mincmorph.c

/* mincmorph.c

   Copyright 2009
   Andrew Janke - a.janke@gmail.com
   Australian National University

   Permission to use, copy, modify, and distribute this software and its
   documentation for any purpose and without fee is hereby granted,
   provided that the above copyright notice appear in all copies.  The
   author and the University make no representations about the
   suitability of this software for any purpose.  It is provided "as is"
   without express or implied warranty.
*/


#include <config.h>
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <sys/param.h>
#include <float.h>
#include <string.h>

#include <volume_io.h>

#include <ParseArgv.h>
#include <time_stamp.h>
#include "kernel_io.h"
#include "kernel_ops.h"

#define INTERNAL_PREC NC_FLOAT         /* should be NC_FLOAT or NC_DOUBLE */
#define DEF_DOUBLE -DBL_MAX

/* function prototypes */
char    *get_real_from_string(char *string, double *value);
char    *get_string_from_string(char *string, char **value);
void     calc_volume_range(VIO_Volume * vol, double *min, double *max);
void     print_version_info(void);

/* kernel names for pretty output */
char    *KERN_names[] = { "NULL", "2D04", "2D08", "3D06", "3D26" };

/* typedefs */
typedef enum {
   UNDEF = 0,
   BINARISE, CLAMP, PAD, ERODE, DILATE, MDILATE,
   MFILTER, OPEN, CLOSE, LPASS, HPASS, CONVOLVE, 
   DISTANCE, GROUP, READ_KERNEL, WRITE, LCORR
   } op_types;

typedef struct {
   op_types type;
   char     op_c;
   char    *kernel_fn;
   kern_types kernel_id;
   char    *cmpfile;
   char    *outfile;
   double   range[2];
   double   foreground;
   double   background;
   } Operation;

/* Argument variables */
int      verbose = FALSE;
int      clobber = FALSE;
int      is_signed = FALSE;
nc_type  dtype = NC_SHORT;
double   range[2] = { -DBL_MAX, DBL_MAX };
double   foreground = 1.0;
double   background = 0.0;
kern_types kernel_id = K_NULL;
char    *kernel_fn = NULL;
char    *succ_txt = "B";

char     successive_help[] = "Successive operations (Maximum: 100) \
\n\tB[floor:ceil:fg:bg] - binarise in the range, using foreground and background \
\n\tK[floor:ceil:bg] - clamp betwen the specified range. Set other voxels to 'bg' (default: 0) \
\n\tP[bg] - pad volume with respect to the current kernel using 'bg' (default: 0)\
\n\tE - erosion \
\n\tD - dilation \
\n\tM - median dilation \
\n\tN - median filter \
\n\tO - open \
\n\tC - close \
\n\tL - lowpass filter \
\n\tH - highpass filter \
\n\tX - convolve \
\n\tF - distance transform (binary input only - not checked) \
\n\tG - Label the groups in the volume in ascending order \
\n\tR[TYPE|file.kern] - (2D04|2D08|3D06|3D26) or read in a kernel file \
\n\tW[file.mnc] - write out current results \
\n\tI[cmp.mnc] - local xcorr between current file and cmp.mnc \
\n\tDefault: ";

/* Argument table */
ArgvInfo argTable[] = {
   {NULL, ARGV_HELP, (char *)NULL, (char *)NULL,
    "General options:"},
   {"-version", ARGV_FUNC, (char *)print_version_info, (char *)NULL,
    "print version info and exit"},
   {"-verbose", ARGV_CONSTANT, (char *)TRUE, (char *)&verbose,
    "be verbose"},
   {"-clobber", ARGV_CONSTANT, (char *)TRUE, (char *)&clobber,
    "clobber existing files"},

