// 3D phase unwrapping, modified for inclusion in scipy by Gregor Thalhammer
// Original file name: Hussein_3D_unwrapper_with_mask_and_wrap_around_option.c

//This program was written by Hussein Abdul-Rahman and Munther Gdeisat to program the three-dimensional phase unwrapper
//entitled "Fast three-dimensional phase-unwrapping algorithm based on sorting by
//reliability following a noncontinuous path"
//by  Hussein Abdul-Rahman, Munther A. Gdeisat, David R. Burton, and Michael J. Lalor,
//published in the Proceedings of SPIE -
//The International Society for Optical Engineering, Vol. 5856, No. 1, 2005, pp. 32-40
//This program was written by Munther Gdeisat, Liverpool John Moores University, United Kingdom.
//Date 31st August 2007
//The wrapped phase volume is assumed to be of floating point data type. The resultant unwrapped phase volume is also of floating point type.
//Read the data from the file frame by frame
//The mask is of byte data type.
//When the mask is 255 this means that the voxel is valid
//When the mask is 0 this means that the voxel is invalid (noisy or corrupted voxel)
//This program takes into consideration the image wrap around problem encountered in MRI imaging.

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>

#ifndef M_PI
#define M_PI 3.1415926535897932384626433832795
#endif

#define PI M_PI
#define TWOPI (2 * M_PI)

#define NOMASK 0
#define MASK 1

typedef struct
{
  double mod;
  int x_connectivity;
  int y_connectivity;
  int z_connectivity;
  int no_of_edges;
} params_t;

//VOXELM information
struct VOXELM
{
  int increment;		//No. of 2*pi to add to the voxel to unwrap it
  int number_of_voxels_in_group;//No. of voxel in the voxel group
  double value;			//value of the voxel
  double reliability;
  unsigned char input_mask;	//MASK voxel is masked. NOMASK voxel is not masked
  unsigned char extended_mask;	//MASK voxel is masked. NOMASK voxel is not masked
  int group;			//group No.
  int new_group;
  struct VOXELM *head;		//pointer to the first voxel in the group in the linked list
  struct VOXELM *last;		//pointer to the last voxel in the group
  struct VOXELM *next;		//pointer to the next voxel in the group
};

typedef struct VOXELM VOXELM;

//the EDGE is the line that connects two voxels.
//if we have S voxels, then we have S horizontal edges and S vertical edges
struct EDGE
{
  double reliab;			//reliabilty of the edge and it depends on the two voxels
  VOXELM *pointer_1;		//pointer to the first voxel
  VOXELM *pointer_2;		//pointer to the second voxel
  int increment;		//No. of 2*pi to add to one of the
				//voxels to unwrap it with respect to
				//the second
};

typedef struct EDGE EDGE;

//---------------start quicker_sort algorithm --------------------------------
#define swap(x,y) {EDGE t; t=x; x=y; y=t;}
#define order(x,y) if (x.reliab > y.reliab) swap(x,y)
#define o2(x,y) order(x,y)
#define o3(x,y,z) o2(x,y); o2(x,z); o2(y,z)

typedef enum {yes, no} yes_no;

yes_no find_pivot(EDGE *left, EDGE *right, double *pivot_ptr)
{
	EDGE a, b, c, *p;

	a = *left;
	b = *(left + (right - left) /2 );
	c = *right;
	o3(a,b,c);

	if (a.reliab < b.reliab)
	{
		*pivot_ptr = b.reliab;
		return yes;
	}

	if (b.reliab < c.reliab)
	{
		*pivot_ptr = c.reliab;
		return yes;
	}

	for (p = left + 1; p <= right; ++p)
	{
		if (p->reliab != left->reliab)
		{
			*pivot_ptr = (p->reliab < left->reliab) ? left->reliab : p->reliab;
			return yes;
		}
	}
    return no;
}

EDGE *partition(EDGE *left, EDGE *right, double pivot)
{
	while (left <= right)
	{
		while (left->reliab < pivot)
			++left;
		while (right->reliab >= pivot)
			--right;
		if (left < right)
		{
			swap (*left, *right);
			++left;
			--right;
		}
	}
	return left;
}

void quicker_sort(EDGE *left, EDGE *right)
{
	EDGE *p;
	double pivot;

	if (find_pivot(left, right, &pivot) == yes)
	{
		p = partition(left, right, pivot);
		quicker_sort(left, p - 1);
		quicker_sort(p, right);
	}
}

//--------------end quicker_sort algorithm -----------------------------------

//--------------------start initialize voxels ----------------------------------
//initiale voxels. See the explanation of the voxel class above.
//initially every voxel is assumed to belong to a group consisting of only itself
void  initialiseVOXELs(double *WrappedVolume, unsigned char *input_mask, unsigned char *extended_mask, VOXELM *voxel, int volume_width, int volume_height, int volume_depth)
{
  VOXELM *voxel_pointer = voxel;
  double *wrapped_volume_pointer = WrappedVolume;
  unsigned char *input_mask_pointer = input_mask;
  unsigned char *extended_mask_pointer = extended_mask;
  int n, i, j;

  for (n=0; n < volume_depth; n++)
    {
      for (i=0; i < volume_height; i++)
        {
	  for (j=0; j < volume_width; j++)
	    {
	      voxel_pointer->increment = 0;
	      voxel_pointer->number_of_voxels_in_group = 1;
	      voxel_pointer->value = *wrapped_volume_pointer;
	      voxel_pointer->reliability = 9999999 + rand();
	      voxel_pointer->input_mask = *input_mask_pointer;
	      voxel_pointer->extended_mask = *extended_mask_pointer;
	      voxel_pointer->head = voxel_pointer;
	      voxel_pointer->last = voxel_pointer;
	      voxel_pointer->next = NULL;
	      voxel_pointer->new_group = 0;
	      voxel_pointer->group = -1;
	      voxel_pointer++;
	      wrapped_volume_pointer++;
	      input_mask_pointer++;
	      extended_mask_pointer++;
	    }
        }
    }
}
//-------------------end initialize voxels -----------

