStat].sourceColumns>maxSourceColumns)
maxSourceColumns = stat[iStat].sourceColumns;
}
if (!(statWorkArray=malloc(sizeof(*statWorkArray)*maxSourceColumns)))
SDDS_Bomb("allocation failure (statWorkArray)");
if (!setupOutputFile(&outData, output, &inData, stat, stats)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
inputData = NULL;
while ((code=SDDS_ReadPage(&inData))>0) {
if (!SDDS_CopyPage(&outData, &inData)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if ((rows = SDDS_CountRowsOfInterest(&inData))) {
if (!(outputData = (double*)malloc(sizeof(*outputData)*rows)))
SDDS_Bomb("memory allocation failure");
if (!(posColumnName = (char**)malloc(sizeof(*posColumnName)*rows)))
SDDS_Bomb("memory allocation failure");
for (iStat=0; iStat<stats; iStat++) {
if (!(inputData = (double**)malloc(sizeof(*inputData)*stat[iStat].sourceColumns)))
SDDS_Bomb("memory allocation failure");
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (!(inputData[iColumn] = SDDS_GetColumnInDoubles(&inData, stat[iStat].sourceColumn[iColumn])))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (row=0; row<rows; row++)
outputData[row] = DBL_MAX;
switch (stat[iStat].optionCode) {
case SET_MINIMUM:
for (row=0; row<rows; row++) {
value1 = DBL_MAX;
posColIndex = 0;
posColumnName[row] = NULL;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
if (inputData[iColumn][row]<value1) {
value1 = inputData[iColumn][row];
posColIndex = iColumn;
}
}
outputData[row] = value1;
if (stat[iStat].positionColumn)
posColumnName[row] = stat[iStat].sourceColumn[posColIndex];
}
break;
case SET_MAXIMUM:
for (row=0; row<rows; row++) {
posColIndex = 0;
value1 = -DBL_MAX;
posColumnName[row] = NULL;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
if (inputData[iColumn][row]>value1) {
posColIndex = iColumn;
value1 = inputData[iColumn][row];
}
}
outputData[row] = value1;
if (stat[iStat].positionColumn)
posColumnName[row] = stat[iStat].sourceColumn[posColIndex];
}
break;
case SET_MEAN:
for (row=0; row<rows; row++) {
value1 = 0;
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
value1 += inputData[iColumn][row];
count ++;
}
if (count)
outputData[row] = value1/count;
}
break;
case SET_MEDIAN:
for (row=0; row<rows; row++) {
for (iColumn=count=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
statWorkArray[count] = inputData[iColumn][row];
count++;
}
if (count)
compute_median(outputData+row, statWorkArray, count);
}
break;
case SET_STANDARDDEVIATION:
for (row=0; row<rows; row++) {
value1 = 0;
value2 = 0;
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
value1 += inputData[iColumn][row];
value2 += inputData[iColumn][row]*inputData[iColumn][row];
count ++;
}
if (count>1) {
if ((value1 = value2/count - sqr(value1/count))<=0)
outputData[row] = 0;
else
outputData[row] = sqrt(value1*count/(count-1.0));
}
}
break;
case SET_SIGMA:
for (row=0; row<rows; row++) {
value1 = 0;
value2 = 0;
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
value1 += inputData[iColumn][row];
value2 += inputData[iColumn][row]*inputData[iColumn][row];
count ++;
}
if (count>1) {
if ((value1 = value2/count - sqr(value1/count))<=0)
outputData[row] = 0;
else
outputData[row] = sqrt(value1/(count-1.0));
}
}
break;
case SET_RMS:
for (row=0; row<rows; row++) {
value1 = 0;
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
value1 += sqr(inputData[iColumn][row]);
count ++;
}
if (count)
outputData[row] = sqrt(value1/count);
}
break;
case SET_SUM:
for (row=0; row<rows; row++) {
value1 = 0;
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
value1 += ipow(inputData[iColumn][row], stat[iStat].sumPower);
count ++;
}
if (count)
outputData[row] = value1;
}
break;
case SET_COUNT:
for (row=0; row<rows; row++) {
count = 0;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
count++;
}
