MaxResults suboptSampler(Model B, PoSition **Pos, SimTime *S)
{
int **nNumMotifs,
**startPos, /* startPos[MotifType][motifnum] */
i, j, seed_run = 0, t, k;
int maxnum; /* maximum number of motif in one type motif */
register Mlist M;
MaxResults maxData, locMax;
RPType RP;
IPtype IP; /* for quick access of input data */
PoSition *Pos_t; /* Pos_t=Pos[t] */
int n; /* BT 2/7/97 */
int nPos;
int sum;
double dCurrProb;
#ifdef _MPI_
MPI_Status status;
double dTempInfo[4];
#endif
IP=B->IP;
RP = B->RP;
init_maxdata(&maxData);
init_maxdata(&locMax);
BeginTime(S);
#ifdef _MPI_
if( ! IP->is_defined[cl_hm] )
{
/* get the go ahead to start */
Gibbs_MPI_Recv( B, &dTempInfo, 4, MPI_DOUBLE, MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD,
&status );
if( status.MPI_TAG == G_MPI_DONE )
return maxData;
if( IP->is_defined[cl_X] && B->AN->bExchange )
{
B->AN->currTemp = dTempInfo[0];
B->AN->dMinTemp = B->AN->currTemp;
B->AN->dMaxTemp = B->AN->currTemp;
PrintTempOut(IP->Datafiles->mpiTemp_fpt, "currTemp = %f maxTemp = %f minTemp = %f\n",
B->AN->currTemp, B->AN->dMaxTemp, B->AN->dMinTemp );
}
}
#endif
/* save the inital number of motifs */
for(t = 0; t < IP->nNumMotifTypes; t++) /* BT 2/7/97 */
{
RP->nPriorMotifSites[t][FORWARD] = IP->nNumMotifs[t][FORWARD];
RP->nPriorMotifSites[t][REVERSE] = IP->nNumMotifs[t][REVERSE];
}
/* copy the original counts into current counts */
copy_counts(B);
nNumMotifs = copy_motif_num(IP);
zero_motifs(IP); /* set motif count to zero */
/* If not running Wilcox test initialize random number gerator. */
/* Wilcox already did this */
if( ! IP->is_defined[cl_l] ) /* BT 7/23/97 */
sRandom(B, IP->lSeedVal);
/* calculate the probability of NULL model */
/* IP->dnull_map = CalcMapProb(B, IP->is_defined[cl_R]); */
IP->dnull_map = CalcNullMap(B); /* 2/16/2001 */
reset_motif_num(nNumMotifs,IP);
/* mark all possible motif sites */
if( ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B);
maxnum = findMaxNumMotif(IP);
if( IP->is_defined[cl_E] ||
RP->nUseSpacingProb || IP->is_defined[cl_T] ) /* BT 11/20/2000 */
{
CountAlignments( B, Pos );
SaveAlignmentCounts( B );
}
/* allocate space for start positions of motifs */
NEWP(startPos,IP->nNumMotifTypes, int);
for(i = 0; i <IP->nNumMotifTypes ; i++)
NEW(startPos[i],maxnum, int);
/* Loop through for a number of different seeds */
while(seed_run++ < IP->nSeeds)
{
if( IP->is_defined[cl_X] )
{
/* if( ! B->AN->bExchange )
B->AN->currTemp = B->AN->dMaxTemp; */
if( ! IP->is_defined[cl_Z] )
printf( "Current temperature: %7.2f\n", B->AN->currTemp );
}
IP->nSeedRun = seed_run;
if(!IP->is_defined[cl_F])
initMask(B);
if( IP->is_defined[cl_X] )
init_maxdata( &(B->AN->results[seed_run]) );
/* initialize the Pos */
for(t=0;t<IP->nNumMotifTypes;t++)
{
Pos_t=Pos[t];
for(i = 0; i < IP->nSeqLen; i++)
{
Pos_t[i].nInMotif=FALSE;
Pos_t[i].nMotifStartPos=FALSE;
}
}
for( t= 0; t < IP->nNumMotifTypes; t++ ) /* BT 5/23/97 */
{
IP->nMotifLen[t] = IP->nInputMotifLen[t]; /* restore original lengths */
SetPossibleSites( B, t ); /* restore original site count */
}
if( IP->is_defined[cl_d] && ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B);
if( ! IP->site_samp ) /* BT 7/16/97 */
set_posterior_prob(IP, B->C); /* Set initial posterior prob */
/* random select a set of motifs */
if( ! IP->is_defined[cl_V] ) /* BT 04/16/03 */
{
if( B->InitPos == NULL || seed_run > 1 )
