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diff --git a/src/silx/io/specfile/src/sfdata.c b/src/silx/io/specfile/src/sfdata.c
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+# /*##########################################################################
+# Copyright (C) 1995-2017 European Synchrotron Radiation Facility
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ############################################################################*/
+/************************************************************************
+ *
+ * File: sfdata.c
+ *
+ * Project: SpecFile library
+ *
+ * Description: Functions for getting data
+ *
+ * Author: V.Rey
+ *
+ * Date: $Date: 2005/07/04 15:02:38 $
+ *
+ ************************************************************************/
+/*
+ * Log: $Log: sfdata.c,v $
+ * Log: Revision 1.8 2005/07/04 15:02:38 ahoms
+ * Log: Fixed memory leak in SfNoDataLines
+ * Log:
+ * Log: Revision 1.7 2004/01/20 09:23:50 sole
+ * Log: Small change in sfdata (ptr < (to-1)) changed to (ptr <= (to-1))
+ * Log:
+ * Log: Revision 1.6 2003/03/06 16:56:40 sole
+ * Log: Check if to is beyond the scan size in SfData (still not finished but it seems to solve a crash)
+ * Log:
+ * Log: Revision 1.5 2002/12/09 13:04:05 sole
+ * Log: Added a check in SfNoDataLines
+ * Log:
+ * Log: Revision 1.4 2002/11/13 15:02:38 sole
+ * Log: Removed some printing in SfData
+ * Log:
+ * Log: Revision 1.3 2002/11/12 16:22:07 sole
+ * Log: WARNING: Developing version - Improved MCA reading and reading properly the end of the file.
+ * Log:
+ * Log: Revision 1.2 2002/11/12 13:15:52 sole
+ * Log: 1st version from Armando. The idea behind is to take the last line only if it ends with \n
+ * Log:
+ * Log: Revision 3.0 2000/12/20 14:17:19 rey
+ * Log: Python version available
+ * Log:
+ * Revision 2.1 2000/07/31 19:05:11 19:05:11 rey (Vicente Rey-Bakaikoa)
+ * SfUpdate and bug corrected in ReadIndex
+ *
+ * Revision 2.0 2000/04/13 13:28:54 13:28:54 rey (Vicente Rey-Bakaikoa)
+ * New version of the library. Complete rewrite
+ * Adds support for MCA
+ *
+ */
+#include <SpecFile.h>
+#include <SpecFileP.h>
+#include <locale_management.h>
+
+#ifndef _GNU_SOURCE
+#ifdef PYMCA_POSIX
+#include <locale.h>
+#endif
+#endif
+
+#include <ctype.h>
+/*
+ * Define macro
+ */
+#define isnumber(this) ( isdigit(this) || this == '-' || this == '+' || this == '.' || this == 'E' || this == 'e')
+
+/*
+ * Mca continuation character
+ */
+#define MCA_CONT '\\'
+#define D_INFO 3
+
+/*
+ * Declarations
+ */
+DllExport long SfNoDataLines ( SpecFile *sf, long index, int *error );
+DllExport int SfData ( SpecFile *sf, long index, double ***retdata,
+ long **retinfo, int *error );
+DllExport long SfDataAsString ( SpecFile *sf, long index,
+ char ***data, int *error );
+DllExport long SfDataLine ( SpecFile *sf, long index, long line,
+ double **data_line, int *error );
+DllExport long SfDataCol ( SpecFile *sf, long index, long col,
+ double **data_col, int *error );
+DllExport long SfDataColByName( SpecFile *sf, long index,
+ char *label, double **data_col, int *error );
+
+
+/*********************************************************************
+ * Function: long SfNoDataLines( sf, index, error )
+ *
+ * Description: Gets number of data lines in a scan
+ *
+ * Parameters:
+ * Input : (1) File pointer
+ * (2) Index
+ * Output:
+ * (3) error number
+ * Returns:
+ * Number of data lines ,
+ * ( -1 ) => errors.
+ * Possible errors:
+ * SF_ERR_SCAN_NOT_FOUND
+ *
+ *********************************************************************/
+DllExport long
+SfNoDataLines( SpecFile *sf, long index, int *error )
+{
+ long *dinfo = NULL;
+ double **data = NULL;
+ long nrlines = 0;
+ int ret, i;
+
+ ret = SfData(sf,index,&data,&dinfo,error);
+
+ if (ret == -1) {
+ return(-1);
+ }
+ if (dinfo == (long *) NULL){
+ return(-1);
+ }
+ if (dinfo[ROW] < 0){
+ printf("Negative number of points!\n");
+ /*free(dinfo);*/
+ return(-1);
+ }
+
+ nrlines = dinfo[ROW];
+
+ /* now free all stuff that SfData allocated */
+ for (i = 0; i < nrlines; i++)
+ free(data[i]);
+ free(data);
+ free(dinfo);
+
+ return nrlines;
+}
+
+
+
+/*********************************************************************
+ * Function: int SfData(sf, index, data, data_info, error)
+ *
+ * Description: Gets data.
