main(int argc,
char **argv)
{
extern int optind; /* for use of getopt() */
extern char *optarg; /* for use of getopt() */
int ch; /* command-line option letter */
int outarch = NATIVE;
char **field_names = NULL;
int num_fields = 0;
int alloc_fields = 0;
int rflag = NO; /* -r option specified? */
char *rrange; /* arguments of -r option */
long start_rec; /* starting record number */
long end_rec; /* ending record number */
long num_recs; /* number of records to read
(0 means all up to end of file) */
long num_read; /* number of records actually read */
int Aflag = NO; /* annotate Ascii output? */
Annot *annotate = NULL;
int annwidth = 70;
char *iname; /* input file name */
FILE *ifile; /* input stream */
struct header *ihd; /* input file header */
struct fea_data *irec; /* input record */
char *oname; /* output file name */
FILE *ofile; /* output stream */
FieldList list; /* output field list */
int outord = TYPE_ORDER;
FieldSpec **ofields; /* output fields in field or type order */
double rec_freq;
double start_time_offset;
char *fdata;
double *edata;
int type;
int len, i;
long dim[1];
FieldSpec *field;
FieldList source; /* field list of source file */
while ((ch = getopt(argc, argv, "a:f:r:x:A:F")) != EOF)
switch (ch)
{
case 'a':
outarch = ((!strcmp(optarg, "EDR1")) ? EDR1
: (!strcmp(optarg, "EDR2")) ? EDR2
: (!strcmp(optarg, "NATIVE")) ? NATIVE
: (!strcmp(optarg, "ASCII")) ? ASCII
: UNKNOWN);
break;
case 'f':
if (num_fields >= alloc_fields)
{
size_t size;
alloc_fields = num_fields + 1 + num_fields/2;
size = (alloc_fields + 1) * sizeof(char *);
field_names = (char **)
((field_names == NULL)
? malloc(size)
: realloc(field_names, size));
}
field_names[num_fields++] = optarg;
field_names[num_fields] = NULL;
break;
case 'r':
rflag = YES;
rrange = optarg;
break;
case 'x':
debug_level = atoi(optarg);
break;
case 'A':
Aflag = YES;
annwidth = atoi(optarg);
break;
case 'F':
outord = FIELD_ORDER;
break;
default:
SYNTAX;
break;
}
if (argc - optind > 2)
{
fprintf(stderr,
"%s: too many file names specified.\n", ProgName);
SYNTAX;
}
if (argc - optind < 2)
{
fprintf(stderr,
"%s: too few file names specified.\n", ProgName);
SYNTAX;
}
iname = eopen(ProgName,
argv[optind++], "r", FT_FEA, NONE, &ihd, &ifile);
oname = argv[optind++];
start_rec = 1;
end_rec = LONG_MAX;
num_recs = 0;
if (rflag)
{
lrange_switch(rrange, &start_rec, &end_rec, 0);
if (end_rec != LONG_MAX)
num_recs = end_rec - start_rec + 1;
}
REQUIRE(start_rec >= 1, "can't start before beginning of file");
REQUIRE(end_rec >= start_rec, "empty range of records specified");
if (debug_level)
fprintf(stderr,
"start_rec: %ld. end_rec: %ld. num_recs: %ld.\n",
start_rec, end_rec, num_recs);
DebugMsgLevel = debug_level;
DebugMsgFunc = DebugPrint;
irec = allo_fea_rec(ihd);
REQUIRE(irec != NULL, "can't allocate memory for input record");
list = fea_to_FieldList(ihd, irec, field_names, FALSE);
REQUIRE(list != NULL,
"failure converting input header to field list");
switch (outord)
{
case TYPE_ORDER:
if (debug_level)
fprintf(stderr, "making type-ordered field array.\n");
ofields = TypeOrder(list);
break;
case FIELD_ORDER:
if (debug_level)
