void setdatapars(struct data *d)
{
int i;
char rcvrs[MAXRCVRS];
/* Set the sequence mode from seqcon and apptype parameters */
setseqmode(d);
/* Set data dimensions */
setdim(d);
/* Number of segments and echo train length */
/* Number of segments takes precidence, as in the setloop macro */
d->nseg=(int)*val("nseg",&d->p);
if (d->nseg>0) {
d->etl=d->nv/d->nseg;
if (d->nv%d->nseg>0) d->etl++;
} else {
d->etl=(int)*val("etl",&d->p);
if (d->etl>0) {
d->nseg=d->nv/d->etl;
if (d->nv%d->etl>0) d->nseg++;
}
}
if (d->nseg<1) {
d->nseg=d->nv;
d->etl=1;
}
/* Number of echoes */
d->ne=(int)*val("ne",&d->p);
if (d->ne < 1) d->ne=1; /* Set ne to 1 if 'ne' does not exist */
/* Number of receivers */
strcpy(rcvrs,*sval("rcvrs",&d->p));
d->nr=0;
for (i=0;i<strlen(rcvrs);i++)
if (rcvrs[i] == 'y') d->nr++;
/* Number of pss values = slices */
d->ns=nvals("pss",&d->p);
/* There must be at least one block per volume */
d->nblocks=(int)*val("nblocks",&d->p);
if (!d->nblocks) d->nblocks++;
/* Number of points and views for resizing data */
d->fn=(int)*val("fn",&d->p);
d->fn1=(int)*val("fn1",&d->p);
d->fn2=(int)*val("fn2",&d->p);
d->fn3=(int)*val("fn3",&d->p);
/* for cropping csi result */
d->startd1 =(int)*val("snv",&d->p);
d->startd1 += -1;
d->startd2 =(int)*val("snv2",&d->p);
d->startd2 += -1;
d->cropd1 =(int)*val("cnv",&d->p);
d->cropd2 =(int)*val("cnv2",&d->p);
// for reversal of dimensions in csi
d->d1rev = (int)*val("d1rev",&d->p);
d->d2rev = (int)*val("d2rev",&d->p);
d->d3rev = (int)*val("d3rev",&d->p);
/* Navigators */
d->nav=FALSE; /* Default is no navigator */
if (spar(d,"navigator","y")) {
d->nav=TRUE;
d->nnav=nvals("nav_echo",&d->p);
if (d->nnav>0) {
if ((d->navpos = (int *)malloc(d->nnav*sizeof(int))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
for (i=0;i<d->nnav;i++) d->navpos[i]=(int)val("nav_echo",&d->p)[i];
}
}
/* Set profile flag */
d->profile=FALSE;
if (spar(d,"profile","y") && im2D(d)) d->profile=TRUE;
if (spar(d,"profile","yy") && im3D(d)) d->profile=TRUE;
/* Set proj2D flag */
d->proj2D=FALSE;
if (im3D(d)) {
if (spar(d,"profile","yn") || spar(d,"profile","ny")) d->proj2D=TRUE;
}
/* Set number of dimensions */
/* 1Ds are just 1D */
if (im1D(d)) d->ndim=1;
/* Multislice 2Ds and 3Ds both work on volumes, i.e. 3D */
else if (im2D(d)) d->ndim=3;
else if (im3D(d)) d->ndim=3;
/* Set default status of each dimension to flag no data */
if ((d->dimstatus = (int *)malloc(d->ndim*sizeof(int))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
for (i=0;i<d->ndim;i++) d->dimstatus[i]=NONE;
#ifdef DEBUG
fprintf(stdout,"\n%s: %s()\n",__FILE__,__FUNCTION__);
fprintf(stdout," d->nseg = %d\n",d->nseg);
fprintf(stdout," d->etl = %d\n",d->etl);
fprintf(stdout," d->ne = %d\n",d->ne);
fprintf(stdout," d->nr = %d\n",d->nr);
fprintf(stdout," d->ns = %d\n",d->ns);
fprintf(stdout," d->fn = %d\n",d->fn);
fprintf(stdout," d->fn1 = %d\n",d->fn1);
fprintf(stdout," d->fn2 = %d\n",d->fn2);
if (d->nav) {
fprintf(stdout," d->nnav = %d",d->nnav);
fprintf(stdout,", d->navpos = %d",d->navpos[0]);
for (i=1;i<d->nnav;i++) fprintf(stdout,",%d",d->navpos[i]);
fprintf(stdout,"\n");
}
if (d->profile) fprintf(stdout," d->profile = TRUE\n");
if (d->proj2D) fprintf(stdout," d->proj2D = TRUE\n");
fflush(stdout);
#endif
}
Document*
initps(Biobuf *b, int argc, char **argv, uchar *buf, int nbuf)
{
Document *d;
PSInfo *ps;
char *p;
char *q, *r;
char eol;
char *nargv[1];
char fdbuf[20];
char tmp[32];
int fd;
int i;
int incomments;
int cantranslate;
int trailer=0;
int nesting=0;
int dumb=0;
int landscape=0;
long psoff;
long npage, mpage;
Page *page;
Rectangle bbox = Rect(0,0,0,0);
if(argc > 1) {
fprint(2, "can only view one ps file at a time\n");
return nil;
}
fprint(2, "reading through postscript...\n");
if(b == nil){ /* standard input; spool to disk (ouch) */
fd = spooltodisk(buf, nbuf, nil);
sprint(fdbuf, "/dev/fd/%d", fd);
b = Bopen(fdbuf, OREAD);
if(b == nil){
fprint(2, "cannot open disk spool file\n");
wexits("Bopen temp");
}
nargv[0] = fdbuf;
argv = nargv;
}
/* find %!, perhaps after PCL nonsense */
Bseek(b, 0, 0);
psoff = 0;
eol = 0;
for(i=0; i<16; i++){
psoff = Boffset(b);
if(!(p = Brdline(b, eol='\n')) && !(p = Brdline(b, eol='\r'))) {
fprint(2, "cannot find end of first line\n");
wexits("initps");
}
if(p[0]=='\x1B')
p++, psoff++;
if(p[0] == '%' && p[1] == '!')
