/*===========================================================================
  Copyright (C) 2001 European Southern Observatory (ESO)

  This program is free software; you can redistribute it and/or 
  modify it under the terms of the GNU General Public License as 
  published by the Free Software Foundation; either version 2 of 
  the License, or (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public 
  License along with this program; if not, write to the Free 
  Software Foundation, Inc., 675 Massachusetss Ave, Cambridge, 
  MA 02139, USA.

  Corresponding concerning ESO-MIDAS should be addressed as follows:
    Internet e-mail: midas@eso.org
    Postal address: European Southern Observatory
            Data Management Division 
            Karl-Schwarzschild-Strasse 2
            D 85748 Garching bei Muenchen 
            GERMANY
===========================================================================*/
/* Program  : mainstandfast.c                                              */
/* Author   : G. Mulas  -  ITAL_FLAMES Consortium                          */
/* Date     :                                                              */
/*                                                                         */
/* Purpose  : Missing                                                      */
/*                                                                         */
/*                                                                         */
/* Input:  see interface                                                   */ 
/*                                                                      */
/* Output:                                                              */
/*                                                                         */
/* DRS Functions called:                                                   */
/* none                                                                    */ 
/*                                                                         */ 
/* Pseudocode:                                                             */
/* Missing                                                                 */ 
/*                                                                         */ 
/* Version  :                                                              */
/* Last modification date: 2002/08/05                                      */
/* Who     When        Why                Where                            */
/* AMo     02-08-05   Add header         header                            */
/*-------------------------------------------------------------------------*/
/* C functions include files */ 

#ifdef HAVE_CONFIG_H
#  include <config.h>
#endif


#include <ctype.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* MIDAS include files */
#include <flames_readallff.h>
#include <flames_optsynth.h>
#include <flames_writesynth.h>
#include <flames_scatter.h>
#include <flames_write_spectra.h>
#include <flames_prepstand.h>
#include <flames_dostandard.h>
#include <flames_readback.h>
#include <flames_readframe.h>
#include <flames_freeordpos.h>
#include <flames_ffslitmultiply.h>
#include <flames_midas_def.h>
#include <flames_writeback.h>
#include <flames_freeallflats.h>
#include <flames_freespectrum.h>
#include <flames_computeback.h>
#include <flames_freeslitflats.h>
#include <flames_freeframe.h>
/* FLAMES-UVES include files */ 
#include <flames_newmatrix.h>
#include <flames_mainstandfast.h>
#include <uves_msg.h>
#include <flames_readordpos.h>
#include <flames_readslitflats.h>



int flames_mainstandfast(const char *IN_A,
                         const cpl_frameset *fibff_set,
                         const cpl_frameset *slitff_set,
                         const char *IN_D,
                         const char *IN_E,
                         const char *BASENAME,
                         const double *MAXDISCARDFRACT,
                         const int *MAXBACKITERS,
                         const int *BKGPOL,
                         const char *BKGFITINLINE,  //was int*
                         const char *BKGFITMETHOD,
                         const char *BKGBADSCAN,   //was int*
                         const int *BKGBADWIN,
                         const double *BKGBADMAXFRAC,
                         const int *BKGBADMAXTOT,
                         const double *SIGMA,
                         const double *WINDOW,
                         double *OUTPUTD,
                         int *OUTPUTI)
{ 
    char output[200];
    int i=0;
    int unit=0;
    int actvals=0;
    frame_mask **mask=0;
    int bxdegree=0, bydegree=0;
    double kappa=0;
    double kappa2=0;
    int chisqpixels=0, nfittedparams=0;
    int maxbackiters=0;
    double maxdiscardfract=0;
    double chisquare=0;
    frame_data **backframe;
    frame_data **normcover;
    flames_err status=0;
    double ***pfibrecentre=0;
    double halfwinsize=0, phalfwinsize=0;

    flames_frame *ScienceFrame=0;

    allslitflats *Slit_FF=0;

    allflats *Shifted_FF=0;

    orderpos *Order=0;

    //char allfile[CATREC_LEN+2];
    //char slitsfile[CATREC_LEN+2];
    const cpl_frameset* allfile=fibff_set;
    const cpl_frameset* slitsfile=slitff_set;


    char backfile[CATREC_LEN+2];
    char infile[CATREC_LEN+2];
    char catfile[CATREC_LEN+2];
    char orderfile[CATREC_LEN+2];
    int32_t n=0;
    int32_t iframe=0;
    int nval=0;
    int null=0;
    int32_t iorder=0, ifibre=0, ix=0;
    scatterswitch bkgswitch=USEALL;
    scatterswitch2 bkgswitch2=NOBADSCAN;
    int badwinxsize=0;
    int badwinysize=0;
    double badfracthres=0;
    int badtotthres=0;
    char keytype=0;
    int noelem=0;
    int bytelem=0;
    char bkgfitmethod[CATREC_LEN+1];
    int32_t orderoffset=0;
    int32_t realfirstorder=0;
    int32_t reallastorder=0;
    int32_t slitfirstorder=0;
    int32_t slitlastorder=0;
    int32_t negativepixels=0;
    char bkginline=TRUE;

