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Copy pathsimple_edge_warp_3d_mex.cpp
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simple_edge_warp_3d_mex.cpp
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#include <math.h>
#include "mex.h"
#include "matrix.h"
#include "simpleEdge3d_l.h"
struct imorder
{
unsigned int coord;
float val;
};
int queue_comp(const void *queue1_, const void *queue2_)
{
struct imorder *queue1 = (struct imorder *)queue1_;
struct imorder *queue2 = (struct imorder *)queue2_;
if(queue1->val > queue2->val)
return -1;
else if(queue1->val < queue2->val)
return 1;
return 0;
}
void construct_patch(unsigned int *source, bool *patch, int i, int xsize, int ysize, int zsize)
{
int x, y, z, d;
for(d=0;d<3;d++)
for(x=0;x<3;x++)
for(y=0;y<3;y++)
for(z=0;z<3;z++)
patch[x + y*3 + z*3*3 + d*3*3*3] = (bool)(source[ i%(xsize*ysize*zsize) + (x-1) + (y-1)*xsize + (z-1)*xsize*ysize + d*xsize*ysize*zsize]!=0);
}
unsigned int unique_neighbor(unsigned int *source, int i, int xsize, int ysize, int zsize, unsigned int fg_conn)
{
int it, j;
unsigned int neighbor = 0;
unsigned int v = (unsigned int)(i/(xsize*ysize*zsize));
if(fg_conn==6)
{
for(j=0;j<10;j++)
{
it = i%(xsize*ysize*zsize) + offset10[j][v][0] + offset10[j][v][1]*xsize + offset10[j][v][2]*xsize*ysize + offset10[j][v][3]*xsize*ysize*zsize;
if(source[it]!=0)
{
neighbor=(unsigned int)source[it];
break;
}
}
}
else
{
for(j=0;j<32;j++)
{
it = i%(xsize*ysize*zsize) + offset12[j][v][0] + offset12[j][v][1]*xsize + offset12[j][v][2]*xsize*ysize + offset12[j][v][3]*xsize*ysize*zsize;
if(source[it]!=0)
{
neighbor=(unsigned int)source[it];
break;
}
}
}
return neighbor;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
int i, j, k, it, x, y, z, d, linind, linind_pad, imsize, imsize_pad, delregct, delregbct, mask_dim_ct, max_obj_id,;
int *size, *mask_dims;
float binary_threshold;
unsigned int fg_conn, bg_conn, v;
bool *mask, *target, *missclass_points_image, *patch, *queued;
unsigned int *orig_source, *source, *sourceout;
float *orig_target, *target_real;
struct imorder *delreg, *delregb;
imsize = (int)mxGetNumberOfElements(prhs[0]);
size = (int *)mxGetDimensions(prhs[0]);
imsize_pad = (int)(size[0]+2)*(size[1]+2)*(size[2]+2)*size[3];
binary_threshold = (float)((nrhs==3)?0.5:mxGetScalar(prhs[3]));
fg_conn = (unsigned int)((nrhs==4)?6:mxGetScalar(prhs[4]));
if(fg_conn==6)
bg_conn=26;
else
bg_conn=6;
orig_source = (unsigned int *)mxGetData(prhs[0]);
orig_target = (float *)mxGetData(prhs[1]);
mask = (bool *)mxGetData(prhs[2]);
mask_dims = (int *)mxGetDimensions(prhs[2]);
mask_dim_ct = (int)mxGetNumberOfDimensions(prhs[2]);
source = (unsigned int *)mxCalloc(imsize_pad,sizeof(unsigned int));
target_real = (float *)mxCalloc(imsize_pad,sizeof(float));
target = (bool *)mxCalloc(imsize_pad,sizeof(bool));
missclass_points_image = (bool *)mxCalloc(imsize_pad,sizeof(bool));
delreg = (struct imorder *)mxCalloc(imsize_pad,sizeof(struct imorder));
delregb = (struct imorder *)mxCalloc(imsize_pad,sizeof(struct imorder));
patch = (bool *)mxCalloc(81,sizeof(bool));
queued = (bool *)mxCalloc(imsize_pad,sizeof(bool));