   {NULL, ARGV_HELP, NULL, NULL,
    "\nOutfile Options"},
   {"-filetype", ARGV_CONSTANT, (char *)NC_UNSPECIFIED, (char *)&dtype,
    "Use data type of the input file."},
   {"-byte", ARGV_CONSTANT, (char *)NC_BYTE, (char *)&dtype,
    "Write out byte data."},
   {"-short", ARGV_CONSTANT, (char *)NC_SHORT, (char *)&dtype,
    "Write out short integer data. (Default)"},
   {"-int", ARGV_CONSTANT, (char *)NC_INT, (char *)&dtype,
    "Write out long integer data."},
   {"-float", ARGV_CONSTANT, (char *)NC_FLOAT, (char *)&dtype,
    "Write out single-precision data."},
   {"-double", ARGV_CONSTANT, (char *)NC_DOUBLE, (char *)&dtype,
    "Write out double-precision data."},
   {"-signed", ARGV_CONSTANT, (char *)TRUE, (char *)&is_signed,
    "Write signed integer data."},
   {"-unsigned", ARGV_CONSTANT, (char *)FALSE, (char *)&is_signed,
    "Write unsigned integer data."},

   {NULL, ARGV_HELP, NULL, NULL, "\nKernel Options"},
   {"-2D04", ARGV_CONSTANT, (char *)K_2D04, (char *)&kernel_id,
    "Use a 2D 4-connectivity kernel."},
   {"-2D08", ARGV_CONSTANT, (char *)K_2D08, (char *)&kernel_id,
    "Use a 2D 8-connectivity kernel."},
   {"-3D06", ARGV_CONSTANT, (char *)K_3D06, (char *)&kernel_id,
    "Use a 3D 6-connectivity kernel. (default)"},
   {"-3D26", ARGV_CONSTANT, (char *)K_3D26, (char *)&kernel_id,
    "Use a 3D 26-connectivity kernel."},
   {"-kernel", ARGV_STRING, (char *)1, (char *)&kernel_fn,
    "<kernel.kern> read in a custom kernel file"},

   {NULL, ARGV_HELP, NULL, NULL, "\nMorphology Options"},
   {"-floor", ARGV_FLOAT, (char *)1, (char *)&range[0],
    "lowwer value for binarising or clamping"},
   {"-ceil", ARGV_FLOAT, (char *)1, (char *)&range[1],
    "upper value for binarising or clamping (incl)"},
   {"-range", ARGV_FLOAT, (char *)2, (char *)range,
    "range for binarising or clamping (incl)"},
   {"-foreground", ARGV_FLOAT, (char *)1, (char *)&foreground,
    "foreground value"},
   {"-background", ARGV_FLOAT, (char *)1, (char *)&background,
    "background value"},

   {NULL, ARGV_HELP, (char *)NULL, (char *)NULL, "\nSingle morphological operations:"},
   {"-binarise", ARGV_CONSTANT, (char *)"B", (char *)&succ_txt,
    "binarise volume using the input range"},
   {"-clamp", ARGV_CONSTANT, (char *)"K", (char *)&succ_txt,
    "clamp volume using the input range"},
   {"-pad", ARGV_CONSTANT, (char *)"P", (char *)&succ_txt,
    "pad volume with respect to the current kernel (-background to specify value)"},
   {"-erosion", ARGV_CONSTANT, (char *)"E", (char *)&succ_txt,
    "do a single erosion"},
   {"-dilation", ARGV_CONSTANT, (char *)"D", (char *)&succ_txt,
    "do a single dilation"},
   {"-median_dilation", ARGV_CONSTANT, (char *)"M", (char *)&succ_txt,
    "do a single median dilation"},
   {"-median_filter", ARGV_CONSTANT, (char *)"N", (char *)&succ_txt,
    "do a single median filter"},
   {"-open", ARGV_CONSTANT, (char *)"O", (char *)&succ_txt,
    "open:            dilation(erosion(X))"},
   {"-close", ARGV_CONSTANT, (char *)"C", (char *)&succ_txt,
    "close:           erosion(dilation(X))"},
   {"-lowpass", ARGV_CONSTANT, (char *)"L", (char *)&succ_txt,
    "lowpass filter:  close(open(X))"},
   {"-highpass", ARGV_CONSTANT, (char *)"H", (char *)&succ_txt,
    "highpass filter: X - lowpass(X)"},
   {"-convolve", ARGV_CONSTANT, (char *)"X", (char *)&succ_txt,
    "convolve file with kernel"},
   {"-distance", ARGV_CONSTANT, (char *)"F", (char *)&succ_txt,
    "distance transform"},
   {"-group", ARGV_CONSTANT, (char *)"G", (char *)&succ_txt,
    "label groups in ascending order"},