+ * Parameters:
+ * Input : (1) File pointer
+ * (2) Index
+ * Output:
+ * (3) Data array
+ * (4) Data info : [0] => no_lines
+ * [1] => no_columns
+ * [2] = ( 0 ) => regular
+ * ( 1 ) => not regular !
+ * (5) error number
+ * Returns:
+ * ( 0 ) => OK
+ * ( -1 ) => errors occured
+ * Possible errors:
+ * SF_ERR_MEMORY_ALLOC
+ * SF_ERR_FILE_READ
+ * SF_ERR_SCAN_NOT_FOUND
+ * SF_ERR_LINE_NOT_FOUND
+ *
+ * Remark: The memory allocated should be freed by the application
+ *
+ *********************************************************************/
+DllExport int
+SfData( SpecFile *sf, long index, double ***retdata, long **retinfo, int *error )
+{
+ long *dinfo = NULL;
+ double **data = NULL;
+ double *dataline = NULL;
+ long headersize;
+
+ char *ptr,
+ *from,
+ *to;
+
+ char strval[100];
+ double val;
+ double valline[512];
+ long cols,
+ maxcol=512;
+ long rows;
+ int i;
+#ifndef _GNU_SOURCE
+#ifdef PYMCA_POSIX
+ char *currentLocaleBuffer;
+ char localeBuffer[21];
+#endif
+#endif
+
+ if (index <= 0 ){
+ return(-1);
+ }
+
+ if (sfSetCurrent(sf,index,error) == -1 )
+ return(-1);
+
+
+ /*
+ * Copy if already there
+ */
+ if (sf->data_info != (long *)NULL) {
+ dinfo = ( long * ) malloc ( sizeof(long) * D_INFO);
+ dinfo[ROW] = sf->data_info[ROW];
+ dinfo[COL] = sf->data_info[COL];
+ dinfo[REG] = sf->data_info[REG];
+ data = ( double **) malloc ( sizeof(double *) * dinfo[ROW]);
+ for (i=0;i<dinfo[ROW];i++) {
+ data[i] = (double *)malloc (sizeof(double) * dinfo[COL]);
+ memcpy(data[i],sf->data[i],sizeof(double) * dinfo[COL]);
+ }
+ *retdata = data;
+ *retinfo = dinfo;
+ return(0);
+ }
+ /*
+ * else do the job
+ */
+
+ if ( ((SpecScan *)sf->current->contents)->data_offset == -1 ) {
+ *retdata = data;
+ *retinfo = dinfo;
+ return(-1);
+ }
+
+ headersize = ((SpecScan *)sf->current->contents)->data_offset
+ - ((SpecScan *)sf->current->contents)->offset;
+
+ from = sf->scanbuffer + headersize;
+ to = sf->scanbuffer + ((SpecScan *)sf->current->contents)->size;
+ if (to > sf->scanbuffer+sf->scansize){
+ /* the -32 found "experimentaly" */
+ ptr = sf->scanbuffer+sf->scansize - 32;
+ while (*ptr != '\n') ptr--;
+ to=ptr;
+ /*printf("I let it crash ...\n");*/
+ }
+ i=0;
+ ptr = from;
+ rows = -1;
+ cols = -1;
+ /*
+ * Alloc memory
+ */
+ if ( (data = (double **) malloc (sizeof(double *)) ) == (double **)NULL) {
+ *error = SF_ERR_MEMORY_ALLOC;
+ return(-1);
+ }
+
+ if ( (dinfo = (long *) malloc(sizeof(long) * D_INFO) ) == (long *)NULL) {
+ free(data);
+ *error = SF_ERR_MEMORY_ALLOC;
+ return(-1);
+ }
+ ptr = from;
+ dinfo[ROW] = dinfo[COL] = dinfo[REG] = 0;
+
+#ifndef _GNU_SOURCE
+#ifdef PYMCA_POSIX
+ currentLocaleBuffer = setlocale(LC_NUMERIC, NULL);
+ strcpy(localeBuffer, currentLocaleBuffer);
+ setlocale(LC_NUMERIC, "C\0");
+#endif
+#endif
+ for ( ; ptr < to; ptr++) {
+ /* get a complete line */
+ i=0;
+ cols=0;
+ /*I should be at the start of a line */
+ while(*(ptr) != '\n'){
+ if (*(ptr-1) == '\n'){
+ /*I am at the start of a line */
+ while(*ptr == '#'){
+ if (ptr >= to)
+ break;
+ for (; ptr < to; ptr++){
+ if (*ptr == '\n'){
+ break;