break;
}
if(i == 16){
werrstr("not ps");
return nil;
}
/* page counting */
npage = 0;
mpage = 16;
page = emalloc(mpage*sizeof(*page));
memset(page, 0, mpage*sizeof(*page));
cantranslate = goodps;
incomments = 1;
Keepreading:
while(p = Brdline(b, eol)) {
if(p[0] == '%')
if(chatty) fprint(2, "ps %.*s\n", utfnlen(p, Blinelen(b)-1), p);
if(npage == mpage) {
mpage *= 2;
page = erealloc(page, mpage*sizeof(*page));
memset(&page[npage], 0, npage*sizeof(*page));
}
if(p[0] != '%' || p[1] != '%')
continue;
if(prefix(p, "%%BeginDocument")) {
nesting++;
continue;
}
if(nesting > 0 && prefix(p, "%%EndDocument")) {
nesting--;
continue;
}
if(nesting)
continue;
if(prefix(p, "%%EndComment")) {
incomments = 0;
continue;
}
if(reverse == -1 && prefix(p, "%%PageOrder")) {
/* glean whether we should reverse the viewing order */
p[Blinelen(b)-1] = 0;
if(strstr(p, "Ascend"))
reverse = 0;
else if(strstr(p, "Descend"))
reverse = 1;
else if(strstr(p, "Special"))
dumb = 1;
p[Blinelen(b)-1] = '\n';
continue;
} else if(prefix(p, "%%Trailer")) {
incomments = 1;
page[npage].offset = Boffset(b)-Blinelen(b);
trailer = 1;
continue;
} else if(incomments && prefix(p, "%%Orientation")) {
if(strstr(p, "Landscape"))
landscape = 1;
} else if(incomments && Dx(bbox)==0 && prefix(p, q="%%BoundingBox")) {
bbox = rdbbox(p+strlen(q)+1);
if(chatty)
/* can't use %R because haven't initdraw() */
fprint(2, "document bbox [%d %d %d %d]\n",
RECT(bbox));
continue;
}
/*
* If they use the initgraphics command, we can't play our translation tricks.
*/
p[Blinelen(b)-1] = 0;
if((q=strstr(p, "initgraphics")) && ((r=strchr(p, '%'))==nil || r > q))
cantranslate = 0;
p[Blinelen(b)-1] = eol;
if(!prefix(p, "%%Page:"))
continue;
/*
* figure out of the %%Page: line contains a page number
* or some other page description to use in the menu bar.
*
* lines look like %%Page: x y or %%Page: x
* we prefer just x, and will generate our
* own if necessary.
*/
p[Blinelen(b)-1] = 0;
if(chatty) fprint(2, "page %s\n", p);
r = p+7;
while(*r == ' ' || *r == '\t')
r++;
q = r;
while(*q && *q != ' ' && *q != '\t')
q++;
free(page[npage].name);
if(*r) {
if(*r == '"' && *q == '"')
r++, q--;
if(*q)
*q = 0;
page[npage].name = estrdup(r);
*q = 'x';
} else {
snprint(tmp, sizeof tmp, "p %ld", npage+1);
page[npage].name = estrdup(tmp);
}
/*
* store the offset info for later viewing
*/
trailer = 0;
p[Blinelen(b)-1] = eol;
page[npage++].offset = Boffset(b)-Blinelen(b);
}
if(Blinelen(b) > 0){
fprint(2, "page: linelen %d\n", Blinelen(b));
Bseek(b, Blinelen(b), 1);
goto Keepreading;
}
if(Dx(bbox) == 0 || Dy(bbox) == 0)
bbox = Rect(0,0,612,792); /* 8½×11 */
/*
* if we didn't find any pages, assume the document
* is one big page
*/
if(npage == 0) {
dumb = 1;
if(chatty) fprint(2, "don't know where pages are\n");
reverse = 0;
goodps = 0;
trailer = 0;
page[npage].name = "p 1";
page[npage++].offset = 0;
}
if(npage+2 > mpage) {
mpage += 2;
page = erealloc(page, mpage*sizeof(*page));
memset(&page[mpage-2], 0, 2*sizeof(*page));
}
if(!trailer)
page[npage].offset = Boffset(b);
Bseek(b, 0, 2); /* EOF */
page[npage+1].offset = Boffset(b);
d = emalloc(sizeof(*d));
ps = emalloc(sizeof(*ps));
ps->page = page;
ps->npage = npage;
ps->bbox = bbox;
ps->psoff = psoff;
d->extra = ps;
d->npage = ps->npage;
d->b = b;
d->drawpage = psdrawpage;
d->pagename = pspagename;
d->fwdonly = ps->clueless = dumb;
d->docname = argv[0];
/*
* "tag" the doc as an image for now since there still is the "blank page"
* problem for ps files.