   {NULL, ARGV_HELP, (char *)NULL, (char *)NULL,
    "\nSuccessive morphological operations:"},
   {"-successive", ARGV_STRING, (char *)1, (char *)&succ_txt, successive_help},

   {NULL, ARGV_HELP, NULL, NULL, ""},
   {NULL, ARGV_END, NULL, NULL, NULL}
   };

int main(int argc, char *argv[])
{
   int      c;
   char    *arg_string;
   char    *infile;
   char    *outfile;

   VIO_Volume *volume;
   VIO_Volume *cmpvol;
   Kernel  *kernel;
   int      num_ops;
   Operation operation[100];
   Operation *op;
   char    *tmp_str;
   char     ext_txt[256];
   char     tmp_filename[MAXPATHLEN];
   double   tmp_double[4];
   double   min, max;
   char    *ptr;

   char    *axis_order[3] = { MIzspace, MIyspace, MIxspace };

   /* Save time stamp and args */
   arg_string = time_stamp(argc, argv);

   /* Get arguments */
   if(ParseArgv(&argc, argv, argTable, 0) || (argc < 2)){
      fprintf(stderr, "\nUsage: %s [options] <in.mnc> <out.mnc>\n", argv[0]);
      fprintf(stderr, "       %s -help\n\n", argv[0]);
      exit(EXIT_FAILURE);
      }
   infile = argv[1];
   outfile = argv[2];

   /* check for the infile */
   if(access(infile, F_OK) != 0){
      fprintf(stderr, "%s: Couldn't find %s\n\n", argv[0], infile);
      exit(EXIT_FAILURE);
      }

   /* check for the outfile */
   if(access(outfile, F_OK) == 0 && !clobber){
      fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0], outfile);
      exit(EXIT_FAILURE);
      }

   /* check kernel args */
   if(kernel_fn != NULL && kernel_id != K_NULL){
      fprintf(stderr, "%s: specify either a kernel file or a set kernel (not both)\n\n",
              argv[0], outfile);
      exit(EXIT_FAILURE);
      }

   /* set the default kernel */
   if(kernel_fn == NULL && kernel_id == K_NULL){
      kernel_id = K_3D06;
      }

   /* add the implicit read kernel operation */
   num_ops = 0;
   op = &operation[num_ops++];

   op->type = READ_KERNEL;
   op->kernel_fn = kernel_fn;
   op->kernel_id = kernel_id;

   /* setup operations and check them... */
   if(verbose){
      fprintf(stdout, "---Checking Operation(s): %s---\n", succ_txt);
      }

   ptr = succ_txt;
   while(ptr[0] != '\0'){

      /* set up counters and extra text */
      strcpy(ext_txt, "");
      op = &operation[num_ops++];

      /* get the operation type */
      op->op_c = ptr[0];
      ptr++;

      switch (op->op_c){
      case 'B':
         op->type = BINARISE;

         /* get 4 possible values */
         ptr = get_real_from_string(ptr, &tmp_double[0]);
         ptr = get_real_from_string(ptr, &tmp_double[1]);
         ptr = get_real_from_string(ptr, &tmp_double[2]);
         ptr = get_real_from_string(ptr, &tmp_double[3]);
         op->range[0] = (tmp_double[0] == DEF_DOUBLE) ? range[0] : tmp_double[0];
         op->range[1] = (tmp_double[1] == DEF_DOUBLE) ? range[1] : tmp_double[1];
         op->foreground = (tmp_double[2] == DEF_DOUBLE) ? foreground : tmp_double[2];
         op->background = (tmp_double[3] == DEF_DOUBLE) ? background : tmp_double[3];

         sprintf(ext_txt, "range: [%g:%g] fg/bg: [%g:%g]", op->range[0],
                 op->range[1], op->foreground, op->background);
         break;

      case 'K':
         op->type = CLAMP;

         /* get 3 possible values */
         ptr = get_real_from_string(ptr, &tmp_double[0]);
         ptr = get_real_from_string(ptr, &tmp_double[1]);
         ptr = get_real_from_string(ptr, &tmp_double[2]);
         op->range[0] = (tmp_double[0] == DEF_DOUBLE) ? range[0] : tmp_double[0];
         op->range[1] = (tmp_double[1] == DEF_DOUBLE) ? range[1] : tmp_double[1];
         op->background = (tmp_double[2] == DEF_DOUBLE) ? background : tmp_double[2];

         sprintf(ext_txt, "range: [%g:%g] fg/bg: [%g:%g]", op->range[0],
                 op->range[1], op->foreground, op->background);
         break;

      case 'P':
         op->type = PAD;