    frame_data *fdvecbuf1=0;
    frame_data *fdvecbuf2=0;
    frame_data *fdvecbuf3=0;



    frame_mask *fmvecbuf1=0;
    frame_mask *fmvecbuf2=0;
    frame_mask *fmvecbuf3=0;
    frame_data pixelvalue=0;


    int32_t lastiyixindex=0;
    int32_t iorderifibreixstart=0;
    int32_t iorderifibreixend=0;
    int32_t iorderifibreindex=0;
    int32_t iorderifibreixoffset=0;
    int32_t iorderifibreixindex=0;
    int32_t ixiorderifibreindex=0;

    memset(output, 0, 200);
    memset(bkgfitmethod, 0, CATREC_LEN+1);

    bkgswitch = USEALL;

    SCSPRO("standfast"); /* Get into MIDAS Env. */

    /* Read once and for all, here at the beginning, what MIDAS keywords we
    need */

    /* get input frame name from MIDAS env.*/
    SCKGETC(IN_A,1,CATREC_LEN+1,&nval,infile);

    /* read input table name */
    SCKGETC(IN_D,1,160,&nval,backfile);

    /* read order table name */
    SCKGETC(IN_E,1,160,&nval,orderfile);

    /* read output base name */
    if (SCKGETC(BASENAME,1,160,&nval,catfile)!=0) {
        /* problems reading BASENAME */
        SCTPUT("Error reading the base name for output spectra");
        return flames_midas_fail();
    }

    /* initialise MAXDISCARDFRACT from keyword */
    if (SCKRDD(MAXDISCARDFRACT, 1, 1, &actvals, &maxdiscardfract, &unit,
                    &null) != 0) {
        /* problems reading MAXDISCARDFRACT */
        SCTPUT("Error reading the MAXDISCARDFRACT keyword");
        return flames_midas_fail();
    }
    /* initialise MAXBACKITERS from keyword */
    if (SCKRDI(MAXBACKITERS, 1, 1, &actvals, &maxbackiters, &unit,
                    &null) != 0) {
        /* problems reading MAXBACKITERS */
        SCTPUT("Error reading the MAXBACKITERS keyword");
        return flames_midas_fail();
    }

    /* initialise background fitting scalars */
    if (SCKRDI(BKGPOL, 1, 1, &actvals, &bxdegree, &unit, &null)
                    != 0) {
        /* problems reading xdegree */
        SCTPUT("Error reading the x degree of the background polynomial");
        return flames_midas_fail();
    }
    if (SCKRDI(BKGPOL, 2, 1, &actvals, &bydegree, &unit, &null)
                    != 0) {
        /* problems reading xdegree */
        SCTPUT("Error reading the y degree of the background polynomial");
        return flames_midas_fail();
    }

    /* Is inline background fitting and subtraction required? */
    if (SCKFND_string(BKGFITINLINE, &keytype, &noelem, &bytelem) != 0) {
        /* SCKFND failed, major problems */
        SCTPUT("Internal MIDAS error in mainopt: SCKFND failed");
        return flames_midas_fail();
    }
    switch(keytype) {
    case 'C':
        /* it exists and it is a character keyword, do read it */
        if (SCKGETC(BKGFITINLINE, 1, CATREC_LEN, &nval, bkgfitmethod)
                        != 0) {
            /* problems reading BKGFITINLINE */
            SCTPUT("Warning: error reading the BKGFITINLINE keyword, falling back to \
default");
        }
        else {
            /* is the string long enough to be unambiguous? */
            if (nval<1) {
                SCTPUT("Warning: BKGFITINLINE is ambiguous, falling back to default");
            }
            else {
                /* convert bkgfitmethod to upper case, to ease the subsequent check */
                for (i=0; i<=(nval-1); i++) bkgfitmethod[i] = toupper(bkgfitmethod[i]);
                /* compare as many letters as we have with the expected values */
                if (strncmp("YES", bkgfitmethod, (size_t) nval) == 0)
                    bkginline = TRUE;
                else if (strncmp("NO", bkgfitmethod, (size_t) nval)
                                == 0) bkginline = FALSE;
                else {
                    SCTPUT("Warning: unsupported BKGFITINLINE value, falling back to \
default");
                }
            }
        }
        break;
    case ' ':
        /* the keyword does not exist at all */
        SCTPUT("Warning: BKGFITINLINE is undefined, falling back to default");
        break;
    default:
        /* the keyword is of the wrong type */
        SCTPUT("Warning: BKGFITINLINE is not a string, falling back to default");
        break;
    }