//gamma function in the paper
double wrap(double voxel_value)
{
  double wrapped_voxel_value;
  if (voxel_value > PI)	wrapped_voxel_value = voxel_value - TWOPI;
  else if (voxel_value < -PI)	wrapped_voxel_value = voxel_value + TWOPI;
  else wrapped_voxel_value = voxel_value;
  return wrapped_voxel_value;
}

// voxelL_value is the left voxel,	voxelR_value is the right voxel
int find_wrap(double voxelL_value, double voxelR_value)
{
  double difference;
  int wrap_value;
  difference = voxelL_value - voxelR_value;

  if (difference > PI)	wrap_value = -1;
  else if (difference < -PI)	wrap_value = 1;
  else wrap_value = 0;

  return wrap_value;
}

void extend_mask(unsigned char *input_mask, unsigned char *extended_mask, int volume_width, int volume_height, int volume_depth, params_t *params)
{
  int n, i, j;
  int vw = volume_width, vh = volume_height, vd = volume_depth;
  int fs  = volume_width * volume_height;	//frame size
  int frame_size = volume_width * volume_height;
  int volume_size = volume_width * volume_height * volume_depth;	//volume size
  int vs = volume_size;
  unsigned char *IMP = input_mask    + frame_size + volume_width + 1;	//input mask pointer
  unsigned char *EMP = extended_mask + frame_size + volume_width + 1;	//extended mask pointer

  //extend the mask for the volume except borders
  for (n=1; n < volume_depth - 1; n++)
    {
      for (i=1; i < volume_height - 1; i++)
        {
	  for (j=1; j < volume_width - 1; j++)
	    {
	      if( (*IMP) == NOMASK		&& (*(IMP - 1) == NOMASK)		&& (*(IMP + 1) == NOMASK) &&
		  (*(IMP + vw) == NOMASK)	&& (*(IMP + vw - 1) == NOMASK)		&& (*(IMP + vw + 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)	&& (*(IMP - vw - 1) == NOMASK)		&& (*(IMP - vw + 1) == NOMASK) &&
		  (*(IMP + fs) == NOMASK)	&& (*(IMP + fs - 1) == NOMASK)		&& (*(IMP + fs + 1) == NOMASK) &&
		  (*(IMP + fs - vw) == NOMASK)	&& (*(IMP + fs - vw - 1) == NOMASK)	&& (*(IMP + fs - vw + 1) == NOMASK) &&
		  (*(IMP + fs + vw) == NOMASK)	&& (*(IMP + fs + vw - 1) == NOMASK)	&& (*(IMP + fs + vw + 1) == NOMASK) &&
		  (*(IMP - fs) == NOMASK)	&& (*(IMP - fs - 1) == NOMASK)		&& (*(IMP - fs + 1) == NOMASK) &&
		  (*(IMP - fs - vw) == NOMASK)	&& (*(IMP - fs - vw - 1) == NOMASK)	&& (*(IMP - fs - vw + 1) == NOMASK) &&
		  (*(IMP - fs + vw) == NOMASK)	&& (*(IMP - fs + vw - 1) == NOMASK)	&& (*(IMP - fs + vw + 1) == NOMASK))
		{
		  *EMP = NOMASK;
		}
	      ++EMP;
	      ++IMP;
	    }
	  EMP += 2;
	  IMP += 2;
	}
      EMP += 2 * volume_width;
      IMP += 2 * volume_width;
    }

  if (params->x_connectivity == 1)
    {
      //extend the mask to the front side of the phase volume
      IMP = input_mask    + frame_size + volume_width;	//input mask pointer
      EMP = extended_mask + frame_size + volume_width;	//extended mask pointer
      for (n=1; n < volume_depth - 1; n++)
	{
	  for (i=1; i < volume_height - 1; i++)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP + vw - 1) == NOMASK)		&& (*(IMP + 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP + vw) == NOMASK)	&&
		  (*(IMP - fs) == NOMASK)		&& (*(IMP + fs) == NOMASK) &&
		  (*(IMP - 1) == NOMASK)		&& (*(IMP + vw + 1) == NOMASK) &&
		  (*(IMP - vw + 1) == NOMASK)		&& (*(IMP + 2 * vw - 1) == NOMASK) &&
		  (*(IMP - fs - 1) == NOMASK)		&& (*(IMP + fs + vw + 1) == NOMASK) &&
		  (*(IMP - fs - vw) == NOMASK)		&& (*(IMP + fs + vw) == NOMASK) &&
		  (*(IMP - fs - vw + 1) == NOMASK)	&& (*(IMP + fs + 2 * vw - 1) == NOMASK) &&
		  (*(IMP - fs + vw - 1) == NOMASK)	&& (*(IMP + fs + 1) == NOMASK)	&&
		  (*(IMP - fs + 1) == NOMASK)		&& (*(IMP + fs + vw - 1) == NOMASK) &&
		  (*(IMP - fs + 2 * vw - 1) == NOMASK)	&& (*(IMP + fs - vw + 1) == NOMASK) &&
		  (*(IMP - fs + vw) == NOMASK)		&& (*(IMP + fs - vw) == NOMASK) &&
		  (*(IMP - fs + vw + 1) == NOMASK)	&& (*(IMP + fs - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP += vw;
	      IMP += vw;
	    }
	  EMP += 2 * vw;
	  IMP += 2 *vw;
	}

