fslio.c

来自「DTMK软件开发包,此为开源软件,是一款很好的医学图像开发资源.」· C语言 代码 · 共 1,842 行 · 第 1/5 页

  size_t volbytes, offset, orig_offset;
  size_t n;
  short xdim,ydim,zdim,v,wordsize;

  if (fslio==NULL)  FSLIOERR("FslReadTimeSeries: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {

    FslGetDim(fslio,&xdim,&ydim,&zdim,&v);
    
    if ((xVox<0) || (xVox >=xdim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
    if ((yVox<0) || (yVox >=ydim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
    if ((zVox<0) || (zVox >=zdim)) FSLIOERR("FslReadTimeSeries: voxel outside valid range");
    
    wordsize = fslio->niftiptr->nbyper;
    volbytes = xdim * ydim * zdim * wordsize;
    
    orig_offset = znztell(fslio->fileptr);
    offset = ((ydim * zVox + yVox) * xdim + xVox) * wordsize;
    znzseek(fslio->fileptr,offset,SEEK_CUR);
    
    for (n=0; n<nvols; n++) {
      if (n>0) znzseek(fslio->fileptr, volbytes - wordsize, SEEK_CUR);
      if (znzread((char *)buffer+(n*wordsize), 1, wordsize,fslio->fileptr) != wordsize)
        FSLIOERR("FslReadTimeSeries: failed to read values"); 
      if (fslio->niftiptr->byteorder != nifti_short_order())
        nifti_swap_Nbytes(1,fslio->niftiptr->swapsize,
                          (char *)buffer+(n*wordsize));
    }
    
    /* restore file pointer to original position */
    znzseek(fslio->fileptr,orig_offset,SEEK_SET);
    return n;

  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
  return 0;
}


size_t FslReadCplxVolumes(FSLIO *fslio, void *buffer, size_t nvols, char mode)
{
  if (fslio==NULL)  FSLIOERR("FslReadCplxVolumes: Null pointer passed for FSLIO");
  fprintf(stderr,"Warning:: FslReadCplxVolumes is not yet supported\n");
  return 0;
}

size_t FslWriteCplxVolumes(FSLIO *fslio, void *buffer, size_t nvols, char mode)
{
  if (fslio==NULL)  FSLIOERR("FslWriteCplxVolumes: Null pointer passed for FSLIO");
  fprintf(stderr,"Warning:: FslWriteCplxVolumes is not yet supported\n");
  return 0;
}

int FslSeekVolume(FSLIO *fslio, size_t vols)
{
  int offset;
  if (fslio==NULL)  FSLIOERR("FslSeekVolume: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    offset = fslio->niftiptr->iname_offset + 
      vols * FslGetVolSize(fslio) * fslio->niftiptr->nbyper;
    if (znz_isnull(fslio->fileptr)) FSLIOERR("FslSeekVolume: Null file pointer");
    return znzseek(fslio->fileptr,offset,SEEK_SET);
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
  return 0;
}


size_t FslGetVolSize(FSLIO *fslio)
{
  /* returns number of voxels per 3D volume */
  if (fslio==NULL)  FSLIOERR("FslGetVolSize: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    return (fslio->niftiptr->nx * fslio->niftiptr->ny * fslio->niftiptr->nz);
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
  return 0;
}


void FslSetDim(FSLIO *fslio, short x, short y, short z, short v)
{
  int ndim;
  if (fslio==NULL)  FSLIOERR("FslSetDim: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {

    ndim=4;
    if (v<=1) {ndim--; if (z<=1) {ndim--; if (y<=1) {ndim--; if (x<=1) {ndim--;}}}}

    fslio->niftiptr->ndim = ndim;

    if (x>=1) fslio->niftiptr->nx = x; else fslio->niftiptr->nx=1;
    if (y>=1) fslio->niftiptr->ny = y; else fslio->niftiptr->ny=1;
    if (z>=1) fslio->niftiptr->nz = z; else fslio->niftiptr->nz=1;
    if (v>=1) fslio->niftiptr->nt = v; else fslio->niftiptr->nt=1;
    fslio->niftiptr->nu = 1;
    fslio->niftiptr->nv = 1;
    fslio->niftiptr->nw = 1;