    /* before trying to read it, make sure that BKGFITMETHOD exists and it is
    of the appropriate type */
    if (SCKFND_string(BKGFITMETHOD, &keytype, &noelem, &bytelem) != 0) {
        /* SCKFND failed, give up! */
        SCTPUT("Internal MIDAS error in mainopt: SCKFND failed");
        return flames_midas_fail();
    }
    switch(keytype) {
    case 'C':
        /* it exists and it is a character keyword, go ahead and read it */
        if (SCKGETC(BKGFITMETHOD, 1, CATREC_LEN, &nval, bkgfitmethod)
                        != 0) {
            /* problems reading BKGFITMETHOD */
            SCTPUT("Warning: error reading the BKGFITMETHOD keyword, falling back to \
default");
        }
        else {
            /* is the string long enough to be unambiguous? */
            if (nval<2) {
                /* no, fall back to the default */
                SCTPUT("Warning: BKGFITMETHOD is ambiguous, falling back to default");
            }
            else {
                /* convert bkgfitmethod to upper case, to ease the subsequent check */
                for (i=0; i<=(nval-1); i++) bkgfitmethod[i] = toupper(bkgfitmethod[i]);
                /* compare as many letters as we have with the expected values */
                if (strncmp("ALL", bkgfitmethod, (size_t) nval) == 0)
                    bkgswitch = USEALL;
                else if (strncmp("MEDIAN", bkgfitmethod, (size_t) nval)
                                == 0) bkgswitch = USEMEDIAN;
                else if (strncmp("MINIMUM", bkgfitmethod, (size_t) nval)
                                == 0) bkgswitch = USEMINIMUM;
                else if (strncmp("AVERAGE", bkgfitmethod, (size_t) nval)
                                == 0) bkgswitch = USEAVERAGE;
                else {
                    SCTPUT("Warning: unsupported BKGFITMETHOD value, falling back to \
default");
                }
            }
        }
        break;
    case ' ':
        /* the keyword does not exist at all */
        SCTPUT("Warning: BKGFITMETHOD is undefined, falling back to default");
        break;
    default:
        /* the keyword is of the wrong type */
        SCTPUT("Warning: BKGFITMETHOD is not a string, falling back to default");
        break;
    }

    /* before trying to read it, make sure that BKGFITMETHOD exists and it is
    of the appropriate type */
    if (SCKFND_string(BKGBADSCAN, &keytype, &noelem, &bytelem) != 0) {
        /* SCKFND failed, give up! */
        SCTPUT("Internal MIDAS error in mainopt: SCKFND failed");
        return flames_midas_fail();
    }
    switch(keytype) {
    case 'C':
        /* it exists and it is a character keyword, go ahead and read it */
        if (SCKGETC(BKGBADSCAN, 1, CATREC_LEN, &nval, bkgfitmethod)
                        != 0) {
            /* problems reading BKGFITMETHOD */
            SCTPUT("Warning: error reading the BKGBADSCAN keyword, falling back to \
default");
        }
        else {
            /* is the string long enough to be unambiguous? */
            if (nval<1) {
                /* no, fall back to the default */
                SCTPUT("Warning: BKGBADSCAN is ambiguous, falling back to default");
            }
            else {
                /* convert bkgfitmethod to upper case, to ease the subsequent check */
                for (i=0; i<=(nval-1); i++) bkgfitmethod[i] = toupper(bkgfitmethod[i]);
                /* compare as many letters as we have with the expected values */
                if (strncmp("NONE", bkgfitmethod, (size_t) nval) == 0)
                    bkgswitch2 = NOBADSCAN;
                else if (strncmp("FRACTION", bkgfitmethod, (size_t) nval)
                                == 0) bkgswitch2 = FRACBADSCAN;
                else if (strncmp("ABSOLUTE", bkgfitmethod, (size_t) nval)
                                == 0) bkgswitch2 = ABSBADSCAN;
                else {
                    SCTPUT("Warning: unsupported BKGBADSCAN value, falling back to \
default");
                }
            }
        }
        break;
    case ' ':
        /* the keyword does not exist at all */
        SCTPUT("Warning: BKGBADSCAN is undefined, falling back to default");
        break;
    default:
        /* the keyword is of the wrong type */
        SCTPUT("Warning: BKGBADSCAN is not a string, falling back to default");
        break;
    }