{
if( IP->is_defined[cl_A] )
{
set_posterior_prob(IP, B->C);
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
IP->nNumMotifs[t][FORWARD] = 0;
IP->nNumMotifs[t][REVERSE] = 0;
}
}
set_random_sequences(B, Pos, startPos); /* set alignment &*/
}
else
{
SetInitSequences( B, Pos, startPos ); /* BT 8/5/98 */
set_posterior_prob(IP, B->First);
if( RP->bUsePosMatrix )
InitializePosMatrix( B );
else if( RP->bUseTrans )
InitializeTransMatrix( B );
}
}
else
{
if( B->InitPos == NULL )
{
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
IP->nNumMotifs[t][FORWARD] = 0;
IP->nNumMotifs[t][REVERSE] = 0;
}
}
else
{
SetInitSequences( B, Pos, startPos );
set_counts( B ); /* BT 10/23/03 */
set_posterior_prob(IP, B->First);
}
set_posterior_prob(IP, B->C);
}
reset_counts(B, startPos, Pos); /* its counts */
if( B->InitPos != NULL && seed_run == 1 )
{
RP->dInitProb = CalcMapProb( B, IP->is_defined[cl_R] );
if( ! IP->inCentroidAlign )
{
fprintf( IP->Datafiles->out_fpt, "seed = %d Initial MAP = %.5f sites = %d \n",
IP->nSeedRun,
RP->dInitProb,
TotalNumMotifs( B ));
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf(IP->Datafiles->out_fpt,
"Motif %d Map = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
}
#ifdef _MPI_
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"rank = %d process = %d seed = %d Initial MAP = %.5f sites = %d\n",
IP->nRank,
IP->nMPIProcesses,
IP->nSeedRun,
RP->dInitProb,
TotalNumMotifs( B ) );
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"%d Motif = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
PrintTempOut( IP->Datafiles->mpiTemp_fpt,
"Bkgnd = %.5f Beta = %.5f Null = %.5f\n",
CalcBkgndMap(B, IP->is_defined[cl_R]),
CalcBetaMap( B, IP->is_defined[cl_R]),
IP->dnull_map );
#else
fprintf( stdout, "seed = %d Initial MAP = %.5f sites = %d\n",
IP->nSeedRun,
B->RP->dInitProb,
TotalNumMotifs( B ) );
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"%d Motif = %.5f Frag = %.5f\n", t,
CalcMotifMap(B, t, IP->is_defined[cl_R]),
CalcMotifFragMap(B, t, IP->is_defined[cl_R]) );
}
fprintf( stdout,
"Bkgnd = %.5f Beta = %.5f Seq = %.5f Null = %.5f\n",
CalcBkgndMap(B, IP->is_defined[cl_R]),
CalcBetaMap( B, IP->is_defined[cl_R]),
CalcSitePerSeqMap( B ),
IP->dnull_map );
#endif
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"-----------------------------------------------------------\n" );
fprintf( stdout, " MOTIF %c\n\n", (char)(97 + t));
DumpMotifPositions( t, B, Pos, stdout );
fprintf( stdout, "%d sites\n", NUMMOTIFS( IP->nNumMotifs[t]) );
}
fflush( stdout );
}
/* create a motif element list */
M = set_motif_info(IP, startPos, B->Seq);
#ifdef _DEBUG_
/* ==================================================================== */
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
fprintf( stdout,
"-----------------------------------------------------------\n" );
fprintf( stdout, " MOTIF %c\n\n", (char)(97 + t));
DumpMotifPositions( t, B, Pos, stdout );
fprintf( stdout, "%d sites\n", NUMMOTIFS( IP->nNumMotifs[t]) );
DumpCounts( B, t, stdout );
fflush( stdout );
}
/* ==================================================================== */
#endif
if( ! IP->is_defined[cl_Z] )
{
put_prior(B);
fprintf(stdout, "\r** %d **\n", seed_run);
fflush( stdout ); /* BT 9/19/97 */
}
if(seed_run > 1)
{
RestoreAlignmentCounts( B );
if(IP->site_samp)