    /* deal with stupid redundancies */
    fslio->niftiptr->dim[0] = fslio->niftiptr->ndim ;
    fslio->niftiptr->dim[1] = fslio->niftiptr->nx;
    fslio->niftiptr->dim[2] = fslio->niftiptr->ny;
    fslio->niftiptr->dim[3] = fslio->niftiptr->nz;
    fslio->niftiptr->dim[4] = fslio->niftiptr->nt;
    fslio->niftiptr->dim[5] = fslio->niftiptr->nu;
    fslio->niftiptr->dim[6] = fslio->niftiptr->nv;
    fslio->niftiptr->dim[7] = fslio->niftiptr->nw;

    fslio->niftiptr->nvox =  fslio->niftiptr->nx * fslio->niftiptr->ny * fslio->niftiptr->nz
      * fslio->niftiptr->nt * fslio->niftiptr->nu * fslio->niftiptr->nv * fslio->niftiptr->nw ;

  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetDim(FSLIO *fslio, short *x, short *y, short *z, short *v)
{
  if (fslio==NULL)  FSLIOERR("FslGetDim: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    *x = fslio->niftiptr->nx;
    *y = fslio->niftiptr->ny;
    *z = fslio->niftiptr->nz;
    *v = fslio->niftiptr->nt;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetDimensionality(FSLIO *fslio, size_t dim)
{
  if (fslio==NULL)  FSLIOERR("FslSetDimensionality: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    fslio->niftiptr->ndim = dim;
    fslio->niftiptr->dim[0] = dim;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetDimensionality(FSLIO *fslio, size_t *dim)
{
  if (fslio==NULL)  FSLIOERR("FslGetDimensionality: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    *dim = fslio->niftiptr->ndim;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetVoxDim(FSLIO *fslio, float x, float y, float z, float tr)
{
  if (fslio==NULL)  FSLIOERR("FslSetVoxDim: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    fslio->niftiptr->dx = fabs(x);
    fslio->niftiptr->dy = fabs(y);
    fslio->niftiptr->dz = fabs(z);
    fslio->niftiptr->dt = fabs(tr);
    fslio->niftiptr->pixdim[1] = fabs(x);
    fslio->niftiptr->pixdim[2] = fabs(y);
    fslio->niftiptr->pixdim[3] = fabs(z);
    fslio->niftiptr->pixdim[4] = fabs(tr);
    /* set the units to mm and seconds */
    fslio->niftiptr->xyz_units  = NIFTI_UNITS_MM;
    fslio->niftiptr->time_units = NIFTI_UNITS_SEC;
 }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetVoxDim(FSLIO *fslio, float *x, float *y, float *z, float *tr)
{
  if (fslio==NULL)  FSLIOERR("FslGetVoxDim: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    *x = fabs(fslio->niftiptr->dx);
    *y = fabs(fslio->niftiptr->dy);
    *z = fabs(fslio->niftiptr->dz);
    *tr = fabs(fslio->niftiptr->dt);
    /* now check the units and convert to mm and sec */
    if (fslio->niftiptr->xyz_units == NIFTI_UNITS_METER) 
    { *x *= 1000.0;   *y *= 1000.0;   *z *= 1000.0; }
    if (fslio->niftiptr->xyz_units == NIFTI_UNITS_MICRON) 
    { *x /= 1000.0;   *y /= 1000.0;   *z /= 1000.0; }
    if (fslio->niftiptr->xyz_units == NIFTI_UNITS_MSEC) 
    { *tr /= 1000.0; }
    if (fslio->niftiptr->xyz_units == NIFTI_UNITS_USEC) 
    { *tr /= 1000000.0; }
    /* if it is Hz or other frequency then leave it */
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetCalMinMax(FSLIO *fslio, float *min, float *max)
{
  if (fslio==NULL)  FSLIOERR("FslGetCalMinMax: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    *min = fslio->niftiptr->cal_min;
    *max = fslio->niftiptr->cal_max;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetCalMinMax(FSLIO *fslio, float  min, float  max)
{
  if (fslio==NULL)  FSLIOERR("FslSetCalMinMax: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    fslio->niftiptr->cal_min = min;
    fslio->niftiptr->cal_max = max;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetAuxFile(FSLIO *fslio,char *aux_file)
{
  if (fslio==NULL)  FSLIOERR("FslGetAuxFile: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    strncpy(aux_file,fslio->niftiptr->aux_file, 24);
    aux_file[23] = '\0';
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetAuxFile(FSLIO *fslio,const char *aux_file)
{
  if (fslio==NULL)  FSLIOERR("FslSetAuxFile: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    strncpy(fslio->niftiptr->aux_file, aux_file, 24);
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetVoxUnits(FSLIO *fslio, const char *units)
{
  int unitcode=0;
  if (fslio==NULL)  FSLIOERR("FslSetVoxUnits: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    if (strcmp(units,nifti_units_string(NIFTI_UNITS_METER))==0) {
      unitcode = NIFTI_UNITS_METER;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MM))==0) {
      unitcode = NIFTI_UNITS_MM;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MICRON))==0) {
      unitcode = NIFTI_UNITS_MICRON;
    }
    fslio->niftiptr->xyz_units  = unitcode;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetVoxUnits(FSLIO *fslio, char *units)
{
  if (fslio==NULL)  FSLIOERR("FslGetVoxUnits: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    strcpy(units,nifti_units_string(fslio->niftiptr->xyz_units));
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}

