示例#1
0
文件: mincio.c 项目: BIC-MNI/BEaST
int write_minc(char *filename, float *image, image_metadata *meta,VIO_BOOL binary_mask){
  VIO_Volume volume;
  int i,j,k,index;
  float min=FLT_MAX,max=FLT_MIN;
  VIO_Real dummy[3];

  if(binary_mask)
  {
    volume = create_volume(3,NULL,NC_BYTE,FALSE,0.0,1.0);
    printf("Writing a binary volume...\n");
  }
  else 
    volume = create_volume(3,NULL,NC_FLOAT,FALSE,FLT_MIN,FLT_MAX);
  
  if(!volume)
    return STATUS_ERR;
  
  if(!binary_mask)
  {
    for (i=0;i<meta->length[0];i++){
      for (j=0;j<meta->length[1];j++){
        for (k=0;k<meta->length[2];k++){	  
          index=i*meta->length[2]*meta->length[1] + j*meta->length[2] + k;
          min=MIN(min,image[index]);
          max=MAX(max,image[index]);
        }
      }
    }
    set_volume_real_range(volume,min,max);
  } else {
    set_volume_real_range(volume,0.0,1.0);
  }
  
  set_volume_sizes(volume,meta->length);
  dummy[0]=meta->start[0];
  dummy[1]=meta->start[1];
  dummy[2]=meta->start[2];
  set_volume_starts(volume,dummy);
  dummy[0]=meta->step[0];
  dummy[1]=meta->step[1];
  dummy[2]=meta->step[2];
  set_volume_separations(volume,dummy);

  alloc_volume_data(volume);
    
  get_volume(image, volume, meta->length);

  if(!binary_mask)
    output_volume( filename, NC_FLOAT,FALSE,min, max,volume,meta->history,(minc_output_options *)NULL);
  else
    output_volume( filename, NC_BYTE,FALSE,0, 1.0,volume,meta->history,(minc_output_options *)NULL);
    
  delete_volume(volume);

  return STATUS_OK;
}
示例#2
0
文件: mincio.c 项目: BIC-MNI/BEaST
int write_volume(char *name, VIO_Volume vol, float *data){
  int i,j,k,index,sizes[5];
  float min=FLT_MAX,max=FLT_MIN;

  fprintf(stderr,"Writing %s\n",name);

  get_volume_sizes(vol,sizes);

  for (i=0;i<sizes[0];i++){
    for (j=0;j<sizes[1];j++){
      for (k=0;k<sizes[2];k++){	  
	index=i*sizes[2]*sizes[1] + j*sizes[2] + k;
	min=MIN(min,data[index]);
	max=MAX(max,data[index]);
      }
    }
  }
  
  set_volume_real_range(vol,min,max);

  get_volume(data, vol, sizes);

  output_volume( name, NC_FLOAT,FALSE,min,max,vol,NULL, (minc_output_options *)NULL);

  return STATUS_OK;
}
示例#3
0
void save_volume(VIO_Volume d, char *filename)
{
  VIO_Status status;

  status = output_volume(filename,NC_UNSPECIFIED, FALSE, 0.0, 0.0, d, (char *)NULL,
                         (minc_output_options *)NULL);

  if (status != OK)
    print_error_and_line_num("problems writing  volume `%s'.",__FILE__, __LINE__, filename);

}
示例#4
0
int main(int argc, char *argv[]) {
  int v1, v2, v3, v4;
  int sizes[VIO_MAX_DIMENSIONS], grid_sizes[4];
  int n_concat_transforms, i;
  VIO_STR arg_string;
  char *input_volume_name;
  char *input_xfm;
  VIO_STR outfile;
  VIO_Real w1, w2, w3;
  VIO_Real nw1, nw2, nw3;
  VIO_Real original[3], transformed[3];
  VIO_Real value;
  VIO_Real cosine[3];
  VIO_Real original_separation[3], grid_separation[4];
  VIO_Real original_starts[3], grid_starts[4];
  VIO_Volume eval_volume, new_grid;
  VIO_General_transform xfm, *voxel_to_world;
  VIO_STR *dimnames, dimnames_grid[4];
  VIO_progress_struct progress;
  
  arg_string = time_stamp(argc, argv);

