/*
The portable graymap format is a lowest common denominator
grayscale file format. The definition is as follows:
- A "magic number" for identifying the file type. A pgm
file's magic number is the two characters "P5".
- Whitespace (blanks, TABs, CRs, LFs).
- A width, formatted as ASCII characters in decimal.
- Whitespace.
- A height, again in ASCII decimal.
- Whitespace.
- The maximum gray value (Maxval), again in ASCII decimal.
Must be less than 65536.
- Newline or other single whitespace character.
- A raster of Width * Height gray values, proceeding
through the image in normal English reading order. Each
gray value is a number from 0 through Maxval, with 0
being black and Maxval being white. Each gray value is
represented in pure binary by either 1 or 2 bytes. If
the Maxval is less than 256, it is 1 byte. Otherwise,
it is 2 bytes. The most significant byte is first.
- Characters from a "#" to the next end-of-line, before
the maxval line, are comments and are ignored.
*/
int readPgmImage(const char *name,_image *im)
{
char string[256];
int x=0, y=0;
int max=0;
fgetns( string, 255, im );
if ( strncmp(string, PGM_MAGIC, strlen(PGM_MAGIC) ) ) {
fprintf( stderr, "readPgmImage: bad magic string in \'%s\'\n", name );
return( -1 );
}
do {
fgetns( string, 255, im );
if ( string[0] != '#' ) {
if ( x == 0 && y == 0 ) {
sscanf( string, "%d %d", &x, &y );
}
else if ( max == 0 ) {
sscanf( string, "%d", &max );
}
}
} while ( max == 0 );
im->xdim = x;
im->ydim = y;
im->zdim = 1;
im->vdim = 1;
im->wordKind = WK_FIXED;
im->sign = SGN_UNSIGNED;
if ( max < 256 ) im->wdim = 1;
else if ( max < 65536 ) {
im->wdim = 2;
fprintf( stderr, "readPgmImage: Warning, data of \'%s\' may have to be swapped\n", name );
}
else {
fprintf( stderr, "readPgmImage: max value too large (%d) in \'%s\'\n", max, name );
return( -1 );
}
im->data = ImageIO_alloc( x*y );
ImageIO_read( im, im->data, x*y );
return 1;
}
int _readAnalyzeHeader( _image* im, const char* name,
struct dsr *analyzeHeader )
{
unsigned int i ;
/* compile time endianness */
ENDIANNESS ARCHITECTURE_ENDIANNESS = _getEndianness();
if(im->openMode != OM_CLOSE) {
ImageIO_read( im, analyzeHeader, sizeof(struct dsr) );
if( analyzeHeader->hk.sizeof_hdr == sizeof(struct dsr) )
{
im->endianness = ARCHITECTURE_ENDIANNESS ;
}
else
{
_swapAnalyzeHdr( analyzeHeader );
if( analyzeHeader->hk.sizeof_hdr != sizeof(struct dsr) )
{
fprintf (stderr,
"_readAnalyzeHeader: error: unknown magic (%d)...\n",
analyzeHeader->hk.sizeof_hdr );
return -1;
}
if( ARCHITECTURE_ENDIANNESS == END_LITTLE )
{
im->endianness = END_BIG;
}
else
{
im->endianness = END_LITTLE;
}
}
if ( analyzeHeader->dime.dim[0] > 4 ) {
fprintf (stderr,
"_readAnalyzeHeader: error: dimensionality not supported (%d)...\n",
analyzeHeader->dime.dim[0] );
return -1;
}
im->xdim = analyzeHeader->dime.dim[1];
im->ydim = analyzeHeader->dime.dim[2];
im->zdim = analyzeHeader->dime.dim[3];
/* 0 time-points is a convention for one volume only at MNI */
/* Corrected by X. Pennec following a bug report by Irina Kezele at MNI */
if( analyzeHeader->dime.dim[4] == 0 ){
fprintf (stderr,
"_readAnalyzeHeader: warning: time dimension / number if volume (dim[4]) is 0. Assuming this means 1 (otherwise there would be no image...). \n");
analyzeHeader->dime.dim[4] = 1;
}
/* Analyze doesn't support vector images.
