OSErr writeHeader( IMAGE *im, char *basename )
/* creates an analyze style header based on the struct im */
{
FILE *f;
char buff[256];
dsr theDSR;
OSErr error = noErr;
sprintf( buff, "%s.hdr", basename );
f = fopen( buff, "wb" );
if( !f ) {
return WRITE_ERROR;
}
error = EmptyAnaHdr( &theDSR, "From Signa", im->dim.scanspacing, im->dim.x,
im->dim.y, im->dim.n_slices, im->dim.timePts, axial );
if( error ) ILError( error, "Creating analyze header" );
if( pcByteOrder() ) {
error = swapHdrBytes( &theDSR );
if( error ) ILError( error, "swapping header bytes" );
printf( "\nWARNING: Computer and data differ in byte order\n" );
}
error = ck_fwrite( &theDSR, sizeof( dsr ), 1, f );
if( error ) ILError( error, buff );
ck_fclose( f );
return error;
}
/****************************** DoSwap ***************************
* This is where the work will be done
*************************************************************************************/
OSErr DoSwap( FILE *inFile, FILE *outFile )
{
OSErr error = noErr;
long theTimePt;
void *inData, *outData;
long bufSize;
int elemSize;
void *buf;
int count;
elemSize = sizeof( float );
bufSize = u.id.xs * u.id.ys * elemSize;
buf = ck_malloc( bufSize, "swap buffer" );
for( count=0; count<u.id.zs; count++ ) {
if( u.Verbose ) {
printf( "." );
}
error = ck_fread( buf, sizeof( char ), bufSize, inFile );
ILError( error, "DoSwap" );
error = vbyteswap( buf, u.id.xs * u.id.ys, T_FLOAT );
ILError( error, "DoSwap" );
error = ck_fwrite( buf, sizeof( char ), bufSize, outFile );
ILError( error, "DoSwap" );
}
return error;
}
/* Advance LINES on LF's infile, copying lines to OUTFILE */
static void
lf_copy (struct line_filter *lf, lin lines, FILE *outfile)
{
char *start = lf->bufpos;
while (lines)
{
lf->bufpos = (char *) memchr (lf->bufpos, '\n', lf->buflim - lf->bufpos);
if (! lf->bufpos)
{
ck_fwrite (start, lf->buflim - start, outfile);
if (! lf_refill (lf))
return;
start = lf->bufpos;
}
else
{
--lines;
++lf->bufpos;
}
}
ck_fwrite (start, lf->bufpos - start, outfile);
}
int main( int argc, char **argv )
{
IMAGE im;
dsr myDSR;
short tmp;
FILE *fp;
char inName[256], outName[256];
OSErr error = noErr;
printf( "%s - Treat times points in an analyze header as slices\n", argv[0] );
printf( "WARNING -- this tool will overwrite the original header\n" );
if( argc == 1 ) {
printf( "Enter the name of an analyze image file ( xxx.img ): " );
scanf( "%s", inName );
} else {
strcpy( inName, argv[1] );
}
error = UC_Readheader( inName, &im );
ILError( error, "reading input header" );
tmp = im.dim.n_slices;
im.dim.n_slices = im.dim.timePts;
im.dim.timePts = tmp;
error = dsrFromIMAGE( &im, &myDSR );
ILError( error, "Creating analyze header" );
strcpy( outName, inName );
sprintf( strrchr( outName, '.' ), ".hdr" );
printf( "Header will be overwritten to %s\n", outName );
error = ck_fopen( &fp, outName, "wb" );
ILError( error, "opening output header" );
error = ck_fwrite( &myDSR, sizeof( dsr ), 1, fp );
ILError( error, "writing analyze header" );
error = ck_fclose( fp );
ILError( error, "closing header file" );
return 0;
}
/* interpret an edit command */
static bool
edit (struct line_filter *left, char const *lname, lin lline, lin llen,
struct line_filter *right, char const *rname, lin rline, lin rlen,
FILE *outfile)
{
for (;;)
{
int cmd0, cmd1;
bool gotcmd = false;
cmd1 = 0; /* Pacify `gcc -W'. */
while (! gotcmd)
{
if (putchar ('%') != '%')
perror_fatal (_("write failed"));
ck_fflush (stdout);
cmd0 = skip_white ();
switch (cmd0)
{
case '1': case '2': case 'l': case 'r':
case 's': case 'v': case 'q':
if (skip_white () != '\n')
{
give_help ();
flush_line ();
continue;
}
gotcmd = true;
break;
case 'e':
cmd1 = skip_white ();
switch (cmd1)
{
case '1': case '2': case 'b': case 'd': case 'l': case 'r':
if (skip_white () != '\n')
{
give_help ();
flush_line ();
continue;
}
gotcmd = true;
break;
case '\n':
gotcmd = true;
break;