*/
d->type = Tgfx;
if(spawngs(&ps->gs, "-dSAFER") < 0)
return nil;
if(!cantranslate)
bbox.min = ZP;
setdim(&ps->gs, bbox, ppi, landscape);
if(goodps){
/*
* We want to only send the page (i.e. not header and trailer) information
* for each page, so initialize the device by sending the header now.
*/
pswritepage(d, ps->gs.gsfd, -1);
waitgs(&ps->gs);
}
if(dumb) {
fprint(ps->gs.gsfd, "(%s) run\n", argv[0]);
fprint(ps->gs.gsfd, "(/dev/fd/3) (w) file dup (THIS IS NOT A PLAN9 BITMAP 01234567890123456789012345678901234567890123456789\\n) writestring flushfile\n");
}
ps->bbox = bbox;
return d;
}
void defaultEPI(struct data *d)
{
int DISCARD=-1;
int refEPI=FALSE,refSGE=FALSE;
int getscaleref=FALSE;
double oversample;
struct data ref1,ref2,ref3,ref4,ref5,ref6;
struct segscale scale1,scale2;
enum {
OFF = 0,
POINTWISE = 1,
TRIPLE = 2,
SCALED_TRIPLE = 3
} epi_pc;
setnvolsEPI(d); /* Set the number of data volumes */
d->nv=(int)*val("nphase",&d->p); /* Set d->nv for dimorder2D */
d->pssorder=sliceorder(d,d->ns,"pss"); /* Fill pssorder with the slice order */
d->dim2order=phaseorder(d,d->nv,d->nv,"par_does_not_exist"); /* Set dim2order=-1 for sequential phase encode order */
d->dim3order=phaseorder(d,d->nv,d->nv,"sgepelist"); /* Fill dim3order with the standard gradient echo phase encode order */
d->nv2=d->nv; /* Set d->nv2 for dim3order */
d->nv=(int)*val("nseg",&d->p); /* Use d->nv for the number of shots */
/* Set EPI correction scheme */
if (spar(d,"epi_pc","POINTWISE")) epi_pc=POINTWISE;
else if (spar(d,"epi_pc","TRIPLE")) epi_pc=TRIPLE;
else if (spar(d,"epi_pc","SCALED_TRIPLE")) epi_pc=SCALED_TRIPLE;
else epi_pc=OFF;
/* Check whether to output or discard reference scans */
if (spar(d,"imRF","y")) refEPI=TRUE;
if (spar(d,"imSGE","y")) refSGE=TRUE;
/* Set reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
initdatafrom(d,&ref1);
initdatafrom(d,&ref3); /* ref3 used in pointwise phase correction of inverted
reference scans if reference output is selected */
}
if (epi_pc > POINTWISE) { /* Triple reference phase corrections */
initdatafrom(d,&ref2);
initdatafrom(d,&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
initdatafrom(d,&ref5);
initdatafrom(d,&ref6);
}
/* Set default of no compressed segment scaling just in case it's never set */
scale1.data=FALSE;
scale2.data=FALSE;
/* Loop over data blocks */
for (d->block=0;d->block<d->nblocks;d->block++) {
if (interupt) return; /* Interupt/cancel from VnmrJ */
d->outvol=0; /* Initialise output data volume (that will not include reference scans) */
for (d->vol=0;d->vol<d->nvols;d->vol++) { /* Loop over "volumes" */
setoutvolEPI(d); /* Set output data volume */
if (d->outvol>d->endvol) break; /* Break if last requested volume has been processed */
getblockEPI(d,d->vol,NDCC); /* Get block without applying dbh.lvl and dbh.tlt */
zeromax(d); /* Zero max structure & coordinates of maximum */
zeronoise(d); /* Zero values in noise structure */
#ifdef DEBUG
fprintf(stdout,"\n%s: %s()\n",__FILE__,__FUNCTION__);
switch (epi_pc) {
case OFF: fprintf(stdout," Correction: OFF \n"); break;
case POINTWISE: fprintf(stdout," Correction: POINTWISE \n"); break;
case TRIPLE: fprintf(stdout," Correction: TRIPLE \n"); break;
case SCALED_TRIPLE: fprintf(stdout," Correction: SCALED_TRIPLE \n"); break;
}
fflush(stdout);
#endif
/* Process data as directed by image parameter */
switch ((int)getelem(d,"image",d->vol)) {
case 0: /* Reference, no phase-encode */
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
if (epi_pc > OFF) { /* If there is phase correction */
ftnpEPI(d); /* FT along readout dimension */
clear2Ddata(&ref1); /* Clear ref1 */
copy2Ddata(d,&ref1); /* Copy to ref1 */
ref1.datamode=EPIREF; /* Flag as EPIREF data */
} else { /* else there is no phase correction */
ref1.datamode=NONE; /* Flag as no data */
if (refEPI) ftnpEPI(d); /* FT along readout dimension */
}
setsegscale(d,&scale1); /* Set scaling for compressed segments */
segscale(d,&scale1); /* Scale compressed segments */
if (refEPI) /* If reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -1: /* Inverted Readout Reference, with phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if triple or scaled triple reference phase correction */