      //extend the mask to the rear side of the phase volume
      IMP = input_mask    + frame_size + 2 * volume_width - 1;	//input mask pointer
      EMP = extended_mask + frame_size + 2 * volume_width - 1;	//extended mask pointer
      for (n=1; n < volume_depth - 1; n++)
	{
	  for (i=1; i < volume_height - 1; i++)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP - vw + 1) == NOMASK)	&& (*(IMP - 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP + vw) == NOMASK) &&
		  (*(IMP - fs) == NOMASK)		&& (*(IMP + fs) == NOMASK) &&
		  (*(IMP - vw - 1) == NOMASK)		&& (*(IMP + 1) == NOMASK) &&
		  (*(IMP + vw - 1) == NOMASK)		&& (*(IMP - 2 * vw + 1) == NOMASK) &&
		  (*(IMP - fs - vw - 1) == NOMASK)	&& (*(IMP + fs + 1) == NOMASK)	&&
		  (*(IMP - fs - 2 * vw + 1) == NOMASK)	&& (*(IMP + fs + vw - 1) == NOMASK) &&
		  (*(IMP - fs - 1) == NOMASK)		&& (*(IMP + fs - vw + 1) == NOMASK) &&
		  (*(IMP - fs - vw + 1) == NOMASK)	&& (*(IMP + fs - 1) == NOMASK)	&&
		  (*(IMP - fs - vw) == NOMASK)		&& (*(IMP + fs + vw) == NOMASK) &&
		  (*(IMP - fs + vw - 1) == NOMASK)	&& (*(IMP + fs - 2 * vw + 1) == NOMASK) &&
		  (*(IMP - fs + vw) == NOMASK)		&& (*(IMP + fs - vw) == NOMASK) &&
		  (*(IMP - fs + 1) == NOMASK)		&& (*(IMP + fs - vw - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP += vw;
	      IMP += vw;
	    }
	  EMP += 2 * vw;
	  IMP += 2 *vw;
	}
    }

  if (params->y_connectivity == 1)
    {
      //extend the mask to the left side of the phase volume
      IMP = input_mask + frame_size + 1;
      EMP = extended_mask + frame_size + 1;
      for (n=1; n < volume_depth - 1; n++)
	{
	  for (j=1; j < volume_width - 1; j++)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP - 1) == NOMASK) && (*(IMP + 1) == NOMASK) &&
		  (*(IMP + fs - vw) == NOMASK)		&& (*(IMP + vw) == NOMASK) &&
		  (*(IMP - fs) == NOMASK)		&& (*(IMP + fs) == NOMASK) &&
		  (*(IMP + fs - vw - 1) == NOMASK)	&& (*(IMP + vw + 1) == NOMASK) &&
		  (*(IMP + fs - vw + 1) == NOMASK)	&& (*(IMP + vw - 1) == NOMASK) &&
		  (*(IMP - vw - 1) == NOMASK)		&& (*(IMP + fs + vw + 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP + fs + vw) == NOMASK) &&
		  (*(IMP - vw + 1) == NOMASK)		&& (*(IMP + fs + vw - 1) == NOMASK) &&
		  (*(IMP - fs - 1) == NOMASK)		&& (*(IMP + fs + 1) == NOMASK)	&&
		  (*(IMP - fs + 1) == NOMASK)		&& (*(IMP + fs - 1) == NOMASK) &&
		  (*(IMP - fs + vw - 1) == NOMASK)	&& (*(IMP + 2 * fs - vw + 1) == NOMASK) &&
		  (*(IMP - fs + vw) == NOMASK)		&& (*(IMP + 2 * fs - vw) == NOMASK) &&
		  (*(IMP - fs + vw + 1) == NOMASK)	&& (*(IMP + 2 * fs - vw - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP++;
	      IMP++;
	    }
	  EMP += fs - vw + 2;
	  IMP += fs - vw + 2;
	}