+ }
+ };
+ /* on exit is equal to newline */
+ if (ptr < to) {
+ ptr++;
+ }
+ }
+ if (*ptr == '@') {
+ /*
+ * read all mca block: go while in buffer ( ptr < to - 1 )
+ * and while a newline is preceded by a slash
+ */
+ for ( ptr = ptr + 2;
+ (*ptr != '\n' || (*(ptr-1) == MCA_CONT)) && ptr < to ;
+ ptr++);
+ if (ptr >= to){
+ break;
+ }
+ }
+ while(*ptr == '#'){
+ if (ptr >= to)
+ break;
+ for (; ptr < to; ptr++){
+ if (*ptr == '\n'){
+ break;
+ }
+ };
+ /* on exit is equal to newline */
+ if (ptr < to) {
+ ptr++;
+ }
+ }
+ /* first characters of buffer
+ */
+ while (*ptr == ' ' && ptr < to) ptr++; /* get rid of empty spaces */
+ }
+ /*
+ * in the middle of a line
+ */
+ if (*ptr == ' ' || *ptr == '\t' ) {
+ strval[i] = '\0';
+ i = 0;
+ val = PyMcaAtof(strval);
+ valline[cols] = val;
+ cols++;
+ if (cols >= maxcol) return(-1);
+ while(*(ptr+1) == ' ' || *(ptr+1) == '\t') ptr++;
+ } else {
+ if isnumber(*ptr){
+ strval[i] = *ptr;
+ i++;
+ }
+ }
+ if (ptr >= (to-1)){
+ break;
+ }
+ ptr++;
+ }
+ if ((*(ptr)== '\n') && (i != 0)){
+ strval[i] = '\0';
+ val = PyMcaAtof(strval);
+ valline[cols] = val;
+ cols++;
+ if (cols >= maxcol) return(-1);
+ /*while(*(ptr+1) == ' ' || *(ptr+1) == '\t') ptr++;*/
+ }
+ /*printf("%c",*ptr);*/
+ /* diffract31 crash -> changed from i!=0 to i==0 */
+ /*cols>0 necessary scan 59 of 31oct98 */
+ if ((ptr < to) && (cols >0)) {
+ rows++;
+ /*cols++;*/
+ if (cols >= maxcol) return(-1);
+ /* printf("Adding a new row, nrows = %ld, ncols= %ld\n",rows,cols);*/
+ /*printf("info col = %d cols = %d\n", dinfo[COL], cols);*/
+ if (dinfo[COL] != 0 && cols != dinfo[COL]) {
+ ;
+ /*diffract31 crash -> nextline uncommented */
+ dinfo[REG] = 1;
+ } else {
+ dinfo[COL] = cols;
+ }
+ if(dinfo[COL]==cols){
+ dataline = (double *)malloc(sizeof(double) * cols);
+ memcpy(dataline,valline,sizeof(double) * cols);
+ data = (double **) realloc ( data, sizeof(double) * (rows+1));
+ data[rows] = dataline;
+ dinfo[ROW]=rows+1;
+ }else{
+ printf("Error on scan %d line %d\n", (int) index, (int) (rows+1));
+ /* just ignore the line instead of stopping there with a
+ break; */
+ rows--;
+ }
+ }
+ }
+
+#ifndef _GNU_SOURCE
+#ifdef PYMCA_POSIX
+ setlocale(LC_NUMERIC, localeBuffer);
+#endif
+#endif
+ /*
+ * make a copy in specfile structure
+ */
+ if ( dinfo[ROW] != 0 && dinfo[REG] == 0) {
+ if (sf->data_info != (long *)NULL){
+ printf("I should not be here!/n");
+ sf->data_info[ROW] = dinfo[ROW];
+ sf->data_info[COL] = dinfo[COL];
+ sf->data_info[REG] = dinfo[REG];
+ for (i=0;i<dinfo[ROW];i++) {
+ sf->data[i]= (double *)realloc (sf->data[i],sizeof(double) * dinfo[COL]);
+ if (sf->data[i] == (double *) NULL){
+ printf("Realloc problem");
+ return (-1);
+ }
+ memcpy(sf->data[i],data[i],sizeof(double) * dinfo[COL]);
+ }
+ *retdata = data;
+ *retinfo = dinfo;
+ return(0);
+ }else{
+ sf->data_info = ( long * ) malloc ( sizeof(long) * D_INFO);
+ sf->data_info[ROW] = dinfo[ROW];
+ sf->data_info[COL] = dinfo[COL];
+ sf->data_info[REG] = dinfo[REG];
+ sf->data = ( double **) malloc ( sizeof(double *) * dinfo[ROW]);
+ if (sf->data == (double **) NULL){