clear2Ddata(&ref2); /* Clear ref2 */
copy2Ddata(d,&ref2); /* Copy to ref2 */
ref2.datamode=EPIREF; /* Flag ref2 as EPIREF data */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (ref3.datamode == EPIREF) { /* if there is ref3 reference data */
phaseEPI(d,&ref3); /* Phase correct with the reference */
}
navcorrEPI(d); /* Phase correct with the navigator */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case -2: /* Inverted Readout Reference, no phase-encode */
#ifdef DEBUG
fprintf(stdout," Processing reference -2 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (refEPI) w2Dfdfs(d,VJ,FLT32,d->vol);
ftnpEPI(d); /* FT along readout dimension */
setsegscale(d,&scale2); /* Set scaling for compressed segments */
segscale(d,&scale2); /* Scale compressed segments */
if (epi_pc > POINTWISE) { /* if old triple or triple reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
if (ref2.datamode == EPIREF) { /* if there is ref2 reference data */
phaseEPIref(&ref2,&ref3,&ref4); /* Phase correct ref2 data using ref3 and put result in ref4 */
/* analyseEPInav(&ref4); // Analyse the navigators */
stripEPInav(&ref4); /* Strip the navigator scans */
ftnvEPI(&ref4); /* FT along phase encode dimension */
revreadEPI(&ref4); /* Reverse the data in readout dimension */
getscaleref=TRUE; /* Flag to store the next regular image for scaling in SCALED_TRIPLE */
}
}
if (refEPI) { /* if reference output is requested */
if (epi_pc == POINTWISE) { /* if pointwise reference phase correction */
clear2Ddata(&ref3); /* Clear ref3 */
copy2Ddata(d,&ref3); /* Copy to ref3 */
ref3.datamode=EPIREF; /* Flag ref3 as EPIREF data */
}
revreadEPI(d); /* Reverse the data in readout dimension */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
}
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
case 1: /* Regular image */
#ifdef DEBUG
fprintf(stdout," Processing image 1 data ...\n");
fflush(stdout);
#endif
setblockEPI(d); /* Set block for 2D data (d->nv > 1) and navigators */
if (d->outvol>=d->startvol)
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
switch (epi_pc) {
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
clear2Ddata(&ref5); /* Clear ref5 */
copy2Ddata(d,&ref5); /* Copy to ref5 */
ref5.datamode=EPIREF; /* Flag ref5 as EPIREF data */
prepEPIref(&ref5,&ref1); /* Prepare ref5 data so it can be used to scale ref4 data */
}
break;
default:
break;
}
ftnpEPI(d); /* FT along readout dimension */
segscale(d,&scale1); /* Scale compressed segments */
phaseEPI(d,&ref1); /* Phase correct with the reference */
navcorrEPI(d); /* Phase correct with the navigator */
/* analyseEPInav(d); // Analyse the navigators */
stripEPInav(d); /* Strip the navigator scans */
ftnvEPI(d); /* FT along phase encode dimension */
switch (epi_pc) {
case TRIPLE: /* Triple reference phase correction */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
break;
case SCALED_TRIPLE: /* Scaled triple reference phase correction */
if (getscaleref) { /* If the scale reference has just been acquired */
addEPIref(d,&ref4); /* Add ref4 data to cancel N/2 ghost */
getscaleref=FALSE; /* Flag that scale reference has been acquired */
} else {
addscaledEPIref(d,&ref4,&ref5); /* Scale ref4 data according to d/ref5, then add to d */
}
break;
default:
break;
}
if (d->outvol>=d->startvol) {
phasedata2D(d,VJ); /* Phase data if required */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Write 2D fdf data from volume */
wnifti(d,VJ,FLT32,d->vol);
}
break;
default: /* Reference Standard Gradient Echo */
setblockSGE(d);
if (refSGE) w2Dfdfs(d,VJ,FLT32,d->vol); /* Output raw data for the volume, if requested */
shiftdata2D(d,STD); /* Shift FID data for fft */
zeronoise(d); /* Zero any noise measurement */
equalizenoise(d,STD); /* Scale for equal noise in all receivers */
phaseramp2D(d,READ); /* Phase ramp the data to correct for readout offset pro */
phaseramp2D(d,PHASE); /* Phase ramp the data to correct for phase encode offset ppe */
weightdata2D(d,STD); /* Weight data using standard VnmrJ parameters */