default:
give_help ();
flush_line ();
continue;
}
break;
case EOF:
if (feof (stdin))
{
gotcmd = true;
cmd0 = 'q';
break;
}
/* Fall through. */
default:
flush_line ();
/* Fall through. */
case '\n':
give_help ();
continue;
}
}
switch (cmd0)
{
case '1': case 'l':
lf_copy (left, llen, outfile);
lf_skip (right, rlen);
return true;
case '2': case 'r':
lf_copy (right, rlen, outfile);
lf_skip (left, llen);
return true;
case 's':
suppress_common_lines = true;
break;
case 'v':
suppress_common_lines = false;
break;
case 'q':
return false;
case 'e':
{
int fd;
if (tmpname)
tmp = fopen (tmpname, "w");
else
{
if ((fd = temporary_file ()) < 0)
perror_fatal ("mkstemp");
tmp = fdopen (fd, "w");
}
if (! tmp)
perror_fatal (tmpname);
switch (cmd1)
{
case 'd':
if (llen)
{
if (llen == 1)
fprintf (tmp, "--- %s %ld\n", lname, (long int) lline);
else
fprintf (tmp, "--- %s %ld,%ld\n", lname,
(long int) lline,
(long int) (lline + llen - 1));
}
/* Fall through. */
case '1': case 'b': case 'l':
lf_copy (left, llen, tmp);
break;
default:
lf_skip (left, llen);
break;
}
switch (cmd1)
{
case 'd':
if (rlen)
{
if (rlen == 1)
fprintf (tmp, "+++ %s %ld\n", rname, (long int) rline);
else
fprintf (tmp, "+++ %s %ld,%ld\n", rname,
(long int) rline,
(long int) (rline + rlen - 1));
}
/* Fall through. */
case '2': case 'b': case 'r':
lf_copy (right, rlen, tmp);
break;
default:
lf_skip (right, rlen);
break;
}
ck_fclose (tmp);
{
int wstatus;
int werrno = 0;
ignore_SIGINT = true;
checksigs ();
{
#if ! (HAVE_WORKING_FORK || HAVE_WORKING_VFORK)
char *command =
xmalloc (quote_system_arg (0, editor_program)
+ 1 + strlen (tmpname) + 1);
sprintf (command + quote_system_arg (command, editor_program),
" %s", tmpname);
wstatus = system (command);
if (wstatus == -1)
werrno = errno;
free (command);
#else
pid_t pid;
pid = vfork ();
if (pid == 0)
{
char const *argv[3];
int i = 0;
argv[i++] = editor_program;
argv[i++] = tmpname;
argv[i] = 0;
execvp (editor_program, (char **) argv);
_exit (errno == ENOENT ? 127 : 126);
}
if (pid < 0)
perror_fatal ("fork");
while (waitpid (pid, &wstatus, 0) < 0)
if (errno == EINTR)
checksigs ();
else
perror_fatal ("waitpid");
#endif
}
ignore_SIGINT = false;
check_child_status (werrno, wstatus, EXIT_SUCCESS,
editor_program);
}
{
char buf[SDIFF_BUFSIZE];
size_t size;
tmp = ck_fopen (tmpname, "r");
while ((size = ck_fread (buf, SDIFF_BUFSIZE, tmp)) != 0)
{
checksigs ();
ck_fwrite (buf, size, outfile);
}
ck_fclose (tmp);
}
return true;
}
default:
give_help ();
break;
}
}
}
int G2A (int argc, char *argv[] )
{
char origname[128]; // original name
char newname [128]; // renumbered name
char command [255]; // command buffer
char *TempName;
char *numstring;
char ImageName[128];
int counter = 0;
int number;
char *p;
char nameFileName[255];
char analyzeFileName[255];
char headerFileName[255];
char baseName[255];
short verbose = true;
FILE *nameFile;
FILE *TempFile;
FILE *dataFile;
FILE *procFile;
FILE *headerFile;
FILE *inFile;
int i;
IMAGE im;
short count;
short *dataBuff;
Boolean DebugMode = false;
static char id[] = "$Revision: 1.21 $$Date: 2006/06/09 18:40:34 $";
OSErr error = noErr;
if( argc < 2 ) {
print_usage( argv[0] );
}
// setup an output file name, based on the last input file name
sprintf( baseName, "%s", argv[argc-1] ); // output file name
p = strrchr( baseName, 'I' );
*p = '\0'; // null terminate
error = OpenProcFile( argc, argv, baseName, id, &procFile );
ILError( error, "Opening Proc file" );
sprintf( nameFileName, "%s.NAME_FILE", baseName );
fprintf( procFile, "Associated name file ... %s\n", nameFileName );
sprintf( headerFileName, "%s.GenesisHdrs", baseName );
fprintf( procFile, "Associated headers file ... %s\n", headerFileName );
// corrected names will be stored temporarily in nameFile
error = CreateTempFile( &TempFile, &TempName );
ILError( error, TempName );
// use UC_ReadHeader to determine image dimensions, etc...