  /* Check arguments   */
  if(ParseArgv(&argc, argv, argTable, 0) || (argc != 4)){
    fprintf(stderr, "\nUsage: %s [options] input.mnc input.xfm output_grid.mnc\n", argv[0]);
    fprintf(stderr, "       %s -help\n\n", argv[0]);
    exit(EXIT_FAILURE);
  }

  input_volume_name = argv[1];
  input_xfm = argv[2];
  outfile = argv[3];

  /* check for the infile and outfile */
  if(access(input_volume_name, F_OK) != 0){
    fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_volume_name);
    exit(EXIT_FAILURE);
  }
  if(access(input_xfm, F_OK) != 0) {
    fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], input_xfm);
    exit(EXIT_FAILURE);
  }
  if(access(outfile, F_OK) == 0 && !clobber){
    fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0], outfile);
    exit(EXIT_FAILURE);
  }

  /*--- input the volume */
  /*
  if( input_volume( input_volume_name, 3, NULL, MI_ORIGINAL_TYPE, 
                    FALSE, 0.0, 0.0, TRUE, &eval_volume,(minc_input_options *) NULL ) != OK )
    return( 1 );
  */

  if (input_volume_header_only( input_volume_name, 3, NULL, &eval_volume,(minc_input_options *) NULL ) != VIO_OK ) { 
    return( 1 );
  }

  /* get information about the volume */
  get_volume_sizes( eval_volume, sizes );
  voxel_to_world = get_voxel_to_world_transform(eval_volume);
  dimnames = get_volume_dimension_names(eval_volume);
  get_volume_separations(eval_volume, original_separation);
  get_volume_starts(eval_volume, original_starts);

  /* create new 4D volume, last three dims same as other volume,
     first dimension being the vector dimension. */
  for(i=1; i < 4; i++) {
    dimnames_grid[i] = dimnames[i-1];
    grid_separation[i] = original_separation[i-1];
    grid_sizes[i] = sizes[i-1];
    grid_starts[i] = original_starts[i-1];
  }
  dimnames_grid[0] = "vector_dimension";
  grid_sizes[0] = 3;
  grid_separation[0] = 1;
  grid_starts[0] = 0;

  new_grid = create_volume(4, dimnames_grid, NC_SHORT, FALSE, 0.0, 0.0);

  //set_voxel_to_world_transform(new_grid, voxel_to_world);
  // initialize the new grid volume, otherwise the output will be
  // garbage...
  set_volume_real_range(new_grid, -100, 100);
  set_volume_sizes(new_grid, grid_sizes);

  set_volume_separations(new_grid, grid_separation);
  set_volume_starts(new_grid, grid_starts);
  /*
  for (i=0; i < 3; i++) {
    get_volume_direction_cosine(eval_volume, i, cosine);
    set_volume_direction_cosine(new_grid, i+1, cosine);
  }
  */

  alloc_volume_data(new_grid);

  /* get the transforms */
  if( input_transform_file( input_xfm, &xfm ) != VIO_OK )
    return( 1 );

  /* see how many transforms will be applied */
  n_concat_transforms = get_n_concated_transforms( &xfm );
  printf("Number of transforms to be applied: %d\n", n_concat_transforms);

  initialize_progress_report(&progress, FALSE, sizes[0], "Processing");


  /* evaluate the transform at every voxel, keep the displacement
     in the three cardinal directions */
  for( v1 = 0;  v1 < sizes[0];  ++v1 ) {
    update_progress_report(&progress, v1 + 1);
    for( v2 = 0;  v2 < sizes[1];  ++v2 ) {
      for( v3 = 0;  v3 < sizes[2];  ++v3 ) {
        convert_3D_voxel_to_world(eval_volume, 
                                  v1, v2, v3, 
                                  &original[0], &original[1], &original[2]);
        general_transform_point(&xfm, 
                                original[0], original[1], original[2], 
                                &transformed[0], &transformed[1], &transformed[2]);
        for(i=0; i < 3; i++) {
          value = transformed[i] - original[i];
          set_volume_real_value(new_grid, i, v1, v2, v3, 0, value);
        }
      }
    }
  }

  terminate_progress_report(&progress);

  printf("Outputting volume.\n");

  output_volume(outfile, MI_ORIGINAL_TYPE, TRUE, 0.0, 0.0, new_grid, arg_string, NULL);

  return(0);