    /* if neighborhood bad pixel scanning was requested, read the other
    keywords needed */
    if (bkgswitch2 == FRACBADSCAN) {
        if ((SCKRDI(BKGBADWIN, 1, 1, &actvals, &badwinxsize, &unit, &null) != 0)
                        || (SCKRDI(BKGBADWIN, 2, 1, &actvals, &badwinysize, &unit, &null)
                                        != 0)) {
            SCTPUT("Error reading the BKGBADWIN keyword");
            return flames_midas_fail();
        }
        if (SCKRDD(BKGBADMAXFRAC, 1, 1, &actvals, &badfracthres, &unit,
                        &null) != 0) {
            SCTPUT("Error reading the BKGBADMAXFRAC keyword");
            return flames_midas_fail();
        }
        /* check the values read for consistence */
        if ((badwinxsize < 0) || (badwinysize < 0)) {
            SCTPUT("Warning: BKGBADWIN values must be non negative, disabling \
BKGBADSCAN");
            bkgswitch2 = NOBADSCAN;
        }
        if (badfracthres < 0) {
            SCTPUT("Warning: BKGBADMAXFRAC value must be non negative, disabling \
BKGBADSCAN");
            bkgswitch2 = NOBADSCAN;
        }
    }
    else if (bkgswitch2 == ABSBADSCAN) {
        if ((SCKRDI(BKGBADWIN, 1, 1, &actvals, &badwinxsize, &unit, &null) != 0)
                        || (SCKRDI(BKGBADWIN, 2, 1, &actvals, &badwinysize, &unit, &null)
                                        != 0)) {
            SCTPUT("Error reading the BKGBADWIN keyword");
            return flames_midas_fail();
        }
        if (SCKRDI(BKGBADMAXTOT, 1, 1, &actvals, &badtotthres, &unit,
                        &null) != 0) {
            SCTPUT("Error reading the BKGBADMAXTOT keyword");
            return flames_midas_fail();
        }
        /* check the values read for consistence */
        if ((badwinxsize < 0) || (badwinysize < 0)) {
            SCTPUT("Warning: BKGBADWIN values must be non negative, disabling \
BKGBADSCAN");
            bkgswitch2 = NOBADSCAN;
        }
        if (badtotthres < 0) {
            SCTPUT("Warning: BKGBADMAXTOT value must be non negative, disabling \
BKGBADSCAN");
            bkgswitch2 = NOBADSCAN;
        }
    }

    /* read the kappa factor to be used later in kappa-sigma clipping */
    if ((status=SCKRDD(SIGMA, 1, 1, &actvals, &kappa, &unit, &null))!=0) {
        /* something went wrong while reading the kappa-sigma factor */
        sprintf(output, "Error %d while reading SIGMA keyword", status);
        SCTPUT(output);
        return flames_midas_fail();
    }
    /* compute once and for all the square of kappa, as we will be using that */
    kappa2 = kappa*kappa;

    /* read the integration window size, to be used later in
    standard extraction */
    if ((status=SCKRDD(WINDOW, 1, 1, &actvals, &halfwinsize, &unit, &null))
                    !=0) {
        /* something went wrong while reading the kappa-sigma factor */
        sprintf(output, "Error %d while reading WINDOW keyword", status);
        SCTPUT(output);
        return flames_midas_fail();
    }
    /* compute once and for all halfwinsize, as we will be using that */
    halfwinsize /= 2;


    /* Link the MIDAS names of the frames to the physical ones */

    if(!(ScienceFrame = calloc(1, sizeof(flames_frame)))) {
        SCTPUT("Allocation error during ScienceFrame memory allocation");
        return flames_midas_fail();
    }

    /* Read the data of the frames and put them in the right C structures */

    /* let's read the Science Frame */
    sprintf(output, "I'm reading the frame %s", infile);
    SCTPUT(output);

    if (readframe(ScienceFrame, infile) != NOERR) {
        SCTPUT("Error while reading the frame");
        return flames_midas_fail();
    }

    /* Read the table data and then put them in the C structures */
    sprintf(output,"Reading the order/fibre table...");
    SCTPUT(output);
    if(!(Order = calloc(1, sizeof(orderpos)))) {
        SCTPUT("Allocation error during the allocation of Order structure");
        return flames_midas_fail();
    }
    /* use the readordpos function to read the descriptors */
    if (readordpos(orderfile, Order) != NOERR) {
        SCTPUT("Error while reading the order table");
        return flames_midas_fail();
    }
    /* does the order table match the Science frame chip? */
    if(Order->chipchoice != ScienceFrame->chipchoice) {
        /* no, it doesn't */
        SCTPUT("Error: chip mismatch between Science frame and order table");
        return flames_midas_fail();
    }

    /* initialise firstorder and lastorder in ScienceFrame from Order */
    ScienceFrame->firstorder = Order->firstorder;
    ScienceFrame->lastorder = Order->lastorder;
    ScienceFrame->tab_io_oshift = Order->tab_io_oshift;

    /* allocate and initialise the frame which will contain the
    estimated background. This will remain zero if no background fitting 
    was required*/
    lastiyixindex = (ScienceFrame->subrows*ScienceFrame->subcols)-1;
    backframe = fdmatrix(0, ScienceFrame->subrows-1, 0,
                    ScienceFrame->subcols-1);
    memset(&backframe[0][0], 0,
           ScienceFrame->subrows*ScienceFrame->subcols*sizeof(frame_data));

    if (bkginline==TRUE) {
        /* Inline background fitting and subtraction required */