         /* get 1 possible value */
         ptr = get_real_from_string(ptr, &tmp_double[0]);
         op->background = (tmp_double[0] == DEF_DOUBLE) ? background : tmp_double[0];

         sprintf(ext_txt, "fill value: %g", op->background);
         break;

      case 'E':
         op->type = ERODE;
         break;

      case 'D':
         op->type = DILATE;
         break;

      case 'M':
         op->type = MDILATE;
         break;

      case 'N':
         op->type = MFILTER;
         break;

      case 'O':
         op->type = OPEN;
         break;

      case 'C':
         op->type = CLOSE;
         break;

      case 'L':
         op->type = LPASS;
         break;

      case 'H':
         op->type = HPASS;
         break;

      case 'X':
         op->type = CONVOLVE;
         break;

      case 'F':
         op->type = DISTANCE;
         break;

      case 'G':
         op->type = GROUP;
         break;

      case 'R':
         op->type = READ_KERNEL;

         /* get the filename */
         ptr = get_string_from_string(ptr, &tmp_str);
         if(tmp_str == NULL){
            fprintf(stderr, "%s: R[TYPE|file.kern] requires a file or kernel name\n\n",
                    argv[0]);
            exit(EXIT_FAILURE);
            }

         /* check if the input kernel is an inbuilt one */
         op->kernel_id = K_NULL;
         for(c = 1; c <= n_inbuilt_kern; c++){
            if(strcmp(tmp_str, KERN_names[c]) == 0){
               op->kernel_id = (kern_types) c;
               }
            }

         /* if no inbuilt found, assume it's a file */
         if(op->kernel_id == K_NULL){

            /* set up and check for the real filename */
            (void)realpath(tmp_str, tmp_filename);
            if(access(tmp_filename, F_OK) != 0){
               fprintf(stderr, "%s: Couldn't find kernel file: %s\n\n", argv[0],
                       tmp_filename);
               exit(EXIT_FAILURE);
               }

            op->kernel_fn = strdup(tmp_filename);
            sprintf(ext_txt, "kernel_fn: %s", op->kernel_fn);
            }
         else {
            sprintf(ext_txt, "inbuilt_kernel[%d]: %s", op->kernel_id,
                    KERN_names[op->kernel_id]);
            }
         break;

      case 'W':
         op->type = WRITE;

         /* get the filename */
         ptr = get_string_from_string(ptr, &op->outfile);

         if(op->outfile == NULL){
            fprintf(stderr, "%s: W[file.mnc] _requires_ a filename\n\n", argv[0]);
            exit(EXIT_FAILURE);
            }
         
         /* check for the outfile */
         if(access(op->outfile, F_OK) == 0 && !clobber){
            fprintf(stderr, "%s: %s exists! (use -clobber to overwrite)\n\n", argv[0],
                    op->outfile);
            exit(EXIT_FAILURE);
            }

         sprintf(ext_txt, "filename: %s", op->outfile);
         break;

      case 'I':
         op->type = LCORR;

         /* get the filenames */
         ptr = get_string_from_string(ptr, &op->cmpfile);

         if(op->cmpfile == NULL){
            fprintf(stderr, "%s: I[cmp.mnc] requires a filename\n\n", argv[0]);
            exit(EXIT_FAILURE);
            }
         
         /* check for cmpfile */
         if(access(op->cmpfile, F_OK) != 0){
            fprintf(stderr, "%s: Couldn't find compare file: %s\n\n", argv[0], op->cmpfile);
            exit(EXIT_FAILURE);
            }

         sprintf(ext_txt, "compare filename: %s", op->cmpfile);
         break;

      default:
         fprintf(stderr, "\nUnknown op: %c\n\n  %s -help  for operations\n\n",
                 op->op_c, argv[0]);
         exit(EXIT_FAILURE);
         }

      if(verbose){
         fprintf(stdout, "  Op[%02d] %c = %d\t\t%s\n", num_ops, op->op_c, op->type,
                 ext_txt);
         }
      }