}
示例#5
0
int main(int argc, char *argv[])
{
   char   **infiles;
   int      n_infiles;
   char    *out_fn;
   char    *history;
   VIO_progress_struct progress;
   VIO_Volume   totals, weights;
   int      i, j, k, v;
   double   min, max;
   double   w_min, w_max;
   long     num_missed;
   double   weight, value;
   double   initial_weight;

   VIO_Real     dummy[3];

   int      sizes[MAX_VAR_DIMS];
   double   starts[MAX_VAR_DIMS];
   double   steps[MAX_VAR_DIMS];
   
   long     t = 0;

   /* start the time counter */
   current_realtime_seconds();
   
   /* get the history string */
   history = time_stamp(argc, argv);

   /* get args */
   if(ParseArgv(&argc, argv, argTable, 0) || (argc < 3)){
      fprintf(stderr,
              "\nUsage: %s [options] <in1.mnc> [<in2.mnc> [...]] <out.mnc>\n", argv[0]);
      fprintf(stderr,
              "       %s [options] -arb_path pth.conf <infile.raw> <out.mnc>\n", argv[0]);
      fprintf(stderr, "       %s -help\n\n", argv[0]);
      exit(EXIT_FAILURE);
      }

   /* get file names */
   n_infiles = argc - 2;
   infiles = (char **)malloc(sizeof(char *) * n_infiles);
   for(i = 0; i < n_infiles; i++){
      infiles[i] = argv[i + 1];
      }
   out_fn = argv[argc - 1];

   /* check for infiles and outfile */
   for(i = 0; i < n_infiles; i++){
      if(!file_exists(infiles[i])){
         fprintf(stderr, "%s: Couldn't find input file %s.\n\n", argv[0], infiles[i]);
         exit(EXIT_FAILURE);
         }
      }
   if(!clobber && file_exists(out_fn)){
      fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0], out_fn);
      exit(EXIT_FAILURE);
      }

   /* check for weights_fn if required */
   if(weights_fn != NULL){
      if(!clobber && file_exists(weights_fn)){
         fprintf(stderr, "%s: %s exists, -clobber to overwrite.\n\n", argv[0],
                 weights_fn);
         exit(EXIT_FAILURE);
         }
      }

   /* set up parameters for reconstruction */
   if(out_dtype == NC_UNSPECIFIED){
      out_dtype = in_dtype;
      }
   if(out_is_signed == DEF_BOOL){
      out_is_signed = in_is_signed;
      }

   /* check vector dimension size */
   if(vect_size < 1){
      fprintf(stderr, "%s: -vector (%d) must be 1 or greater.\n\n", argv[0], vect_size);
      exit(EXIT_FAILURE);
      }

   /* check sigma */
   if(regrid_sigma[0] <= 0 || regrid_sigma[1] <= 0 || regrid_sigma[2] <= 0 ){
      fprintf(stderr, "%s: -sigma must be greater than 0\n\n", argv[0]);
      exit(EXIT_FAILURE);
      }

   /* read in the output file config from a file is specified */
   if(out_config_fn != NULL){
      int      ext_args_c;
      char    *ext_args[32];           /* max possible is 32 arguments */

      ext_args_c = read_config_file(out_config_fn, ext_args);
      if(ParseArgv(&ext_args_c, ext_args, argTable,
                   ARGV_DONT_SKIP_FIRST_ARG | ARGV_NO_LEFTOVERS | ARGV_NO_DEFAULTS)){
         fprintf(stderr, "\nError in parameters in %s\n", out_config_fn);
         exit(EXIT_FAILURE);
         }
      }

   if(verbose){
      fprintf_vol_def(stdout, &out_inf);
      }

   /* transpose the geometry arrays */
   /* out_inf.*[] are in world xyz order, perm[] is the permutation
      array to map world xyz to the right voxel order in the volume */
   for(i = 0; i < WORLD_NDIMS; i++){
      sizes[i] = out_inf.nelem[perm[i]];  /* sizes, starts, steps are in voxel volume order. */
      starts[i] = out_inf.start[perm[i]];
      steps[i] = out_inf.step[perm[i]];
      }
   sizes[WORLD_NDIMS] = vect_size;