fprintf(stderr, "making field-ordered field array.\n");
ofields = FieldOrder(list);
break;
default:
REQUIRE(0, "output order neither TYPE_ORDER nor FIELD_ORDER");
break;
}
if (debug_level)
fprintf(stderr, "setting field ordering.\n");
REQUIRE(SetFieldOrdering(&list, outord),
"can't set field ordering of output");
rec_freq = get_genhd_val("record_freq", ihd, 1.0);
type = genhd_type("record_freq", &len, ihd);
if (type != HD_UNDEF)
{
field = AddGlobalField(&list, "recordFreq", 0, NULL, EDOUBLE, NULL);
*(double *) field->data = rec_freq;
}
type = genhd_type("start_time", &len, ihd);
if (type != HD_UNDEF && rec_freq != 0)
{
start_time_offset = (start_rec - 1) / rec_freq;
fdata = (char *) get_genhd("start_time", ihd);
edata = (double *) type_convert((long) len, fdata, type,
(char *) NULL, DOUBLE,
(void (*)()) NULL);
if (start_time_offset != 0)
{
for (i = 0; i < len; i++)
edata[i] += start_time_offset;
}
dim[0] = len;
AddGlobalField(&list, "startTime", 1, dim, EDOUBLE, edata);
}
source = fea_to_FieldList(ihd, NULL, NULL, TRUE);
(void) AddSource(&list, 0, iname, source);
(void) AddCommandLine(&list, GetCommandLine(argc, argv));
if (debug_level)
fprintf(stderr, "annwidth %d.\n", annwidth);
if (Aflag)
{
annotate = (Annot *) malloc(sizeof(Annot));
annotate->position = 0;
annotate->indent = 0;
annotate->width = annwidth;
annotate->recnum = 0;
}
if (debug_level)
fprintf(stderr, "writing Esignal header.\n");
REQUIRE(OpenOut(oname, list, outarch, &ofile, annotate),
"write header failed");
if (ofile == stdout)
oname = "<stdout>";
num_read = start_rec - 1;
if (debug_level)
fprintf(stderr, "skipping %ld records.\n", num_read);
/* skiprec(ifile, num_read, size_rec(ihd)); */
fea_skiprec(ifile, num_read, ihd);
while (num_read++ < end_rec && get_fea_rec(irec, ihd, ifile) != EOF)
{
if (debug_level > 2)
fprintf(stderr, "Record number %ld read.\n", num_read);
WriteRecord(ofields, outarch, ofile, annotate);
}
if (--num_read < end_rec && num_recs != 0)
fprintf(stderr, "fea2esig: only %ld records read.\n",
num_read - (start_rec - 1));
exit(0);
/*NOTREACHED*/
}
main(int argc,
char **argv)
{
extern int optind; /* for use of getopt() */
extern char *optarg; /* for use of getopt() */
int ch; /* command-line option letter */
static char *ProgName = "esig2fea"; /* name of this program */
static char *Version = SCCS_VERSION; /* program SCCS version */
static char *Date = SCCS_DATE; /* program SCCS date */
char **field_names = NULL;
int num_fields = 0;
int alloc_fields = 0;
int rflag = NO; /* -r option specified? */
char *rrange; /* arguments of -r option */
long start_rec; /* starting record number */
long end_rec; /* ending record number */
long num_recs; /* number of records to read
(0 means all up to end of file) */
long num_read; /* number of records actually read */
char *iname; /* input file name */
FILE *ifile; /* input stream */
FieldList list; /* input field list */
int inord; /* input: field order or type order? */
FieldSpec **ifields; /* input fields in field or type order */
char *subtype = NULL; /* FEA subtype name */
int subtype_code = NONE; /* numeric subtype code */