+ printf("malloc1 problem");
+ return (-1);
+ }
+ for (i=0;i<dinfo[ROW];i++) {
+ sf->data[i] = (double *)malloc (sizeof(double) * dinfo[COL]);
+ if (sf->data[i] == (double *) NULL){
+ printf("malloc2 problem");
+ return (-1);
+ }
+ memcpy(sf->data[i],data[i],sizeof(double) * dinfo[COL]);
+ }
+ }
+ } else {
+ if (dinfo[REG] == 0) {
+ ;
+ /*printf("Not Freeing data:!\n");*/
+ /* I can be in the case of an mca without scan points */
+ /*free(data);
+ return(-1);*/
+ }
+ }
+ *retinfo = dinfo;
+ *retdata = data;
+ return( 0 );
+}
+
+
+DllExport long
+SfDataCol ( SpecFile *sf, long index, long col, double **retdata, int *error )
+{
+ double *datacol=NULL;
+
+ long *dinfo = NULL;
+ double **data = NULL;
+
+ long selection;
+ int i,ret;
+
+ ret = SfData(sf,index,&data,&dinfo,error);
+
+ if (ret == -1) {
+ *error = SF_ERR_COL_NOT_FOUND;
+ *retdata = datacol;
+ return(-1);
+ }
+
+ if (col < 0) {
+ selection = dinfo[COL] + col;
+ } else {
+ selection = col - 1;
+ }
+if (selection > dinfo[COL] - 1) {
+selection=dinfo[COL] - 1;
+}
+ if ( selection < 0 || selection > dinfo[COL] - 1) {
+ *error = SF_ERR_COL_NOT_FOUND;
+ if ( dinfo != (long *)NULL) {
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ }
+ free(dinfo);
+ return(-1);
+ }
+
+ datacol = (double *) malloc( sizeof(double) * dinfo[ROW]);
+ if (datacol == (double *)NULL) {
+ *error = SF_ERR_MEMORY_ALLOC;
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+ return(-1);
+ }
+
+ for (i=0;i<dinfo[ROW];i++) {
+ datacol[i] = data[i][selection];
+ }
+
+ ret = dinfo[ROW];
+
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+
+ *retdata = datacol;
+ return(ret);
+}
+
+
+DllExport long
+SfDataLine( SpecFile *sf, long index, long line, double **retdata, int *error )
+{
+ double *datarow=NULL;
+
+ long *dinfo = NULL;
+ double **data = NULL;
+
+ long selection;
+ int ret;
+
+ ret = SfData(sf,index,&data,&dinfo,error);
+
+ if (ret == -1) {
+ *error = SF_ERR_LINE_NOT_FOUND;
+ *retdata = datarow;
+ return(-1);
+ }
+
+ if (line < 0) {
+ selection = dinfo[ROW] + line;
+ } else {
+ selection = line - 1;
+ }
+
+ if ( selection < 0 || selection > dinfo[ROW] - 1) {
+ *error = SF_ERR_LINE_NOT_FOUND;
+ if ( dinfo != (long *)NULL) {
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ }
+ free(dinfo);
+ return(-1);
+ }
+
+ datarow = (double *) malloc( sizeof(double) * dinfo[COL]);
+ if (datarow == (double *)NULL) {
+ *error = SF_ERR_MEMORY_ALLOC;
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+ return(-1);
+ }
+
+
+ memcpy(datarow,data[selection],sizeof(double) * dinfo[COL]);
+
+ ret = dinfo[COL];
+
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+
+ *retdata = datarow;
+ return(ret);
+}
+
+
+DllExport long
+SfDataColByName( SpecFile *sf, long index, char *label, double **retdata, int *error )
+{
+
+ double *datacol;
+
+ long *dinfo = NULL;
+ double **data = NULL;
+
+ int i,ret;
+
+ char **labels = NULL;
+
+ long nb_lab,
+ idx;
+
+ short tofree=0;
+
+ if ( sfSetCurrent(sf,index,error) == -1) {
+ *retdata = (double *)NULL;
+ return(-1);
+ }
+
+ if ( sf->no_labels != -1 ) {