The forth dimension relates to time. */
if( analyzeHeader->dime.dim[4] != 1 )
{
fprintf (stderr,
"_readAnalyzeHeader: error: time dimension not supported (%d)...\n",
analyzeHeader->dime.dim[4] );
return -1;
}
im->vectMode = VM_SCALAR;
im->vx = analyzeHeader->dime.pixdim[1];
im->vy = analyzeHeader->dime.pixdim[2];
im->vz = analyzeHeader->dime.pixdim[3];
if( im->vx == 0.0 ) im->vx = 1.0 ;
if( im->vy == 0.0 ) im->vy = im->vx ;
if( im->vz == 0.0 ) im->vz = im->vy ;
switch(analyzeHeader->dime.datatype)
{
case DT_BINARY:
case DT_UNSIGNED_CHAR:
case DT_SIGNED_SHORT:
case DT_SIGNED_INT:
case DT_FLOAT:
case DT_COMPLEX:
case DT_DOUBLE:
im->vdim = 1;
break ;
case DT_RGB:
im->vdim = 3;
break ;
default:
fprintf (stderr,
"_readAnalyzeHeader: error: data type not supported (%d)...\n",
analyzeHeader->dime.datatype );
return -1;
}
switch(analyzeHeader->dime.datatype)
{
case DT_BINARY:
case DT_UNSIGNED_CHAR:
case DT_SIGNED_SHORT:
case DT_SIGNED_INT:
case DT_RGB:
im->wordKind = WK_FIXED;
break ;
case DT_FLOAT:
case DT_COMPLEX:
case DT_DOUBLE:
im->wordKind = WK_FLOAT;
break ;
default:
fprintf (stderr,
"_readAnalyzeHeader: error: data type not supported (%d)...\n",
analyzeHeader->dime.datatype );
return -1;
}
switch(analyzeHeader->dime.datatype)
{
case DT_BINARY:
case DT_UNSIGNED_CHAR:
case DT_RGB:
im->sign = SGN_UNSIGNED;
break ;
case DT_SIGNED_SHORT:
case DT_SIGNED_INT:
case DT_FLOAT:
case DT_COMPLEX:
case DT_DOUBLE:
im->sign = SGN_SIGNED;
break ;
default:
fprintf (stderr,
"_readAnalyzeHeader: error: data type not supported (%d)...\n",
analyzeHeader->dime.datatype );
return -1;
}
im->wdim = analyzeHeader->dime.bitpix;
if( analyzeHeader->dime.datatype == DT_RGB )
{
im->wdim /= 3 ;
}
if(im->wdim != 8 && im->wdim != 16 && im->wdim != 32 && im->wdim != 64)
{
fprintf (stderr,
"_readAnalyzeHeader: error: pixel size not supported (%d)...\n",
analyzeHeader->dime.bitpix );
return -1;
}
im->wdim >>= 3 ;
/* There are 17 optional data fields
be careful in the allocation
*/
im->nuser = 1 + 17 ;
im->user = (char **) ImageIO_alloc(im->nuser * sizeof(char *));
for ( i=0; i<im->nuser; i++ ) im->user[i] = NULL;
i = 0 ;
im->user[i] = (char *) ImageIO_alloc((strlen("Data lost in the Analyze -> ImageIO conversion:") + 1));
sprintf( im->user[i++], "Data lost in the Analyze -> ImageIO conversion:" );
im->user[i] = (char *) ImageIO_alloc((strlen(" descrip: ") + 1 + strlen(analyzeHeader->hist.descrip) ));
sprintf( im->user[i++], " descrip: %s", analyzeHeader->hist.descrip );
im->user[i] = (char *) ImageIO_alloc((strlen(" aux_file: ") + 1 + strlen(analyzeHeader->hist.descrip) ));
sprintf( im->user[i++], " aux_file: %s", analyzeHeader->hist.descrip );
im->user[i] = (char *) ImageIO_alloc((strlen(" orient: ") + 1+ 2));
sprintf( im->user[i++], " orient: %d", analyzeHeader->hist.orient );
im->user[i] = (char *) ImageIO_alloc((strlen(" originator: ") + 1 + strlen(analyzeHeader->hist.originator) ));
sprintf( im->user[i++], " originator: %s", analyzeHeader->hist.originator );
im->user[i] = (char *) ImageIO_alloc((strlen(" generated: ") + 1 + strlen(analyzeHeader->hist.generated) ));
