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;
}
int main(int argc, char **argv)
{
FILE *fileID;
COLUMN_DATA_STRUCTURES *columnValues;
PARAMETER_DATA_STRUCTURES *parameterValues;
SDDS_DATASET SDDS_dataset;
SCANNED_ARG *s_arg;
long i, j, k, n, i_arg;
int32_t rows;
int32_t maxRows=10000, initRows=10000, row;
long par, col, page, size, readline=1, fillin=0;
int32_t ptrSize=0;
char *input, *output, s[1024], *ptr, *ptr2, data[10240],temp[10240];
unsigned long pipeFlags=0,majorOrderFlag;
long noWarnings=0, tmpfile_used=0, columnOrder=0, whitespace=1;
short shortValue;
int32_t longValue;
float floatValue;
double doubleValue;
char stringValue[SDDS_MAXLINE];
char characterValue;
char buffer[124], buffer2[124];
long *parameterIndex, *columnIndex;
long binary=0, noRowCount=0, inputBinary=0, count=0;
char separator;
char commentCharacters[20];
short checkComment=0;
short commentFound;
long parameters=0, columns=0;
long skiplines=0;
short abort=0, recover=1, columnMajorOrder=0;
input = output = NULL;
separator = ' ';
columnValues = NULL;
parameterValues = NULL;
parameterIndex = columnIndex = NULL;
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_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_OUTPUTMODE:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -outputMode syntax");
switch (match_string(s_arg[i_arg].list[1], mode_name, MODES, 0)) {
case ASCII_MODE:
binary = 0;
break;
case BINARY_MODE:
binary = 1;
break;
default:
SDDS_Bomb("invalid -outputMode syntax");
break;
}
break;
case SET_INPUTMODE:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -inputMode syntax");
switch (match_string(s_arg[i_arg].list[1], mode_name, MODES, 0)) {
case ASCII_MODE:
inputBinary = 0;
break;
case BINARY_MODE:
inputBinary = 1;
break;
default:
SDDS_Bomb("invalid -inputMode syntax");
break;
}
break;
case SET_SEPARATOR:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -separator syntax");
separator = s_arg[i_arg].list[1][0];
whitespace = 0;
break;
case SET_COMMENT:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -commentCharacters syntax");
sprintf(commentCharacters, "%s", s_arg[i_arg].list[1]);
checkComment=1;
break;
case SET_FILLIN:
fillin=1;
break;
case SET_NOROWCOUNT:
if (s_arg[i_arg].n_items!=1)
SDDS_Bomb("invalid -noRowCount syntax");
noRowCount = 1;
break;
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_PARAMETER:
if (s_arg[i_arg].n_items<3)
SDDS_Bomb("invalid -parameter syntax");
count=1;
parameters++;
parameterValues = trealloc(parameterValues, sizeof(*parameterValues)*(parameters));
SDDS_CopyString(¶meterValues[parameters-1].name, s_arg[i_arg].list[1]);
parameterValues[parameters-1].units = NULL;
parameterValues[parameters-1].description = NULL;
parameterValues[parameters-1].symbol = NULL;
switch (match_string(s_arg[i_arg].list[2], type_name, DATATYPES, 0)) {
case TYPE_SHORT:
parameterValues[parameters-1].type = SDDS_SHORT;
break;
case TYPE_LONG:
parameterValues[parameters-1].type = SDDS_LONG;
break;
case TYPE_FLOAT:
parameterValues[parameters-1].type = SDDS_FLOAT;
break;
case TYPE_DOUBLE:
parameterValues[parameters-1].type = SDDS_DOUBLE;
break;
case TYPE_STRING:
parameterValues[parameters-1].type = SDDS_STRING;
break;
case TYPE_CHARACTER:
parameterValues[parameters-1].type = SDDS_CHARACTER;
break;
default:
SDDS_Bomb("invalid -parameter type");
break;
}
for (i=3;i<s_arg[i_arg].n_items;i++) {
if (!(ptr=strchr(s_arg[i_arg].list[i], '=')))
SDDS_Bomb("invalid -parameter syntax");
*ptr++ = 0;
switch (match_string(s_arg[i_arg].list[i], header_elements, HEADERELEMENTS, 0)) {
case HEADER_UNITS:
SDDS_CopyString(¶meterValues[parameters-1].units, ptr);
break;
case HEADER_DESCRIPTION:
SDDS_CopyString(¶meterValues[parameters-1].description, ptr);
break;
case HEADER_SYMBOL:
SDDS_CopyString(¶meterValues[parameters-1].symbol, ptr);
break;
case HEADER_COUNT:
if (sscanf(ptr, "%ld", &count)!=1 ||
count<=0)
SDDS_Bomb("invalid parameter count value");
sprintf(buffer, "%s", parameterValues[parameters-1].name);
sprintf(buffer2, "%s1", buffer);
free(parameterValues[parameters-1].name);
SDDS_CopyString(¶meterValues[parameters-1].name, buffer2);
break;
default:
SDDS_Bomb("invalid -parameter syntax");
break;
}
}
for (i=2;i<=count;i++) {
parameters++;
parameterValues = trealloc(parameterValues, sizeof(*parameterValues)*(parameters));
sprintf(buffer2, "%s%ld", buffer, i);
SDDS_CopyString(¶meterValues[parameters-1].name, buffer2);
parameterValues[parameters-1].units = NULL;
parameterValues[parameters-1].description = NULL;
parameterValues[parameters-1].symbol = NULL;
parameterValues[parameters-1].type = parameterValues[parameters-2].type;
if (parameterValues[parameters-2].units)
SDDS_CopyString(¶meterValues[parameters-1].units, parameterValues[parameters-2].units);
if (parameterValues[parameters-2].description)
SDDS_CopyString(¶meterValues[parameters-1].description, parameterValues[parameters-2].description);
if (parameterValues[parameters-2].symbol)
SDDS_CopyString(¶meterValues[parameters-1].symbol, parameterValues[parameters-2].symbol);
}
break;
case SET_COLUMN:
if (s_arg[i_arg].n_items<3)
SDDS_Bomb("invalid -column syntax");
count=1;
columns++;
columnValues = trealloc(columnValues, sizeof(*columnValues)*(columns));
SDDS_CopyString(&columnValues[columns-1].name, s_arg[i_arg].list[1]);
columnValues[columns-1].elements = 0;
columnValues[columns-1].values = NULL;
columnValues[columns-1].stringValues = NULL;
columnValues[columns-1].units = NULL;
columnValues[columns-1].description = NULL;
columnValues[columns-1].symbol = NULL;
columnValues[columns-1].skip = 0;
switch (match_string(s_arg[i_arg].list[2], type_name, DATATYPES, 0)) {
case TYPE_SHORT:
columnValues[columns-1].type = SDDS_SHORT;
break;
case TYPE_LONG:
columnValues[columns-1].type = SDDS_LONG;
break;
case TYPE_FLOAT:
columnValues[columns-1].type = SDDS_FLOAT;
break;
case TYPE_DOUBLE:
columnValues[columns-1].type = SDDS_DOUBLE;
break;
case TYPE_STRING:
columnValues[columns-1].type = SDDS_STRING;
break;
case TYPE_CHARACTER:
columnValues[columns-1].type = SDDS_CHARACTER;
break;
default:
SDDS_Bomb("invalid -column type");
break;
}
for (i=3;i<s_arg[i_arg].n_items;i++) {
if (!(ptr=strchr(s_arg[i_arg].list[i], '=')))
SDDS_Bomb("invalid -column syntax");
*ptr++ = 0;
switch (match_string(s_arg[i_arg].list[i], header_elements, HEADERELEMENTS, 0)) {
case HEADER_UNITS:
SDDS_CopyString(&columnValues[columns-1].units, ptr);
break;
case HEADER_DESCRIPTION:
SDDS_CopyString(&columnValues[columns-1].description, ptr);
break;
case HEADER_SYMBOL:
SDDS_CopyString(&columnValues[columns-1].symbol, ptr);
break;
case HEADER_COUNT:
if (sscanf(ptr, "%ld", &count)!=1 ||
count<=0)
SDDS_Bomb("invalid column count value");
sprintf(buffer, "%s", columnValues[columns-1].name);
sprintf(buffer2, "%s1", buffer);
free(columnValues[columns-1].name);
SDDS_CopyString(&columnValues[columns-1].name, buffer2);
break;
default:
SDDS_Bomb("invalid -column syntax");
break;
}
}
for (i=2;i<=count;i++) {
columns++;
columnValues = trealloc(columnValues, sizeof(*columnValues)*(columns));
sprintf(buffer2, "%s%ld", buffer, i);
SDDS_CopyString(&columnValues[columns-1].name, buffer2);
columnValues[columns-1].elements = 0;
columnValues[columns-1].values = NULL;
columnValues[columns-1].stringValues = NULL;
columnValues[columns-1].units = NULL;
columnValues[columns-1].description = NULL;
columnValues[columns-1].symbol = NULL;
columnValues[columns-1].type = columnValues[columns-2].type;
if (columnValues[columns-2].units)
SDDS_CopyString(&columnValues[columns-1].units, columnValues[columns-2].units);
if (columnValues[columns-2].description)
SDDS_CopyString(&columnValues[columns-1].description, columnValues[columns-2].description);
if (columnValues[columns-2].symbol)
SDDS_CopyString(&columnValues[columns-1].symbol, columnValues[columns-2].symbol);
}
break;
case SET_SKIPCOLUMN:
if (s_arg[i_arg].n_items!=2)
SDDS_Bomb("invalid -skipcolumn syntax");
count=1;
columns++;
columnValues = trealloc(columnValues, sizeof(*columnValues)*(columns));
columnValues[columns-1].name = NULL;
columnValues[columns-1].elements = 0;
columnValues[columns-1].values = NULL;
columnValues[columns-1].stringValues = NULL;
columnValues[columns-1].units = NULL;
columnValues[columns-1].description = NULL;
columnValues[columns-1].symbol = NULL;
columnValues[columns-1].skip = 1;
switch (match_string(s_arg[i_arg].list[1], type_name, DATATYPES, 0)) {
case TYPE_SHORT:
columnValues[columns-1].type = SDDS_SHORT;
break;
case TYPE_LONG:
columnValues[columns-1].type = SDDS_LONG;
break;
case TYPE_FLOAT:
columnValues[columns-1].type = SDDS_FLOAT;
break;
case TYPE_DOUBLE:
columnValues[columns-1].type = SDDS_DOUBLE;
break;
case TYPE_STRING:
columnValues[columns-1].type = SDDS_STRING;
break;
case TYPE_CHARACTER:
columnValues[columns-1].type = SDDS_CHARACTER;
break;
default:
SDDS_Bomb("invalid -skipcolumn type");
break;
}
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:
if (s_arg[i_arg].n_items!=1)
SDDS_Bomb("invalid -nowarnings syntax");
noWarnings = 1;
break;
case SET_SKIPLINES:
if (s_arg[i_arg].n_items!=2 ||