outputData[row] = count;
}
break;
case SET_MAD:
for (row=0; row<rows; row++) {
for (iColumn=count=value1=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
statWorkArray[count] = inputData[iColumn][row];
count++;
}
if (count)
computeMoments(NULL, NULL, NULL, &outputData[row],
statWorkArray, count);
}
break;
case SET_DRANGE:
for (row=0; row<rows; row++) {
for (iColumn=count=value1=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
statWorkArray[count] = inputData[iColumn][row];
count++;
}
if (count &&
compute_percentiles(decileResult, decilePoint, 2,
statWorkArray, count))
outputData[row] = decileResult[1] - decileResult[0];
}
break;
case SET_QRANGE:
for (row=0; row<rows; row++) {
for (iColumn=count=value1=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
statWorkArray[count] = inputData[iColumn][row];
count++;
}
if (count &&
compute_percentiles(quartileResult, quartilePoint, 2,
statWorkArray, count))
outputData[row] = quartileResult[1] - quartileResult[0];
}
break;
case SET_SMALLEST:
for (row=0; row<rows; row++) {
value1 = DBL_MAX;
posColIndex = 0;
posColumnName[row] = NULL;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
if ((value2=fabs(inputData[iColumn][row]))<value1) {
posColIndex = iColumn;
value1 = value2;
}
}
outputData[row] = value1;
if (stat[iStat].positionColumn)
posColumnName[row] = stat[iStat].sourceColumn[posColIndex];
}
break;
case SET_LARGEST:
for (row=0; row<rows; row++) {
value1 = 0;
posColIndex = 0;
posColumnName[row] = NULL;
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
if ((value2=fabs(inputData[iColumn][row]))>value1) {
posColIndex = iColumn;
value1 = value2;
}
}
outputData[row] = value1;
if (stat[iStat].positionColumn)
posColumnName[row] = stat[iStat].sourceColumn[posColIndex];
}
break;
case SET_SPREAD:
for (row=0; row<rows; row++) {
value1 = DBL_MAX; /* min */
value2 = -DBL_MAX; /* max */
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
if (inputData[iColumn][row]<value1)
value1 = inputData[iColumn][row];
if (inputData[iColumn][row]>value2)
value2 = inputData[iColumn][row];
}
outputData[row] = value2-value1;
}
break;
case SET_PERCENTILE:
for (row=0; row<rows; row++) {
for (iColumn=count=value1=0; iColumn<stat[iStat].sourceColumns; iColumn++) {
if (stat[iStat].flags&TOPLIMIT_GIVEN &&
inputData[iColumn][row]>stat[iStat].topLimit)
continue;
if (stat[iStat].flags&BOTTOMLIMIT_GIVEN &&
inputData[iColumn][row]<stat[iStat].bottomLimit)
continue;
statWorkArray[count] = inputData[iColumn][row];
count++;
}
outputData[row] = HUGE_VAL;
if (count)
compute_percentiles(&outputData[row], &stat[iStat].percent, 1, statWorkArray, count);
}
break;
default:
SDDS_Bomb("invalid statistic code (accumulation loop)");
break;
}
if (!SDDS_SetColumn(&outData, SDDS_SET_BY_INDEX, outputData, rows, stat[iStat].resultIndex))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (stat[iStat].positionColumn) {
if (!SDDS_SetColumn(&outData, SDDS_SET_BY_INDEX, posColumnName, rows,
stat[iStat].positionColumnIndex))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++)
free(inputData[iColumn]);
free(inputData);
inputData = NULL;
}
free(outputData);
outputData = NULL;
free(posColumnName);
posColumnName = NULL;
}
if (!SDDS_WritePage(&outData))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free_scanargs(&scanned, argc);
for (iStat=0; iStat<stats; iStat++) {
if (stat[iStat].positionColumn) free(stat[iStat].positionColumn);
for (iColumn=0; iColumn<stat[iStat].sourceColumns; iColumn++)
free(stat[iStat].sourceColumn[iColumn]);
free(stat[iStat].sourceColumn);
}
free(request);
free(stat);
if (statWorkArray) free(statWorkArray);
if (!SDDS_Terminate(&inData) || !SDDS_Terminate(&outData)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
if (tmpFileUsed && !replaceFileAndBackUp(input, output))
exit(1);
return 0;
}