   /* add an implicit write statment to the end if needed */
   if(operation[num_ops - 1].type != WRITE){
      operation[num_ops].type = WRITE;
      operation[num_ops].outfile = outfile;
      num_ops++;
      }

   /* malloc space for volume structure and read in infile */
   volume = (VIO_Volume *) malloc(sizeof(VIO_Volume));
   input_volume(infile, MAX_VAR_DIMS, axis_order,
                INTERNAL_PREC, TRUE, 0.0, 0.0, TRUE, volume, NULL);
   get_type_range(get_volume_data_type(*volume), &min, &max);
   set_volume_real_range(*volume, min, max);

   /* init and then do some operations */
   kernel = new_kernel(0);

   if(verbose){
      fprintf(stdout, "\n---Doing %d Operation(s)---\n", num_ops);
      }
   for(c = 0; c < num_ops; c++){
      op = &operation[c];

      switch (op->type){
      case BINARISE:
         volume = binarise(volume, op->range[0], op->range[1],
                           op->foreground, op->background);
         break;

      case CLAMP:
         volume = clamp(volume, op->range[0], op->range[1], op->background);
         break;

      case PAD:
         volume = pad(kernel, volume, op->background);
         break;

      case ERODE:
         volume = erosion_kernel(kernel, volume);
         break;

      case DILATE:
         volume = dilation_kernel(kernel, volume);
         break;

      case MDILATE:
         volume = median_dilation_kernel(kernel, volume);
         break;

      case MFILTER:
         volume = median_filter_kernel(kernel, volume);
         break;

      case OPEN:
         volume = erosion_kernel(kernel, volume);
         volume = dilation_kernel(kernel, volume);
         break;

      case CLOSE:
         volume = dilation_kernel(kernel, volume);
         volume = erosion_kernel(kernel, volume);
         break;

      case LPASS:
         volume = erosion_kernel(kernel, volume);
         volume = dilation_kernel(kernel, volume);
         volume = dilation_kernel(kernel, volume);
         volume = erosion_kernel(kernel, volume);
         break;

      case HPASS:
         fprintf(stderr, "%s: GNFARK! Highpass Not implemented yet..\n\n", argv[0]);
         break;

      case CONVOLVE:
         volume = convolve_kernel(kernel, volume);
         break;

      case DISTANCE:
         volume = distance_kernel(kernel, volume, background);
         break;

      case GROUP:
         volume = group_kernel(kernel, volume, background);
         break;

      case READ_KERNEL:
         /* free the existing kernel then set the pointer to the new one */
         free(kernel);

         /* read in the kernel or set the kernel to an inbuilt one */
         if(op->kernel_id == K_NULL){
            kernel = new_kernel(0);
            if(input_kernel(op->kernel_fn, kernel) != OK){
               fprintf(stderr, "%s: Died reading in kernel file: %s\n\n", argv[0],
                       op->kernel_fn);
               exit(EXIT_FAILURE);
               }
            }
         else {

            switch (op->kernel_id){
            case K_2D04:
               kernel = get_2D04_kernel();
               break;

            case K_2D08:
               kernel = get_2D08_kernel();
               break;

            case K_3D06:
               kernel = get_3D06_kernel();
               break;

            case K_3D26:
               kernel = get_3D26_kernel();
               break;

            default:
               fprintf(stderr, "%s: This shouldn't happen -- much bad\n\n", argv[0]);
               exit(EXIT_FAILURE);
               }
            }

         setup_pad_values(kernel);
         if(verbose){
            fprintf(stdout, "Input kernel:\n");
            print_kernel(kernel);
            }
         break;

      case WRITE:
         if(op->outfile == NULL){
            fprintf(stdout, "%s: WRITE passed a NULL pointer! - this is bad\n\n",
                    argv[0]);
            exit(EXIT_FAILURE);
            }

         if(verbose){
            fprintf(stdout, "Outputting to %s\n", op->outfile);
            }

         /* get the resulting range */
         calc_volume_range(volume, &min, &max);

