// Copyright (C) 2006,2007,2008,2009, George Hobbs, Russel Edwards

/*

* This file is part of TEMPO2.

*

* TEMPO2 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 3 of the License, or

* (at your option) any later version.

* TEMPO2 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 TEMPO2. If not, see <http://www.gnu.org/licenses/>.

*/

/*

* If you use TEMPO2 then please acknowledge it by citing

* Hobbs, Edwards & Manchester (2006) MNRAS, Vol 369, Issue 2,

* pp. 655-672 (bibtex: 2006MNRAS.369..655H)

* or Edwards, Hobbs & Manchester (2006) MNRAS, VOl 372, Issue 4,

* pp. 1549-1574 (bibtex: 2006MNRAS.372.1549E) when discussing the

* timing model.

*/

#include <stdio.h>

#include <stdlib.h>

#include "tempo2.h"

#include <math.h>

#include <string.h>

void preProcessSimple (pulsar *psr)

{

const char *CVS_verNum = "$Id$";

if (displayCVSversion == 1) CVSdisplayVersion("preProcessSimple.C","preProcessSimple()",CVS_verNum);

preProcessSimple1 (psr, 0, -1);

preProcessSimple2 (psr, 0, 0, 0, 0);

preProcessSimple3 (psr);

}

void preProcessSimple1 (pulsar *psr, int tempo1, double thelast)

{

logdbg("In preProcessSimple1");

ECLIPTIC_OBLIQUITY = ECLIPTIC_OBLIQUITY_VAL;

int i = 0;

/* Check whitening */

if (psr->param[param_wave_om].paramSet[0] == 1 && psr->param[param_wave_om].val[0] == 0.0) /* Set fundamental frequency */

{

longdouble first=-1,last=-1;

for (i=0;i<psr->nobs;i++)

{

if (psr->obsn[i].deleted==0 && first==-1) first=psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && last==-1) last=psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && psr->obsn[i].sat < first) first = psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && psr->obsn[i].sat > last) last = psr->obsn[i].sat;

}

psr->param[param_wave_om].val[0] = 2.0*M_PI/(last-first)/

(1.0+4.0/(double)(psr->nWhite));

fprintf(stderr, "%.3le\n", (double)psr->param[param_wave_om].val[0]);

}

/* Check whitening */

if (psr->param[param_wave_dm].paramSet[0] == 1 && psr->param[param_wave_dm].val[0] == 0.0) /* Set fundamental frequency */

{

longdouble first=-1,last=-1;

for (i=0;i<psr->nobs;i++)

{

if (psr->obsn[i].deleted==0 && first==-1) first=psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && last==-1) last=psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && psr->obsn[i].sat < first) first = psr->obsn[i].sat;

if (psr->obsn[i].deleted==0 && psr->obsn[i].sat > last) last = psr->obsn[i].sat;

}

psr->param[param_wave_dm].val[0] = 2.0*M_PI/(last-first)/

(1.0+4.0/(double)(psr->nWhite));

}

/* Set tempo emulation mode */

if (psr->param[param_ephver].paramSet[0]==1)

{

if (psr->param[param_ephver].val[0] < 5)

{

printf("************************************************* \n");

printf("Warning: you are running in tempo1 emulation mode \n");

printf("************************************************* \n");

tempo1 = 1;

}

else

tempo1 = 0;

}

else if (tempo1 == 1)

{

psr->param[param_ephver].paramSet[0]=1;

psr->param[param_ephver].val[0]=2;

}

else

{

psr->param[param_ephver].paramSet[0]=1;

psr->param[param_ephver].val[0]=5;

}

if (thelast>0)

/* Define the start parameter based upon the last observation */

{

psr->param[param_start].val[0] = psr->obsn[psr->nobs-1].sat-thelast;

psr->param[param_start].fitFlag[0] = 1;

psr->param[param_start].paramSet[0] = 1;

}

psr->tempo1 = 0;

if (tempo1 == 1)

{

psr->tempo1 = 1;

psr->units = TDB_UNITS;

psr->timeEphemeris = FB90_TIMEEPH;

psr->dilateFreq = 0;

psr->planetShapiro=0;

psr->t2cMethod = T2C_TEMPO;

psr->correctTroposphere = 0;

psr->ne_sw = 9.961;

ECLIPTIC_OBLIQUITY = 84381.412;

}

/* XXXX Hack!! -- removed - should use transform plugin*/

/* Problem, if a function is not called then the compiler does not include

* it in the library - so the plugin cannot find it */

if (psr->units==100) /* SI_UNITS) */

transform_units(psr, TDB_UNITS, SI_UNITS);

}

void preProcessSimple2 (pulsar *psr,

float startdmmjd, int ndm, float* dmvals, int trimonly)