for(d=0;d<size[3];d++)
{
for(x=0;x<size[0];x++)
{
for(y=0;y<size[1];y++)
{
for(z=0;z<size[2];z++)
{
linind_pad = (x+1) + (y+1)*(size[0]+2) + (z+1)*(size[0]+2)*(size[1]+2) + d*(size[0]+2)*(size[1]+2)*(size[2]+2);
linind = x + y*size[0] + z*size[0]*size[1] + d*size[0]*size[1]*size[2];
source[linind_pad] = (unsigned int)(orig_source[linind]);
target_real[linind_pad] = (float)(orig_target[linind]);
target[linind_pad] = (bool)(target_real[linind_pad]>binary_threshold);
}
}
}
}
bool found_fg,found_bg;
int i_pad;
bool object_wise_warp=false;
int obj_id;
if(mask_dim_ct==5)
{
// We should really check the maximum value of the segmented components now to see how many objects we need to allocate
max_obj_id=0;
for(i=0;i<linind;i++)
{
if(orig_source[i] > max_obj_id)
max_obj_id = (int)orig_source[i];
}
if(mxGetDimensions(prhs[2])[4]<max_obj_id)
mexErrMsgTxt("You must provide more masks than the highest labeled object in the image.");
object_wise_warp=true;
}
int max_obj_ct = object_wise_warp?max_obj_id:1;
bool cur_edge_bg;
for(obj_id=0;obj_id<max_obj_ct;obj_id++)
{
j=0;
for(i=0;i<imsize;i++)// We can redo this so the mask neighborhood doesn't need to be padded
{
d=(int)(i/(size[0]*size[1]*size[2]));
x=i%size[0]+1;
y=(int)(i/size[0])%size[1]+1;
z=(int)(i/(size[0]*size[1]))%size[2]+1;
i_pad = x + y*(size[0]+2) + z*(size[0]+2)*(size[1]+2) + d*(size[0]+2)*(size[1]+2)*(size[2]+2);
missclass_points_image[i_pad] = (bool)(mask[i+obj_id*imsize] && ((source[i_pad]!=0)!=target[i_pad]));
if(object_wise_warp)
missclass_points_image[i_pad] &= (source[i_pad]==i+1) || (source[i_pad]==0);
if(missclass_points_image[i_pad])
{
v = (unsigned int)(i_pad/((size[0]+2)*(size[1]+2)*(size[2]+2)));
// First check for fg pixel, then check for bg pixel
found_bg=false;
found_fg=false;
if(fg_conn==6)
{
for(k=0;k<10;k++)
{
it = i_pad%((size[0]+2)*(size[1]+2)*(size[2]+2)) + offset10[0][v][0] + offset10[0][v][1]*(size[0]+2) + offset10[0][v][2]*(size[0]+2)*(size[1]+2) + offset10[0][v][3]*(size[0]+2)*(size[1]+2)*(size[2]+2);
if((object_wise_warp && source[it]==(obj_id+1)) || (!object_wise_warp && source[it]!=0))
{
found_fg=true;
break;
}
}
for(k=0;k<32;k++)
{
it = i_pad%((size[0]+2)*(size[1]+2)*(size[2]+2)) + offset12[0][v][0] + offset12[0][v][1]*(size[0]+2) + offset12[0][v][2]*(size[0]+2)*(size[1]+2) + offset12[0][v][3]*(size[0]+2)*(size[1]+2)*(size[2]+2);
if(source[it]==0)
{
found_bg=true;
break;
}
}
}
else
{
for(k=0;k<32;k++)
{
it = i_pad%((size[0]+2)*(size[1]+2)*(size[2]+2)) + offset12[0][v][0] + offset12[0][v][1]*(size[0]+2) + offset12[0][v][2]*(size[0]+2)*(size[1]+2) + offset12[0][v][3]*(size[0]+2)*(size[1]+2)*(size[2]+2);
if((object_wise_warp && source[it]==(obj_id+1)) || (!object_wise_warp && source[it]!=0))
{
found_fg=true;
break;
}
}
for(k=0;k<10;k++)
{
it = i_pad%((size[0]+2)*(size[1]+2)*(size[2]+2)) + offset10[0][v][0] + offset10[0][v][1]*(size[0]+2) + offset10[0][v][2]*(size[0]+2)*(size[1]+2) + offset10[0][v][3]*(size[0]+2)*(size[1]+2)*(size[2]+2);
if(source[it]==0)
{
found_bg=true;
break;
}
}
}
// We are still only considering i_pad, which we are already sure belongs to the object of interest.
