/*
* return 0 - no update found
* return 1 - found update
*/
int get_matching_sig(unsigned int csig, int cpf, void *mc, int rev)
{
struct microcode_header_intel *mc_header = mc;
struct extended_sigtable *ext_header;
unsigned long total_size = get_totalsize(mc_header);
int ext_sigcount, i;
struct extended_signature *ext_sig;
if (update_match_cpu(csig, cpf, mc_header->sig, mc_header->pf))
return 1;
/* Look for ext. headers: */
if (total_size <= get_datasize(mc_header) + MC_HEADER_SIZE)
return 0;
ext_header = mc + get_datasize(mc_header) + MC_HEADER_SIZE;
ext_sigcount = ext_header->count;
ext_sig = (void *)ext_header + EXT_HEADER_SIZE;
for (i = 0; i < ext_sigcount; i++) {
if (update_match_cpu(csig, cpf, ext_sig->sig, ext_sig->pf))
return 1;
ext_sig++;
}
return 0;
}
static MAPTYPE *get_maps_3dvol(const mxArray *ptr, int *n)
{
int num_dims, jj, t, dtype = 0;
const mwSize *dims;
MAPTYPE *maps;
unsigned char *dptr;
if (mxIsDouble(ptr)) dtype = SPM_DOUBLE;
else if (mxIsSingle(ptr)) dtype = SPM_FLOAT;
else if (mxIsInt32 (ptr)) dtype = SPM_SIGNED_INT;
else if (mxIsUint32(ptr)) dtype = SPM_UNSIGNED_INT;
else if (mxIsInt16 (ptr)) dtype = SPM_SIGNED_SHORT;
else if (mxIsUint16(ptr)) dtype = SPM_UNSIGNED_SHORT;
else if (mxIsInt8 (ptr)) dtype = SPM_SIGNED_CHAR;
else if (mxIsUint8 (ptr)) dtype = SPM_UNSIGNED_CHAR;
else mexErrMsgTxt("Unknown volume datatype.");
maps = (MAPTYPE *)mxCalloc(1, sizeof(MAPTYPE));
num_dims = mxGetNumberOfDimensions(ptr);
if (num_dims > 3)
{
mexErrMsgTxt("Too many dimensions.");
}
dims = mxGetDimensions(ptr);
for(jj=0; jj<num_dims; jj++)
maps->dim[jj]=dims[jj];
for(jj=num_dims; jj<3; jj++)
maps->dim[jj]=1;
for(jj=0; jj<16; jj++)
maps->mat[jj] = 0.0;
for(jj=0; jj<4; jj++)
maps->mat[jj + jj*4] = 1.0;
maps->dtype = dtype;
maps->data = (void **)mxCalloc(maps->dim[2],sizeof(void *));
maps->scale = (double *)mxCalloc(maps->dim[2],sizeof(double));
maps->offset = (double *)mxCalloc(maps->dim[2],sizeof(double));
t = maps->dim[0]*maps->dim[1]*get_datasize(maps->dtype)/8;
dptr = (unsigned char *)mxGetPr(ptr);
for(jj=0; jj<maps->dim[2]; jj++)
{
maps->scale[jj] = 1.0;
maps->offset[jj] = 0.0;
maps->data[jj] = &(dptr[jj*t]);
}
maps->addr = 0;
maps->len = 0;
*n = 1;
return(maps);
}
block_datastr *blkdev_write_block(UID id,char *data)
{
int size;
char *copy_ptr;
block_datastr *ret;
block_datastr *bp;
char *temp;
int i=0;
ret = bp = find_freeblock(); // get free block pointer
printf("%x\n", ret);
size = get_datasize(data); // get size of data
printf("%d\n", size);
while(size > 0){
if(bcb.blocksleft <= 0)
{
printf("No have empty block");
return NULL;
}
bp->next = (unsigned int)(bp->next)|(0x1); // check block to be used
if(size > BLOCK_SIZE)
{
MemCpy(bp->data, data, BLOCK_SIZE);