zerofill2D(d,STD); /* Zero fill data using standard VnmrJ parameters */
fft2D(d,STD); /* 2D fft */
phasedata2D(d,VJ); /* Phase data if required */
shiftdata2D(d,STD); /* Shift data to get images */
oversample=*val("oversample",&d->p); /* Check to see if there is oversampling */
if (oversample>1) zoomEPI(d); /* If oversampled, zoom to get the requested FOV */
if (refSGE) /* If standard gradient echo reference output is requested */
w2Dfdfs(d,VJ,FLT32,d->vol); /* Output data for the volume */
else w2Dfdfs(d,VJ,FLT32,DISCARD); /* Else use DISCARD to flag skip the volume */
wnifti(d,VJ,FLT32,DISCARD);
break;
} /* end image parameter switch */
clear2Ddata(d); /* Clear data volume from memory */
setdim(d); /* Reset data dimensions in case data has been zerofilled (sets d->nv=1) */
d->nv=*val("nseg",&d->p); /* Use d->nv for the number of shots */
d->nv2=(int)*val("nphase",&d->p); /* Use d->nv2 for number of standard gradient echo phase encodes */
d->dimstatus[0] = NONE; /* Make sure ZEROFILL status is not set, otherwise setdim will be called in getblock() */
d->dimstatus[1] = NONE; /* Make sure ZEROFILL status is not set, otherwise setdim will be called in getblock() */
} /* end volume loop */
} /* end data block loop */
/* Clear all reference data */
if (epi_pc > OFF) { /* Pointwise or triple reference phase correction */
clear2Dall(&ref1);
clear2Dall(&ref3);
}
if (epi_pc > POINTWISE) { /* Triple and scaled triple reference phase correction */
clear2Dall(&ref2);
clear2Dall(&ref4);
}
if (epi_pc > TRIPLE) { /* Scaled triple reference phase correction */
clear2Dall(&ref5);
clear2Dall(&ref6);
}
clear2Dall(d); /* Clear everything from memory */
}
void
emulate(void)
{
char buf[BUFS+1];
int i;
int n;
int c;
int operand[10];
int noperand;
int savex, savey, saveattr, saveisgraphics;
int isgraphics;
int g0set, g1set;
int dch;
isgraphics = 0;
g0set = 'B'; /* US ASCII */
g1set = 'B'; /* US ASCII */
savex = savey = 0;
yscrmin = 0;
yscrmax = ymax;
saveattr = 0;
saveisgraphics = 0;
/* set initial tab stops to DEC-standard 8-column spacing */
for(c=0; (c+=8)<nelem(tabcol);)
tabcol[c] = 1;
for (;;) {
if (y > ymax) {
x = 0;
newline();
}
buf[0] = get_next_char();
buf[1] = '\0';
switch(buf[0]) {
case '\000':
case '\001':
case '\002':
case '\003':
case '\004':
case '\005':
case '\006':
goto Default;
case '\007': /* bell */
ringbell();
break;
case '\010': /* backspace */
if (x > 0)
--x;
break;
case '\011': /* tab to next tab stop; if none, to right margin */
for(c=x+1; c<nelem(tabcol) && !tabcol[c]; c++)
;
if(c < nelem(tabcol))
x = c;
else
x = xmax;
break;
case '\012': /* linefeed */
case '\013':
case '\014':
newline();
if (ttystate[cs->raw].nlcr)
x = 0;
break;
case '\015': /* carriage return */
x = 0;
if (ttystate[cs->raw].crnl)
newline();
break;
case '\016': /* SO: invoke G1 char set */
isgraphics = (isdigit(g1set));
break;
case '\017': /* SI: invoke G0 char set */
isgraphics = (isdigit(g0set));
break;
case '\020': /* DLE */
case '\021': /* DC1 */
case '\022': /* XON */
case '\023': /* DC3 */
case '\024': /* XOFF */
case '\025': /* NAK */
case '\026': /* SYN */
case '\027': /* ETB */
case '\030': /* CAN: cancel escape sequence, display checkerboard (not implemented) */
case '\031': /* EM */
case '\032': /* SUB: same as CAN */
goto Default;
;
/* ESC, \033, is handled below */
case '\034': /* FS */
case '\035': /* GS */
case '\036': /* RS */
case '\037': /* US */
break;
case '\177': /* delete: ignored */
break;
case '\033':
switch(dch = get_next_char()){
/*
* 1 - graphic processor option on (no-op; not installed)
*/
case '1':
break;
/*
* 2 - graphic processor option off (no-op; not installed)
*/
case '2':
break;
/*
* 7 - save cursor position.
*/
case '7':
//print("save\n");
savex = x;
savey = y;
saveattr = attr;
saveisgraphics = isgraphics;
break;
/*
* 8 - restore cursor position.
*/
case '8':
//print("restore\n");
x = savex;
y = savey;
attr = saveattr;
isgraphics = saveisgraphics;
break;
/*
* c - Reset terminal.
*/
case 'c':
print("resetterminal\n");
cursoron = 1;
ttystate[cs->raw].nlcr = 0;
break;
/*
* D - active position down a line, scroll if at bottom margin.