error = UC_Readheader( argv[argc-1], &im );
if( error ) ILError( error, "Read Image" );
// rename the files and create name list into the file called TempName
for( i=argc-1; i>0; i-- )
{
strcpy( origname, argv[i] );
strcpy( newname, argv[i] );
numstring = strrchr( newname, 'I' ) + 1;
number = atoi( numstring );
sprintf( numstring, "%0.3d.MR", number );
fprintf( TempFile, "%s\n", newname );
if( strcmp( origname, newname ) || DebugMode ) {
if( verbose ) {
printf( "i:%d\t%s --> %s\n", i, origname, newname );
}
sprintf( command, "mv %s %s\n", origname, newname );
fprintf( procFile, "\tRenamed %s to %s\n", origname, newname );
system( command );
}
}
error = ck_fclose( TempFile );
ILError( error, TempName );
// Sort the contents of the temporary nameFile and place it into the permanent version
sprintf( command, "sort %s > %s", TempName, nameFileName );
system( command );
if( false ) {
DBG( command );
printf( "\nContents of name file\n" );
sprintf( command, "cat %s", nameFileName );
DBG( command );
system( command );
}
// now, place the name of the header file at the beginning of a file */
error = CreateTempFile( &TempFile, &TempName );
ILError ( error, TempName );
fprintf( TempFile, "%s\n", headerFileName );
error = ck_fclose( TempFile );
ILError( error, TempName );
// add the file names to the end
sprintf( command, "cat %s >> %s\n", nameFileName, TempName );
system( command );
// and rename this file
sprintf( command, "mv %s %s\n", TempName, nameFileName );
system( command );
if( false ) {
printf( "new Contents of name file" );
sprintf( command, "cat %s", nameFileName );
DBG( command );
system( command );
}
im.dim.n_slices = argc - 1;
error = CreateHeader( ANALYZE, &im, baseName );
if( error ) ILError( error, "Writing Header" );
sprintf( analyzeFileName, "%s.img", baseName );
error = ck_fopen( &dataFile, analyzeFileName, "wb" );
ILError( error, "data file" );
error = ck_fopen( &nameFile, nameFileName, "rb" );
ILError( error, "name file" );
error = ck_fopen( &headerFile, headerFileName, "wb" );
ILError( error, "header file" );
if( im.dim.x * im.dim.y * sizeof(short) < SIGHDRSIZE ) {
dataBuff = (short *)ck_malloc( SIGHDRSIZE, "data buffer" );
} else {
dataBuff = (short *)ck_malloc( im.dim.x * im.dim.y * sizeof(short), "data buffer" );
}
count = fscanf( nameFile, "%s", headerFileName ); // just read past this.
count = fscanf( nameFile, "%s", ImageName );
if( false ) { DBG( ImageName ); }
printf( "\n\tPatience for a moment\n" );
while( count>0 ) {
printf( "%d of %d complete\n", counter++, argc - 1 );
error = ck_fopen( &inFile, ImageName, "rb" );
ILError( error, "Opening image" );
error = ck_fread ( dataBuff, sizeof( char ), SIGHDRSIZE, inFile );
ILError( error, "Reading header" );
error = ck_fwrite( dataBuff, sizeof( char ), SIGHDRSIZE, headerFile );
ILError( error, "Writing image header" );
error = ck_fread ( dataBuff, sizeof( short ), im.dim.x * im.dim.y, inFile );
ILError( error, "Reading image data" );
error = ck_fwrite( dataBuff, sizeof( short ), im.dim.x * im.dim.y, dataFile );
ILError( error, "Writing image data" );
ck_fclose( inFile );
count = fscanf( nameFile, "%s", ImageName );
}
printf( "\n\nCreated Analyze (4D) file: %s\n", analyzeFileName );
printf( "\tSave these files!: %s and %s\n\n", nameFileName, headerFileName );
printf( "To create corresponding genesis images from an analyze file named XXX.img, use:\n" );
printf( "\tAnalyze2Genesis -n %s -i XXX.img\n", nameFileName );
free( dataBuff );
error = ck_fclose( headerFile );
if( error ) ILError( error, headerFileName );
error = ck_fclose( nameFile );
if( error ) ILError( error, nameFileName );
error = ck_fclose( dataFile );
if( error ) ILError( error, analyzeFileName );
error = ck_fclose( procFile );
if( error ) ILError( error, "proc file" );
return error;
}
/********************************** 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;
}