locMax = site_sampler(B, Pos, M);
else if( IP->is_defined[cl_bayes] )
locMax = bayes_sampler(B, Pos, M, seed_run);
else if( IP->is_defined[cl_E] )
locMax = rsite_sampler(B, Pos, M, seed_run);
else
locMax = motif_sampler(B,Pos,M);
if( IP->is_defined[cl_X] )
CopyMaxResults( &(B->AN->results[seed_run]), &locMax, B );
dCurrProb = locMax.dProbability;
if(locMax.dProbability > maxData.dProbability)
{
/* Check to see if current run is max */
free_maxdata(&maxData, IP);
maxData = locMax;
maxData.nSuboptSeed = seed_run;
if( (! IP->is_defined[cl_Z]) && IP->is_defined[cl_opt] )
print_maxData(IP->nNumMotifTypes, maxData);
}
else
free_maxdata(&locMax, IP);
}
else
{ /* Set Maximum first time through */
if(IP->site_samp)
maxData = site_sampler(B, Pos, M);
else if( IP->is_defined[cl_bayes] )
maxData = bayes_sampler(B, Pos, M, seed_run);
else if( IP->is_defined[cl_E] )
maxData = rsite_sampler(B, Pos, M, seed_run);
else
maxData = motif_sampler(B,Pos,M);
dCurrProb = maxData.dProbability;
maxData.nSuboptSeed = seed_run;
if( IP->is_defined[cl_X] )
CopyMaxResults( &(B->AN->results[seed_run]), &maxData, B );
if( (! IP->is_defined[cl_Z]) && IP->is_defined[cl_opt] )
print_maxData(IP->nNumMotifTypes, maxData);
}
reset_motif_num(nNumMotifs, IP);
copy_counts(B); /* Counts w/o motifs */
free_motifs(B, M);
#ifdef _MPI_
if( IP->is_defined[cl_hm] )
{
if( seed_run == IP->nSeeds )
SendSuboptMsg( B, G_MPI_SUBOPT_DONE, seed_run );
else
SendSuboptMsg( B, G_MPI_SEED_DONE, seed_run );
}
else
{
dTempInfo[1] = dCurrProb;
dTempInfo[3] = 0;
if( IP->is_defined[cl_opt] )
{
for(t = 0; t < IP->nNumMotifTypes; t++)
{
dTempInfo[3] += (double) maxData.nNumMotifs[t];
}
}
Gibbs_MPI_Send( B, dTempInfo, 4, MPI_DOUBLE, 0, G_MPI_DATA, MPI_COMM_WORLD );
}
Gibbs_MPI_Recv( B, dTempInfo, 4, MPI_DOUBLE, 0, MPI_ANY_TAG, MPI_COMM_WORLD,
&status );
if( status.MPI_TAG == G_MPI_DONE )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt, "Received MPI_DONE signal\n" );
break;
}
else if( status.MPI_TAG == G_MPI_FINISH )
{
PrintTempOut( IP->Datafiles->mpiTemp_fpt, "Received subopt end signal\n" );
break;
}
#endif
}/* end of while loop, at this time we have MaxData */
FREEP(startPos,IP->nNumMotifTypes );
if(!IP->is_defined[cl_F] && maxData.F)
{
for(t = 0; t < IP->nNumMotifTypes; t++) /* BT 2/7/97 */
{
for(n = 0; n < B->F->nMaxLen[t]; n++)
B->F->nColMask[t][n] = maxData.F->nColMask[t][n];
B->F->FragWidth[t] = maxData.F->FragWidth[t];
for( n = 0; n < IP->nMotifLen[t]; n++ )
B->F->fragPos[t][n] = maxData.F->fragPos[t][n];
}
}
for(t = 0; t < IP->nNumMotifTypes; t++)
{ /* Add in motifs */
if( maxData.nMotifLen )
IP->nMotifLen[t] = maxData.nMotifLen[t];
/* Reset Pos in case width changed */
if( ! IP->inCentroidAlign )
set_indicator_vector(Pos, B->Seq, B); /* BT 9/12/97 */
if( maxData.nNumMotifs )
{
for(i = 0; i < maxData.nNumMotifs[t]; i++) /* from the maximum */
adjust_counts(B, ADD, maxData.nMotifLoc[i][t], /* alignment */
t, maxData.RevComp[i][t]);
}
}
if( maxData.nNumMotifs )
{
setMotifNum(IP, maxData); /* BT 5/30/97 */
}
if( IP->is_defined[cl_u] )
print_info(B, maxData, TRUE, SUBOPT); /* BT 3/19/97 */
if( IP->is_defined[cl_d] && IP->is_defined[cl_q] )
GetWidthCounts( B );
FREEP(nNumMotifs, IP->nNumMotifTypes);
free(nNumMotifs);
if( IP->is_defined[cl_Q] ) /* BT 3/27/98 */
{
fprintf( IP->Datafiles->occur_fpt, "seq pos pos2 motif count\n" );