{

logdbg("In preProcessSimple2");

int i=0, j=0, k=0;

for (i=0;i<psr->nobs;i++)

{

//psr->obsn[i].efac = 1.0;

//psr->obsn[i].equad = 0.0;

/* Check whether any error = 0 */

if (psr->fitMode==1 && psr->obsn[i].toaErr==0)

{

printf("Error: the uncertainty for TOA %d (MJD %f) is equal to zero\n ",i+1,(double)psr->obsn[i].sat);

exit(1);

}

for (k=0; k<6; k++) /* zero these vectors for first call to tt2tb */

{

psr->obsn[i].earthMoonBary_ssb[k] = 0.0;

psr->obsn[i].earthMoonBary_earth[k] = 0.0;

psr->obsn[i].observatory_earth[k] = 0.0;

psr->obsn[i].earth_ssb[k] = 0.0;

}

// Correctly taking note of the phase offset

psr->obsn[i].sat += ((psr->obsn[i].phaseOffset/psr->param[param_f].val[0])/SECDAY);

for (k=0;k<psr->nToffset;k++) /* Calculate time offsets */

{

char offsetSite[256], obsSite[256];

lookup_observatory_alias(psr->tOffsetSite[k], offsetSite);

lookup_observatory_alias(psr->obsn[i].telID, obsSite);

if ((psr->tOffset_f1[k]==0.0 || (psr->obsn[i].freq > psr->tOffset_f1[k])) &&

(psr->tOffset_f2[k]==0.0 || (psr->obsn[i].freq < psr->tOffset_f2[k])) &&

(psr->tOffset_t1[k]==0.0 || (psr->obsn[i].sat > psr->tOffset_t1[k])) &&

(psr->tOffset_t2[k]==0.0 || (psr->obsn[i].sat < psr->tOffset_t2[k])) &&

(strcmp(offsetSite,"0")==0 ||

strcmp(offsetSite,obsSite)==0))

{

int use=1;

/* Check for flags */

if (strlen(psr->tOffsetFlags[k])>0)

{

char *myStr,str1[1000],flagID[100];

use=0;

strcpy(str1,psr->tOffsetFlags[k]);

myStr = strtok(str1," ");

do {

if (myStr[0]=='-' && (myStr[1]<48 || myStr[1]>57)) /* Look for flag */

{

strcpy(flagID,myStr);

myStr = strtok(NULL," ");

for (int l=0;l<psr->obsn[i].nFlags;l++)

{

if (strcmp(flagID,psr->obsn[i].flagID[l])==0

&& strcmp(myStr,psr->obsn[i].flagVal[l])==0)

{

use=1;

break;

}

}

}

} while ((myStr = strtok(NULL," "))!=NULL);

}

if (use==1) {psr->obsn[i].sat += psr->tOffset[k]/SECDAY;}

}

}

/* Check filtering */

if (strlen(psr->filterStr)>0)

{

char flag[100],filtS[1000],*filt;

strcpy(filtS,psr->filterStr);

filt = strtok(filtS," ");

strcpy(flag,filt);

while (filt != NULL)

{

if (filt[0]=='-') strcpy(flag,filt);

else

{

for (j=0;j<psr->obsn[i].nFlags;j++)

{

if (strcmp(psr->obsn[i].flagID[j],flag)==0 &&

strcmp(psr->obsn[i].flagVal[j],filt)==0)

psr->obsn[i].deleted=1;

}

}

filt = strtok(NULL," ");

}

}

/* Check filtering for 'pass' */

if (strlen(psr->passStr)>0)

{

char flag[100],filtS[1000],*filt;

int found;

strcpy(filtS,psr->passStr);

filt = strtok(filtS," ");

found=0;

while ( filt != NULL && found==0)

{

if (filt[0]=='-') // Have a flag

strcpy(flag,filt);

else

{

for (j=0;j<psr->obsn[i].nFlags;j++)

{

if (strcmp(psr->obsn[i].flagID[j],flag)==0 &&

strcmp(psr->obsn[i].flagVal[j],filt)==0)

{

found=1;

break;

}

}

}

filt = strtok(NULL," ");

}

if (found==0)

psr->obsn[i].deleted=1;

}

/* CHECK JUMPS */

for (k=1;k<=psr->nJumps;k++)

{

int yes=0;

char str1[100],str2[100],str3[100],str4[100],str5[100];

double val1, val2;

/* Must parse jump string to determine whether this observation should jump or not */

int nread = sscanf(psr->jumpStr[k],"%s %s %s",str1,str2,str3);

if (strcasecmp(str1,"MJD")==0 || strcasecmp(str1,"FREQ")==0)

{

sscanf(str2,"%lf",&val1);

sscanf(str3,"%lf",&val2);

if (strcasecmp(str1,"MJD")==0) {

if (psr->obsn[i].sat >= val1 && psr->obsn[i].sat < val2) {

yes=1;