bp->next = (unsigned int)(bp->next)|(unsigned int)find_freeblock();
bp = (unsigned int)(bp->next)&0xFFFFFFFE;
}
else
{
MemCpy(bp->data, data, size);
}
size = size - BLOCK_SIZE;
bcb.blocksleft--;
}
return ret;
}
static void get_map_dat(int i, const mxArray *ptr, MAPTYPE *maps)
{
mxArray *tmp;
double *pr;
int num_dims, j, t, dtype = 0;
const mwSize *dims;
unsigned char *dptr;
tmp=mxGetField(ptr,i,"dat");
if (tmp == (mxArray *)0)
{
free_maps(maps,i);
mexErrMsgTxt("Cant find dat.");
}
if (mxIsDouble(tmp)) dtype = SPM_DOUBLE;
else if (mxIsSingle(tmp)) dtype = SPM_FLOAT;
else if (mxIsInt32 (tmp)) dtype = SPM_SIGNED_INT;
else if (mxIsUint32(tmp)) dtype = SPM_UNSIGNED_INT;
else if (mxIsInt16 (tmp)) dtype = SPM_SIGNED_SHORT;
else if (mxIsUint16(tmp)) dtype = SPM_UNSIGNED_SHORT;
else if (mxIsInt8 (tmp)) dtype = SPM_SIGNED_CHAR;
else if (mxIsUint8 (tmp)) dtype = SPM_UNSIGNED_CHAR;
else
{
free_maps(maps,i);
mexErrMsgTxt("Unknown volume datatype.");
}
dptr = (unsigned char *)mxGetPr(tmp);
num_dims = mxGetNumberOfDimensions(tmp);
if (num_dims > 3)
{
free_maps(maps,i);
mexErrMsgTxt("Too many dimensions.");
}
dims = mxGetDimensions(tmp);
for(j=0; j<num_dims; j++)
maps[i].dim[j]=dims[j];
for(j=num_dims; j<3; j++)
maps[i].dim[j]=1;
tmp=mxGetField(ptr,i,"dim");
if (tmp != (mxArray *)0)
{
if (mxGetM(tmp)*mxGetN(tmp) != 3)
{
free_maps(maps,i);
mexErrMsgTxt("Wrong sized dim.");
}
pr = mxGetPr(tmp);
if (maps[i].dim[0] != (mwSize)fabs(pr[0]) ||
maps[i].dim[1] != (mwSize)fabs(pr[1]) ||
maps[i].dim[2] != (mwSize)fabs(pr[2]))
{
free_maps(maps,i);
mexErrMsgTxt("Incompatible volume dimensions in dim.");
}
}
tmp=mxGetField(ptr,i,"dt");
if (tmp != (mxArray *)0)
{
if (mxGetM(tmp)*mxGetN(tmp) != 1 && mxGetM(tmp)*mxGetN(tmp) != 2)
{
free_maps(maps,i);
mexErrMsgTxt("Wrong sized dt.");
}
pr = mxGetPr(tmp);
if (dtype != (int)fabs(pr[0]))
{
free_maps(maps,i);
mexErrMsgTxt("Incompatible datatype in dt.");
}
}
maps[i].addr = 0;
maps[i].len = 0;
maps[i].dtype = dtype;
maps[i].data = (void **)mxCalloc(maps[i].dim[2],sizeof(void *));
maps[i].scale = (double *)mxCalloc(maps[i].dim[2],sizeof(double));
maps[i].offset = (double *)mxCalloc(maps[i].dim[2],sizeof(double));
t = maps[i].dim[0]*maps[i].dim[1]*get_datasize(maps[i].dtype)/8;
tmp = mxGetField(ptr,i,"pinfo");
if (tmp != (mxArray *)0)
{
if ((mxGetM(tmp) != 2 && mxGetM(tmp) != 3) || (mxGetN(tmp) != 1 && mxGetN(tmp) != maps[i].dim[2]))
{
free_maps(maps,i+1);
mexErrMsgTxt("Wrong sized pinfo.");
}
if (mxGetM(tmp) == 3 && mxGetPr(tmp)[2] != 0)
{
free_maps(maps,i+1);
mexErrMsgTxt("pinfo(3) must equal 0 to read dat field.");
}
pr = mxGetPr(tmp);
if (mxGetN(tmp) == 1)
for(j=0; j<maps[i].dim[2]; j++)
{
maps[i].scale[j] = pr[0];
maps[i].offset[j] = pr[1];
maps[i].data[j] = &(dptr[j*t]);
}
else