        SCTPUT("*** Step 1: Background fitting and subtraction ***\n");

        sprintf(output, "I'm reading the background table %s", backfile);
        SCTPUT(output); /* Display text w/o storing it into MIDAS logfile */

        /* read in the background table */
        if ((status=readback(&(ScienceFrame->back), backfile, bxdegree, bydegree))
                        != NOERR) {
            /* something went wrong while reading the background table */
            sprintf(output, "Error %d while reading the background table", status);
            SCTPUT(output);
            return flames_midas_fail();
        }

        /* Calculate the fit model of the background */

        SCTPUT("Start the background fitting procedure");

        if (ScienceFrame->back.Window_Number > 0) {
            if (scatter(ScienceFrame, Order, bkgswitch, bkgswitch2, badwinxsize,
                            badwinysize, badfracthres, badtotthres, kappa2,
                            (int32_t) maxbackiters, maxdiscardfract, OUTPUTI)) {
                SCTPUT("Error executing the scatter function");
                return flames_midas_fail();
            }
            /* compute the estimated background */
            if (computeback(ScienceFrame, backframe) != NOERR) {
                SCTPUT("Error computing fitted background");
                return flames_midas_fail();
            }
            /* subtract the estimated background from the data frame */
            /* the error of the estimated background is assumed to be negligible */
            SCTPUT("Subtracting fitted background from Science Frame");
            fdvecbuf1 = ScienceFrame->frame_array[0];
            fdvecbuf2 = backframe[0];
            for (ix=0; ix<=lastiyixindex; ix++) {
                fdvecbuf1[ix] -= fdvecbuf2[ix];
            }
            /* some more black magic to make the thing more robust: scan the frame
    for any negative pixel values; if any are found, compare them to the
    standard deviation: if the negative value is not compatible with zero, 
    mark that pixel as bad */
            negativepixels=0;
            fdvecbuf1 = ScienceFrame->frame_array[0];
            fdvecbuf2 = ScienceFrame->frame_sigma[0];
            fmvecbuf1 = ScienceFrame->badpixel[0];
            for (ix=0; ix<=lastiyixindex; ix++) {
                if (fmvecbuf1[ix]==0 && (pixelvalue=fdvecbuf1[ix])<0) {
                    if ((pixelvalue*pixelvalue)>4*fdvecbuf2[ix]) {
                        fmvecbuf1[ix]=1;
                        negativepixels++;
                    }
                }
            }

            if (negativepixels!=0) {
                sprintf(output, "Warning: %d pixels result lower than fitted \
background", negativepixels);
                SCTPUT(output);
                SCTPUT("either they are unmasked bad pixels or some contamination is");
                SCTPUT("skewing background determination");
            }
            SCTPUT("Writing fitted background frame to middumma.bdf");
            if (writeback(ScienceFrame, "middumma.bdf", backframe)!=NOERR)
                SCTPUT("Warning: error writing background frame to disk");
        }
        else {
            SCTPUT("Error: no regions available for background estimation");
            return flames_midas_fail();
        }

    }

    /* Allocate memory for the Shifted_FF structure */

    if(!(Shifted_FF = calloc(1, sizeof(allflats)))) {
        SCTPUT("Allocation error during Shifted_FF structure memory allocation");
        return flames_midas_fail();
    }

    /* let's read the fibre FFs */

    sprintf(output, "I'm reading the fibre FF frames");
    SCTPUT(output);
    if (readallff(allfile, Shifted_FF) != NOERR) {
        SCTPUT("Error while reading the fibre Flat Field frames");
        return flames_midas_fail();
    }

    /* is this fibre FF frames set shiftable? */
    if (Shifted_FF->shiftable != 'y') {
        sprintf(output, "The fibre FF set is not slit-flatfielded");
        SCTPUT(output);
        return flames_midas_fail();
    }

    if (ScienceFrame->nflats != 0) {
        /* I need to deallocate the yshift vector and to reallocate it with
      a different size */
        free_dvector(ScienceFrame->yshift, 0, ScienceFrame->nflats-1);
    }
    /* set ScienceFrame->nflats equal to Shifted_FF->nflats, and allocate
    ScienceFrame->yshift accordingly */
    ScienceFrame->nflats = Shifted_FF->nflats;
    ScienceFrame->yshift = dvector(0, ScienceFrame->nflats-1);
    /* here, in the "fast" version, set the yshifts to zero
    with the simulated data the shifts ARE zero! */
    for (iframe=0; iframe <= (Shifted_FF->nflats-1); iframe++)
        ScienceFrame->yshift[iframe]=0;