sscanf(s_arg[i_arg].list[1], "%ld", &skiplines)!=1 ||
skiplines<=0)
SDDS_Bomb("invalid -skiplines syntax");
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("plaindata2sdds", &input, &output, pipeFlags, noWarnings, &tmpfile_used);
if (!columns && !parameters)
SDDS_Bomb("you must specify one of the -column or the -parameter options");
if (skiplines && inputBinary)
SDDS_Bomb("-skiplines does not work with binary input files");
if (!input) {
if (inputBinary) {
#if defined(_WIN32)
if (_setmode(_fileno(stdin), _O_BINARY) == -1) {
fprintf(stderr, "error: unable to set stdin to binary mode\n");
exit(1);
}
#endif
}
fileID = stdin;
} else {
if (!fexists(input)) {
fprintf(stderr, "input file not found\n");
exit(1);
}
if (inputBinary) {
fileID = fopen(input, "rb");
} else {
fileID = fopen(input, "r");
}
}
if (fileID == NULL) {
fprintf(stderr, "unable to open input file for reading\n");
exit(1);
}
if (!SDDS_InitializeOutput(&SDDS_dataset, binary?SDDS_BINARY:SDDS_ASCII,
1, NULL, NULL, output))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
SDDS_dataset.layout.data_mode.column_major = columnMajorOrder;
if (parameters) {
parameterIndex = tmalloc(sizeof(*parameterIndex)*parameters);
}
if (columns) {
columnIndex = tmalloc(sizeof(*columnIndex)*columns);
}
for (i=0; i<parameters; i++) {
if ((parameterIndex[i] =
SDDS_DefineParameter(&SDDS_dataset, parameterValues[i].name, parameterValues[i].symbol,
parameterValues[i].units, parameterValues[i].description, NULL,
parameterValues[i].type, 0))<0) {
sprintf(s, "Problem defining parameter %s.", parameterValues[i].name);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
for (i=0; i<columns; i++) {
if (columnValues[i].skip)
continue;
if ((columnIndex[i] =
SDDS_DefineColumn(&SDDS_dataset, columnValues[i].name, columnValues[i].symbol, \
columnValues[i].units, columnValues[i].description, NULL,
columnValues[i].type, 0))<0) {
sprintf(s, "Problem defining column %s.", columnValues[i].name);
SDDS_SetError(s);
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (!SDDS_WriteLayout(&SDDS_dataset))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_StartPage(&SDDS_dataset, initRows))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row = par = col = page = 0;
while (inputBinary) {
row = par = col = 0;
if (fread(&rows,sizeof(rows),1,fileID) != 1) {
if (page == 0) {
SDDS_SetError("Unable to read number of rows");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
if (!SDDS_Terminate(&SDDS_dataset))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (k=0;k<columns;k++) {
if (columnValues[k].type == SDDS_STRING) {
SDDS_FreeStringArray(columnValues[k].stringValues,columnValues[k].elements);
} else {
free(columnValues[k].values);
}
}
return 0;
}
}
page++;
for (par=0;par<parameters;par++) {
switch (parameterValues[par].type) {
case SDDS_SHORT:
if (fread(&shortValue,2,1,fileID) != 1) {
SDDS_SetError("Unable to read short parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,shortValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_LONG:
if (fread(&longValue,4,1,fileID) != 1) {
SDDS_SetError("Unable to read long parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,longValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_FLOAT:
if (fread(&floatValue,4,1,fileID) != 1) {
SDDS_SetError("Unable to read float parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,floatValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_DOUBLE:
if (fread(&doubleValue,8,1,fileID) != 1) {
SDDS_SetError("Unable to read double parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,doubleValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_STRING:
if (fread(&size,4,1,fileID) != 1) {
SDDS_SetError("Unable to read string parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (size>SDDS_MAXLINE-1)
SDDS_Bomb("String is too long");
if (size > 0) {
if (fread(&stringValue,size,1,fileID) != 1) {
SDDS_SetError("Unable to read string parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
stringValue[size] = 0;
} else {
strcpy(stringValue,"");
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,stringValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_CHARACTER:
if (fread(&characterValue,1,1,fileID) != 1) {
SDDS_SetError("Unable to read character parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,characterValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
}
}
for (i=0;i<columns;i++) {
if (rows > columnValues[i].elements) {
if (columnValues[i].type == SDDS_STRING) {
columnValues[i].stringValues = AllocateColumnStringData(columnValues[i].stringValues, rows, columnValues[i].elements);
} else {
columnValues[i].values = AllocateColumnData(columnValues[i].type, columnValues[i].values, rows);
}
columnValues[i].elements = rows;
}
}
if (columnOrder) {
for (col=0;col<columns;col++) {
switch (columnValues[col].type) {
case SDDS_SHORT:
for (i=0;i<rows;i++) {
if (fread((short*)(columnValues[col].values)+i,2,1,fileID) != 1) {
SDDS_SetError("Unable to read short column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_LONG:
for (i=0;i<rows;i++) {
if (fread((int32_t*)(columnValues[col].values)+i,4,1,fileID) != 1) {
SDDS_SetError("Unable to read long column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_FLOAT:
for (i=0;i<rows;i++) {
if (fread((float*)(columnValues[col].values)+i,4,1,fileID) != 1) {
SDDS_SetError("Unable to read float column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_DOUBLE:
for (i=0;i<rows;i++) {
if (fread((double*)(columnValues[col].values)+i,8,1,fileID) != 1) {
SDDS_SetError("Unable to read double double");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_STRING:
for (i=0;i<rows;i++) {
if (fread(&size,4,1,fileID) != 1) {
SDDS_SetError("Unable to read string column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (size>SDDS_MAXLINE-1)
SDDS_Bomb("String is too long");
columnValues[col].stringValues[i] = malloc(size + 1);
if (size > 0) {
if (fread(columnValues[col].stringValues[i],size,1,fileID) != 1) {
SDDS_SetError("Unable to read string column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
columnValues[col].stringValues[i][size] = 0;
} else {
strcpy(columnValues[col].stringValues[i],"");
}
}
break;
case SDDS_CHARACTER:
for (i=0;i<rows;i++) {
if (fread((char*)(columnValues[col].values)+i,1,1,fileID) != 1) {
SDDS_SetError("Unable to read character column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
}
}
} else {
for (i=0;i<rows;i++) {
for (col=0;col<columns;col++) {
switch (columnValues[col].type) {
case SDDS_SHORT:
if (fread((short*)(columnValues[col].values)+i,2,1,fileID) != 1) {
SDDS_SetError("Unable to read short column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
break;
case SDDS_LONG:
if (fread((int32_t*)(columnValues[col].values)+i,4,1,fileID) != 1) {
SDDS_SetError("Unable to read long column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
break;
case SDDS_FLOAT:
if (fread((float*)(columnValues[col].values)+i,4,1,fileID) != 1) {
SDDS_SetError("Unable to read float column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
break;
case SDDS_DOUBLE:
if (fread(((double*)(columnValues[col].values)+i),8,1,fileID) != 1) {
SDDS_SetError("Unable to read double column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
break;
case SDDS_STRING:
if (fread(&size,4,1,fileID) != 1) {
SDDS_SetError("Unable to read string column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (size>SDDS_MAXLINE-1)
SDDS_Bomb("String is too long");
columnValues[col].stringValues[i] = malloc(size + 1);
if (size > 0) {
if (fread(columnValues[col].stringValues[i],size,1,fileID) != 1) {
SDDS_SetError("Unable to read string column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
columnValues[col].stringValues[i][size] = 0;
} else {
strcpy(columnValues[col].stringValues[i],"");
}
break;
case SDDS_CHARACTER:
if (fread(((char*)(columnValues[col].values)+i),1,1,fileID) != 1) {
SDDS_SetError("Unable to read character column");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
break;
}
}
}
}
if (rows > maxRows) {
if (!SDDS_LengthenTable(&SDDS_dataset, rows - maxRows)) {
SDDS_SetError("Unable to lengthen table");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = rows;
}
j=n;
for (i=0;i<columns;i++) {
if (columnValues[i].skip)
continue;
if (columnValues[i].type == SDDS_STRING) {
SetColumnData(columnValues[i].type, &SDDS_dataset, columnValues[i].stringValues, rows, n);
} else {
SetColumnData(columnValues[i].type, &SDDS_dataset, columnValues[i].values, rows, n);
}
n++;
}
if (!SDDS_WritePage(&SDDS_dataset)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = 10000;
if (!SDDS_StartPage(&SDDS_dataset, initRows))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
row = par = col = n = 0;
rows = -1;
ptr = NULL;
ptr = SDDS_Malloc(sizeof(*ptr)*(ptrSize=2048));
/* ptr2 = NULL;
ptr2 = SDDS_Malloc(sizeof(*ptr)*(ptrSize=2048));*/
ptr[0] = 0;
while (1) {
if (readline) {
while (skiplines > 0) {
fgets(ptr, ptrSize, fileID);
skiplines--;
}
if (!fgetsSkipCommentsResize(&ptr,&ptrSize,fileID, '!'))