      //extend the mask to the right side of the phase volume
      IMP = input_mask + 2 * frame_size - volume_width + 1;
      EMP = extended_mask + 2 * frame_size - volume_width + 1;
      for (n=1; n < volume_depth - 1; n++)
	{
	  for (j=1; j < volume_width - 1; j++)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP + 1) == NOMASK) && (*(IMP - 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP - fs + vw) == NOMASK)	&&
		  (*(IMP - fs) == NOMASK)		&& (*(IMP + fs) == NOMASK) &&
		  (*(IMP - vw - 1) == NOMASK)		&& (*(IMP - fs + vw + 1) == NOMASK) &&
		  (*(IMP - vw + 1) == NOMASK)		&& (*(IMP - fs + vw - 1) == NOMASK) &&
		  (*(IMP - fs - vw - 1) == NOMASK)	&& (*(IMP + vw + 1) == NOMASK)	&&
		  (*(IMP - fs - vw + 1) == NOMASK)	&& (*(IMP + vw - 1) == NOMASK) &&
		  (*(IMP - fs - vw) == NOMASK)		&& (*(IMP + vw) == NOMASK) &&
		  (*(IMP - fs - 1) == NOMASK)		&& (*(IMP + fs + 1) == NOMASK)	&&
		  (*(IMP - fs + 1) == NOMASK)		&& (*(IMP + fs - 1) == NOMASK) &&
		  (*(IMP - 2 * fs + vw - 1) == NOMASK)	&& (*(IMP + fs - vw + 1) == NOMASK) &&
		  (*(IMP - 2 * fs + vw) == NOMASK)	&& (*(IMP + fs - vw) == NOMASK) &&
		  (*(IMP - 2 * fs + vw + 1) == NOMASK)	&& (*(IMP + fs - vw - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP++;
	      IMP++;
	    }
	  EMP += fs - vw + 2;
	  IMP += fs - vw + 2;
	}
    }

  if (params->z_connectivity == 1)
    {
      //extend the mask to the bottom side of the phase volume
      IMP = input_mask + volume_width + 1;
      EMP = extended_mask + volume_width + 1;
      for (i=1; i < volume_height - 1; ++i)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP - 1) == NOMASK)		&& (*(IMP + 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP + vw) == NOMASK)	&&
		  (*(IMP + fs) == NOMASK)		&& (*(IMP + vs  -  fs) == NOMASK) &&
		  (*(IMP - vw - 1) == NOMASK)		&& (*(IMP + vw + 1) == NOMASK) &&
		  (*(IMP - vw + 1) == NOMASK)		&& (*(IMP + vw - 1) == NOMASK) &&
		  (*(IMP + vs - fs - vw - 1) == NOMASK)	&& (*(IMP + fs + vw + 1) == NOMASK) &&
		  (*(IMP + vs - fs - vw) == NOMASK)	&& (*(IMP + fs + vw) == NOMASK) &&
		  (*(IMP + vs - fs - vw + 1) == NOMASK)	&& (*(IMP + fs + vw - 1) == NOMASK) &&
		  (*(IMP + vs - fs - 1) == NOMASK)	&& (*(IMP + fs + 1) == NOMASK)	&&
		  (*(IMP + vs - fs + 1) == NOMASK)	&& (*(IMP + fs - 1) == NOMASK) &&
		  (*(IMP + vs - fs + vw - 1) == NOMASK)	&& (*(IMP + fs - vw + 1) == NOMASK) &&
		  (*(IMP + vs - fs + vw) == NOMASK)	&& (*(IMP + fs - vw) == NOMASK) &&
		  (*(IMP + vs - fs + vw + 1) == NOMASK)	&& (*(IMP + fs - vw - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP++;
	      IMP++;
	    }
	  EMP += 2;
	  IMP += 2;
	}

      //extend the mask to the top side of the phase volume
      IMP = input_mask + volume_size - frame_size + volume_width + 1;
      EMP = extended_mask + volume_size - frame_size + volume_width + 1;
      for (i=1; i < volume_height - 1; ++i)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if( (*IMP) == NOMASK			&& (*(IMP + 1) == NOMASK)		&& (*(IMP - 1) == NOMASK) &&
		  (*(IMP - vw) == NOMASK)		&& (*(IMP - fs + vw) == NOMASK)	&&
		  (*(IMP - fs) == NOMASK)		&& (*(IMP - vs + fs) == NOMASK) &&
		  (*(IMP - vw - 1) == NOMASK)		&& (*(IMP + vw + 1) == NOMASK) &&
		  (*(IMP - vw + 1) == NOMASK)		&& (*(IMP + vw - 1) == NOMASK) &&
		  (*(IMP - fs - vw - 1) == NOMASK)	&& (*(IMP - vs + fs + vw + 1) == NOMASK) &&
		  (*(IMP - fs - vw + 1) == NOMASK)	&& (*(IMP - vs + fs + vw - 1) == NOMASK) &&
		  (*(IMP - fs - vw) == NOMASK)		&& (*(IMP - vs + fs + vw) == NOMASK) &&
		  (*(IMP - fs - 1) == NOMASK)		&& (*(IMP - vs + fs + 1) == NOMASK)	&&
		  (*(IMP - fs + 1) == NOMASK)		&& (*(IMP - vs + fs - 1) == NOMASK) &&
		  (*(IMP - fs + vw - 1) == NOMASK)	&& (*(IMP - vs + fs - vw + 1) == NOMASK) &&
		  (*(IMP - fs + vw) == NOMASK)		&& (*(IMP - vs + fs - vw) == NOMASK) &&
		  (*(IMP - fs + vw + 1) == NOMASK)	&& (*(IMP - vs + fs - vw - 1) == NOMASK) )
		{
		  *EMP = NOMASK;
		}
	      EMP++;
	      IMP++;
	    }
	  EMP += 2;
	  IMP += 2;
	}
    }
}

void calculate_reliability(double *wrappedVolume, VOXELM *voxel, int volume_width, int volume_height, int volume_depth, params_t *params)
{
  int frame_size  = volume_width * volume_height;
  int volume_size = volume_width * volume_height * volume_depth;
  VOXELM *voxel_pointer;
  double H, V, N, D1, D2, D3, D4, D5, D6, D7, D8, D9, D10;
  double *WVP;
  int n, i, j;