* (Original VT100 had a bug: tracked new-line/line-feed mode.)
*/
case 'D':
if(++y > yscrmax) {
y = yscrmax;
scroll(yscrmin+1, yscrmax+1, yscrmin, yscrmax);
}
break;
/*
* E - active position to start of next line, scroll if at bottom margin.
*/
case 'E':
x = 0;
if(++y > yscrmax) {
y = yscrmax;
scroll(yscrmin+1, yscrmax+1, yscrmin, yscrmax);
}
break;
/*
* H - set tab stop at current column.
* (This is cursor home in VT52 mode (not implemented).)
*/
case 'H':
if(x < nelem(tabcol))
tabcol[x] = 1;
break;
/*
* M - active position up a line, scroll if at top margin..
*/
case 'M':
if(--y < yscrmin) {
y = yscrmin;
scroll(yscrmin, yscrmax, yscrmin+1, yscrmin);
}
break;
/*
* Z - identification. the terminal
* emulator will return the response
* code for a generic VT100.
*/
case 'Z':
Ident:
sendnchars2(7, "\033[?1;2c"); /* VT100 with AVO option */
// sendnchars2(5, "\033[?6c"); /* VT102 (insert/delete-char, etc.) */
break;
/*
* < - enter ANSI mode
*/
case '<':
break;
/*
* > - set numeric keypad mode on (not implemented)
*/
case '>':
break;
/*
* = - set numeric keypad mode off (not implemented)
*/
case '=':
break;
/*
* # - Takes a one-digit argument
*/
case '#':
switch(get_next_char()){
case '3': /* Top half of double-height line */
case '4': /* Bottom half of double-height line */
case '5': /* Single-width single-height line */
case '6': /* Double-width line */
case '7': /* Screen print */
case '8': /* Fill screen with E's */
break;
}
break;
/*
* ( - switch G0 character set
*/
case '(':
g0set = get_next_char();
break;
/*
* - switch G1 character set
*/
case ')':
g1set = get_next_char();
break;
/*
* Received left bracket.
*/
case '[':
/*
* A semi-colon or ? delimits arguments.
*/
memset(operand, 0, sizeof(operand));
operand[0] = number(buf, &i);
noperand = 1;
while(buf[0] == ';' || buf[0] == '?'){
if(noperand < nelem(operand)){
noperand++;
operand[noperand-1] = number(buf, nil);
} else
number(buf, nil);
}
/*
* do escape2 stuff
*/
switch(dch = buf[0]){
/*
* c - same as ESC Z: what are you?
*/
case 'c':
goto Ident;
/*
* g - various tabstop manipulation
*/
case 'g':
switch(operand[0]){
case 0: /* clear tab at current column */
if(x < nelem(tabcol))
tabcol[x] = 0;
break;
case 3: /* clear all tabs */
memset(tabcol, 0, sizeof tabcol);
break;
}
break;
/*
* l - clear various options.
*/
case 'l':
if(noperand == 1){
switch(operand[0]){
case 20: /* set line feed mode */
ttystate[cs->raw].nlcr = 1;
break;
case 30: /* screen invisible (? not supported through VT220) */
break;
}
}else while(--noperand > 0){
switch(operand[noperand]){
case 1: /* set cursor keys to send ANSI functions: ESC [ A..D */
break;
case 2: /* set VT52 mode (not implemented) */
break;
case 3: /* set 80 columns */
setdim(-1, 80);
break;
case 4: /* set jump scrolling */
break;
case 5: /* set normal video on screen */
break;
case 6: /* set origin to absolute */
originrelative = 0;
x = y = 0;
break;
case 7: /* reset auto-wrap mode */
wraparound = 0;
break;
case 8: /* reset auto-repeat mode */
break;
case 9: /* reset interlacing mode */
break;
case 25: /* text cursor off (VT220) */
cursoron = 0;
break;
}
}
break;
/*
* s - some dec private stuff. actually [ ? num s, but we can't detect it.
*/
case 's':
break;
/*
* h - set various options.
*/
case 'h':
if(noperand == 1){
switch(operand[0]){
default:
break;
case 20: /* set newline mode */
ttystate[cs->raw].nlcr = 0;
break;
case 30: /* screen visible (? not supported through VT220) */
break;
}
}else while(--noperand > 0){
switch(operand[noperand]){
default:
break;
case 1: /* set cursor keys to send application function: ESC O A..D */
break;
case 2: /* set ANSI */
break;
case 3: /* set 132 columns */
setdim(-1, 132);
break;
case 4: /* set smooth scrolling */
break;
case 5: /* set screen to reverse video (not implemented) */
break;
case 6: /* set origin to relative */
originrelative = 1;
x = 0;
y = yscrmin;
break;
case 7: /* set auto-wrap mode */
wraparound = 1;
break;
case 8: /* set auto-repeat mode */
break;
case 9: /* set interlacing mode */
break;
case 25: /* text cursor on (VT220) */
cursoron = 1;
break;
}
}
break;
/*
* m - change character attrs.