}

}

else if (strcasecmp(str1,"FREQ")==0) {

if (psr->obsn[i].freq >= val1 && psr->obsn[i].freq < val2) {

yes=1;

}

}

}

if (strcasecmp(str1,"NAME")==0 && strstr(psr->obsn[i].fname,str2)!=NULL)

yes=1;

if (strcasecmp(str1,"TEL")==0)

{

char selectedSite[256], obsSite[256];

lookup_observatory_alias(str2, selectedSite);

lookup_observatory_alias(psr->obsn[i].telID, obsSite);

if (strcasecmp(selectedSite, obsSite)!=0)

yes=1;

}

else if (str1[0]=='-')

{

int jj;

for (jj=0;jj<psr->obsn[i].nFlags;jj++)

{

if (strcmp(psr->obsn[i].flagID[jj],str1)==0 &&

strcmp(psr->obsn[i].flagVal[jj],str2)==0)

yes=1;

}

}

if (yes==1) {psr->obsn[i].jump[psr->obsn[i].obsNjump]=k; (psr->obsn[i].obsNjump)++;}

}

// Check for time offset flags

for (k=0;k<psr->obsn[i].nFlags;k++)

{

if (strcmp(psr->obsn[i].flagID[k],"-to")==0)

{

longdouble v;

v = parse_longdouble(psr->obsn[i].flagVal[k]);

psr->obsn[i].sat += v/SECDAY;

}

}

// Check for dm updates

if (startdmmjd && ndm && dmvals)

{

//float dm; //not needed any more

if ((int)(psr->obsn[i].sat-startdmmjd+0.5) > 0)

{

if ((int)(psr->obsn[i].sat-startdmmjd+0.5) >= ndm)

psr->obsn[i].deleted=1;

else if (trimonly == 0) // set flags only if really correcting for dm, not only trimming the data

{

strcpy(psr->obsn[i].flagID[psr->obsn[i].nFlags],"-dm");

sprintf(psr->obsn[i].flagVal[psr->obsn[i].nFlags],"%g",dmvals[(int)(psr->obsn[i].sat-startdmmjd+0.5)]);

psr->obsn[i].nFlags++;

if (psr->obsn[i].nFlags >= MAX_FLAGS)

{

printf("Number of different flags in the .tim file > MAX_FLAGS (%d)\n",MAX_FLAGS);

exit(1);

}

//dm = dmvals[(int)(psr->obsn[i].sat-startdmmjd+0.5)];

}

}

else

{

psr->obsn[i].deleted=1;

}

}

}

logdbg("Complete preProcessSimple2");

}

void preProcessSimple3 (pulsar *psr)

{

int i,j,k,l;

logdbg("Start preProcessSimple3");

//

// Check fjump

//

if (strlen(psr->fjumpID)>0)

{

char val[MAX_JUMPS][16];

int nval[MAX_JUMPS];

int nf=0;

int found;

// Find flag corresponding to longest data set

for (i=0;i<psr->nobs;i++)

{

if (psr->obsn[i].deleted==0)

{

for (k=0;k<psr->obsn[i].nFlags;k++)

{

if (strcmp(psr->obsn[i].flagID[k],psr->fjumpID)==0)

{

found=0;

for (l=0;l<nf;l++)

{

if (strcmp(psr->obsn[i].flagVal[k],val[l])==0)

{

found=1;

break;

}

}

if (found==0)

{

strcpy(val[nf],psr->obsn[i].flagVal[k]);

nf++;

if (nf >= MAX_JUMPS)

{

printf("preProcessSimple3: Number of different flags in the .tim file > MAX_JUMPS (%d)\n",MAX_JUMPS);

exit(1);

}

}

}

}

}

}

// Now create jumps

for (l=1;l<nf;l++)

{

psr->nJumps++;

sprintf(psr->jumpStr[psr->nJumps],"%s %s",psr->fjumpID,val[l]);

for (i=0;i<psr->nobs;i++)

{

for (k=0;k<psr->obsn[i].nFlags;k++)

{

if (strcmp(psr->obsn[i].flagVal[k],val[l])==0)

psr->obsn[i].jump[(psr->obsn[i].obsNjump)++]=psr->nJumps;

}

}

psr->fitJump[psr->nJumps]=1;

}

}

// Now link phase jumps to a particular site-arrival-time

for (i=0;i<psr->nPhaseJump;i++)

{

if ((psr->phaseJumpID[i] = -1))

{

// Find closest TOA

if (i==0) printf("WARNING: Use of phase jumps => .tim file must be sorted in time order\n");

for (k=1;k<psr->nobs;k++)

{

if ((double)psr->obsn[k].sat > (double)psr->phaseJump[i])

{

psr->phaseJumpID[i]=k-1;

break;

}

}

}

}

logdbg("Complete preProcessSimple3");

}