         /* set the range to something sensible (if possible) */
         if(dtype == NC_BYTE && is_signed == FALSE){
            if(min >= 0 && max < 255){
               fprintf(stdout, "BYTE data, setting 1:1 mapping (0-256)\n");
               min = 0;
               max = 255;
               }
            }
         set_volume_real_range(*volume, min, max);

         output_modified_volume(op->outfile,
                                dtype, is_signed,
                                0.0, 0.0, *volume, infile, arg_string, NULL);
         break;

      case LCORR:
         if(op->cmpfile == NULL){
            fprintf(stdout, "%s: LCORR passed a NULL pointer! - this is bad\n\n",
                    argv[0]);
            exit(EXIT_FAILURE);
            }

         if(verbose){
            fprintf(stdout, "Comparing to %s\n", op->cmpfile);
            }
         
         /* malloc space for volume structure and read cmpfile */
         cmpvol = (VIO_Volume *) malloc(sizeof(VIO_Volume));
         input_volume(op->cmpfile, MAX_VAR_DIMS, axis_order,
            INTERNAL_PREC, TRUE, 0.0, 0.0, TRUE, cmpvol, NULL);
         
         /* run the local correlation */
         volume = lcorr_kernel(kernel, volume, cmpvol);
         
         /* clean up */
         delete_volume(*cmpvol);
         free(cmpvol);
         
         break;

      default:
         fprintf(stderr, "\n%s: Unknown operation (This is very bad, call Houston)\n\n", argv[0]);
         exit(EXIT_FAILURE);
         }
      }

   /* jump through operations freeing stuff */
   // free(op.kernel);

   delete_volume(*volume);
   return (EXIT_SUCCESS);
   }

/* get a real from a char* stream                   */
/* with possible trailing or leading square bracket */
/* and possible leading ':'                         */
/* return the string advanced to the next token or  */
/* as it was input if nothing found                 */
char    *get_real_from_string(char *string, double *value)
{
   char    *ptr;

   /* skip a [ or : else we probably don't belong here */
   if(string[0] == '[' || string[0] == ':'){
      string++;
      }

   /* get a double */
   *value = strtod(&string[0], &ptr);

   /* if nothing found return a default value */
   if(&string[0] == ptr){
      *value = DEF_DOUBLE;
      }

   /* skip over a possible ']' */
   if(ptr[0] == ']'){
      ptr++;
      }

   return ptr;
   }

/* get a copy of the string between [ and ] from a char*      */
/* return the string advanced to the next token or            */
/* as it was input if nothing found                           */
char    *get_string_from_string(char *string, char **value)
{
   int      offset;
   char    *malloc_string;

   /* initialise the return values first */
   *value = NULL;

   /* get the string if there is one */
   if(string[0] == '['){
      string++;

      /* get the length of the string in question */
      offset = strcspn(string, "]");

      /* alloc some space for the string */
      malloc_string = (char *)malloc((offset + 1) * sizeof(char));

      /* get a copy of it and append the null charater */
      strncpy(malloc_string, string, offset);
      malloc_string[offset] = '\0';

      /* store the result */
      *value = malloc_string;

      /* increment the pointer and skip over a possible '[' */
      string += offset;
      if(string[0] == ']'){
         string++;
         }
      }

   return string;
   }

void calc_volume_range(VIO_Volume * vol, double *min, double *max)
{

   int      x, y, z;
   int      sizes[MAX_VAR_DIMS];
   double   value;
   VIO_progress_struct progress;

   *min = DBL_MAX;
   *max = -DBL_MIN;

   get_volume_sizes(*vol, sizes);

   initialize_progress_report(&progress, FALSE, sizes[2], "Finding Range");
   for(z = sizes[0]; z--;){
      for(y = sizes[1]; y--;){
         for(x = sizes[2]; x--;){

            value = get_volume_voxel_value(*vol, z, y, x, 0, 0);
            if(value < *min){
               *min = value;
               }
            else if(value > *max){
               *max = value;
               }
            }
         }
      update_progress_report(&progress, z + 1);
      }
   terminate_progress_report(&progress);

   if (*min == *max) {
       *max = *min + 1.0;
   }

   if(verbose){
      fprintf(stdout, "Found range of [%g:%g]\n", *min, *max);
      }
   }

void print_version_info(void)
{
   fprintf(stdout, "%s version %s\n", PACKAGE, VERSION);
   fprintf(stdout, "Comments to %s\n", PACKAGE_BUGREPORT);
   fprintf(stdout, "\n");
   exit(EXIT_SUCCESS);
   }