*/
case 'm':
setattr(noperand, operand);
break;
/*
* n - request various reports
*/
case 'n':
switch(operand[0]){
case 5: /* status */
sendnchars2(4, "\033[0n"); /* terminal ok */
break;
case 6: /* cursor position */
sendnchars2(sprint(buf, "\033[%d;%dR",
originrelative ? y+1 - yscrmin : y+1, x+1), buf);
break;
}
break;
/*
* q - turn on list of LEDs; turn off others.
*/
case 'q':
break;
/*
* r - change scrolling region. operand[0] is
* min scrolling region and operand[1] is max
* scrolling region.
*/
case 'r':
yscrmin = 0;
yscrmax = ymax;
switch(noperand){
case 2:
yscrmax = operand[1]-1;
if(yscrmax > ymax)
yscrmax = ymax;
case 1:
yscrmin = operand[0]-1;
if(yscrmin < 0)
yscrmin = 0;
}
x = 0;
y = yscrmin;
break;
/*
* x - report terminal parameters
*/
case 'x':
sendnchars2(20, "\033[3;1;1;120;120;1;0x");
break;
/*
* y - invoke confidence test
*/
case 'y':
break;
/*
* A - cursor up.
*/
case 'e':
case 'A':
fixops(operand);
y -= operand[0];
if(y < yscrmin)
y = yscrmin;
olines -= operand[0];
if(olines < 0)
olines = 0;
break;
/*
* B - cursor down
*/
case 'B':
fixops(operand);
y += operand[0];
if(y > yscrmax)
y=yscrmax;
break;
/*
* C - cursor right
*/
case 'a':
case 'C':
fixops(operand);
x += operand[0];
/*
* VT-100-UG says not to go past the
* right margin.
*/
if(x > xmax)
x = xmax;
break;
/*
* D - cursor left
*/
case 'D':
fixops(operand);
x -= operand[0];
if(x < 0)
x = 0;
break;
/*
* G - cursor to column
*/
case '\'':
case 'G':
fixops(operand);
x = operand[0] - 1;
if(x > xmax)
x = xmax;
break;
/*
* H and f - cursor motion. operand[0] is row and
* operand[1] is column, origin 1.
*/
case 'H':
case 'f':
fixops(operand+1);
x = operand[1] - 1;
if(x > xmax)
x = xmax;
/* fallthrough */
/*
* d - cursor to line n (xterm)
*/
case 'd':
fixops(operand);
y = operand[0] - 1;
if(originrelative){
y += yscrmin;
if(y > yscrmax)
y = yscrmax;
}else{
if(y > ymax)
y = ymax;
}
break;
/*
* J - clear some or all of the display.
*/
case 'J':
switch (operand[0]) {
/*
* operand 2: whole screen.
*/
case 2:
clear(Rpt(pt(0, 0), pt(xmax+1, ymax+1)));
break;
/*
* operand 1: start of screen to active position, inclusive.
*/
case 1:
clear(Rpt(pt(0, 0), pt(xmax+1, y)));
clear(Rpt(pt(0, y), pt(x+1, y+1)));
break;
/*
* Default: active position to end of screen, inclusive.
*/
default:
clear(Rpt(pt(x, y), pt(xmax+1, y+1)));
clear(Rpt(pt(0, y+1), pt(xmax+1, ymax+1)));
break;
}
break;
/*
* K - clear some or all of the line.
*/
case 'K':
switch (operand[0]) {
/*
* operand 2: whole line.
*/
case 2:
clear(Rpt(pt(0, y), pt(xmax+1, y+1)));
break;
/*
* operand 1: start of line to active position, inclusive.
*/
case 1:
clear(Rpt(pt(0, y), pt(x+1, y+1)));
break;
/*
* Default: active position to end of line, inclusive.
*/
default:
clear(Rpt(pt(x, y), pt(xmax+1, y+1)));
break;
}
break;
/*
* P - delete character(s) from right of cursor (xterm)
*/
case 'P':
fixops(operand);
i = x + operand[0];
draw(screen, Rpt(pt(x, y), pt(xmax+1, y+1)), screen, nil, pt(i, y));
clear(Rpt(pt(xmax-operand[0], y), pt(xmax+1, y+1)));
break;
/*
* @ - insert blank(s) to right of cursor (xterm)
*/
case '@':
fixops(operand);
i = x + operand[0];
draw(screen, Rpt(pt(i, y), pt(xmax+1, y+1)), screen, nil, pt(x, y));
clear(Rpt(pt(x, y), pt(i, y+1)));
break;
/*
* X - erase character(s) at cursor and to the right (xterm)
*/
case 'X':
fixops(operand);
i = x + operand[0];
clear(Rpt(pt(x, y), pt(i, y+1)));
break;
/*
* L - insert a line at cursor position (VT102 and later)
*/
case 'L':
fixops(operand);
for(i = 0; i < operand[0]; ++i)
scroll(y, yscrmax, y+1, y);
break;
/*
* M - delete a line at cursor position (VT102 and later)
*/
case 'M':
fixops(operand);
for(i = 0; i < operand[0]; ++i)
scroll(y+1, yscrmax+1, y, yscrmax);
break;
/*
* S,T - scroll up/down (xterm)
*/
case 'T':
fixops(operand);
for(i = 0; i < operand[0]; ++i)
scroll(yscrmin, yscrmax, yscrmin+1, yscrmin);
break;
case 'S':
fixops(operand);
for(i = 0; i < operand[0]; ++i)
scroll(yscrmin+1, yscrmax+1, yscrmin, yscrmin);
break;
case '=': /* ? not supported through VT220 */
number(buf, nil);
switch(buf[0]) {
case 'h':
case 'l':
break;
}
break;
/*
* Anything else we ignore for now...