   /* create the totals volume */
   totals = create_volume((vect_size > 1) ? 4 : 3,
                          (vect_size > 1) ? std_dimorder_v : std_dimorder,
                          out_dtype, out_is_signed, 0.0, 0.0);
   set_volume_sizes(totals, sizes);
   set_volume_starts(totals, starts);
   set_volume_separations(totals, steps);
   for(i = 0; i < WORLD_NDIMS; i++){
      /* out_inf.dircos is in world x,y,z order, we have to use the perm array to 
         map each direction to the right voxel axis. */
      set_volume_direction_cosine(totals, i, out_inf.dircos[perm[i]]);
      }
   alloc_volume_data(totals);

   /* create the "weights" volume */
   weights = create_volume(3, std_dimorder, out_dtype, out_is_signed, 0.0, 0.0);
   set_volume_sizes(weights, sizes);
   set_volume_starts(weights, starts);
   set_volume_separations(weights, steps);
   for(i = 0; i < WORLD_NDIMS; i++){
      set_volume_direction_cosine(weights, i, out_inf.dircos[perm[i]]);
      }
   alloc_volume_data(weights);

   /* down below in regrid_loop, Andrew makes a nasty direct reference to the
      voxel_to_world transformation in the volume.  This
      transformation is not necessarily up to date, particularly when
      non-default direction cosines are used.  In volume_io, the
      direction cosines are set and a FLAG is also set to indicate
      that the voxel-to-world xform is not up to date.  If the stanrd
      volume_io general transform code is used, it checks internally
      to see if the matrix is up to date, and if not it is recomputed.

      So here, we'll (LC + MK) force an update by calling a general
      transform.  */

//   convert_world_to_voxel(weights, (Real) 0, (Real) 0, (Real) 0, dummy);
//   convert_world_to_voxel(totals, (Real) 0, (Real) 0, (Real) 0, dummy);

   fprintf(stderr, "2Sizes: [%d:%d:%d] \n", sizes[perm[0]], sizes[perm[1]], sizes[perm[2]]);
   
   /* initialize weights to be arbitray large value if using NEAREST */
   /* volume interpolation else initialize all to zero */
   if(regrid_type == NEAREST_FUNC && ap_coord_fn == NULL){
      initial_weight = LARGE_INITIAL_WEIGHT;
      }
   else{
      initial_weight = 0.0;
      }
   
   /* initialize weights and totals */   
   for(k = sizes[Z_IDX]; k--;){
      for(j = sizes[Y_IDX]; j--;){
         for(i = sizes[X_IDX]; i--;){
            set_volume_real_value(weights, k, j, i, 0, 0, initial_weight);
            for(v = vect_size; v--;){
               set_volume_real_value(totals, k, j, i, v, 0, 0.0);
               }
            }
         }
      }

   /* if regridding via an arbitrary path */
   if(ap_coord_fn != NULL){

      if(n_infiles > 1){
         fprintf(stderr, "%s: arb_path only works for one input file (so far).\n\n",
                 argv[0]);
         exit(EXIT_FAILURE);
         }

      /* print some pretty output */
      if(verbose){
         fprintf(stdout, " | Input data:      %s\n", infiles[0]);
         fprintf(stdout, " | Arb path:        %s\n", ap_coord_fn);
         fprintf(stdout, " | Output range:    [%g:%g]\n", out_range[0], out_range[1]);
         fprintf(stdout, " | Output file:     %s\n", out_fn);
         }

      regrid_arb_path(ap_coord_fn, infiles[0], max_buffer_size_in_kb,
                      &totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
      }

   /* else if regridding via a series of input minc file(s) */
   else {
      for(i = 0; i < n_infiles; i++){
         if(verbose){
            fprintf(stdout, " | Input file:      %s\n", infiles[i]);
            }
         regrid_minc(infiles[i], max_buffer_size_in_kb,
                     &totals, &weights, vect_size, regrid_range[0], regrid_range[1]);
         }
      }