void FslSetTimeUnits(FSLIO *fslio, const char *units)
{
  int unitcode=0;
  if (fslio==NULL)  FSLIOERR("FslSetTimeUnits: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    if (strcmp(units,nifti_units_string(NIFTI_UNITS_HZ))==0) {
      unitcode = NIFTI_UNITS_HZ;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_PPM))==0) {
      unitcode = NIFTI_UNITS_PPM;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_RADS))==0) {
      unitcode = NIFTI_UNITS_RADS;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_SEC))==0) {
      unitcode = NIFTI_UNITS_SEC;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_MSEC))==0) {
        fprintf(stderr,"Warning::Setting time units to msec is not fully recommended in fslio\n");
        unitcode = NIFTI_UNITS_MSEC;
    } else if (strcmp(units,nifti_units_string(NIFTI_UNITS_USEC))==0) {
        fprintf(stderr,"Warning::Setting time units to msec is not fully recommended in fslio\n");
        unitcode = NIFTI_UNITS_USEC;
    }
    fslio->niftiptr->time_units = unitcode;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslGetTimeUnits(FSLIO *fslio, char *units)
{
  if (fslio==NULL)  FSLIOERR("FslGetTimeUnits: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    strcpy(units,nifti_units_string(fslio->niftiptr->time_units));
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}


void FslSetDataType(FSLIO *fslio, short t)
{
  int nbytepix=0, ss=0;
  if (fslio==NULL)  FSLIOERR("FslSetDataType: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    fslio->niftiptr->datatype = t;
    nifti_datatype_sizes(t,&nbytepix,&ss);
    fslio->niftiptr->nbyper = nbytepix;
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
}

size_t FslGetDataType(FSLIO *fslio, short *t)
{
    /* returns bits per pixel */
  int nbytepix=32, ss=0;
  if (fslio==NULL)  FSLIOERR("FslGetDataType: Null pointer passed for FSLIO");
  if (fslio->niftiptr!=NULL) {
    *t = fslio->niftiptr->datatype;
    nifti_datatype_sizes(*t,&nbytepix,&ss);
  }
  if (fslio->mincptr!=NULL) {
    fprintf(stderr,"Warning:: Minc is not yet supported\n");
  }
  return (size_t) 8 * nbytepix;
}


void FslGetMMCoord(mat44 stdmat, float voxx, float voxy, float voxz, 
                   float *mmx, float *mmy, float *mmz) 
{
    *mmx = stdmat.m[0][0] * voxx + stdmat.m[0][1] * voxy + stdmat.m[0][2] * voxz 
        + stdmat.m[0][3];