for( i = 0; i < IP->nNumSequences; i++ )
{
for( j = 0; j < SequenceLength( B, i ); j++ )
{
nPos = SequenceStartPos( B, i ) + j;
for( t = 0; t < IP->nNumMotifTypes; t++ )
{
for( sum = 0, k = 1; k <= IP->nSeeds; k++ )
{
sum += IP->nAlignCnts[k][t][i][j];
}
fprintf( IP->Datafiles->occur_fpt, "%5d %5d %5d %5d %5d\n",
i, j, nPos, t, sum );
}
}
fflush( IP->Datafiles->occur_fpt );
}
}
if( ! IP->is_defined[cl_Z] && ! IP->is_defined[cl_nopt] )
printf( "Max subopt MAP found on seed %d\n", maxData.nSuboptSeed );
return maxData;
}
void process_cmd(char *readbuf, int length) {
typedef enum pipe_cmd_type{ca,im,tl,px,bo,tv,an,as,at,ac,ab,sh,co,br,sa,is,vs,rl,ec,em,wb,mm,ie,ce,ro,fl,ri,ss,qu,pv,bi,ru,md,sc,rs,bu,mn,mt,mi,mb,me,mx,mf,vm,vp,wd,sy,cn,st} pipe_cmd_type;
char pipe_cmds[] = "ca,im,tl,px,bo,tv,an,as,at,ac,ab,sh,co,br,sa,is,vs,rl,ec,em,wb,mm,ie,ce,ro,fl,ri,ss,qu,pv,bi,ru,md,sc,rs,bu,mn,mt,mi,mb,me,mx,mf,vm,vp,wd,sy,cn,st";
pipe_cmd_type pipe_cmd;
int parcount;
char pars[128][10];
long int par0;
char cmd[3];
char par[MAX_COMMAND_LEN];
char *parstring=0, *temp;
int key = -1;
if (length < 2 || length > (MAX_COMMAND_LEN - 2)) return;
//Get cmd
strncpy(cmd, readbuf, 2);
//find 2 letter command and translate into enum
temp = strstr(pipe_cmds, cmd);
if (temp == NULL) return;
pipe_cmd = (pipe_cmd_type)((temp - pipe_cmds) / 3);
if(length > 3) {
strcpy(par, readbuf + 3);
par[length-3] = 0;
//extract space separated numeric parameters
// and make separate string parameter (strtok changes the original)
asprintf(&parstring, "%s", par);
parcount = 0;
temp = strtok(par, " ");
while(parcount<10 && temp != NULL) {
strcpy(pars[parcount], temp);
parcount++;
temp = strtok(NULL, " ");
}
par0 = strtol(pars[0], NULL, 10);
} else {
par0 = 0;
}
switch(pipe_cmd) {
case ca:
if(par0 == 1) {
if (parcount > 1) {
long vtime = strtol(pars[1], NULL, 10);
video_stoptime = time(NULL) + vtime;
printLog("Capturing %d seconds\n", vtime);
}
start_video(0);
} else {
stop_video(0);
}
break;
case im:
capt_img();
break;
case tl:
if(par0) {
timelapse = 1;
lapse_cnt = 1;
updateStatus();
printLog("Timelapse started\n");
}
else {
image2_cnt++;
timelapse = 0;
updateStatus();
printLog("Timelapse stopped\n");
}
break;
case px:
stop_all();
addUserValue(c_video_width, pars[0]);
addUserValue(c_video_height, pars[1]);
addUserValue(c_video_fps, pars[2]);
addUserValue(c_MP4Box_fps, pars[3]);
addUserValue(c_image_width, pars[4]);
addUserValue(c_image_height, pars[5]);
start_all(0);
break;
case bo:
addUserValue(c_MP4Box, pars[0]);
break;
case tv:
addUserValue(c_tl_interval, pars[0]);
break;
case an:
addUserValue(c_annotation, parstring);
break;
case as:
addUserValue(c_anno_text_size, pars[0]);
break;
case at:
addUserValue(c_anno3_custom_text_colour, pars[0]);
addUserValue(c_anno3_custom_text_Y, pars[1]);
addUserValue(c_anno3_custom_text_U, pars[2]);
addUserValue(c_anno3_custom_text_V, pars[3]);
break;
case ac:
addUserValue(c_anno3_custom_background_colour, pars[0]);
addUserValue(c_anno3_custom_background_Y, pars[1]);
addUserValue(c_anno3_custom_background_U, pars[2]);
addUserValue(c_anno3_custom_background_V, pars[3]);
break;
case ab:
addUserValue(c_anno_background, pars[0]);
break;
case sh:
key = c_sharpness;
break;
case co:
key = c_contrast;
break;
case br:
key = c_brightness;
break;
case sa:
key = c_saturation;
break;
case is:
key = c_iso;
break;