break;
commentFound=0;
if (checkComment) {
for (i=0; i<strlen(commentCharacters); i++) {
if (ptr[0] == commentCharacters[i]) {
commentFound=1;
}
}
}
if (commentFound == 1) {
continue;
}
if (ptr[strlen(ptr)-1] == '\n')
ptr[strlen(ptr)-1] = 0;
strcpy(temp,ptr);
/*skip empty lines*/
if (getToken(temp,data,10240,separator,whitespace)<0)
continue;
} else {
readline = 1;
}
if (par < parameters) {
switch (parameterValues[par].type) {
case SDDS_SHORT:
if (sscanf(ptr,"%hd",&shortValue) != 1) {
SDDS_SetError("Invalid short parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,shortValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_LONG:
if (sscanf(ptr,"%" SCNd32 ,&longValue) != 1) {
SDDS_SetError("Invalid long parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,longValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_FLOAT:
ConvertDNotationToENotation(ptr);
if (sscanf(ptr,"%f",&floatValue) != 1) {
SDDS_SetError("Invalid float parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,floatValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_DOUBLE:
ConvertDNotationToENotation(ptr);
if (sscanf(ptr,"%lf",&doubleValue) != 1) {
SDDS_SetError("Invalid double parameter");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,doubleValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_STRING:
SDDS_GetToken(ptr,stringValue,SDDS_MAXLINE);
SDDS_InterpretEscapes(stringValue);
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,stringValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
case SDDS_CHARACTER:
SDDS_InterpretEscapes(ptr);
characterValue = ptr[0];
if (!SDDS_SetParameters(&SDDS_dataset,SDDS_SET_BY_INDEX|SDDS_PASS_BY_VALUE,par,characterValue,-1))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
}
par++;
} else if ((rows == -1) && (!noRowCount)) {
if (sscanf(ptr,"%ld",&rows) != 1) {
SDDS_SetError("Invalid row count");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
} else if ((columns > 0) && ((row < rows) || (noRowCount))) {
if (columnOrder) {
if (noRowCount) {
cp_str(&ptr2,ptr);
rows = 0;
while (getToken(ptr2,data,10240,separator,whitespace) >= 0) {
rows++;
}
free(ptr2);
}
if (rows > columnValues[col].elements) {
if (columnValues[col].type == SDDS_STRING) {
columnValues[col].stringValues = AllocateColumnStringData(columnValues[col].stringValues, rows, columnValues[col].elements);
} else {
columnValues[col].values = AllocateColumnData(columnValues[col].type, columnValues[col].values, rows);
}
columnValues[col].elements = rows;
}
switch (columnValues[col].type) {
case SDDS_SHORT:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid short column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (sscanf(data,"%hd",((short*)(columnValues[col].values)+row)) != 1) {
SDDS_SetError("Invalid short column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_LONG:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid long column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (sscanf(data,"%" SCNd32,((int32_t*)(columnValues[col].values)+row)) != 1) {
SDDS_SetError("Invalid long column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_FLOAT:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid float column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
ConvertDNotationToENotation(data);
if (sscanf(data,"%f",((float*)(columnValues[col].values)+row)) != 1) {
SDDS_SetError("Invalid float column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_DOUBLE:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid double column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
ConvertDNotationToENotation(data);
if (sscanf(data,"%lf",((double*)(columnValues[col].values)+row)) != 1) {
SDDS_SetError("Invalid double column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_STRING:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid string column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
SDDS_InterpretEscapes(data);
columnValues[col].stringValues[row] = malloc(strlen(data) + 1);
strcpy(columnValues[col].stringValues[row],data);
}
break;
case SDDS_CHARACTER:
for (row=0;row<rows;row++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
SDDS_SetError("Invalid character column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
SDDS_InterpretEscapes(data);
*((char*)(columnValues[col].values)+row) = data[0];
}
break;
}
if (rows > maxRows) {
if (!SDDS_LengthenTable(&SDDS_dataset, rows - maxRows)) {
SDDS_SetError("Unable to lengthen table");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = rows;
}
if (columnValues[col].skip == 0) {
if (columnValues[col].type == SDDS_STRING) {
SetColumnData(columnValues[col].type, &SDDS_dataset, columnValues[col].stringValues, rows, col);
} else {
SetColumnData(columnValues[col].type, &SDDS_dataset, columnValues[col].values, rows, col);
}
n++;
}
col++;
row = 0;
} else {
if (noRowCount) {
if (row == 0) {
rows = 3;
} else if (row == rows - 1) {
rows = rows + 3;
for (i=0;i<columns;i++) {
if (rows > columnValues[i].elements) {
if (columnValues[i].type == SDDS_STRING) {
columnValues[i].stringValues = AllocateColumnStringData(columnValues[i].stringValues, rows, columnValues[i].elements);
} else {
columnValues[i].values = AllocateColumnData(columnValues[i].type, columnValues[i].values, rows);
}
}
columnValues[i].elements = rows;
}
}
}
if (row == 0)
for (i=0;i<columns;i++) {
if (rows > columnValues[i].elements) {
if (columnValues[i].type == SDDS_STRING) {
columnValues[i].stringValues = AllocateColumnStringData(columnValues[i].stringValues, rows, columnValues[i].elements);
} else {
columnValues[i].values = AllocateColumnData(columnValues[i].type, columnValues[i].values, rows);
}
}
columnValues[i].elements = rows;
}
if (noRowCount) {
cp_str(&ptr2,ptr);
i = 0;
while (getToken(ptr2,data,10240,separator,whitespace) >= 0)
i++;
free(ptr2);
if ((i != columns) && (parameters>0 && i==1)) {
if (row > 0) {
if (row > maxRows) {
if (!SDDS_LengthenTable(&SDDS_dataset, row - maxRows)) {
SDDS_SetError("Unable to lengthen table");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = row;
}
n=0;
for (j=0;j<columns;j++) {
if (columnValues[j].skip)
continue;
if (columnValues[j].type == SDDS_STRING) {
SetColumnData(columnValues[j].type, &SDDS_dataset, columnValues[j].stringValues, row, n);
} else {
SetColumnData(columnValues[j].type, &SDDS_dataset, columnValues[j].values, row, n);
}
n++;
}
if (!SDDS_WritePage(&SDDS_dataset))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
maxRows = 10000;
if (!SDDS_StartPage(&SDDS_dataset, initRows))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row = par = col = 0;
rows = -1;
}
readline = 0;
continue;
}
}
for (i=0;i<columns;i++) {
if (getToken(ptr,data,10240,separator,whitespace) < 0) {
if (!fillin) {
SDDS_SetError("Invalid column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else {
switch (columnValues[i].type) {
case SDDS_SHORT:
case SDDS_LONG:
case SDDS_FLOAT:
case SDDS_DOUBLE:
data[0]='0';
data[1]='\0';
break;
case SDDS_STRING:
case SDDS_CHARACTER:
data[0]='\0';
break;
}
}
}
switch (columnValues[i].type) {
case SDDS_SHORT:
if (sscanf(data,"%hd",((short*)(columnValues[i].values)+row)) != 1) {
if (recover) {
abort=1;
row--;
} else {
SDDS_SetError("Invalid short column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_LONG:
if (sscanf(data,"%" SCNd32,((int32_t*)(columnValues[i].values)+row)) != 1) {
if (recover) {
abort=1;
row--;
} else {
SDDS_SetError("Invalid long column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_FLOAT:
ConvertDNotationToENotation(data);
if (sscanf(data,"%f",((float*)(columnValues[i].values)+row)) != 1) {
if (recover) {
abort=1;
row--;
} else {
SDDS_SetError("Invalid float column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_DOUBLE:
ConvertDNotationToENotation(data);
if (sscanf(data,"%lf",((double*)(columnValues[i].values)+row)) != 1) {
if (recover) {
abort=1;
row--;
} else {
SDDS_SetError("Invalid double column element");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
break;
case SDDS_STRING:
SDDS_InterpretEscapes(data);
columnValues[i].stringValues[row] = malloc(strlen(data) + 1);
strcpy(columnValues[i].stringValues[row],data);
break;
case SDDS_CHARACTER:
SDDS_InterpretEscapes(data);
*((char*)(columnValues[i].values)+row) = data[0];
break;
}
if (recover && abort) {
break;
}
}
row++;
if ((row == rows) && (!noRowCount)) {
if (rows > maxRows) {
if (!SDDS_LengthenTable(&SDDS_dataset, rows - maxRows)) {
SDDS_SetError("Unable to lengthen table");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = rows;
}
n=0;
for (i=0;i<columns;i++) {
if (columnValues[i].skip)
continue;
if (columnValues[i].type == SDDS_STRING) {
SetColumnData(columnValues[i].type, &SDDS_dataset, columnValues[i].stringValues, rows, n);
} else {
SetColumnData(columnValues[i].type, &SDDS_dataset, columnValues[i].values, rows, n);
}
n++;
}
}
}
}
if ((par == parameters) &&
(((!noRowCount) && (rows != -1)) || (noRowCount)) &&
(((columnOrder) && (col == columns)) || ((columns > 0) && (row == rows)) || (columns == 0))) {
if (!SDDS_WritePage(&SDDS_dataset)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = 10000;
if (!SDDS_StartPage(&SDDS_dataset, initRows))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
row = par = col = 0;
rows = -1;
}
ptr[0] = 0;
}
if (noRowCount) {
if (row > 0) {
if (row > maxRows) {
if (!SDDS_LengthenTable(&SDDS_dataset, row - maxRows)) {
SDDS_SetError("Unable to lengthen table");
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = row;
}
n=0;
for (j=0;j<columns;j++) {
if (columnValues[j].skip)
continue;
if (columnValues[j].type == SDDS_STRING) {
SetColumnData(columnValues[j].type, &SDDS_dataset, columnValues[j].stringValues, row, n);
} else {
SetColumnData(columnValues[j].type, &SDDS_dataset, columnValues[j].values, row, n);
}
n++;
}
if (!SDDS_WritePage(&SDDS_dataset)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
maxRows = 10000;
}
}
for (i=0;i<columns;i++) {
if (columnValues[i].type == SDDS_STRING) {
for (j=0;j<columnValues[i].elements;j++) {
free(columnValues[i].stringValues[j]);
}
free(columnValues[i].stringValues);
} else {
free(columnValues[i].values);
}
if (columnValues[i].name) free(columnValues[i].name);
if (columnValues[i].units) free(columnValues[i].units);
if (columnValues[i].description) free(columnValues[i].description);
if (columnValues[i].symbol) free(columnValues[i].symbol);
}
for (i=0;i<parameters;i++) {
free(parameterValues[i].name);
if (parameterValues[i].units) free(parameterValues[i].units);
if (parameterValues[i].description) free(parameterValues[i].description);
if (parameterValues[i].symbol) free(parameterValues[i].symbol);
}
if (columnValues) free(columnValues);
if (parameterValues) free(parameterValues);
if (columnIndex) free(columnIndex);
if (parameterIndex) free(parameterIndex);
if (ptr) free(ptr);
if (!SDDS_Terminate(&SDDS_dataset))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free_scanargs(&s_arg,argc);
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)
{
SCANNED_ARG *scanned;
SDDS_TABLE inputPage, *copiedPage, outputPage;
long copiedPages;
char *inputfile, *outputfile;
char **column, **excludeColumn=NULL;
int32_t columns;
long excludeColumns;
char *indParameterName;
char **copyColumn;
int32_t copyColumns;
long verbose;
long slopeErrors;
long iArg,i;
double *indVar;
char *indVarUnits;
char **intColumn,**slopeColumn,**slopeSigmaColumn;
char *Units,*slopeUnits;
double *depVar;
long order;
double *coef,*coefsigma,*weight,*diff,chi;
long iCol,iRow,iPage;
long rows;
double *slope, slope2, slopeAve, slopeSigma;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long generateIndex;
short columnMajorOrder=-1;
copiedPage = NULL;
slopeSigmaColumn = NULL;
slopeUnits = Units = indVarUnits = NULL;
rows = 0;
slope = NULL;
slope2 = 0;
coef = coefsigma = weight = diff = slope = NULL;
argc = scanargs(&scanned, argc, argv);
if (argc == 1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
columns = excludeColumns = 0;
column = excludeColumn = NULL;
indParameterName = NULL;
verbose = 0;
slopeErrors = 0;
pipeFlags = 0;
tmpfile_used=0;
noWarnings=0;
for (iArg = 1; iArg<argc; iArg++) {
if (scanned[iArg].arg_type == OPTION) {
delete_chars(scanned[iArg].list[0], "_");
switch (match_string(scanned[iArg].list[0], commandline_option, COMMANDLINE_OPTIONS, UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
scanned[iArg].n_items--;
if (scanned[iArg].n_items>0 &&
(!scanItemList(&majorOrderFlag, scanned[iArg].list+1, &scanned[iArg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_INDEPENDENT_PARAMETER:
if (!(indParameterName = scanned[iArg].list[1]))
SDDS_Bomb("no string given for option -independentVariable");
break;
case CLO_COLUMNS:
if (columns)
SDDS_Bomb("only one -columns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -columns syntax");
column = tmalloc(sizeof(*column)*(columns = scanned[iArg].n_items-1));
for (i = 0; i<columns; i++)
column[i] = scanned[iArg].list[i+1];
break;
case CLO_EXCLUDE:
if (excludeColumns)
SDDS_Bomb("only one -excludecolumns option may be given");
if (scanned[iArg].n_items<2)
SDDS_Bomb("invalid -excludecolumns syntax");
excludeColumn = tmalloc(sizeof(*excludeColumn)*(excludeColumns = scanned[iArg].n_items-1));
for (i = 0; i<excludeColumns; i++)
excludeColumn[i] = scanned[iArg].list[i+1];
break;
case CLO_VERBOSE:
verbose = 1;
break;
case CLO_PIPE:
if (!processPipeOption(scanned[iArg].list+1, scanned[iArg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_SLOPE_ERRORS:
slopeErrors = 1;
break;
default:
SDDS_Bomb("unrecognized option given");
break;
}
}
else {
if (!inputfile)
inputfile = scanned[iArg].list[0];
else if (!outputfile)
outputfile = scanned[iArg].list[0];
else
SDDS_Bomb("too many filenames given");
}
}
processFilenames("sddsvslopes", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (!indParameterName)
SDDS_Bomb("independentVariable not given");
if (!excludeColumns) {
excludeColumn = defaultExcludedColumn;
excludeColumns = DEFAULT_EXCLUDED_COLUMNS;
}
if (verbose)
fprintf(stderr,"Reading file %s.\n",inputfile);
SDDS_InitializeInput(&inputPage, inputfile);
copiedPages = 0;
while (SDDS_ReadTable(&inputPage)>0) {
if (!copiedPages) {
copiedPage = (SDDS_TABLE*)malloc(sizeof(SDDS_TABLE));
rows = SDDS_CountRowsOfInterest(&inputPage);
}
else {
copiedPage = (SDDS_TABLE*)realloc(copiedPage, (copiedPages+1)*sizeof(SDDS_TABLE));
}
if (!SDDS_InitializeCopy(&copiedPage[copiedPages], &inputPage, NULL, "m"))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (!SDDS_CopyTable(&copiedPage[copiedPages], &inputPage))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
copiedPages++;
}
if (copiedPages<2) {
fprintf(stderr,"Insufficient data (i.e. number of data pages) to fit a straight line.\n");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Rootname", NULL, SDDS_STRING, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
switch(SDDS_CheckColumn(&inputPage, "Index", NULL, SDDS_LONG, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
generateIndex = 0;
break;
case SDDS_CHECK_NONEXISTENT:
generateIndex = 1;
break;
default:
fprintf(stderr,"Something wrong with column %s.\n", "Rootname");
exit(1);
}
/****************\
* make array of independent variable
\**************/
indVar = (double*)malloc(sizeof(*indVar)*copiedPages);
switch(SDDS_CheckParameter(&inputPage, indParameterName, NULL, SDDS_DOUBLE, NULL)) {
case SDDS_CHECK_WRONGUNITS:
case SDDS_CHECK_OKAY:
break;
default:
fprintf(stderr,"Something wrong with parameter %s.\n", indParameterName);
exit(1);
}
for (iPage = 0; iPage<copiedPages; iPage++) {
if (!SDDS_GetParameter(&copiedPage[iPage],indParameterName,&indVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!SDDS_GetParameterInformation(&inputPage, "units", &indVarUnits, SDDS_GET_BY_NAME, indParameterName))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!indVarUnits) {
indVarUnits = (char *) malloc(sizeof(*indVarUnits));
indVarUnits[0] = 0;
}
/************************************\
* get columns of interest. use set_multicolumn_flags to simply
* return new values for array column.