  WVP = wrappedVolume + frame_size + volume_width + 1;
  voxel_pointer = voxel + frame_size + volume_width + 1;
  for (n=1; n < volume_depth - 1; n++)
    {
      for (i=1; i < volume_height - 1; i++)
        {
	  for (j=1; j < volume_width - 1; j++)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP - 1) - *WVP) - wrap(*WVP - *(WVP + 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP + frame_size));
		  D1 = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1));
		  D2 = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + volume_width - 1));
		  D3 = wrap(*(WVP - frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width + 1));
		  D4 = wrap(*(WVP - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width));
		  D5 = wrap(*(WVP - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width - 1));
		  D6 = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D7 = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  D8 = wrap(*(WVP - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width + 1));
		  D9 = wrap(*(WVP - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width));
		  D10 = wrap(*(WVP - frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer++;
	      WVP++;
	    }
	  voxel_pointer += 2;
	  WVP += 2;
	}
      voxel_pointer += 2 * volume_width;
      WVP += 2 * volume_width;
    }

  if (params->x_connectivity == 1)
    {
      //calculating reliability for the front side of the phase volume...add volume_width
      WVP = wrappedVolume + frame_size + volume_width;
      voxel_pointer = voxel + frame_size + volume_width;
      for (n=1; n < volume_depth - 1; ++n)
	{
	  for (i=1; i < volume_height - 1; ++i)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP + frame_size));
		  D1 = wrap(*(WVP - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1));
		  D2 = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + 2 * volume_width - 1));
		  D3 = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width + 1));
		  D4 = wrap(*(WVP - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width));
		  D5 = wrap(*(WVP - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 2 * volume_width - 1));
		  D6 = wrap(*(WVP - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D7 = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width - 1));
		  D8 = wrap(*(WVP - frame_size + 2 * volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width + 1));
		  D9 = wrap(*(WVP - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width));
		  D10 = wrap(*(WVP - frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer += volume_width;
	      WVP += volume_width;
	    }
	  voxel_pointer += 2 * volume_width;
	  WVP += 2 * volume_width;
	}

      //calculating reliability for the rear side of the phase volume..... subtract volume_width
      WVP = wrappedVolume + frame_size + 2 * volume_width - 1;
      voxel_pointer = voxel + frame_size + 2 * volume_width - 1;
      for (n=1; n < volume_depth - 1; ++n)
	{
	  for (i=1; i < volume_height - 1; ++i)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP - 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP + frame_size));
		  D1 = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + 1));
		  D2 = wrap(*(WVP + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP - 2 * volume_width + 1));
		  D3 = wrap(*(WVP - frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D4 = wrap(*(WVP - frame_size - 2 * volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width - 1));
		  D5 = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width + 1));
		  D6 = wrap(*(WVP - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  D7 = wrap(*(WVP - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width));
		  D8 = wrap(*(WVP - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 2 * volume_width + 1));
		  D9 = wrap(*(WVP - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width));
		  D10 = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer += volume_width;
	      WVP += volume_width;
	    }
	  voxel_pointer += 2 * volume_width;
	  WVP += 2 * volume_width;
	}
    }

  if (params->y_connectivity == 1)
    {
      //calculating reliability for the left side of the phase volume...add frame_size
      WVP = wrappedVolume + frame_size + 1;
      voxel_pointer = voxel + frame_size + 1;
      for (n=1; n < volume_depth - 1; ++n)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP - 1) - *WVP) - wrap(*WVP - *(WVP + 1));
		  V  = wrap(*(WVP + frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP + frame_size));
		  D1  = wrap(*(WVP + frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1));
		  D2  = wrap(*(WVP + frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + volume_width - 1));
		  D3  = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width + 1));
		  D4  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width));
		  D5  = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width - 1));
		  D6  = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D7  = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  D8  = wrap(*(WVP - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + 2 * frame_size - volume_width + 1));
		  D9  = wrap(*(WVP - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + 2 * frame_size - volume_width));
		  D10  = wrap(*(WVP - frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + 2 * frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer++;
	      WVP++;
	    }
	  voxel_pointer += frame_size - volume_width + 2;
	  WVP += frame_size - volume_width + 2;
	}

      //calculating reliability for the right side of the phase volume...subtract frame_size
      WVP = wrappedVolume + 2 * frame_size - volume_width + 1;
      voxel_pointer = voxel + 2 * frame_size - volume_width + 1;
      for (n=1; n < volume_depth - 1; ++n)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP + 1) - *WVP) - wrap(*WVP - *(WVP - 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP - frame_size + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP + frame_size));
		  D1  = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP - frame_size + volume_width + 1));
		  D2  = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP - frame_size + volume_width - 1));
		  D3  = wrap(*(WVP - frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1)	);
		  D4  = wrap(*(WVP - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + volume_width -	1));
		  D5  = wrap(*(WVP - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  D6  = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D7  = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  D8  = wrap(*(WVP - 2 * frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width + 1));
		  D9  = wrap(*(WVP - 2 * frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width));
		  D10  = wrap(*(WVP - 2 * frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer++;
	      WVP++;
	    }
	  voxel_pointer += frame_size - volume_width + 2;
	  WVP += frame_size - volume_width + 2;
	}
    }