FieldSpec *fld; /* spec of various special fields */
char *oname; /* output file name */
FILE *ofile; /* output stream */
struct header *ohd; /* output file header */
struct fea_data *orec; /* output record */
int outord = TYPE_ORDER;
char *version; /* version from input preamble */
int arch; /* architecture from input preamble */
long pre_size; /* preamble size */
long hdr_size; /* header size (bytes) from preamble */
long rec_size; /* record size from preamble */
double rec_freq;
double start_time_offset;
double *data;
long len, i;
struct header *source; /* embedded source-file header */
while ((ch = getopt(argc, argv, "f:r:x:FT:")) != EOF)
switch (ch)
{
case 'f':
if (num_fields >= alloc_fields)
{
size_t size;
alloc_fields = num_fields + 1 + num_fields/2;
size = (alloc_fields + 1) * sizeof(char *);
field_names = (char **)
((field_names == NULL)
? malloc(size)
: realloc(field_names, size));
}
field_names[num_fields++] = optarg;
field_names[num_fields] = NULL;
break;
case 'r':
rflag = YES;
rrange = optarg;
break;
case 'x':
debug_level = atoi(optarg);
break;
case 'F':
outord = FIELD_ORDER;
break;
case 'T':
subtype = optarg;
break;
default:
SYNTAX;
break;
}
if (argc - optind > 2)
{
fprintf(stderr,
"%s: too many file names specified.\n", ProgName);
SYNTAX;
}
if (argc - optind < 2)
{
fprintf(stderr,
"%s: too few file names specified.\n", ProgName);
SYNTAX;
}
DebugMsgLevel = debug_level;
DebugMsgFunc = DebugPrint;
iname = argv[optind++];
list = OpenIn(iname, &version,
&arch, &pre_size, &hdr_size, &rec_size, &ifile);
REQUIRE(list != NULL, "read header failed");
if (ifile == stdin)
iname = "<stdin>";
oname = argv[optind++];
start_rec = 0;
end_rec = LONG_MAX;
num_recs = 0; /* 0 means continue to end of file */
if (rflag)
{
lrange_switch(rrange, &start_rec, &end_rec, 0);
if (end_rec != LONG_MAX)
num_recs = end_rec - start_rec + 1;
}
REQUIRE(start_rec >= 0, "can't start before beginning of file");
REQUIRE(end_rec >= start_rec, "empty range of records specified");
if (debug_level)
fprintf(stderr,
"start_rec: %ld. end_rec: %ld. num_recs: %ld.\n",
start_rec, end_rec, num_recs);
REQUIRE(GetFieldOrdering(list, &inord),
"cant get field ordering of input");
switch (inord)
{
case TYPE_ORDER:
if (debug_level)
fprintf(stderr, "making type-ordered field array.\n");
ifields = TypeOrder(list);
break;
case FIELD_ORDER:
if (debug_level)
fprintf(stderr, "making field-ordered field array.\n");
ifields = FieldOrder(list);
break;
default:
REQUIRE(0, "input order neither TYPE_ORDER nor FIELD_ORDER");
break;
}
ohd = FieldList_to_fea(list, &orec, field_names, FALSE);
REQUIRE(ohd != NULL,
"failure converting input field list to header & record struct");
if (subtype != NULL)
{
subtype_code = lin_search(fea_file_type, subtype);
if (subtype_code == -1)
fprintf(stderr, "%s: unknown FEA file subtype \"%s\" ignored.\n",
ProgName, subtype);
else
ohd->hd.fea->fea_type = subtype_code;
}
if (outord == FIELD_ORDER)
ohd->hd.fea->field_order = YES;
fld = FindField(list, "recordFreq");
if (fld != NULL && fld->occurrence == GLOBAL && fld->data != NULL)
{
(void) type_convert(1L, (char *) fld->data, ElibTypeToEsps(fld->type),