for(j=0; j<maps[i].dim[2]; j++)
{
maps[i].scale[j] = pr[0+j*2];
maps[i].offset[j] = pr[1+j*2];
maps[i].data[j] = &(dptr[j*t]);
}
}
else
for(j=0; j<maps[i].dim[2]; j++)
{
maps[i].scale[j] = 1.0;
maps[i].offset[j] = 0.0;
maps[i].data[j] = &(dptr[j*t]);
}
tmp=mxGetField(ptr,i,"mat");
if (tmp != (mxArray *)0)
{
if (mxGetM(tmp) != 4 || mxGetN(tmp) != 4)
{
free_maps(maps,i+1);
mexErrMsgTxt("Wrong sized mat.");
}
pr = mxGetPr(tmp);
for(j=0; j<16; j++)
maps[i].mat[j] = pr[j];
}
else
{
for(j=0; j<16; j++)
maps[i].mat[j] = 0.0;
for(j=0; j<4; j++)
maps[i].mat[j + j*4] = 1.0;
}
}
int microcode_sanity_check(void *mc, int print_err)
{
unsigned long total_size, data_size, ext_table_size;
struct microcode_header_intel *mc_header = mc;
struct extended_sigtable *ext_header = NULL;
int sum, orig_sum, ext_sigcount = 0, i;
struct extended_signature *ext_sig;
total_size = get_totalsize(mc_header);
data_size = get_datasize(mc_header);
if (data_size + MC_HEADER_SIZE > total_size) {
if (print_err)
pr_err("error! Bad data size in microcode data file\n");
return -EINVAL;
}
if (mc_header->ldrver != 1 || mc_header->hdrver != 1) {
if (print_err)
pr_err("error! Unknown microcode update format\n");
return -EINVAL;
}
ext_table_size = total_size - (MC_HEADER_SIZE + data_size);
if (ext_table_size) {
if ((ext_table_size < EXT_HEADER_SIZE)
|| ((ext_table_size - EXT_HEADER_SIZE) % EXT_SIGNATURE_SIZE)) {
if (print_err)
pr_err("error! Small exttable size in microcode data file\n");
return -EINVAL;
}
ext_header = mc + MC_HEADER_SIZE + data_size;
if (ext_table_size != exttable_size(ext_header)) {
if (print_err)
pr_err("error! Bad exttable size in microcode data file\n");
return -EFAULT;
}
ext_sigcount = ext_header->count;
}
/* check extended table checksum */
if (ext_table_size) {
int ext_table_sum = 0;
int *ext_tablep = (int *)ext_header;
i = ext_table_size / DWSIZE;
while (i--)
ext_table_sum += ext_tablep[i];
if (ext_table_sum) {
if (print_err)
pr_warn("aborting, bad extended signature table checksum\n");
return -EINVAL;
}
}
/* calculate the checksum */
orig_sum = 0;
i = (MC_HEADER_SIZE + data_size) / DWSIZE;
while (i--)
orig_sum += ((int *)mc)[i];
if (orig_sum) {
if (print_err)
pr_err("aborting, bad checksum\n");
return -EINVAL;
}
if (!ext_table_size)
return 0;
/* check extended signature checksum */
for (i = 0; i < ext_sigcount; i++) {
ext_sig = (void *)ext_header + EXT_HEADER_SIZE +
EXT_SIGNATURE_SIZE * i;
sum = orig_sum
- (mc_header->sig + mc_header->pf + mc_header->cksum)
+ (ext_sig->sig + ext_sig->pf + ext_sig->cksum);
if (sum) {
if (print_err)
pr_err("aborting, bad checksum\n");
return -EINVAL;
}
}
return 0;
}
int main(int argc, char **argv)
{
static char id[] = "$Revision: 1.5 $$Date: 2002/09/10 22:14:51 $";