+ nb_lab = sf->no_labels;
+ labels = sf->labels;
+ } else {
+ nb_lab = SfAllLabels(sf,index,&labels,error);
+ tofree = 1;
+ }
+
+ if ( nb_lab == 0 || nb_lab == -1) {
+ *retdata = (double *)NULL;
+ return(-1);
+ }
+
+ for (idx=0;idx<nb_lab;idx++)
+ if (!strcmp(label,labels[idx])) break;
+
+ if ( idx == nb_lab ) {
+ if (tofree) freeArrNZ((void ***)&labels,nb_lab);
+ *error = SF_ERR_COL_NOT_FOUND;
+ *retdata = (double *)NULL;
+ return(-1);
+ }
+
+ ret = SfData(sf,index,&data,&dinfo,error);
+
+ if (ret == -1) {
+ *retdata = (double *)NULL;
+ return(-1);
+ }
+
+ datacol = (double *) malloc( sizeof(double) * dinfo[ROW]);
+ if (datacol == (double *)NULL) {
+ *error = SF_ERR_MEMORY_ALLOC;
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+ *retdata = (double *)NULL;
+ return(-1);
+ }
+
+ for (i=0;i<dinfo[ROW];i++) {
+ datacol[i] = data[i][idx];
+ }
+
+ ret = dinfo[ROW];
+
+ if ( dinfo != (long *)NULL)
+ freeArrNZ((void ***)&data,dinfo[ROW]);
+ free(dinfo);
+
+ *retdata = datacol;
+
+ return(ret);
+}
+
+
+DllExport long
+SfDataAsString( SpecFile *sf, long index, char ***retdata, int *error )
+{
+ char **data=NULL;
+ char oneline[300];
+
+ char *from,
+ *to,
+ *ptr,
+ *dataline;
+
+ long headersize,rows;
+ int i;
+
+ if (sfSetCurrent(sf,index,error) == -1 )
+ return(-1);
+
+ if ( ((SpecScan *)sf->current->contents)->data_offset == -1 ) {
+ *retdata = data;
+ return(-1);
+ }
+
+ data = (char **) malloc (sizeof(char *));
+
+ headersize = ((SpecScan *)sf->current->contents)->data_offset
+ - ((SpecScan *)sf->current->contents)->offset;
+
+ from = sf->scanbuffer + headersize;
+ to = sf->scanbuffer + ((SpecScan *)sf->current->contents)->size;
+
+ rows = -1;
+ i = 0;
+
+ /*
+ * first characters of buffer
+ */
+
+ ptr = from;
+
+ if (isnumber(*ptr)) {
+ rows++;
+ oneline[i] = *ptr;
+ i++;
+ } else if (*ptr == '@') {
+ /*
+ * read all mca block: go while in buffer ( ptr < to - 1 )
+ * and while a newline is preceded by a slash
+ */
+ for ( ptr = ptr + 2;
+ (*(ptr+1) != '\n' || (*ptr == MCA_CONT)) && ptr < to - 1 ;
+ ptr++);
+ }
+
+ /*
+ * continue
+ */
+ ptr++;
+
+ for ( ; ptr < to - 1; ptr++) {
+ /*
+ * check for lines and for mca
+ */
+ if ( *(ptr-1) == '\n' ) {
+
+ if ( i != 0 ) {
+ oneline[i-1] = '\0';
+ i = 0;
+
+ dataline = (char *)strdup(oneline);
+ data = (char **) realloc ( data, sizeof(char *) * (rows +1));
+ data[rows] = dataline;
+ }
+
+ if ( *ptr == '@') { /* Mca --> pass it all */
+ for ( ptr = ptr + 2;
+ (*ptr != '\n' || (*(ptr-1) == MCA_CONT)) && ptr < to ;
+ ptr++);
+ } else if ( *ptr == '#') { /* Comment --> pass one line */
+ for (ptr = ptr + 1; *ptr != '\n';ptr++);
+ } else if ( isnumber(*ptr) ) {
+ rows++;
+ oneline[i] = *ptr;
+ i++;
+ }
+ } else {
+ if (rows == -1) continue;
+
+ oneline[i] = *ptr;
+ i++;
+ }
+ }
+
+ /*
+ * last line
+ */
+
+ if (rows != -1 && i) {
+ oneline[i-1] = '\0';
+ dataline = (char *)strdup(oneline);
+ data = (char **) realloc ( data, sizeof(char *) * (rows+1));
+ data[rows] = dataline;
+ }
+
+ *retdata = data;
+ return(rows+1);
+}
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