(char *) &rec_freq, FDOUBLE, (void (*)()) NULL);
*add_genhd_d("record_freq", NULL, 1, ohd) = rec_freq;
}
else
rec_freq = 1.0;
fld = FindField(list, "startTime");
if (fld != NULL
&& fld->occurrence == GLOBAL && fld->data != NULL && rec_freq != 0)
{
start_time_offset = start_rec / rec_freq;
len = FieldLength(fld);
data = (double *) type_convert(len, (char *) fld->data,
ElibTypeToEsps(fld->type),
(char *) NULL, FDOUBLE,
(void (*)()) NULL);
if (start_time_offset != 0)
{
for (i = 0; i < len; i++)
data[i] += start_time_offset;
}
(void) add_genhd_d("start_time", data, len, ohd);
}
(void) strcpy(ohd->common.prog, ProgName);
(void) strcpy(ohd->common.vers, Version);
(void) strcpy(ohd->common.progdate, Date);
source = FieldList_to_fea(list, NULL, NULL, TRUE);
add_source_file(ohd, savestring(iname), source);
add_comment(ohd, get_cmd_line(argc, argv));
oname = eopen(ProgName,
oname, "w", NONE, NONE, NULL, &ofile);
write_header(ohd, ofile);
num_read = SkipRecs(ifile, start_rec,
RecordSize(list, arch), ifields, arch);
if (num_read != start_rec)
{
fprintf(stderr,
"%s: couldn't reach starting record; only %ld skipped.\n",
ProgName, num_read);
exit(0);
}
for ( ;
num_read <= end_rec && ReadRecord(ifields, arch, ifile);
num_read++)
{
put_fea_rec(orec, ohd, ofile);
}
if (num_read <= end_rec && num_recs != 0)
fprintf(stderr, "esig2fea: only %ld records read.\n",
num_read - start_rec);
exit(0);
/*NOTREACHED*/
}
DoubleAdapter::DoubleAdapter(const ImagePtr image) :
ConstImageAdapter<double>(image->size()), _image(image) {
ConstImageAdapter<double> *adapter = type_convert(image);
doubleimage = std::shared_ptr<ConstImageAdapter<double> >(adapter);
}
/********************************** T2Fit ************************************
* This is where the work will be done
*************************************************************************************/
OSErr T2Fit( FILE *inFile, FILE *outFile )
{
OSErr error = noErr;
long theTimePt;
int i;
float *inData, *outData, *T2, *intercept, *chi2, *Smoother;
long VolSize, outVolBytes, inVolBytes;
float te[ u.inIm.dim.timePts ];
unsigned char *theMask;
short rules;
u.NumOutImages = 0;
VolSize = u.inIm.dim.isoX * u.inIm.dim.isoY * u.inIm.dim.n_slices;
inVolBytes = VolSize * get_datasize( T_FLOAT );
outVolBytes = VolSize * get_datasize( u.outIm.data_type );
T2 = (float *)ck_malloc( inVolBytes, "Storage for R2" );
intercept = (float *)ck_malloc( inVolBytes, "Storage for intercept" );
chi2 = (float *)ck_malloc( inVolBytes, "Storage for chi2" );
outData = (float *)ck_malloc( outVolBytes, "Storage for output data" );
inData = (float *)ck_malloc( inVolBytes * u.inIm.dim.timePts, "Storage for input data" );
theMask = (unsigned char*)ck_malloc( VolSize * sizeof( unsigned char ), "Storage for theMask" );
if( u.Smooth ) {
Smoother = (float *)ck_malloc( inVolBytes * 2, "Storage for smoothing" );
}
// load up te vector
if( u.Verbose ) {
printf( "TE: " );
}
for( i=0; i<u.inIm.dim.timePts; i++ ) {
fscanf(u.TEFile ,"%f", &te[i]);
if( u.Verbose ) {
printf( "%0.3f ", te[i] );
}
}
// We will do everything in float
SetImDatatype( &u.inIm, T_FLOAT );
// Load all of the images into a single matrix