sprintf( im->user[i++], " generated: %s", analyzeHeader->hist.generated );
im->user[i] = (char *) ImageIO_alloc((strlen(" scannum: ") + 1 + strlen(analyzeHeader->hist.scannum) ));
sprintf( im->user[i++], " scannum: %s", analyzeHeader->hist.scannum );
im->user[i] = (char *) ImageIO_alloc((strlen(" patient_id: ") + 1 + strlen(analyzeHeader->hist.patient_id) ));
sprintf( im->user[i++], " patient_id: %s", analyzeHeader->hist.patient_id );
im->user[i] = (char *) ImageIO_alloc((strlen(" exp_date: ") + 1 + strlen(analyzeHeader->hist.exp_date) ));
sprintf( im->user[i++], " exp_date: %s", analyzeHeader->hist.exp_date );
im->user[i] = (char *) ImageIO_alloc((strlen(" exp_time: ") + 1 + strlen(analyzeHeader->hist.exp_time) ));
sprintf( im->user[i++], " exp_time: %s", analyzeHeader->hist.exp_time );
/* A 32 bit int doesn't print on more than 11 chars */
im->user[i] = (char *) ImageIO_alloc((strlen(" views: ") + 11 + 1));
sprintf( im->user[i++], " views: %d", analyzeHeader->hist.views );
im->user[i] = (char *) ImageIO_alloc((strlen(" vols_added: ") + 11 + 1));
sprintf( im->user[i++], " vols_added: %d", analyzeHeader->hist.vols_added );
im->user[i] = (char *) ImageIO_alloc((strlen(" start_field: ") + 11 + 1));
sprintf( im->user[i++], " start_field: %d", analyzeHeader->hist.start_field );
im->user[i] = (char *) ImageIO_alloc((strlen(" field_skip: ") + 11 + 1));
sprintf( im->user[i++], " field_skip: %d", analyzeHeader->hist.field_skip );
im->user[i] = (char *) ImageIO_alloc((strlen(" omax: ") + 11 + 1));
sprintf( im->user[i++], " omax: %d", analyzeHeader->hist.omax );
im->user[i] = (char *) ImageIO_alloc((strlen(" omin: ") + 11 + 1));
sprintf( im->user[i++], " omin: %d", analyzeHeader->hist.omin );
im->user[i] = (char *) ImageIO_alloc((strlen(" smax: ") + 11 + 1));
sprintf( im->user[i++], " smax: %d", analyzeHeader->hist.smax );
im->user[i] = (char *) ImageIO_alloc((strlen(" smin: ") + 11 + 1));
sprintf( im->user[i++], " smin: %d", analyzeHeader->hist.smin );
/* header is read. close header file and open data file. */
if( name != NULL ) {
int length = strlen(name) ;
char* data_filename = (char *) ImageIO_alloc(length+4) ;
if( strcmp( name+length-4, ".hdr" ) )
{
fprintf (stderr,
"_readAnalyzeHeader: error: file header extension must be .hdr\n");
ImageIO_free( data_filename );
return -1;
}
ImageIO_close(im);
strcpy(data_filename,name);
strcpy(data_filename+length-3, "img.gz");
_openReadImage(im,data_filename);
if(!im->fd) {
strcpy(data_filename,name);
strcpy(data_filename+length-3, "img");
_openReadImage(im,data_filename);
if(!im->fd) {
fprintf(stderr, "_readAnalyzeHeader: error: unable to open data file \'%s\'\n", data_filename);
ImageIO_free( data_filename );
return -1;
}
}
ImageIO_free( data_filename );
}
/* check header validity */
if(im->xdim > 0 && im->ydim > 0 && im->zdim > 0 && im->vdim > 0 &&
im->vx > 0.0 && im->vy > 0.0 && im->vz > 0.0 &&
(im->wordKind == WK_FLOAT || (im->wordKind == WK_FIXED &&
im->sign != SGN_UNKNOWN)) &&
im->endianness != END_UNKNOWN) {
return 0;
}
else return -1;
}