case vs:
key = c_video_stabilisation;
break;
case rl:
key = c_raw_layer;
break;
case ec:
key = 1000 + c_exposure_compensation;
break;
case em:
key = 1000 + c_exposure_mode;
break;
case wb:
key = 1000 + c_white_balance;
break;
case mm:
key = 1000 + c_metering_mode;
break;
case ie:
key = 1000 + c_image_effect;
break;
case ce:
addUserValue(c_colour_effect_u, pars[1]);
addUserValue(c_colour_effect_v, pars[2]);
key = c_colour_effect_en;
break;
case ro:
key = c_rotation;
break;
case fl:
if(par0 & 1) addUserValue(c_hflip, "1"); else addUserValue(c_hflip, "0");
if((par0 >> 1) & 1) addUserValue(c_vflip, "1"); else addUserValue(c_vflip, "0");
cam_set(c_hflip);
break;
case ri:
addUserValue(c_sensor_region_y, pars[1]);
addUserValue(c_sensor_region_w, pars[2]);
addUserValue(c_sensor_region_h, pars[3]);
key = c_sensor_region_x;
break;
case ss:
addUserValue(c_shutter_speed, pars[0]);
key = c_shutter_speed;
break;
case qu:
key = c_image_quality;
break;
case pv:
stop_all();
addUserValue(c_quality, pars[0]);
addUserValue(c_width, pars[1]);
addUserValue(c_divider, pars[2]);
start_all(0);
break;
case bi:
stop_all();
addUserValue(c_video_bitrate, pars[0]);
start_all(0);
break;
case st:
stop_all();
addUserValue(c_stat_pass, pars[0]);
start_all(0);
break;
case wd:
addUserValue(c_watchdog_interval, pars[0]);
addUserValue(c_watchdog_errors, pars[1]);
break;
case ru:
if (par0 == 0) {
stop_all();
idle = 1;
printLog("Stream halted\n");
} else {
start_all(1);
idle = 0;
printLog("Stream continued\n");
}
updateStatus();
break;
case mx:
key = c_motion_external;
//If switching to internal with motion detection on then try to kill external motion
if (cfg_val[c_motion_detection] != 0 && !par0) {
if(system("killall motion") == -1) error("Could not stop external motion", 1);
printLog("External motion detection stopped\n");
}
break;
case md:
exec_macro(cfg_stru[c_do_cmd], readbuf);
stop_all();
if (cfg_val[c_motion_external]) {
if(par0 == 0) {
if(system("killall motion") == -1) error("Could not stop external motion", 1);
printLog("External motion detection stopped\n");
}
else {
if (cfg_val[c_motion_detection] == 0) {
if(system("motion") == -1) error("Could not start external motion", 1);
printLog("External motion detection started\n");
} else {
printLog("Motion already running. md 1 ignored\n");
}
}
} else {
if(par0 == 0) {
printLog("Internal motion detection stopped\n");
}
else {
printLog("Internal motion detection started\n");
}
}
cfg_val[c_motion_detection] = par0?1:0;
start_all(0);
updateStatus();
break;
case sc:
set_counts();
printLog("Scan for highest count\n");
break;
case rs:
printLog("Reset settings to defaults\n");
stop_all();
read_config("/etc/raspimjpeg", 1);
saveUserConfig(cfg_stru[c_user_config]);
start_all(0);
break;
case bu:
key = c_video_buffer;
break;
case vp:
stop_all();
addUserValue(c_vector_preview, pars[0]);
start_all(0);
break;
case mn:
key = c_motion_noise;
break;
case mt:
key = c_motion_threshold;
break;
case mi:
key = c_motion_image + 1000;
break;
case mb:
key = c_motion_startframes;
break;
case me:
key = c_motion_stopframes;
break;
case mf:
key = c_motion_file;
break;
case vm:
key = c_vector_mode;
break;
case sy:
exec_macro(parstring, NULL);
break;
case cn:
stop_all();
addUserValue(c_camera_num, pars[0]);
start_all(0);
break;
default:
printLog("Unrecognised pipe command\n");
break;
}