for ( theTimePt = 0; theTimePt < u.inIm.dim.timePts; theTimePt++ ) {
error = GetSelectedVolume( inFile, &u.inIm, inData+theTimePt*VolSize, theTimePt );
RETURNONERROR;
if( u.Smooth ) {
vmov( inData+theTimePt*VolSize, 1, Smoother, 1, VolSize, T_FLOAT );
error = gaussSmooth( &u.inIm, Smoother, inData+theTimePt*VolSize, &u.xSmooth, &u.ySmooth, &u.zSmooth );
RETURNONERROR;
}
RETURNONERROR;
}
// threshold on first images
if( u.autoThresh ) {
error = autoMask( inData, theMask, VolSize, &u.threshold, &u.nonNoise, T_FLOAT );
RETURNONERROR;
} else if( u.threshold != 0 ) {
u.nonNoise = ThreshMask( inData, theMask, VolSize, &u.threshold, T_FLOAT );
} else {
u.nonNoise = VolSize;
}
error = CalcT2( &u.inIm, inData, theMask, te, T2, intercept, chi2 ); RETURNONERROR;
free( inData );
error = type_convert( T2, T_FLOAT,
outData, u.outIm.data_type,
VolSize, &u.outIm.theMinf, &u.outIm.theMaxf, &rules );
if( error && error != CONVERSION_ERROR ) return error;
error = ck_fwrite( outData, 1, outVolBytes, outFile );
u.NumOutImages++;
RETURNONERROR;
error = type_convert( intercept, T_FLOAT,
outData, u.outIm.data_type,
VolSize, &u.outIm.theMinf, &u.outIm.theMaxf, &rules );
if( error && error != CONVERSION_ERROR ) return error;
error = ck_fwrite( outData, 1, outVolBytes, outFile );
u.NumOutImages++;
RETURNONERROR;
if( u.Smooth ) {
free( Smoother );
}
// Make R2 image
for( i=0; i<VolSize; i++ ) {
if( T2[i] !=0 ) {
T2[i] = 1/T2[i];
}
}
error = type_convert( T2, T_FLOAT,
outData, u.outIm.data_type,
VolSize, &u.outIm.theMinf, &u.outIm.theMaxf, &rules );
if( error && error != CONVERSION_ERROR ) return error;
error = ck_fwrite( outData, 1, outVolBytes, outFile );
u.NumOutImages++;
RETURNONERROR;
error = type_convert( chi2, T_FLOAT,
outData, u.outIm.data_type,
VolSize, &u.outIm.theMinf, &u.outIm.theMaxf, &rules );
if( error && error != CONVERSION_ERROR ) return error;
error = ck_fwrite( outData, 1, outVolBytes, outFile );
u.NumOutImages++;
RETURNONERROR;
fprintf( u.ProcFile, "Output file contains maps of T2, M0, R2 and chi2\n" );
fprintf( u.ProcFile, "TE's used: " );
for( i=0; i<u.inIm.dim.timePts; i++ ) {
fprintf( u.ProcFile, "%0.3f ", te[i] );
}
fprintf( u.ProcFile, "\n" );
fprintf( u.ProcFile, "Input data were intensity thresholded at %0.3f\n", u.threshold );
fprintf( u.ProcFile, "Non-Noise Points:\t%ld\n", u.nonNoise );
if( u.Smooth ) {
fprintf( u.ProcFile, "Input images were smoothed with a width of %0.3f mm in x, %0.3f mm in y and %0.3f mm in z\n",
u.xSmooth, u.ySmooth, u.zSmooth );
}
fprintf( stderr, "Output file contains maps of T2, M0, R2 and chi2\n" );
fprintf( stderr, "TE's used: " );
for( i=0; i<u.inIm.dim.timePts; i++ ) {
fprintf( stderr, "%0.3f ", te[i] );
}
fprintf( stderr, "\n" );
fprintf( stderr, "Input data were intensity thresholded at %0.3f\n", u.threshold );
fprintf( stderr, "Non-Noise Points:\t%ld\n\n", u.nonNoise );
if( u.Smooth ) {
fprintf( stderr, "Input images were smoothed with a width of %0.3f mm in x, %0.3f mm in y and %0.3f mm in z\n",
u.xSmooth, u.ySmooth, u.zSmooth );
}
free( theMask );
free( outData );
free( chi2 );
free( intercept );
free( T2 );
return error;
}