\*************************************/
if (!set_multicolumn_flags(&inputPage, &column, &columns, excludeColumn, excludeColumns)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
exit(1);
}
/************************************\
* make column names for the output
\*************************************/
intColumn = (char**)malloc((sizeof(char*)*columns));
slopeColumn = (char**)malloc((sizeof(char*)*columns));
if (slopeErrors)
slopeSigmaColumn = (char**)malloc((sizeof(char*)*columns));
for (i=0; i<columns; i++) {
intColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Intercept")+1)));
strcat(strcpy(intColumn[i], column[i]), "Intercept");
slopeColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("Slope")+1)));
strcat(strcpy(slopeColumn[i], column[i]), "Slope");
if (slopeErrors) {
slopeSigmaColumn[i] = (char*)malloc((sizeof(char)*(strlen(column[i])+strlen("SlopeSigma")+1)));
strcat(strcpy(slopeSigmaColumn[i], column[i]), "SlopeSigma");
}
}
/************************************\
* Write layout for output file
\*************************************/
if (verbose)
fprintf(stderr,"Opening file %s.\n",outputfile);
if(!SDDS_InitializeOutput(&outputPage,SDDS_BINARY,1,
"lsf of sddsvexperiment",NULL,outputfile) ||
0>SDDS_DefineParameter(&outputPage, "InputFile", "InputFile", NULL,
"InputFile", NULL, SDDS_STRING, 0) ||
0>SDDS_DefineParameter(&outputPage, "IndependentVariable", "IndependentVariable", NULL,
"IndependentVariable", NULL, SDDS_STRING, 0) ||
(0>SDDS_DefineColumn(&outputPage,"Index",NULL,NULL,"Rootname index",NULL,SDDS_LONG,0))||
(0>SDDS_DefineColumn(&outputPage,"Rootname",NULL,NULL,NULL,NULL,SDDS_STRING,0)))
SDDS_PrintErrors(stderr,SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (columnMajorOrder!=-1)
outputPage.layout.data_mode.column_major = columnMajorOrder;
else
outputPage.layout.data_mode.column_major = inputPage.layout.data_mode.column_major;
for (iCol=0; iCol<columns; iCol++) {
if (!SDDS_GetColumnInformation(&inputPage, "units", &Units, SDDS_GET_BY_NAME,column[iCol]))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!Units) {
Units = (char*) malloc(sizeof(*Units));
Units[0] = 0;
}
if (0>SDDS_DefineColumn(&outputPage, intColumn[iCol], NULL, Units, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/* units for slopes columns */
if (strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+strlen(indVarUnits)+2));
strcat( strcat( strcpy(slopeUnits, Units), "/"), indVarUnits);
}
if (strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(indVarUnits)+2));
strcat( strcpy( slopeUnits, "1/"), indVarUnits);
}
if (!strlen(indVarUnits) && strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits)*(strlen(Units)+2));
strcpy( slopeUnits, indVarUnits);
}
if (!strlen(indVarUnits) && !strlen(Units) ) {
slopeUnits = (char*)malloc(sizeof(*slopeUnits));
strcpy( slopeUnits, "");
}
if (0>SDDS_DefineColumn(&outputPage, slopeColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (slopeErrors) {
if (0>SDDS_DefineColumn(&outputPage, slopeSigmaColumn[iCol], NULL, slopeUnits, NULL, NULL, SDDS_DOUBLE,0))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
free(slopeUnits);
}
if(!SDDS_WriteLayout(&outputPage) ||
!SDDS_StartTable(&outputPage,rows) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile",inputfile?inputfile:"pipe",NULL) ||
!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, 0,
"IndependentVariable", indParameterName, NULL) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/************************************\
* Copy columns to output file (usually columns Index and Rootname)
\*************************************/
copyColumns = DEFAULT_COPY_COLUMNS;
copyColumn = defaultCopyColumn;
if (!set_multicolumn_flags(&inputPage, ©Column, ©Columns, NULL, 0)) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
exit(1);
}
if(!SDDS_CopyColumns(&outputPage, &inputPage))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
depVar = (double*)malloc(sizeof(*depVar)*copiedPages);
weight = (double*)malloc(sizeof(*weight)*copiedPages);
diff = (double*)malloc(sizeof(*weight)*copiedPages);
order=1;
coef = (double*)malloc(sizeof(*coef)*(order+1));
coefsigma = (double*)malloc(sizeof(*coefsigma)*(order+1));
if(slopeErrors)
slope = (double*)malloc(sizeof(*slope)*copiedPages);
for (iCol=0; iCol<columns; iCol++) {
for (iPage=0; iPage<copiedPages; iPage++)
weight[iPage]=1;
if (verbose)
fprintf(stderr,"Doing column %s.\n", column[iCol]);
for (iRow=0; iRow<rows; iRow++) {
for (iPage=0; iPage<copiedPages; iPage++) {
if (!SDDS_GetValue(&copiedPage[iPage], column[iCol], iRow, &depVar[iPage]))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
if (generateIndex) {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
"Index",iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
intColumn[iCol], coef[0],
slopeColumn[iCol], coef[1], NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if(slopeErrors){
/* recalculate the slope with a subset of points */
slopeAve= slope2 = 0;
for (iPage=0; iPage<copiedPages; iPage++) {
weight[iPage] = 1e10;
if(iPage)
weight[iPage-1] = 1;
if (!(lsfn(indVar, depVar, weight, copiedPages, order, coef, coefsigma, &chi, diff))){
fprintf(stderr,"Problem with call to lsfn\n.");
exit(1);
}
slope[iPage] = coef[1];
slopeAve += slope[iPage];
slope2 += sqr(slope[iPage]);
}
slopeSigma = sqrt(slope2/copiedPages - sqr(slopeAve/copiedPages));
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, iRow,
slopeSigmaColumn[iCol], slopeSigma, NULL))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
}
if( !SDDS_WriteTable(&outputPage)|| SDDS_Terminate(&inputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for (iPage=0; iPage<copiedPages; iPage++) {
if( !SDDS_Terminate(&copiedPage[iPage]) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if( SDDS_Terminate(&outputPage) )
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
SDDS_FreeStringArray(column, columns);
free(column);
SDDS_FreeStringArray(intColumn, columns);
SDDS_FreeStringArray(slopeColumn, columns);
free(intColumn);
free(slopeColumn);
if (slopeErrors) {
SDDS_FreeStringArray(slopeSigmaColumn, columns);
free(slopeSigmaColumn);
}
free(copiedPage);
free(indVar);
free(depVar);
if (weight)
free(weight);
if (diff)
free(diff);
if (slope)
free(slope);
if (coef) free(coef);
if (coefsigma) free(coefsigma);
if (Units) free(Units);
if (indVarUnits) free(indVarUnits);
free_scanargs(&scanned, argc);
return(0);
}
int main(int argc, char **argv)
{
SCANNED_ARG *s_arg;
SDDS_DATASET inputPage, outputPage;
char *inputfile, *outputfile;
char **inputColumnName, **inputStringColumnName, **inputDoubleColumnName;
char **outputStringColumnName, **outputDoubleColumnName, **matchColumn=NULL;
long inputRows, inputDoubleColumns, inputStringColumns, indexColumn=0, matchColumns=0, noOldColumnNamesColumn=0;
long outputRows, outputDoubleColumns, outputStringColumns;
char **inputParameterName;
int32_t inputParameters, inputColumns;
char *inputDescription, *inputContents;
char *outputDescription;
long i, i_arg, col;
char *buffer;
char **columnOfStrings;
long buffer_size;
#define BUFFER_SIZE_INCREMENT 16384
MATRIX *R, *RInv;
long OldStringColumnsDefined;
char *inputStringRows, *outputStringRows;
char **stringArray, *stringParameter;
long token_length;
long verbose;
char format[32];
long digits;
char *Symbol, *Root;
void *parameterPointer;
long ascii;
unsigned long pipeFlags, majorOrderFlag;
long tmpfile_used, noWarnings;
long ipage=0, columnType;
char *oldColumnNames, *newColumnNamesColumn;
short columnMajorOrder=-1;
inputColumnName = outputStringColumnName = outputDoubleColumnName = inputParameterName = NULL;
outputRows = outputDoubleColumns = outputStringColumns = OldStringColumnsDefined = 0;
SDDS_RegisterProgramName(argv[0]);
argc = scanargs(&s_arg, argc, argv);
if (argc==1)
bomb(NULL, USAGE);
inputfile = outputfile = NULL;
verbose = 0;
Symbol = Root = NULL;
ascii = 0;
digits=3;
pipeFlags = 0;
tmpfile_used = 0;
noWarnings = 0;
oldColumnNames = NULL;
newColumnNamesColumn = NULL;
for (i_arg=1; i_arg<argc; i_arg++) {
if (s_arg[i_arg].arg_type==OPTION) {
switch(match_string(s_arg[i_arg].list[0], commandline_option, COMMANDLINE_OPTIONS,
UNIQUE_MATCH)) {
case CLO_MAJOR_ORDER:
majorOrderFlag=0;
s_arg[i_arg].n_items--;
if (s_arg[i_arg].n_items>0 &&
(!scanItemList(&majorOrderFlag, s_arg[i_arg].list+1, &s_arg[i_arg].n_items, 0,
"row", -1, NULL, 0, SDDS_ROW_MAJOR_ORDER,
"column", -1, NULL, 0, SDDS_COLUMN_MAJOR_ORDER,
NULL)))
SDDS_Bomb("invalid -majorOrder syntax/values");
if (majorOrderFlag&SDDS_COLUMN_MAJOR_ORDER)
columnMajorOrder=1;
else if (majorOrderFlag&SDDS_ROW_MAJOR_ORDER)
columnMajorOrder=0;
break;
case CLO_MATCH_COLUMN:
matchColumns = s_arg[i_arg].n_items-1;
matchColumn = s_arg[i_arg].list+1;
break;
case CLO_INDEX_COLUMN:
indexColumn = 1;
break;
case CLO_NO_OLDCOLUMNNAMES:
noOldColumnNamesColumn = 1;
break;
case CLO_VERBOSE:
verbose=1;
break;
case CLO_ASCII:
ascii=1;
break;
case CLO_DIGITS:
if (!(get_long(&digits, s_arg[i_arg].list[1])))
bomb("no string given for option -digits", USAGE);
break;
case CLO_COLUMNROOT:
if (!(Root=s_arg[i_arg].list[1]))
SDDS_Bomb("No root string given");
break;
case CLO_SYMBOL:
if (!(Symbol=s_arg[i_arg].list[1]))
SDDS_Bomb("No symbol string given");
break;
case CLO_PIPE:
if (!processPipeOption(s_arg[i_arg].list+1, s_arg[i_arg].n_items-1, &pipeFlags))
SDDS_Bomb("invalid -pipe syntax");
break;
case CLO_OLDCOLUMNNAMES:
if (!(oldColumnNames=s_arg[i_arg].list[1]))
SDDS_Bomb("No oldColumnNames string given");
break;
case CLO_NEWCOLUMNNAMES:
if (s_arg[i_arg].n_items!=2 ||
SDDS_StringIsBlank(newColumnNamesColumn = s_arg[i_arg].list[1]))
SDDS_Bomb("Invalid -newColumnNames syntax/value");
break;
default:
bomb("unrecognized option given", USAGE);
}
}
else {
if (!inputfile)
inputfile = s_arg[i_arg].list[0];
else if (!outputfile)
outputfile = s_arg[i_arg].list[0];
else
bomb("too many filenames given", USAGE);
}
}
processFilenames("sddstranpose", &inputfile, &outputfile, pipeFlags, noWarnings, &tmpfile_used);
if (newColumnNamesColumn && Root)
SDDS_Bomb("-root and -newColumnNames are incompatible");
if (!SDDS_InitializeInput(&inputPage, inputfile) ||
!(inputParameterName=(char**)SDDS_GetParameterNames(&inputPage, &inputParameters)) ||
!SDDS_GetDescription(&inputPage, &inputDescription, &inputContents))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
if (matchColumns)
inputColumnName = getMatchingSDDSNames(&inputPage, matchColumn, matchColumns, &inputColumns, SDDS_MATCH_COLUMN);
else {
if (!(inputColumnName=(char**)SDDS_GetColumnNames(&inputPage, &inputColumns)))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
}
inputDoubleColumns=0;
inputStringColumns=0;
inputDoubleColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputStringColumnName=(char**)malloc(inputColumns*sizeof(char*));
inputRows = 0;
/*********** \
* read data *
\***********/
while (0<SDDS_ReadTable(&inputPage)) {
ipage ++;
#if defined(DEBUG)
fprintf(stderr, "working on page %ld\n", ipage);
#endif
if (ipage==1) {
SDDS_DeferSavingLayout(1);
if( !SDDS_SetColumnFlags(&inputPage, 0))
SDDS_PrintErrors(stderr, SDDS_EXIT_PrintErrors|SDDS_VERBOSE_PrintErrors);
/* count the string and numerical columns in the input file */
for (i=0;i<inputColumns;i++) {
if ( SDDS_NUMERIC_TYPE( columnType = SDDS_GetColumnType( &inputPage, i))) {
inputDoubleColumnName[inputDoubleColumns]=inputColumnName[i];
inputDoubleColumns++;
}
}
for (i=0; i<inputPage.layout.n_columns; i++) {
if (inputPage.layout.column_definition[i].type == SDDS_STRING ) {
inputStringColumnName[inputStringColumns] = inputPage.layout.column_definition[i].name;
inputStringColumns++;
}
}
if( !(inputRows=SDDS_CountRowsOfInterest(&inputPage)))
SDDS_Bomb("No rows in dataset.");
}
else {
/* these statements are executed on the subsequent pages */
if (inputRows != SDDS_CountRowsOfInterest(&inputPage)) {
SDDS_Bomb("Datasets don't have the same number of rows.\nProcessing stopped before reaching the end of the input file.");
}
}
#if defined(DEBUG)
fprintf(stderr, "row flags set\n");
#endif
if (inputDoubleColumns == 0)
SDDS_Bomb("No numerical columns in file.");
if ((ipage==1) && verbose) {
fprintf(stderr, "No. of double/float/integer columns: %ld.\n", inputDoubleColumns);
fprintf(stderr, "No. of string columns: %ld.\n", inputStringColumns);
fprintf(stderr, "No. of rows: %ld.\n", inputRows);
}
/****************\
* transpose data *
\****************/
if (inputDoubleColumns) {
if (ipage == 1) {
m_alloc(&RInv, inputRows, inputDoubleColumns);
m_alloc(&R, inputDoubleColumns, inputRows);
}
for (col=0;col<inputDoubleColumns;col++){
if (!(R->a[col]=(double*)SDDS_GetColumnInDoubles(&inputPage, inputDoubleColumnName[col]))) {
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (verbose) {
m_show(R, "%9.6le ", "Transpose of input matrix:\n", stdout);
}
m_trans(RInv, R);
}
/***************************\
* determine existence of *
* transposed string columns *
\***************************/
if (ipage == 1) {
OldStringColumnsDefined=0;
switch(SDDS_CheckParameter(&inputPage, OLD_STRING_COLUMN_NAMES, NULL, SDDS_STRING, NULL)){
case SDDS_CHECK_OKAY:
OldStringColumnsDefined=1;
break;
case SDDS_CHECK_NONEXISTENT:
break;
case SDDS_CHECK_WRONGTYPE:
case SDDS_CHECK_WRONGUNITS:
fprintf(stderr, "Something wrong with parameter OldStringColumns.\n");
exit(1);
break;
}
if (OldStringColumnsDefined){
/* decompose OldStringColumns into names of string columns for the output file */
if (!SDDS_GetParameter(&inputPage, OLD_STRING_COLUMN_NAMES, &inputStringRows))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Parameter OldStringColumns: %s.\n", inputStringRows);
}
outputStringColumnName=(char**)malloc(sizeof(char*));
outputStringColumns=0;
buffer_size=BUFFER_SIZE_INCREMENT;
buffer=(char*)malloc(sizeof(char)*buffer_size);
while ( 0 <= (token_length = SDDS_GetToken(inputStringRows, buffer, BUFFER_SIZE_INCREMENT))){
if (!token_length)
SDDS_Bomb("A null string was detected in parameter OldStringColumns.\n");
if (!SDDS_CopyString(&outputStringColumnName[outputStringColumns], buffer))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (verbose) {
fprintf(stderr, "Output string column: %s\n", outputStringColumnName[outputStringColumns]);
}
outputStringColumns++;
}
}
}
/*********************\
* define output page *
\*********************/
if ( ipage == 1 ) {
outputRows = inputDoubleColumns;
outputDoubleColumns = inputRows;
if (inputDescription){
outputDescription = (char*) malloc( sizeof(char) * (strlen("Transpose of ") + strlen(inputDescription) + 1));
strcat(strcpy(outputDescription, "Transpose of "), inputDescription);
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, outputDescription, inputContents, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (!SDDS_InitializeOutput(&outputPage, ascii?SDDS_ASCII:SDDS_BINARY, 1, NULL, NULL, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (columnMajorOrder!=-1)
outputPage.layout.data_mode.column_major = columnMajorOrder;
else
outputPage.layout.data_mode.column_major = inputPage.layout.data_mode.column_major;
/***********************************\
* define names for double columns *
\***********************************/
if (!Root && inputStringColumns ) {
/* use specified string column, or first string column encountered */
if (!newColumnNamesColumn)
/* first string column encountered */
outputDoubleColumnName = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[0]);
else {
/* use specified string column */
if (SDDS_CheckColumn(&inputPage, newColumnNamesColumn, NULL, SDDS_STRING, stderr)!=SDDS_CHECK_OKAY)
SDDS_Bomb("column named with -newColumnNames does not exist in input");
outputDoubleColumnName = (char**)SDDS_GetColumn(&inputPage, newColumnNamesColumn);
}
for (i=1; i<inputRows; i++) {
if (match_string(outputDoubleColumnName[i-1], outputDoubleColumnName+i, inputRows-i, EXACT_MATCH)>=0) {
fprintf(stderr, "Error, duplicate %s found in input file string column %s, can not be used as output column names\n", outputDoubleColumnName[i-1], newColumnNamesColumn ? newColumnNamesColumn : inputStringColumnName[0]);
exit(1);
}
}
}
else {
/* use command line options to produce column names in the output file */
outputDoubleColumnName = (char**) malloc( outputDoubleColumns * sizeof(char*) );
digits = MAX(digits, log10(inputRows) + 1);
if (!Root){
Root = (char*) malloc( sizeof(char) * (strlen("Column")+1) );
strcpy(Root, "Column");
}
if (outputDoubleColumns!=1) {
for ( i=0; i < outputDoubleColumns; i++){
outputDoubleColumnName[i] = (char*) malloc( sizeof(char) * (strlen(Root)+digits+1));
sprintf(format, "%s%%0%ldld", Root, digits);
sprintf(outputDoubleColumnName[i], format, i);
}
}
else {/* only one row to transpose */
outputDoubleColumnName[0] = (char*) malloc( sizeof(char) * (strlen(Root)+1));
strcpy( outputDoubleColumnName[0], Root);
}
}
/*************************\
* define string columns *
\*************************/
if (OldStringColumnsDefined) {
if (!SDDS_DefineSimpleColumns(&outputPage, outputStringColumns,
outputStringColumnName, NULL, SDDS_STRING))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
/* by default there should be at least one string column, that of the old column names. */
if (!noOldColumnNamesColumn) {
outputStringColumns = 1;
outputStringColumnName = (char**) malloc( sizeof(char*));
if (oldColumnNames) {
/* commanline option specification */
outputStringColumnName[0] = oldColumnNames;
}
else {
outputStringColumnName[0] = (char*) malloc( sizeof(char) * (strlen("OldColumnNames") + 1));
strcpy(outputStringColumnName[0], "OldColumnNames");
}
if ( 0 > SDDS_DefineColumn(&outputPage, outputStringColumnName[0], NULL, NULL, NULL, NULL, SDDS_STRING, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
if (indexColumn && !SDDS_DefineSimpleColumn(&outputPage, "Index", NULL, SDDS_LONG))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
/*************************\
* define double columns *
\*************************/
for ( i=0; i < outputDoubleColumns; i++)
if (Symbol){
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], Symbol, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
else {
if (0>SDDS_DefineColumn(&outputPage, outputDoubleColumnName[i], NULL, NULL, NULL,
NULL, SDDS_DOUBLE, 0))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/********************************\
* define string parameters *
* i.e. transposed string columns *
\********************************/
if ( inputStringColumns>1 ) {
if (0>SDDS_DefineParameter(&outputPage, OLD_STRING_COLUMN_NAMES,
NULL, NULL, "Transposed string columns", NULL, SDDS_STRING,
NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
for ( i=0; i < inputStringColumns; i++){
if (0>SDDS_DefineParameter(&outputPage, inputStringColumnName[i], NULL, NULL, "Transposed string column data", NULL,
SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/*************************\
* transfer parameters not *
* associated with old *
* string columns *
\*************************/
if (inputParameters) {
for ( i=0; i < inputParameters; i++) {
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES)))
if ( 0 > SDDS_TransferParameterDefinition(&outputPage, &inputPage, inputParameterName[i], NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
/***************\
* write layout *
\***************/
SDDS_DeferSavingLayout(0);
/* if InputFile is not already transfered ot the output file, then create it. */
switch( SDDS_CheckParameter(&outputPage, "InputFile", NULL, SDDS_STRING, NULL) ) {
case SDDS_CHECK_NONEXISTENT:
if (0>SDDS_DefineParameter(&outputPage, "InputFile", NULL, NULL, "Original matrix file", NULL, SDDS_STRING, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
break;
default:
break;
}
if (!SDDS_WriteLayout(&outputPage) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "table layout defined\n");
#endif
if (!SDDS_StartTable(&outputPage, outputRows) )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (ipage == 1) {
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
"InputFile", inputfile?inputfile:"pipe", NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
/***************************************\
* assign string columns from input *
* to string parameters in output *
\**************************************/
if ( inputStringColumns > 1) {
for ( i=0; i < inputStringColumns; i++){
columnOfStrings = (char**) SDDS_GetColumn(&inputPage, inputStringColumnName[i]);
stringParameter = JoinStrings(columnOfStrings, inputRows, BUFFER_SIZE_INCREMENT);
if ( !SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
inputStringColumnName[i], stringParameter, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(columnOfStrings);
free(stringParameter);
}
outputStringRows = JoinStrings(inputStringColumnName, inputStringColumns, BUFFER_SIZE_INCREMENT);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE,
OLD_STRING_COLUMN_NAMES, outputStringRows, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string parameters assigned\n");
#endif
if (inputParameters){
for ( i=0; i < inputParameters; i++){
if ( (0 > match_string(inputParameterName[i], outputStringColumnName, outputStringColumns, 0) &&
strcasecmp(inputParameterName[i], OLD_STRING_COLUMN_NAMES))) {
parameterPointer = (void*) SDDS_GetParameter(&inputPage, inputParameterName[i], NULL);
if (!SDDS_SetParameters(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputParameterName[i], parameterPointer, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
free(parameterPointer);
}
}
}
#if defined(DEBUG)
fprintf(stderr, "input parameters assigned\n");
#endif
/**********************************\
* assign data to *
* output table part of data set *
\**********************************/
if (outputRows) {
/***************************\
* assign string column data *
\***************************/
if (OldStringColumnsDefined){
for ( i=0 ; i < outputStringColumns; i++){
if (!SDDS_GetParameter(&inputPage, outputStringColumnName[i], &stringParameter))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
stringArray=TokenizeString(stringParameter, outputRows);
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
stringArray, outputRows, outputStringColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
}
else {
if (!noOldColumnNamesColumn && !SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
inputDoubleColumnName, outputRows, outputStringColumnName[0]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "string data columns assigned\n");
#endif
/***************************\
* assign double column data *
\***************************/
for ( i=0 ; i < outputDoubleColumns; i++) /* i is the row index */
if (!SDDS_SetColumn(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_REFERENCE,
RInv->a[i], outputRows, outputDoubleColumnName[i]))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (indexColumn) {
for (i=0; i<outputRows; i++)
if (!SDDS_SetRowValues(&outputPage, SDDS_SET_BY_NAME|SDDS_PASS_BY_VALUE, i, "Index", i, NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
#if defined(DEBUG)
fprintf(stderr, "double data columns assigned\n");
#endif
}
#if defined(DEBUG)
fprintf(stderr, "data assigned\n");
#endif
if (!SDDS_WriteTable(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
#if defined(DEBUG)
fprintf(stderr, "data written out\n");
#endif
}
if (inputDoubleColumns) {
m_free(&RInv);
m_free(&R);
}
if (inputColumnName) {
SDDS_FreeStringArray(inputColumnName, inputColumns);
free(inputColumnName);
}
if (inputStringColumns)
free(inputStringColumnName);
if (inputDescription)
free(inputDescription);
if (inputParameterName) {
SDDS_FreeStringArray(inputParameterName, inputParameters);
free(inputParameterName);
}
if (outputDoubleColumns) {
SDDS_FreeStringArray(outputDoubleColumnName, outputDoubleColumns);
free(outputDoubleColumnName);
}
if (!SDDS_Terminate(&inputPage) || !SDDS_Terminate(&outputPage))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (tmpfile_used && !replaceFileAndBackUp(inputfile, outputfile))
exit(1);
return(0);
}
void SetupOutputFile(char *outputfile, SDDS_DATASET *SDDSout, int mode, SDDS_DATASET *SDDSin, long copyCols, char **copyCol, long copyPars, char **copyPar) {
long i, cols=0, pars=0;
char **column=NULL, **par=NULL;
if (!SDDS_InitializeOutput(SDDSout, SDDS_BINARY, 1, NULL, NULL, outputfile))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (copyCols) {
column = getMatchingSDDSNames(SDDSin, copyCol, copyCols, &cols, SDDS_MATCH_COLUMN);
SDDS_SetColumnFlags(SDDSin, 0);
for (i=0; i<cols; i++) {
if (!SDDS_TransferColumnDefinition(SDDSout, SDDSin, column[i], NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!SDDS_SetColumnsOfInterest(SDDSin, SDDS_MATCH_STRING, column[i], SDDS_OR))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
SDDS_FreeStringArray(column, cols);
}
if (copyPars) {
par = getMatchingSDDSNames(SDDSin, copyPar, copyPars, &pars, SDDS_MATCH_PARAMETER);
for (i=0; i<pars; i++) {
if (!SDDS_TransferParameterDefinition(SDDSout, SDDSin, par[i], NULL))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
SDDS_FreeStringArray(par, pars);
}
if (verbose > 1 ) { fprintf(stdout, "cols %ld pars %ld\n", cols, pars); }
if (!SDDS_DefineSimpleParameter(SDDSout, "sddsxra_mode", NULL, SDDS_LONG) ||
!SDDS_DefineSimpleParameter(SDDSout, "TargetMaterial", NULL, SDDS_STRING) ||
!SDDS_DefineSimpleParameter(SDDSout, "TargetFormula", NULL, SDDS_STRING) ||
!SDDS_DefineSimpleParameter(SDDSout, "MassThickness", "g/cm^2", SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "TargetThickness", "mm", SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "TargetDensity", "g/cm^3", SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "ThetaIn", "degrees", SDDS_DOUBLE) ||
!SDDS_DefineSimpleColumn(SDDSout, "PhotonEnergy", "eV", SDDS_DOUBLE))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (mode!=1 && mode!=6 && mode!=11) {
if (SDDS_DefineColumn(SDDSout, "TotalCS", NULL, "cm^2/g", "Total x-ray cross section",NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "PhotoCS", NULL, "cm^2/g", "Photoelectric cross section",NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "CoherentCS", NULL, "cm^2/g", "Coherent scattering cross section ",NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "IncoherentCS", NULL, "cm^2/g", "Incoherent scattering cross section ",NULL, SDDS_DOUBLE, 0)<0)
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (mode==1 || mode==6) {
if (SDDS_DefineColumn(SDDSout, "RefracIndex_Re", NULL, NULL, "Real part of refractive index", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "RefracIndex_Im", NULL, NULL, "Imaginary part of refractive index", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "delta", NULL, NULL, "Real part of 1 - n", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "beta", NULL, NULL, "Imaginary part 1 - n", NULL, SDDS_DOUBLE, 0)<0)
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
} else if (mode==11) {
if (SDDS_DefineColumn(SDDSout, "F1", NULL, NULL, "Atomic scattering factor f1", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "F2", NULL, NULL, "Atomic scattering factor f2", NULL, SDDS_DOUBLE, 0)<0)
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (mode==6) {
if (SDDS_DefineColumn(SDDSout, "Reflectivity", NULL, "g/cm^3", NULL, NULL, SDDS_DOUBLE, 0)<0 ||
!SDDS_DefineSimpleParameter(SDDSout, "Polarization", NULL, SDDS_DOUBLE))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (mode==2 || mode==4 || mode==12 || mode==14) {
if (SDDS_DefineColumn(SDDSout, "Transmission", NULL, NULL, "Ratio of x-ray beam transmitted through the film target", NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "Absorption", NULL, NULL, "Ratio of x-ray beam absorbed by the film target", NULL, SDDS_DOUBLE, 0)<0 )
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (mode==4 || mode==14 ) {