*/
default:
print("unknown escape2 '%c' (0x%x)\n", dch, dch);
break;
}
break;
/*
* Collapse multiple '\033' to one.
*/
case '\033':
peekc = '\033';
break;
/* set title */
case ']': /* it's actually <esc> ] num ; title <bel> */
{
int ch, fd;
number(buf, nil);
i = 0;
while((ch = get_next_char()) != '\a')
if(i < sizeof buf)
buf[i++] = ch;
fd = open("/dev/label", OWRITE);
write(fd, buf, i);
close(fd);
}
break;
/*
* Ignore other commands.
*/
default:
print("unknown command '%c' (0x%x)\n", dch, dch);
break;
}
break;
default: /* ordinary char */
Default:
if(isgraphics && gmap[(uint8_t) buf[0]])
buf[0] = gmap[(uint8_t) buf[0]];
/* line wrap */
if (x > xmax){
if(wraparound){
x = 0;
newline();
}else{
continue;
}
}
n = 1;
c = 0;
while (!cs->raw && host_avail() && x+n<=xmax && n<BUFS
&& (c = get_next_char())>=' ' && c<'\177') {
buf[n++] = c;
c = 0;
}
buf[n] = 0;
// clear(Rpt(pt(x,y), pt(x+n, y+1)));
drawstring(pt(x, y), buf, attr);
x += n;
peekc = c;
break;
}
}
}
void prescanEPI(struct data *d)
{
int dim1,dim2,dim3,nr;
double oversample;
int nread;
int rampsamp=FALSE,linearsamp=FALSE;
setnvolsEPI(d); /* Set the number of data volumes */
d->nv=(int)*val("nphase",&d->p); /* Set d->nv for dimorder2D */
d->pssorder=sliceorder(d,d->ns,"pss"); /* Fill pssorder with the slice order */
d->dim2order=phaseorder(d,d->nv,d->nv,"par_does_not_exist"); /* Set dim2order=-1 for sequential phase encode order */
d->dim3order=phaseorder(d,d->nv,d->nv,"sgepelist"); /* Fill dim3order with the standard gradient echo phase encode order */
d->nv2=d->nv; /* Set d->nv2 for dim3order */
d->nv=(int)*val("nseg",&d->p); /* Use d->nv for the number of shots */
/* Set data dimensions */
dim3=d->endpos-d->startpos; nr=d->nr;
/* Check for oversampling */
oversample=*val("oversample",&d->p);
if (spar(d,"rampsamp","y")) rampsamp=TRUE;
if (spar(d,"linearsamp","y")) linearsamp=TRUE;
nread=(int)*val("nread",&d->p)/2;
for (d->vol=0;d->vol<d->nvols;d->vol++) { /* loop over "volumes" */
if (interupt) return; /* Interupt/cancel from VnmrJ */
/* Loop over data blocks */
for (d->block=0;d->block<d->nblocks;d->block++) {
getblockEPI(d,d->vol,NDCC); /* Get block without applying dbh.lvl and dbh.tlt */
zeromax(d); /* Zero max structure & coordinates of maximum */
zeronoise(d); /* Zero values in noise structure */
setblockEPI(d);
/* Set data dimensions */
dim1=d->np/2; dim2=d->nv;
if (vnmrj_recon) settep(d,STD);
/* If oversampled or ramp and linear sampling, zoom to get the requested matrix size */
if ((oversample==1) && rampsamp && linearsamp) zoomdata2D(d,(dim1-nread)/2,nread,0,dim2);
else if ((oversample>1) || (rampsamp && linearsamp)) zoomdata2D(d,(dim1-1.5*nread)/2,1.5*nread,0,dim2);
/* Flag the data as IMAGE since magnitude output is combined from multiple receivers */
d->dimstatus[0]+=FFT;
/* We always want to view prescan with same orientation so fix it as though it's axial */
setval(&d->p,"psi",180.0);
setval(&d->p,"phi",0.0);
setval(&d->p,"theta",0.0);
w2Dfdfs(d,VJ,FLT32,d->vol); /* Write 2D fdf raw data from volume */
/* Properly flag the data as FID */
d->dimstatus[0]-=FFT;
clear2Ddata(d); /* Clear data volume from memory */
setdim(d); /* Reset data dimensions in case data has been zerofilled (sets d->nv=1) */
d->nv=*val("nseg",&d->p); /* Use d->nv for the number of shots */
d->dimstatus[0] = NONE; /* Make sure ZEROFILL status is not set, otherwise setdim will be called in getblock() */
d->dimstatus[1] = NONE; /* Make sure ZEROFILL status is not set, otherwise setdim will be called in getblock() */
}
}
}