char *invec, *outvec; /* image vectors */
int timePt;
short rows = 0;
short cols = 0;
int slices;
long MultImSize; /* size of one image */
short SmallX, SmallY; /* X and Y size of single image from multi-display */
int argp=EOF;
char *in_fname = NULL;
char *out_basename = NULL;
char out_fname[128], procfname[128];
FILE *imFile;
FILE *procFile;
IMAGE im;
short dSize;
char typeString[40];
OSErr error = noErr;
while ( (argp=getopt(argc,argv,"o:i:r:c:h?")) != EOF ) {
switch( argp ) {
case 'o': out_basename = optarg; break;
case 'i': in_fname = optarg; break;
case 'c': cols = atoi( optarg ); break;
case 'r': rows = atoi( optarg ); break;
case 'h':
case '?':
default:
print_usage( argv[0] );
exit( -1 );
break;
}
}
if( !out_basename || !in_fname || !rows || !cols ) {
print_usage( argv[0] );
exit(-1);
}
error = UC_Readheader(in_fname, &im);
if( error ) {
ILError( error, "Reading Header" );
}
switch( im.file_type )
{
case BSHORT:
dSize = get_datasize( T_USHORT );
sprintf( typeString, "bshort" );
break;
case BUCHAR:
dSize = get_datasize( T_UCHAR );
sprintf( typeString, "buchar" );
break;
case BFLOAT:
dSize = get_datasize( T_FLOAT );
sprintf( typeString, "bfloat" );
break;
default:
ILError( DATA_OUT_OF_RANGE, "unknown type" );
}
/* Parse output file name and create proc file name */
strcpy( procfname, out_basename );
MultImSize= im.dim.x*im.dim.y;
SmallX = im.dim.x / cols;
SmallY = im.dim.y / rows;
slices = rows * cols;
/* Buffer allocation */
invec = ( char *)ck_malloc( MultImSize * dSize, "image vector" );
outvec = ( char *)ck_malloc( SmallX * SmallY * slices * dSize, "output vector" );
imFile = errfopen( in_fname, "rb" );
error = OpenProcFile( argc, argv, procfname, id, &procFile );
ILError( error, "Opening Proc file" );
for( timePt = 0; timePt < im.dim.timePts; timePt++ ) {
int theSlice = 0;
error = UC_Readimage( imFile, &im, invec, theSlice, timePt );
if( error ) {
ILError( error, "Reading image" );
}
// fool unmdisplay by treating all input as char
error = unmdisplay( outvec, invec, SmallX * dSize, SmallY, slices, T_UCHAR );
if( error ) {
ILError( error, "unmdisplay" );
}
if( im.dim.timePts > 1 ) {
sprintf( out_fname, "%s.%0.3d", out_basename, timePt+1 );
} else {
sprintf( out_fname, "%s", out_basename );
}
fprintf( procFile, "\tCreated %s.%s\n", out_fname, typeString );
error = WriteMGHImage( outvec, out_fname, SmallX, SmallY, (short)slices, im.data_type );
if( error ) {
ILError( error, "Writing output image" );
}
}
error = ck_fclose( imFile );
if( error ) ILError( error, "input file" );
error = ck_fclose( procFile );
if( error ) ILError( error, "proc file" );
free( outvec );
free( invec );
return 0;
}
/********************************** 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;
}