    /* we must multiply the shifted FF frames by the slit FF, hence allocate
    and load the latter */
    if(!(Slit_FF = calloc(1, sizeof(allslitflats)))) {
        SCTPUT("Allocation error during Slit_FF memory allocation");
        return flames_midas_fail();
    }
    /* let's read the slit FFs */
    sprintf(output, "I'm reading the slit FF frames");
    SCTPUT(output);
    if ((status = readslitflats(slitsfile, Slit_FF)) != NOERR) {
        /* problems reading slitflats members from disk */
        SCTPUT("Error while reading the slit Flat Field frames");
        return flames_midas_fail();
    }
    orderoffset = Slit_FF->tab_io_oshift-Order->tab_io_oshift;
    slitfirstorder = Slit_FF->firstorder;
    slitlastorder = Slit_FF->lastorder;
    realfirstorder = Order->firstorder;
    if (orderoffset > 0) realfirstorder += orderoffset;
    reallastorder = Slit_FF->lastorder+orderoffset;
    if (reallastorder > Order->lastorder) reallastorder = Order->lastorder;
    if (realfirstorder > reallastorder) {
        /* this should really never happen with sane data, complain and exit */
        strcpy(output, "Error: The orders in the slit FF(s) and in the order \
table being used do not overlap at all!");
        SCTPUT(output);
        return flames_midas_fail();
    }
    /* make sure we do not attempt extraction for uncovered fibres */
    fmvecbuf1 = Shifted_FF->goodfibres[0][0];
    if (Order->firstorder<realfirstorder) {
        iorderifibreixstart = 0;
        iorderifibreixend = ((realfirstorder-Order->firstorder)*
                        Shifted_FF->maxfibres*Shifted_FF->subcols)-1;
        for (ix=iorderifibreixstart; ix<=iorderifibreixend; ix++) {
            fmvecbuf1[ix] = BADSLICE;
        }
    }
    if (Order->lastorder>reallastorder) {
        iorderifibreixstart = (reallastorder-Order->firstorder+1)*
                        Shifted_FF->maxfibres*Shifted_FF->subcols;
        iorderifibreixend = ((Order->lastorder-Order->firstorder)*
                        Shifted_FF->maxfibres*Shifted_FF->subcols)-1;
        for (ix=iorderifibreixstart; ix<=iorderifibreixend; ix++) {
            fmvecbuf1[ix] = BADSLICE;
        }
    }
    /* correct for the ycorrection, if present */
    if (Order->corrected=='t') {
        for (iframe=0; iframe<=(Slit_FF->nflats-1);iframe++)
            Slit_FF->slit[iframe].yshift -= Order->ycorrection;
    }
    /* do multiply the shifted fibre FF frames by the slit FF, in place
    to save memory */
    SCTPUT("Multiplying the shifted FF frame(s) by the slit FF frame(s)");
    if (ffslitmultiply(Slit_FF, Order, Shifted_FF, Shifted_FF) != NOERR) {
        SCTPUT("Error multiplying the shifted fibre FF by the slit FF");
        return flames_midas_fail();
    }
    /* copy the normalisation factors from the slit FF structure before
    freeing it for good */
    normcover = fdmatrix(0, Slit_FF->lastorder-Slit_FF->firstorder,
                    0, Slit_FF->subcols-1);
    memcpy(normcover[0], Slit_FF->normfactor[0],
           (size_t) ((Slit_FF->lastorder-Slit_FF->firstorder+1)*
                           Slit_FF->subcols)*sizeof(frame_data));
    /* finally free for good the memory for the slit FF */
    if (freeslitflats(Slit_FF)!=NOERR) {
        SCTPUT("Error while freeing the memory for the Slit_FF structure");
        return flames_midas_fail();
    }
    free(Slit_FF);

    SCTPUT("\n*** Step 2: prepare merged bad pixel mask and final \
initialisations ***\n");
    /* allocate the global, merged bad pixel mask and the upper and lower
    integration limits */
    mask=fmmatrix(0,ScienceFrame->subrows-1,0,ScienceFrame->subcols-1);
    if(!mask) {
        SCTPUT("Error allocating mask matrix");
        return flames_midas_fail();
    }
    pfibrecentre = d3tensor(0, Order->lastorder-Order->firstorder,
                    0, ScienceFrame->maxfibres-1,
                    0, ScienceFrame->subcols-1);
    if(!pfibrecentre) {
        SCTPUT("Error allocating pfibrecentre tensor");
        return flames_midas_fail();
    }
    /* it is pointless to use an integration window larger than fibre width */
    if (halfwinsize>Order->halfibrewidth) {
        SCTPUT("Warning: reducing window size to fibre width");
        halfwinsize = Order->halfibrewidth;
    }
    if (fabs(ScienceFrame->substepy) < DEPSILON) {
        /* the y step is too small, exit */
        SCTPUT("Error: the STEP in y is too small");
        return flames_midas_fail();
    }
    phalfwinsize = fabs(halfwinsize/ScienceFrame->substepy);