if (SDDS_DefineColumn(SDDSout, "TotalElectronYieldFront", NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "TotalElectronYieldBack", NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0)<0 ||
SDDS_DefineColumn(SDDSout, "TotalElectronYield", NULL, NULL, NULL, NULL, SDDS_DOUBLE, 0)<0 ||
!SDDS_DefineSimpleParameter(SDDSout, "TargetEfficiency", "g/cm^2", SDDS_DOUBLE))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (mode==20) {
if (!SDDS_DefineSimpleParameter(SDDSout, "ShellID", NULL, SDDS_LONG) ||
!SDDS_DefineSimpleParameter(SDDSout, "ShellName", NULL, SDDS_STRING) ||
!SDDS_DefineSimpleParameter(SDDSout, "EdgeEnergy", "eV", SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "FluorYield", NULL, SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "JumpFactor", NULL, SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "LevelWidth", "eV", SDDS_DOUBLE) ||
!SDDS_DefineSimpleParameter(SDDSout, "ElectronConfig", "e", SDDS_DOUBLE))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
if (!SDDS_WriteLayout(SDDSout))
SDDS_PrintErrors(stdout, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
}
void run_rpn_load(NAMELIST_TEXT *nltext, RUN *run)
{
SDDS_DATASET SDDSin;
long code, foundPage, iColumn, matchRow, rows, iParameter;
int32_t columns, parameters;
char *parameterValue = NULL;
double *data, data1;
char **columnName, **matchColumnData, *memName = NULL;
char **parameterName;
/* process the namelist text */
set_namelist_processing_flags(STICKY_NAMELIST_DEFAULTS);
set_print_namelist_flags(0);
if (processNamelist(&rpn_load, nltext)==NAMELIST_ERROR)
bombElegant(NULL, NULL);
if (echoNamelists) print_namelist(stdout, &rpn_load);
if (match_column && strlen(match_column)) {
if (use_row!=-1) {
fprintf(stdout, "Error: you asked to match a column and also gave use_row.\n");
exitElegant(1);
}
if (!match_column_value || !strlen(match_column_value)) {
fprintf(stdout, "Error: you must give match_column_value with match_column\n");
exitElegant(1);
}
}
if (match_parameter && strlen(match_parameter)) {
if (use_page!=-1) {
fprintf(stdout, "Error: you asked to match a parameter and also gave use_page.\n");
exitElegant(1);
}
if (!match_parameter_value || !strlen(match_parameter_value)) {
fprintf(stdout, "Error: you must give match_parameter_value with match_parameter\n");
exitElegant(1);
}
}
if (!filename || !strlen(filename)) {
fprintf(stdout, "Error: no filename given for rpn_load.\n");
exitElegant(1);
}
filename = compose_filename(filename, run->rootname);
if (!SDDS_InitializeInputFromSearchPath(&SDDSin, filename)) {
fprintf(stdout, "Error: couldn't initialize SDDS input for %s\n",
filename);
exitElegant(1);
}
foundPage = 0;
while ((code=SDDS_ReadPage(&SDDSin))>0) {
if (use_page>0) {
if (code==use_page) {
foundPage = 1;
break;
}
continue;
}
if (match_parameter && strlen(match_parameter)) {
if (!(parameterValue=SDDS_GetParameterAsString(&SDDSin, match_parameter, NULL)))
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors|SDDS_EXIT_PrintErrors);
if (!wild_match(parameterValue, match_parameter_value))
continue;
foundPage = 1;
break;
}
if (use_page==-1 && SDDS_CheckEndOfFile(&SDDSin)==1) {
foundPage = 1;
break;
}
}
if (!foundPage) {
fprintf(stdout, "Error: no appropriate page found\n");
exitElegant(1);
}
if (!load_parameters) {
if ((columnName = SDDS_GetColumnNames(&SDDSin, &columns))==NULL) {
fprintf(stdout, "Warning: No columns in file!\n");
return;
}
rows = SDDS_RowCount(&SDDSin);
matchRow = rows-1;
if (use_row!=-1) {
if (use_row>=rows) {
fprintf(stdout, "Error: number of rows in file (%ld) less than needed for use_row=%ld\n",
rows, use_row);
exitElegant(1);
}
matchRow = use_row;
}
if (match_column) {
if (SDDS_GetNamedColumnType(&SDDSin, match_column)!=SDDS_STRING) {
fprintf(stdout, "Error: column %s nonexistent or not string type.\n",
match_column);
exitElegant(1);
}
if (!(matchColumnData=SDDS_GetColumn(&SDDSin, match_column))) {
fprintf(stdout, "Error: unable to get data for column %s\n", match_column);
exitElegant(1);
}
if (matching_row_number<0) {
/* use last match */
for (matchRow=rows-1; matchRow>=0; matchRow--)
if (wild_match(matchColumnData[matchRow], match_column_value))
break;
} else {
/* use nth match */
for (matchRow=0; matchRow<rows; matchRow++)
if (wild_match(matchColumnData[matchRow], match_column_value) &&
matching_row_number-- == 0)
break;
}
if (matchRow<0 || matchRow>=rows) {
fprintf(stdout, "Error: unable to find match for %s in column %s\n",
match_column_value, match_column);
exitElegant(1);
}
SDDS_FreeStringArray(matchColumnData, rows);
}
for (iColumn=0; iColumn<columns; iColumn++) {
switch (SDDS_GetNamedColumnType(&SDDSin, columnName[iColumn])) {
case SDDS_CHARACTER:
case SDDS_STRING:
break;
default:
if (!(data=SDDS_GetColumnInDoubles(&SDDSin, columnName[iColumn]))) {
fprintf(stdout, "Error: unable to get data for column %s as numerical data.\n",
columnName[iColumn]);
exitElegant(1);
}
if (!(memName=SDDS_Realloc(memName, sizeof(*memName)*((tag?strlen(tag):0)+strlen(columnName[iColumn])+2)))) {
fprintf(stdout, "Memory allocation failure trying to create memory name for loaded data\n");
exitElegant(1);
}
if (tag && strlen(tag))
sprintf(memName, "%s.%s", tag, columnName[iColumn]);
else
sprintf(memName, "%s", columnName[iColumn]);
rpn_store(data[matchRow], NULL, rpn_create_mem(memName, 0));
fprintf(stdout, "%le --> %s\n", data[matchRow], memName);
free(columnName[iColumn]);
free(data);
}
}
if (memName)
free(memName);
if (columnName)
free(columnName);
} else {
/* load data from parameters */
if ((parameterName = SDDS_GetParameterNames(&SDDSin, ¶meters))==NULL) {
fprintf(stdout, "Warning: No parameters in file!\n");
return;
}
for (iParameter=0; iParameter<parameters; iParameter++) {
switch (SDDS_GetNamedParameterType(&SDDSin, parameterName[iParameter])) {
case SDDS_CHARACTER:
case SDDS_STRING:
break;
default:
if (!SDDS_GetParameterAsDouble(&SDDSin, parameterName[iParameter], &data1)) {
fprintf(stdout, "Error: unable to get data for parameter %s as numerical data.\n",
parameterName[iParameter]);
exitElegant(1);
}
if (!(memName=SDDS_Realloc(memName, sizeof(*memName)*((tag?strlen(tag):0)+strlen(parameterName[iParameter])+2)))) {
fprintf(stdout, "Memory allocation failure trying to create memory name for loaded data\n");
exitElegant(1);
}
if (tag && strlen(tag))
sprintf(memName, "%s.%s", tag, parameterName[iParameter]);
else
sprintf(memName, "%s", parameterName[iParameter]);
rpn_store(data1, NULL, rpn_create_mem(memName, 0));
fprintf(stdout, "%le --> %s\n", data1, memName);
free(parameterName[iParameter]);
}
}
if (memName)
free(memName);
if (parameterName)
free(parameterName);
}
}
long expandColumnPairNames(SDDS_DATASET *SDDSin, char ***name, char ***errorName, long names, char **excludeName,
long excludeNames, long typeMode, long typeValue)
{
long i, j, names1, errorNames1, names2;
char **name1, **errorName1, **name2, **errorName2;
if (!names || !*name)
return 0;
name2 = errorName1 = errorName2 = NULL;
names2 = errorNames1 = 0;
for (i=0; i<names; i++) {
switch (typeMode) {
case FIND_ANY_TYPE:
case FIND_NUMERIC_TYPE:
case FIND_INTEGER_TYPE:
case FIND_FLOATING_TYPE:
names1 = SDDS_MatchColumns(SDDSin, excludeNames?NULL:&name1, SDDS_MATCH_STRING, typeMode,
(*name)[i], SDDS_0_PREVIOUS|SDDS_OR);
break;
case FIND_SPECIFIED_TYPE:
if (!SDDS_VALID_TYPE(typeValue))
SDDS_Bomb("invalid type value in expandColumnPairNames");
names1 = SDDS_MatchColumns(SDDSin, excludeNames?NULL:&name1, SDDS_MATCH_STRING, typeMode, typeValue,
(*name)[i], SDDS_0_PREVIOUS|SDDS_OR);
break;
default:
SDDS_Bomb("invalid typeMode in expandColumnPairNames");
exit(1);
break;
}
if (names1==0)
continue;
if (names1==-1) {
SDDS_PrintErrors(stderr, SDDS_VERBOSE_PrintErrors);
SDDS_Bomb("unable to perform column name match in expandColumnPairNames");
}
if (excludeNames) {
for (j=0; j<excludeNames; j++)
if (!(names1=SDDS_MatchColumns(SDDSin, (j==excludeNames-1?&name1:0),
SDDS_MATCH_STRING, FIND_ANY_TYPE,
excludeName[j], SDDS_NEGATE_MATCH|SDDS_AND)))
break;
}
if (!names1)
continue;
moveToStringArray(&name2, &names2, name1, names1);
if (errorName && *errorName && (*errorName)[i]) {
if (strstr((*errorName)[i], "%s")) {
if (!(errorName1 = (char**)malloc(sizeof(*errorName1)*names1)))
SDDS_Bomb("allocation failure in expandColumnPairNames");
errorNames1 = names1;
for (j=0; j<names1; j++) {
if (!(errorName1[j] = (char*)malloc(sizeof(**errorName1)*
strlen(name1[j])+strlen((*errorName)[i])+1)))
SDDS_Bomb("allocation failure in expandColumnPairNames");
replace_stringn(errorName1[j], (*errorName)[i], "%s", name1[j], 1);
if (SDDS_CheckColumn(SDDSin, errorName1[j], NULL, SDDS_ANY_NUMERIC_TYPE, stderr)!=SDDS_CHECK_OKAY)
exit(1);
}
}
else if (names1==1) {
errorNames1 = 1;
if (!(errorName1 = (char**)malloc(sizeof(*errorName1))))
SDDS_Bomb("allocation failure in expandColumnPairNames");
if (!SDDS_CopyString(errorName1, (*errorName)[i]))
return 0;
}
else
SDDS_Bomb("%s template must be employed with error names when primary name has wildcards");
names2 -= names1;
moveToStringArray(&errorName2, &names2, errorName1, errorNames1);
free(errorName1);
free(name1);
}
}
if (names2==0)
return 0;
SDDS_FreeStringArray(*name, names);
*name = name2;
if (errorName) {
if (*errorName)
SDDS_FreeStringArray(*errorName, names);
*errorName = errorName2;
}
return names2;
}