  if (params->z_connectivity == 1)
    {
      //calculating reliability for the bottom side of the phase volume...add volume_size
      WVP = wrappedVolume + volume_width + 1;
      voxel_pointer = voxel + volume_width + 1;
      for (i=1; i < volume_height - 1; ++i)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP - 1) - *WVP) - wrap(*WVP - *(WVP + 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP + frame_size) - *WVP) - wrap(*WVP - *(WVP + volume_size - frame_size));
		  D1  = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1));
		  D2  = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + volume_width - 1));
		  D3  = wrap(*(WVP + volume_size - frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width + 1));
		  D4  = wrap(*(WVP + volume_size - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width));
		  D5  = wrap(*(WVP + volume_size - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + volume_width - 1));
		  D6  = wrap(*(WVP + volume_size - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size + 1));
		  D7  = wrap(*(WVP + volume_size - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - 1));
		  D8  = wrap(*(WVP + volume_size - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width + 1));
		  D9  = wrap(*(WVP + volume_size - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width));
		  D10 = wrap(*(WVP + volume_size - frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer++;
	      WVP++;
	    }
	  voxel_pointer += 2;
	  WVP += 2;
	}

      //calculating reliability for the top side of the phase volume...subtract volume_size
      WVP = wrappedVolume + volume_size - frame_size + volume_width + 1;
      voxel_pointer = voxel + volume_size - frame_size + volume_width + 1;
      for (i=1; i < volume_height - 1; ++i)
	{
	  for (j=1; j < volume_width - 1; ++j)
	    {
	      if (voxel_pointer->extended_mask == NOMASK)
		{
		  H  = wrap(*(WVP + 1) - *WVP) - wrap(*WVP - *(WVP - 1));
		  V  = wrap(*(WVP - volume_width) - *WVP) - wrap(*WVP - *(WVP + volume_width));
		  N  = wrap(*(WVP - frame_size) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size));
		  D1  = wrap(*(WVP - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP + volume_width + 1));
		  D2  = wrap(*(WVP - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP + volume_width - 1));
		  D3  = wrap(*(WVP - frame_size - volume_width - 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size + volume_width + 1));
		  D4  = wrap(*(WVP - frame_size - volume_width + 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size + volume_width - 1));
		  D5  = wrap(*(WVP - frame_size - volume_width) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size + volume_width));
		  D6  = wrap(*(WVP - frame_size - 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size + 1));
		  D7  = wrap(*(WVP - frame_size + 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size - 1));
		  D8  = wrap(*(WVP - frame_size + volume_width - 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size - volume_width + 1));
		  D9  = wrap(*(WVP - frame_size + volume_width) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size - volume_width));
		  D10 = wrap(*(WVP - frame_size + volume_width + 1) - *WVP) - wrap(*WVP - *(WVP - volume_size + frame_size - volume_width - 1));
		  voxel_pointer->reliability = H*H + V*V + N*N + D1*D1 + D2*D2  + D3*D3 + D4*D4  + D5*D5 + D6*D6
		    + D7*D7 + D8*D8 + D9*D9 + D10*D10;
		}
	      voxel_pointer++;
	      WVP++;
	    }
	  voxel_pointer += 2;
	  WVP += 2;
	}
    }
}

//calculate the reliability of the horizontal edges of the volume.  it
//is calculated by adding the reliability of voxel and the relibility
//of its right neighbour. edge is calculated between a voxel and its
//next neighbour
void  horizontalEDGEs(VOXELM *voxel, EDGE *edge, int volume_width, int volume_height, int volume_depth, params_t *params)
{
  int n, i, j;
  EDGE *edge_pointer = edge;
  VOXELM *voxel_pointer = voxel;
  int no_of_edges = params->no_of_edges;

  for (n=0; n < volume_depth; n++)
    {
      for (i = 0; i < volume_height; i++)
	{
	  for (j = 0; j < volume_width - 1; j++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer + 1)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer+1);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer + 1)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer + 1)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer++;
	    }
	  voxel_pointer++;
	}
    }
  if (params->x_connectivity == 1)
    {
      voxel_pointer = voxel + volume_width - 1;
      for (n=0; n < volume_depth; n++)
	{
	  for (i = 0; i < volume_height; i++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer - volume_width + 1)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer - volume_width + 1);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer - volume_width + 1)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer - volume_width + 1)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer += volume_width;
	    }
	}
    }
  params->no_of_edges = no_of_edges;
}

void  verticalEDGEs(VOXELM *voxel, EDGE *edge, int volume_width, int volume_height, int volume_depth, params_t *params)
{
  int n, i, j;
  int no_of_edges = params->no_of_edges;
  VOXELM *voxel_pointer = voxel;
  EDGE *edge_pointer = edge + no_of_edges;
  int frame_size = volume_width * volume_height;
  int next_voxel = frame_size - volume_width;

  for (n=0; n < volume_depth; n++)
    {
      for (i=0; i<volume_height - 1; i++)
	{
	  for (j=0; j < volume_width; j++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer + volume_width)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer + volume_width);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer + volume_width)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer + volume_width)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer++;
	    }
	}
      voxel_pointer += volume_width;
    }