    /* initialise the global, merged bad pixel mask to be used
    in the subsequent standard extraction, initialise the lookup tables for 
    lit fibres in the ScienceFrame and allocate the arrays to store the 
    allocated spectra again in ScienceFrame */
    if (prepstand(ScienceFrame, Shifted_FF, Order, pfibrecentre, normcover,
                    orderoffset, realfirstorder, reallastorder, mask,
                    phalfwinsize)!=NOERR) {
        /* something went wrong in prepstand */
        SCTPUT("Error in prepstand");
        return flames_midas_fail();
    }


    /* Going to do the real spectrum extraction */
    SCTPUT("\n*** Step 3: standard extraction proper ***\n");
    if (dostandard(ScienceFrame, Order, Shifted_FF, mask, pfibrecentre,
                    phalfwinsize, realfirstorder, reallastorder) != NOERR) {
        SCTPUT("Error in dostandard");
        return flames_midas_fail();
    }

    /* free here pfibrecentre, unneeded from now on */
    free_d3tensor(pfibrecentre, 0, Order->lastorder-Order->firstorder,
                  0, ScienceFrame->maxfibres-1,
                  0, ScienceFrame->subcols-1);

    /* free the old bad pixel mask, replace it with the global mask */
    free_fmmatrix(ScienceFrame->badpixel, 0, ScienceFrame->subrows-1, 0,
                  ScienceFrame->subcols-1);
    ScienceFrame->badpixel = mask;

    /* build the fitted Science Frame, do it in place to save memory */
    if (optsynth(ScienceFrame, Shifted_FF, Order, &backframe, &chisquare,
                    &chisqpixels, &nfittedparams)!=NOERR){
        SCTPUT("Error computing the fitted frame");
        return flames_midas_fail();
    }
    SCKWRD(OUTPUTD, &chisquare, 1, 1, &unit);
    SCKWRI(OUTPUTI, &chisqpixels, 1, 1, &unit);
    SCKWRI(OUTPUTI, &nfittedparams, 2, 1, &unit);
    SCTPUT("Writing the synthesized data frame to middummb.bdf");
    SCTPUT("Writing the synthesized sigma frame to middummc.bdf");
    SCTPUT("Writing the overall mask to middummd.bdf");
    if (writesynth(ScienceFrame, "middummb.bdf", "middummc.bdf", "middummd.bdf")
                    != NOERR)
        SCTPUT("Warning: error writing dummy debugging frames");

    SCTPUT("\n*** Step 4: write extrated spectra to disk, clean up and \
exit ***\n");

    /* let's free a bit of memory */

    /* free the estimated background frame, we don't need it any more */
    free_fdmatrix(backframe, 0, ScienceFrame->subrows-1, 0,
                  ScienceFrame->subcols-1);

    /* free the normcover array */
    free_fdmatrix(normcover, 0, Order->lastorder-Order->firstorder,
                  0, ScienceFrame->subcols-1);

    /* Creating the output catalog of the spectra extracted */
    //Fixme: the next 3 lines are useless as that catalog is not used elsewhere
    //SCTPUT("Creating catalog of the spectra extracted");
    //SCCCRE("spectra.cat",F_IMA_TYPE,0);
    //SCTPUT("Created catalog of Spectra");