if(found_fg && found_bg)
{
delreg[j].coord = i_pad;
delreg[j].val = (float)fabs(target_real[i_pad]-binary_threshold);
j++;
}
}
}
delregct = j;
bool changed=true;
while( changed )
{
changed=false;
qsort(delreg,delregct,sizeof(struct imorder),queue_comp);
for(i=0;i<delregct;i++)
delregb[i] = delreg[i];
for(i=0;i<imsize_pad;i++)
queued[i] = false;
delregbct = delregct;
delregct = 0;
for(k=0;k<delregbct;k++)
{
i = delregb[k].coord;
if(missclass_points_image[i])
{
construct_patch(source,patch,i,size[0]+2,size[1]+2,size[2]+2);
if(simpleEdge3d(patch,(unsigned int)(i/((size[0]+2)*(size[1]+2)*(size[2]+2)) +1),fg_conn))
{
source[i] = source[i]==0?unique_neighbor(source,i,size[0]+2,size[1]+2,size[2]+2,fg_conn):0;
missclass_points_image[i] = false;
changed = true;
v = (unsigned int)(i/((size[0]+2)*(size[1]+2)*(size[2]+2)));
for(j=0;j<34;j++) /* all potential neighbors */
{
it = i%((size[0]+2)*(size[1]+2)*(size[2]+2)) + offset12e[j][v][0] + offset12e[j][v][1]*(size[0]+2) + offset12e[j][v][2]*(size[0]+2)*(size[1]+2) + offset12e[j][v][3]*(size[0]+2)*(size[1]+2)*(size[2]+2);
if(!queued[it])
{
if(object_wise_warp)
{
if(source[it]==(obj_id+1) || source[it]==0)
{
// For each edge we add, check whether it satisfies same criteria as initial queue?
queued[it] = true;
delreg[delregct].coord = it;
delreg[delregct].val = (float)fabs(target_real[it]-binary_threshold);
delregct++;
}
}
else
{
queued[it] = true;
delreg[delregct].coord = it;
delreg[delregct].val = (float)fabs(target_real[it]-binary_threshold);
delregct++;
}
}
}
}
}
}
}
}
plhs[0] = mxCreateNumericArray(mxGetNumberOfDimensions(prhs[0]),mxGetDimensions(prhs[0]),mxUINT32_CLASS,mxREAL);
sourceout = (unsigned int *)mxGetData(plhs[0]);
for(d=0;d<size[3];d++)
for(x=0;x<size[0];x++)
for(y=0;y<size[1];y++)
for(z=0;z<size[2];z++)
sourceout[x + y*size[0] + z*size[0]*size[1] + d*size[0]*size[1]*size[2]] = source[(x+1) + (y+1)*(size[0]+2) + (z+1)*(size[0]+2)*(size[1]+2) + d*(size[0]+2)*(size[1]+2)*(size[2]+2)];
mxFree(source);
mxFree(target_real);
mxFree(target);
mxFree(missclass_points_image);
mxFree(patch);
mxFree(queued);
mxFree(delreg);
mxFree(delregb);
return;
}