  if (params->y_connectivity == 1)
    {
      voxel_pointer = voxel + frame_size - volume_width;
      for (n=0; n < volume_depth; n++)
	{
	  for (i = 0; i < volume_width; i++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer - next_voxel)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer - next_voxel);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer - next_voxel)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer - next_voxel)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer++;
	    }
	  voxel_pointer += next_voxel;
	}
    }
  params->no_of_edges = no_of_edges;
}

void  normalEDGEs(VOXELM *voxel, EDGE *edge, int volume_width, int volume_height, int volume_depth, params_t *params)
{
  int n, i, j;
  int no_of_edges = params->no_of_edges;
  int frame_size = volume_width * volume_height;
  int volume_size = volume_width * volume_height * volume_depth;
  VOXELM *voxel_pointer = voxel;
  EDGE *edge_pointer = edge + no_of_edges;
  int next_voxel = volume_size - frame_size;

  for (n=0; n < volume_depth - 1; n++)
    {
      for (i=0; i<volume_height; i++)
	{
	  for (j=0; j < volume_width; j++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer + frame_size)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer + frame_size);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer + frame_size)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer + frame_size)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer++;
	    }
	}
    }


  if (params->z_connectivity == 1)
    {
      voxel_pointer = voxel + next_voxel;
      for (i=0; i < volume_height; i++)
	{
	  for (j = 0; j < volume_width; j++)
	    {
	      if (voxel_pointer->input_mask == NOMASK && (voxel_pointer - next_voxel)->input_mask == NOMASK )
		{
		  edge_pointer->pointer_1 = voxel_pointer;
		  edge_pointer->pointer_2 = (voxel_pointer - next_voxel);
		  edge_pointer->reliab = voxel_pointer->reliability + (voxel_pointer - next_voxel)->reliability;
		  edge_pointer->increment = find_wrap(voxel_pointer->value, (voxel_pointer - next_voxel)->value);
		  edge_pointer++;
		  no_of_edges++;
		}
	      voxel_pointer++;
	    }
	}
    }
  params->no_of_edges = no_of_edges;
}

//gather the voxels of the volume into groups
void  gatherVOXELs(EDGE *edge, params_t *params)
{
  int k;
  VOXELM *VOXEL1;
  VOXELM *VOXEL2;
  VOXELM *group1;
  VOXELM *group2;
  EDGE *pointer_edge = edge;
  int incremento;

  for (k = 0; k < params->no_of_edges; k++)
    {
      VOXEL1 = pointer_edge->pointer_1;
      VOXEL2 = pointer_edge->pointer_2;

      //VOXELM 1 and VOXELM 2 belong to different groups
      //initially each voxel is in a group by itself and one voxel can construct a group
      //no else or else if to this if
      if (VOXEL2->head != VOXEL1->head)
	{
	  //VOXELM 2 is alone in its group
	  //merge this voxel with VOXELM 1 group and find the number of 2 pi to add
	  //to or subtract to unwrap it
	  if ((VOXEL2->next == NULL) && (VOXEL2->head == VOXEL2))
	    {
	      VOXEL1->head->last->next = VOXEL2;
	      VOXEL1->head->last = VOXEL2;
	      (VOXEL1->head->number_of_voxels_in_group)++;
	      VOXEL2->head=VOXEL1->head;
	      VOXEL2->increment = VOXEL1->increment-pointer_edge->increment;
	    }

	  //VOXELM 1 is alone in its group
	  //merge this voxel with VOXELM 2 group and find the number of 2 pi to add
	  //to or subtract to unwrap it
	  else if ((VOXEL1->next == NULL) && (VOXEL1->head == VOXEL1))
	    {
	      VOXEL2->head->last->next = VOXEL1;
	      VOXEL2->head->last = VOXEL1;
	      (VOXEL2->head->number_of_voxels_in_group)++;
	      VOXEL1->head = VOXEL2->head;
	      VOXEL1->increment = VOXEL2->increment+pointer_edge->increment;
	    }

	  //VOXELM 1 and VOXELM 2 both have groups
	  else
            {
	      group1 = VOXEL1->head;
	      group2 = VOXEL2->head;
	      //if the no. of voxels in VOXELM 1 group is larger than the no. of voxels
	      //in VOXELM 2 group.   Merge VOXELM 2 group to VOXELM 1 group
	      //and find the number of wraps between VOXELM 2 group and VOXELM 1 group
	      //to unwrap VOXELM 2 group with respect to VOXELM 1 group.
	      //the no. of wraps will be added to VOXELM 2 grop in the future
	      if (group1->number_of_voxels_in_group > group2->number_of_voxels_in_group)
		{
		  //merge VOXELM 2 with VOXELM 1 group
		  group1->last->next = group2;
		  group1->last = group2->last;
		  group1->number_of_voxels_in_group = group1->number_of_voxels_in_group + group2->number_of_voxels_in_group;
		  incremento = VOXEL1->increment-pointer_edge->increment - VOXEL2->increment;
		  //merge the other voxels in VOXELM 2 group to VOXELM 1 group
		  while (group2 != NULL)
		    {
		      group2->head = group1;
		      group2->increment += incremento;
		      group2 = group2->next;
		    }
		}