   /* initialise min and max counters and divide totals/weights */
   num_missed = 0;
   min = get_volume_real_value(totals, 0, 0, 0, 0, 0);
   max = get_volume_real_value(totals, 0, 0, 0, 0, 0);
   w_min = get_volume_real_value(weights, 0, 0, 0, 0, 0);
   w_max = get_volume_real_value(weights, 0, 0, 0, 0, 0);
   initialize_progress_report(&progress, FALSE, out_inf.nelem[Z_IDX], "Dividing through");
   
   for(i = sizes[perm[0]]; i--;){
      for(j = sizes[perm[1]]; j--;){
         for(k = sizes[perm[2]]; k--;){
            weight = get_volume_real_value(weights, k, j, i, 0, 0);
            if(weight < w_min){
               w_min = weight;
               }
            else if(weight > w_max){
               w_max = weight;
               }
            
            if(weight != 0){
               for(v = vect_size; v--;){
                  value = get_volume_real_value(totals, k, j, i, v, 0) / weight;
                  if(value < min){
                     min = value;
                     }
                  else if(value > max){
                     max = value;
                     }
                  
                  set_volume_real_value(totals, k, j, i, v, 0, value);
                  }
               }
            else {
               num_missed++;
               }
            }
         }
      update_progress_report(&progress, k + 1);
      }
   terminate_progress_report(&progress);

   /* set the volumes range */
   if(verbose){
      fprintf(stdout, " + data range:   [%g:%g]\n", min, max);
      fprintf(stdout, " + weight range: [%g:%g]\n", w_min, w_max);
      }
   set_volume_real_range(totals, min, max);
   set_volume_real_range(weights, w_min, w_max);

   if(num_missed > 0 && verbose){
      int      nvox;

      nvox = out_inf.nelem[X_IDX] * out_inf.nelem[Y_IDX] * out_inf.nelem[Z_IDX];
      fprintf(stdout,
              "\n-regrid_radius possibly too small, no data in %ld/%d[%2.2f%%] voxels\n\n",
              num_missed, nvox, ((float)num_missed / nvox * 100));
      }

   /* rescale data if required */
   if(out_range[0] != -DBL_MAX && out_range[1] != DBL_MAX){
      double   o_min, o_max;

      /* get the existing range */
      get_volume_real_range(totals, &o_min, &o_max);

      /* rescale it */
      scale_volume(&totals, o_min, o_max, out_range[0], out_range[1]);
      }

   /* output the result */
   if(verbose){
      fprintf(stdout, " | Outputting %s...\n", out_fn);
      }
   if(output_volume(out_fn, out_dtype, out_is_signed,
                    0.0, 0.0, totals, history, NULL) != VIO_OK){
      fprintf(stderr, "Problems outputing: %s\n\n", out_fn);
      }

   /* output weights volume if required */
   if(weights_fn != NULL){
      if(verbose){
         fprintf(stdout, " | Outputting %s...\n", weights_fn);
         }
      if(output_volume(weights_fn, out_dtype, out_is_signed,
                       0.0, 0.0, weights, history, NULL) != VIO_OK){
         fprintf(stderr, "Problems outputting: %s\n\n", weights_fn);
         }
      }

   delete_volume(totals);
   delete_volume(weights);
   
   t = current_realtime_seconds();
   printf("Total reconstruction time: %ld hours %ld minutes %ld seconds\n", t/3600, (t/60)%60, t%60);
   
   return (EXIT_SUCCESS);
   }
示例#6
0
int main(int argc, char *argv[])
{
   VIO_Volume 
     volume;
   VIO_Real
     variability,
     rand_val,
     voxel[VIO_MAX_DIMENSIONS];
   int 
     progress_count,
     sizes[VIO_MAX_DIMENSIONS],
     index[VIO_MAX_DIMENSIONS],
     i,j,k;
   VIO_progress_struct
     progress;

   union
     {
       long   l;
       char   c[4];
     } seedval;
   
   time_t t;
   char tmp;

   prog_name = argv[0];