    /* can these spectra be normalised? */
    if ((Order->corrected == 't')&&(Shifted_FF->normalised == 'y')) {
        /* yes, compensation was performed already */
        SCTPUT("Correcting for normalisation factors");
        fdvecbuf1 = Shifted_FF->normfactors[0][0];
        fdvecbuf2 = Shifted_FF->normsigmas[0][0];
        fmvecbuf1 = Shifted_FF->goodfibres[0][0];
        fdvecbuf3 = ScienceFrame->spectrum[0][0];
        frame_data* fdvecbuf4 = ScienceFrame->normsigma[0][0];
        frame_data* fdvecbuf5 = ScienceFrame->specsigma[0][0];
        frame_data* fdvecbuf6 = ScienceFrame->normspec[0][0];
        frame_mask* fmvecbuf2 = ScienceFrame->specmask[0][0];
        frame_mask* fmvecbuf3 = ScienceFrame->normmask[0][0];
        for (ifibre=0; ifibre<=(ScienceFrame->maxfibres-1); ifibre++) {
            /* is this fibre lit? */
            if ((ScienceFrame->fibremask[ifibre] == TRUE) &&
                            (Shifted_FF->fibremask[ifibre] == TRUE)) {
                for (iorder=0; iorder<=(Order->lastorder-Order->firstorder); iorder++) {
                    iorderifibreindex = (iorder*ScienceFrame->maxfibres)+ifibre;
                    iorderifibreixoffset = iorderifibreindex*ScienceFrame->subcols;
                    for (ix=0; ix<=(ScienceFrame->subcols-1); ix++) {
                        iorderifibreixindex = iorderifibreixoffset+ix;
                        ixiorderifibreindex = (ix*(1+Order->lastorder-Order->firstorder)*
                                        ScienceFrame->maxfibres)+iorderifibreindex;
                        /* can this fibre be corrected here? */
                        if ((fmvecbuf2[ixiorderifibreindex]==1) &&
                                        (fmvecbuf1[iorderifibreixindex]==GOODSLICE)) {
                            /* yes, therefore correct and propagate errors */
                            frame_data normvalue = fdvecbuf1[iorderifibreixindex];
                            frame_data normvalue2 = normvalue*normvalue;
                            pixelvalue = ScienceFrame->spectrum[ix][iorder][ifibre];
                            fdvecbuf4[ixiorderifibreindex] =
                                            (fdvecbuf5[ixiorderifibreindex]/normvalue2) +
                                            ((pixelvalue*pixelvalue)*fdvecbuf2[iorderifibreixindex]/
                                                            (normvalue2*normvalue2));
                            fdvecbuf6[ixiorderifibreindex] =
                                            fdvecbuf3[ixiorderifibreindex]/normvalue;
                            fmvecbuf3[ixiorderifibreindex] = 1;
                        }
                        /* no, mark this slice as bad */
                        else {
                            fmvecbuf3[ixiorderifibreindex] = 0;
                            fdvecbuf6[ixiorderifibreindex] = 0;
                            fdvecbuf4[ixiorderifibreindex] = 0;
                        }
                    }
                }
            }
        }
    }
    else {
        SCTPUT("Warning: no correction factors available");
        fdvecbuf1 = ScienceFrame->normspec[0][0];
        fdvecbuf2 = ScienceFrame->normsigma[0][0];
        fmvecbuf1 = ScienceFrame->normmask[0][0];
        for (ifibre=0; ifibre<=(ScienceFrame->maxfibres-1); ifibre++) {
            /* is this fibre lit? */
            if ((ScienceFrame->fibremask[ifibre] == TRUE) &&
                            (Shifted_FF->fibremask[ifibre] == TRUE)) {
                for (iorder=0; iorder<=(Order->lastorder-Order->firstorder); iorder++) {
                    iorderifibreindex = (iorder*ScienceFrame->maxfibres)+ifibre;
                    for (ix=0; ix<=(ScienceFrame->subcols-1); ix++) {
                        ixiorderifibreindex = (ix*(1+Order->lastorder-Order->firstorder)*
                                        ScienceFrame->maxfibres)+iorderifibreindex;
                        fmvecbuf1[ixiorderifibreindex] = 0;
                        fdvecbuf1[ixiorderifibreindex] = 0;
                        fdvecbuf2[ixiorderifibreindex] = 0;
                    }
                }
            }
        }
    }

    for (n=0; n<ScienceFrame->maxfibres; n++) {
        if(ScienceFrame->fibremask[n] == TRUE) {
            if (n==0) sprintf(output,"Writing spectrum for the first fibre...");
            else if (n==1) sprintf(output,"Writing spectrum for the second fibre...");
            else if (n==2) sprintf(output,"Writing spectrum for the third fibre...");
            else sprintf(output,"Writing spectrum for the %d-th fibre...", n+1);
            SCTPUT(output);
            status=Write_Spectra(ScienceFrame, n, catfile);
            if (status) SCTPUT("Error during the writing on disk");
            else if (n==0) sprintf(output,"Spectrum for the first fibre written");
            else if (n==1) sprintf(output,"Spectrum for the second fibre written");
            else if (n==2) sprintf(output,"Spectrum for the third fibre written");
            else sprintf(output,"Spectrum for the %d-th fibre written", n+1);
            SCTPUT(output);
        }
    }

    /* finally free for good the ScienceFrame (including the spectrum),
    Shifted_FF and Order */
    if (free_spectrum(ScienceFrame)!=NOERR) {
        SCTPUT("Error while freeing the spectrum in the ScienceFrame structure");
        return flames_midas_fail();
    }
    if (freeframe(ScienceFrame)!=NOERR) {
        SCTPUT("Error while freeing the memory of the ScienceFrame structure");
        return flames_midas_fail();
    }
    free(ScienceFrame);
    if (freeallflats(Shifted_FF)!=NOERR) {
        SCTPUT("Error while freeing the memory of the Shifted_FF structure");
        return flames_midas_fail();
    }
    free(Shifted_FF);
    if (freeordpos(Order)!=NOERR) {
        SCTPUT("Error while freeing the memory of the Order structure");
        return flames_midas_fail();
    }
    free(Order);

    SCTPUT("\n*** Standard extraction complete ***\n");

    return SCSEPI();

}