	      //if the no. of voxels in VOXELM 2 group is larger than the no. of voxels
	      //in VOXELM 1 group.   Merge VOXELM 1 group to VOXELM 2 group
	      //and find the number of wraps between VOXELM 2 group and VOXELM 1 group
	      //to unwrap VOXELM 1 group with respect to VOXELM 2 group.
	      //the no. of wraps will be added to VOXELM 1 grop in the future
	      else
                {
		  //merge VOXELM 1 with VOXELM 2 group
		  group2->last->next = group1;
		  group2->last = group1->last;
		  group2->number_of_voxels_in_group = group2->number_of_voxels_in_group + group1->number_of_voxels_in_group;
		  incremento = VOXEL2->increment + pointer_edge->increment - VOXEL1->increment;
		  //merge the other voxels in VOXELM 2 group to VOXELM 1 group
		  while (group1 != NULL)
		    {
		      group1->head = group2;
		      group1->increment += incremento;
		      group1 = group1->next;
		    } // while

                } // else
            } //else
        } //if
      pointer_edge++;
    }
}

//unwrap the volume
void unwrapVolume(VOXELM *voxel, int volume_width, int volume_height, int volume_depth)
{
  int i;
  int volume_size = volume_width * volume_height * volume_depth;
  VOXELM *voxel_pointer=voxel;

  for (i = 0; i < volume_size; i++)
    {
      voxel_pointer->value += TWOPI * (double)(voxel_pointer->increment);
      voxel_pointer++;
    }
}

//set the masked voxels (mask = 0) to the minimum of the unwrapper phase
void  maskVolume(VOXELM *voxel, unsigned char *input_mask, int volume_width, int volume_height, int volume_depth)
{
  int volume_width_plus_one  = volume_width + 1;
  int volume_height_plus_one  = volume_height + 1;
  int volume_width_minus_one = volume_width - 1;
  int volume_height_minus_one = volume_height - 1;

  VOXELM *pointer_voxel = voxel;
  unsigned char *IMP = input_mask;	//input mask pointer
  double min=99999999.;
  int i, j;
  int volume_size = volume_width * volume_height * volume_depth;

  //find the minimum of the unwrapped phase
  for (i = 0; i < volume_size; i++)
    {
      if ((pointer_voxel->value < min) && (*IMP == NOMASK))
	min = pointer_voxel->value;

      pointer_voxel++;
      IMP++;
    }

  pointer_voxel = voxel;
  IMP = input_mask;

  //set the masked voxels to minimum
  for (i = 0; i < volume_size; i++)
    {
      if ((*IMP) == MASK)
	{
	  pointer_voxel->value = min;
	}
      pointer_voxel++;
      IMP++;
    }
}

//the input to this unwrapper is an array that contains the wrapped
//phase map.  copy the volume on the buffer passed to this unwrapper
//to over-write the unwrapped phase map on the buffer of the wrapped
//phase map.
void  returnVolume(VOXELM *voxel, double *unwrappedVolume, int volume_width, int volume_height, int volume_depth)
{
  int i;
  int volume_size = volume_width * volume_height * volume_depth;
  double *unwrappedVolume_pointer = unwrappedVolume;
  VOXELM *voxel_pointer = voxel;

  for (i=0; i < volume_size; i++)
    {
      *unwrappedVolume_pointer = voxel_pointer->value;
      voxel_pointer++;
      unwrappedVolume_pointer++;
    }
}

//the main function of the unwrapper
void
unwrap3D(double* wrapped_volume, double* unwrapped_volume, unsigned char* input_mask,
	 int volume_width, int volume_height, int volume_depth,
	 int wrap_around_x, int wrap_around_y, int wrap_around_z)
{
  params_t params = {TWOPI, wrap_around_x, wrap_around_y, wrap_around_z, 0};
  unsigned char *extended_mask;
  VOXELM *voxel;
  EDGE *edge;
  int volume_size = volume_height * volume_width * volume_depth;
  int No_of_Edges_initially = 3 * volume_width * volume_height * volume_depth;

  extended_mask = (unsigned char *) calloc(volume_size, sizeof(unsigned char));
  voxel = (VOXELM *) calloc(volume_size, sizeof(VOXELM));
  edge = (EDGE *) calloc(No_of_Edges_initially, sizeof(EDGE));;

  extend_mask(input_mask, extended_mask, volume_width, volume_height, volume_depth, &params);
  initialiseVOXELs(wrapped_volume, input_mask, extended_mask, voxel, volume_width, volume_height, volume_depth);
  calculate_reliability(wrapped_volume, voxel, volume_width, volume_height, volume_depth, &params);
  horizontalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, &params);
  verticalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, &params);
  normalEDGEs(voxel, edge, volume_width, volume_height, volume_depth, &params);

  if (params.no_of_edges != 0) {
      //sort the EDGEs depending on their reiability. The VOXELs with higher relibility (small value) first
      quicker_sort(edge, edge + params.no_of_edges - 1);
  }

  //gather VOXELs into groups
  gatherVOXELs(edge, &params);

  unwrapVolume(voxel, volume_width, volume_height, volume_depth);
  maskVolume(voxel, input_mask, volume_width, volume_height, volume_depth);

  //copy the volume from VOXELM structure to the unwrapped phase array passed to this function
  returnVolume(voxel, unwrapped_volume, volume_width, volume_height, volume_depth);

  free(edge);
  free(voxel);
  free(extended_mask);
}