   /* Check arguments */
   if (argc != 4) {
      (void) fprintf(stderr, "Usage: %s input.mnc output.mnc std_dev\n",
                     argv[0]);
      exit(EXIT_FAILURE);
   }


   if( input_volume( argv[1], 3, NULL, NC_UNSPECIFIED, FALSE,
                    0.0, 0.0, TRUE, &volume, (minc_input_options *)NULL ) != OK ) {
     (void)fprintf(stderr, "Error opening input volume file %s.\n",
                   argv[1]);
     exit(EXIT_FAILURE);
   }

   variability = atof( argv[3] );

                                /* initialize drand function */
   t = 2*time(NULL);
   seedval.l = t; 
   tmp = seedval.c[0]; seedval.c[0] = seedval.c[3]; seedval.c[3] = tmp; 
   tmp = seedval.c[1]; seedval.c[1] = seedval.c[2]; seedval.c[2] = tmp;
   srand48(seedval.l);



   set_volume_real_range(volume, -5.0*variability, 5.0*variability);

   get_volume_sizes(volume,sizes);
   initialize_progress_report(&progress, FALSE, 
                              sizes[VIO_X]*sizes[VIO_Y]*sizes[VIO_Z]+1,
                              "Randomizing volume");
   progress_count = 0;


   for(i=0; i<MAX_DIMENSIONS; i++) index[i] = 0;

   /* loop over all voxels */
   for(index[X]=0; index[X]<sizes[X]; index[X]++)
     for(index[Y]=0; index[Y]<sizes[Y]; index[Y]++)
       for(index[Z]=0; index[Z]<sizes[Z]; index[Z]++) {
             
         /* get a random value from a gaussian distribution  */

         rand_val = variability * gaussian_random_0_1();

         if (rand_val >  5.0*variability) rand_val =  5.0*variability;
         if (rand_val < -5.0*variability) rand_val = -5.0*variability;
         
         set_volume_real_value(volume,
                               index[0],index[1],index[2],index[3],index[4],
                               rand_val);
         
         progress_count++;
         update_progress_report(&progress, progress_count);
       }
   
   terminate_progress_report(&progress);

   

   /* Write out the random volume */
   if (output_volume(argv[2], NC_UNSPECIFIED, FALSE, 0.0, 0.0, volume, 
                     (char *)NULL, (minc_output_options *)NULL) != OK) {
     (void) fprintf(stderr, "%s: Error writing volume file %s\n",
                     argv[0], argv[2]);
      exit(EXIT_FAILURE);
   }

   exit(EXIT_SUCCESS);
}
示例#7
0
int  main(
    int   argc,
    char  *argv[] )
{
    Volume         volume;
    STRING         input_filename, output_filename;
    int            n_slices, n_components;
    pixels_struct  *pixels;
    nc_type        vol_type;
    BOOLEAN        two_d_allowed;

    initialize_argument_processing( argc, argv );

    if( !get_string_argument( NULL, &output_filename ) ||
        !get_int_argument( 0, &n_components ) )
    {
        print( "Usage: %s output.mnc  3|4|23|24 input1.rgb input2.rgb ...\n", argv[0] );
        return( 1 );
    }

    if( n_components > 100 )
    {
        vol_type = NC_FLOAT;
        n_components -= 100;
    }
    else
        vol_type = NC_BYTE;

    if( n_components > 20 )
    {
        two_d_allowed = TRUE;
        n_components -= 20;
    }
    else
    {
        two_d_allowed = FALSE;
    }

    n_slices = 0;
    pixels = NULL;

    while( get_string_argument( "", &input_filename ) )
    {
        SET_ARRAY_SIZE( pixels, n_slices, n_slices+1, DEFAULT_CHUNK_SIZE );

        if( input_rgb_file( input_filename, &pixels[n_slices] ) != OK )
            return( 1 );

        ++n_slices;
    }

    volume = convert_pixels_to_volume( n_components, n_slices,
                                       (two_d_allowed && n_slices == 1) ? 2 : 3,
                                       vol_type, pixels );

    if( volume != NULL )
    {
        (void) output_volume( output_filename, NC_UNSPECIFIED, FALSE,
                              0.0, 0.0,
                              volume, "Converted from pixels",
                              (minc_output_options *) NULL );

        delete_volume( volume );
    }

    return( 0 );
}