diff options
author | taw27 <taw27@bf6ca9ba-c028-0410-8290-897cf20841d1> | 2007-03-31 15:00:56 +0000 |
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committer | taw27 <taw27@bf6ca9ba-c028-0410-8290-897cf20841d1> | 2007-03-31 15:00:56 +0000 |
commit | f72af885e7beb97127e4300d635ab156b4336094 (patch) | |
tree | fb755678de8654eb58dc23f96cd9ef601aa2ed0a /src/itrans-stat.c | |
parent | 9f50a7efb9e16373c8f1d03abf6ad96235045139 (diff) |
More fussiness:
Tidy itrans-stat.c
Display units for pixel_size
Display appropriate peak search algorithm for cache files (i.e. none)
Tweak credits
git-svn-id: svn://cook.msm.cam.ac.uk:745/diff-tomo/dtr@19 bf6ca9ba-c028-0410-8290-897cf20841d1
Diffstat (limited to 'src/itrans-stat.c')
-rw-r--r-- | src/itrans-stat.c | 330 |
1 files changed, 193 insertions, 137 deletions
diff --git a/src/itrans-stat.c b/src/itrans-stat.c index 9a876a8..c2369ec 100644 --- a/src/itrans-stat.c +++ b/src/itrans-stat.c @@ -4,7 +4,7 @@ * Peak detection by iterative statistical analysis and processing * * (c) 2007 Gordon Ball <gfb21@cam.ac.uk> - * Thomas WHite <taw27@cam.ac.uk> + * Thomas White <taw27@cam.ac.uk> * * dtr - Diffraction Tomography Reconstruction * @@ -22,7 +22,7 @@ #include "imagedisplay.h" #include "utils.h" -/* +/* * Create a gsl_matrix for performing image operations on * from a raw image and control context * Converting to gsl_matrix because many of the required operations @@ -30,34 +30,36 @@ * Renormalises matrix to 0->1 */ static gsl_matrix *itrans_peaksearch_stat_createImageMatrix(ControlContext *ctx, int16_t *image) { + gsl_matrix *raw; + int i, j; + raw = gsl_matrix_alloc(ctx->width,ctx->height); - - int i,j; - for ( i=0; i<raw->size1;i++) { - for (j=0; j<raw->size2;j++) { - gsl_matrix_set(raw,i,j,(double)image[i+j*ctx->width]); + for ( i=0; i<raw->size1; i++ ) { + for ( j=0; j<raw->size2; j++ ) { + gsl_matrix_set(raw, i, j, (double)image[i+j*ctx->width]); } } - //printf("Created %dx%d matrix\n",ctx->width,ctx->height); matrix_renormalise(raw); + return raw; + } +/* Find and return the mean value of the matrix */ +static double itrans_peaksearch_stat_image_mean(gsl_matrix *m) { + int i, j; + double mean = 0.; -/* - * Find and return the mean value of the matrix - */ -static double itrans_peaksearch_stat_image_mean(gsl_matrix *m) { - double mean=0.; - int i,j; - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { mean += gsl_matrix_get(m,i,j); } } + return mean / (m->size1 * m->size2); + } /* @@ -65,34 +67,42 @@ static double itrans_peaksearch_stat_image_mean(gsl_matrix *m) { * \sqrt(\sum((x-mean)^2)/n) */ static double itrans_peaksearch_stat_image_sigma(gsl_matrix *m, double mean) { - double diff2=0; + int i,j; - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { + double diff2 = 0; + + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { diff2 += (gsl_matrix_get(m,i,j)-mean)*(gsl_matrix_get(m,i,j)-mean); } } + return sqrt(diff2/(m->size1 * m->size2)); + } /* * Filter all pixels with value < mean + k*sigma to 0 - * Set all matching pixels to 1 + * Set all matching pixels to 1 d */ static void itrans_peaksearch_stat_sigma_filter(gsl_matrix *m, double k) { + double mean,sigma; int i,j; + mean = itrans_peaksearch_stat_image_mean(m); sigma = itrans_peaksearch_stat_image_sigma(m,mean); - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { + + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { if (gsl_matrix_get(m,i,j) >= mean+k*sigma) { - gsl_matrix_set(m,i,j,1.); + gsl_matrix_set(m, i, j, 1.); } else { - gsl_matrix_set(m,i,j,0.); + gsl_matrix_set(m, i, j, 0.); } } } + } /* @@ -101,20 +111,25 @@ static void itrans_peaksearch_stat_sigma_filter(gsl_matrix *m, double k) { * TODO: Use a mask instead of calculating valid points */ static double itrans_peaksearch_stat_circle_mean(gsl_matrix *m, int x, int y, int r, gsl_matrix *mask) { - double mean=0.; - int i,j,n=0; - for (i=x-r;i<=x+r;i++) { - for (j=y-r;j<=y+r;j++) { + + double mean = 0.; + int i, j; + int n = 0; + + for ( i=x-r; i<=x+r; i++ ) { + for ( j=y-r; j<=y+r; j++ ) { //printf("cm: ij=(%d,%d) mask=(%d,%d)\n",i,j,i-x+r,j-y+r); - if (gsl_matrix_get(mask,i-x+r,j-y+r)>0.) { - mean += gsl_matrix_get(m,i,j); + if ( gsl_matrix_get(mask,i-x+r,j-y+r)>0. ) { + mean += gsl_matrix_get(m, i, j); //printf("cm: (%d,%d) mean=%lf val=%lf\n",i,j,mean,gsl_matrix_get(m,i,j)); n++; } } } + //printf("cm: (%d,%d) summean=%lf n=%d\n",x,y,mean,n); return mean/n; + } /* @@ -123,35 +138,44 @@ static double itrans_peaksearch_stat_circle_mean(gsl_matrix *m, int x, int y, in * TODO: Use a mask instead of calculating valid points */ static double itrans_peaksearch_stat_circle_sigma(gsl_matrix *m, int x, int y, int r, gsl_matrix *mask, double mean) { - double diff2=0.; - int i,j,n=0; - for (i=x-r;i<=x+r;i++) { - for (j=y-r;j<=y+r;j++) { - if (gsl_matrix_get(mask,i-x+r,j-y+r)>0) { + + double diff2 = 0.; + int i, j; + int n = 0; + + for ( i=x-r; i<=x+r; i++ ) { + for ( j=y-r; j<=y+r; j++ ) { + if ( gsl_matrix_get(mask, i-x+r, j-y+r) > 0 ) { diff2 += (gsl_matrix_get(m,i,j)-mean)*(gsl_matrix_get(m,i,j)-mean); n++; } } } + return sqrt(diff2/n); + } /* * Calculate a circular mask to save recalculating it every time */ static gsl_matrix *itrans_peaksearch_stat_circle_mask(int r) { + gsl_matrix *m; - m = gsl_matrix_calloc(2*r+1,2*r+1); int i,j; - for (i=0;i<2*r+1;i++) { - for (j=0;j<2*r+1;j++) { - if (sqrt((r-i)*(r-i)+(r-j)*(r-j))<=(double)r) { - gsl_matrix_set(m,i,j,1.); + + m = gsl_matrix_calloc(2*r+1, 2*r+1); + for ( i=0; i<2*r+1; i++ ) { + for ( j=0; j<2*r+1; j++ ) { + if ( sqrt((r-i)*(r-i)+(r-j)*(r-j)) <= r ) { + gsl_matrix_set(m, i, j, 1.); } } } + return m; + } /* @@ -174,51 +198,56 @@ static gsl_matrix *itrans_peaksearch_stat_circle_mask(int r) { * self-referencing problem being dealt with - output being written onto the array before the next point it computed * problem carried over from the OO version where a new object was created by each operation */ - static void itrans_peaksearch_stat_local_sigma_filter(gsl_matrix *m, int r, double k) { - //printf("lsf: starting\n"); + double mean,sigma; double local; - //printf("lsf: generating circle mask\n"); - gsl_matrix *mask = itrans_peaksearch_stat_circle_mask(r); + gsl_matrix *mask; gsl_matrix *new; - new = gsl_matrix_alloc(m->size1,m->size2); int i,j; - //int interval = (m->size1-r)/20; + //int interval; + + mask = itrans_peaksearch_stat_circle_mask(r); + new = gsl_matrix_alloc(m->size1, m->size2); + + //interval = (m->size1-r)/20; //printf("lsf: starting loop\n"); //printf("lsf: "); //for (i=r;i<m->size1-r;i++) { // for (j=r;j<m->size2-r;j++) { - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { - if ((i>=r && i<m->size1-r) && (j>=r && j<m->size2-r)) { + + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { + if ( ((i >= r) && (i < m->size1-r)) && ((j >= r) && (j < m->size2-r)) ) { + //printf("lsf: evaluating (%d,%d)\n",i,j); - mean = itrans_peaksearch_stat_circle_mean(m,i,j,r,mask); + mean = itrans_peaksearch_stat_circle_mean(m, i, j, r, mask); //printf("lsf: mean=%lf",mean); - sigma = itrans_peaksearch_stat_circle_sigma(m,i,j,r,mask,mean); + sigma = itrans_peaksearch_stat_circle_sigma(m, i, j, r, mask, mean); //printf(" sigma=%lf",sigma); - local = gsl_matrix_get(m,i,j); - local += gsl_matrix_get(m,i+1,j) + gsl_matrix_get(m,i-1,j) + gsl_matrix_get(m,i,j+1) + gsl_matrix_get(m,i,j-1); - local += .5*(gsl_matrix_get(m,i+1,j+1) + gsl_matrix_get(m,i-1,j+1) + gsl_matrix_get(m,i+1,j-1) + gsl_matrix_get(m,i-1,j-1)); + local = gsl_matrix_get(m, i, j); + local += gsl_matrix_get(m, i+1, j) + gsl_matrix_get(m, i-1, j) + gsl_matrix_get(m, i, j+1) + gsl_matrix_get(m, i, j-1); + local += .5*(gsl_matrix_get(m, i+1, j+1) + gsl_matrix_get(m, i-1, j+1) + gsl_matrix_get(m, i+1, j-1) + gsl_matrix_get(m, i-1, j-1)); local /= 7.; //printf(" local=%lf\n",local); - if (local > mean+k*sigma) { - gsl_matrix_set(new,i,j,1.); + if ( local > mean+k*sigma ) { + gsl_matrix_set(new, i, j, 1.); } else { - gsl_matrix_set(new,i,j,0.); + gsl_matrix_set(new, i, j, 0.); } + } else { - gsl_matrix_set(new,i,j,0.); + gsl_matrix_set(new, i, j, 0.); } } //if (i % interval == 0) printf("."); } + //printf("done\n"); - gsl_matrix_memcpy(m,new); + gsl_matrix_memcpy(m, new); gsl_matrix_free(new); -} - +} /* * Apply an arbitary kernel to the image - each point takes the value @@ -231,67 +260,80 @@ static void itrans_peaksearch_stat_local_sigma_filter(gsl_matrix *m, int r, doub * Also suffers from self-reference problem */ static void itrans_peaksearch_stat_apply_kernel(gsl_matrix *m, gsl_matrix *kernel) { - int size = kernel->size1; - int half = (size-1)/2; + + int size; + int half; gsl_matrix *l; gsl_matrix_view lv; gsl_matrix *new; - new = gsl_matrix_calloc(m->size1,m->size2); double val; - int i,j,x,y; - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { - if ((i>=half && i<m->size1-half) && (j>=half && j<m->size2-half)) { - lv = gsl_matrix_submatrix(m,i-half,j-half,size,size); + int i, j, x, y; + + size = kernel->size1; + half = (size-1)/2; + new = gsl_matrix_calloc(m->size1, m->size2); + + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { + if ( ((i >= half) && (i < m->size1-half)) && ((j >= half) && (j < m->size2-half)) ) { + + lv = gsl_matrix_submatrix(m, i-half, j-half, size, size); l = &lv.matrix; val = 0.; - for (x=0;x<size;x++) { - for (y=0;y<size;y++) { - val += gsl_matrix_get(l,x,y)*gsl_matrix_get(kernel,x,y); + for ( x=0; x<size; x++ ) { + for ( y=0; y<size; y++ ) { + val += gsl_matrix_get(l, x, y)*gsl_matrix_get(kernel, x, y); } } //gsl_matrix_free(l); gsl_matrix_set(new,i,j,val); + } } } + gsl_matrix_memcpy(m,new); gsl_matrix_free(new); + } -/* - * Generate the simplist possible kernel - a flat one - */ +/* Generate the simplist possible kernel - a flat one */ static gsl_matrix *itrans_peaksearch_stat_generate_flat_kernel(int half) { + gsl_matrix *k; + k = gsl_matrix_alloc(2*half+1,2*half+1); gsl_matrix_set_all(k,1./((2*half+1)*(2*half+1))); + return k; + } -/* - * expands or contracts a gsl_matrix by copying the columns to a new one - */ +/* Expands or contracts a gsl_matrix by copying the columns to a new one */ static gsl_matrix *itrans_peaksearch_stat_matrix_expand(gsl_matrix *m, int oldsize, int newsize) { + gsl_matrix *new; + int j; //printf("me: %d->%d\n",oldsize,newsize); - new = gsl_matrix_calloc(2,newsize); + new = gsl_matrix_calloc(2, newsize); //printf("me: calloc(2,%d)\n",newsize); - int j; - for (j = 0; j < oldsize; j++) { - if (j < newsize) { + for ( j=0; j<oldsize; j++) { + if ( j < newsize ) { //printf("me: copying col %d\n",j); - gsl_matrix_set(new,0,j,gsl_matrix_get(m,0,j)); - gsl_matrix_set(new,1,j,gsl_matrix_get(m,1,j)); + gsl_matrix_set(new, 0, j, gsl_matrix_get(m, 0, j)); + gsl_matrix_set(new, 1, j, gsl_matrix_get(m, 1, j)); } } + //printf("me: freeing old matrix\n"); gsl_matrix_free(m); + //printf("me: new s1=%d s2=%d\n",new->size1,new->size2); - return new; //printf("me: m s1=%d s2=%d\n",m->size1,m->size2); + return new; + } /* @@ -299,30 +341,34 @@ static gsl_matrix *itrans_peaksearch_stat_matrix_expand(gsl_matrix *m, int oldsi * have to return a pointer to com each time because if the matrix size has to be changed then we need to keep * track of the location of the resized instance */ - static gsl_matrix *itrans_peaksearch_stat_do_ff(int i, int j, int* mask, double threshold, gsl_matrix *m, gsl_matrix *com, int *com_n, int *com_size) { - if (i>=0 && i<m->size1) { - if (j>=0 && j<m->size2) { - if (mask[i+j*m->size1]==0) { - if (gsl_matrix_get(m,i,j)>threshold) { + + if ( (i >= 0) && (i < m->size1) ) { + if ( (j >= 0) && (j < m->size2) ) { + if ( mask[i+j*m->size1] == 0 ) { + if ( gsl_matrix_get(m, i, j) > threshold ) { + //printf("dff: found valid point (%d,%d)\n",i,j); - gsl_matrix_set(com,0,*com_n,(double)i); - gsl_matrix_set(com,1,*com_n,(double)j); - *com_n=*com_n+1; - if (*com_n == *com_size) { - com = itrans_peaksearch_stat_matrix_expand(com,*com_size,*com_size*2); + gsl_matrix_set(com, 0, *com_n, i); + gsl_matrix_set(com, 1, *com_n, j); + *com_n = *com_n + 1; + if ( *com_n == *com_size ) { + com = itrans_peaksearch_stat_matrix_expand(com, *com_size, *com_size*2); *com_size *= 2; } - mask[i+j*m->size1]=1; - com = itrans_peaksearch_stat_do_ff(i+1,j,mask,threshold,m,com,com_n,com_size); - com = itrans_peaksearch_stat_do_ff(i-1,j,mask,threshold,m,com,com_n,com_size); - com = itrans_peaksearch_stat_do_ff(i,j+1,mask,threshold,m,com,com_n,com_size); - com = itrans_peaksearch_stat_do_ff(i,j-1,mask,threshold,m,com,com_n,com_size); + mask[i+j*m->size1] = 1; + com = itrans_peaksearch_stat_do_ff(i+1, j, mask,threshold, m, com, com_n, com_size); + com = itrans_peaksearch_stat_do_ff(i-1, j, mask,threshold, m, com, com_n, com_size); + com = itrans_peaksearch_stat_do_ff(i, j+1, mask,threshold, m, com, com_n, com_size); + com = itrans_peaksearch_stat_do_ff(i, j-1, mask,threshold, m, com, com_n, com_size); + } } } } + return com; + } /* @@ -335,84 +381,90 @@ static gsl_matrix *itrans_peaksearch_stat_do_ff(int i, int j, int* mask, double * coordinates in row 1, which should be of the right length * Variable count is set to the number of points found */ - static gsl_matrix *itrans_peaksearch_stat_floodfill(gsl_matrix *m, double threshold, int *count) { - //printf("ff: starting\n"); + int *mask; - mask = calloc(m->size1*m->size2,sizeof(int)); - - int size=32,com_size; - int i,j,k,n=0; + int size, com_size, i, j, k, n; int com_n; gsl_matrix *p; gsl_matrix *com; - p = gsl_matrix_calloc(2,size); - - double com_x,com_y; + double com_x, com_y; + + mask = calloc(m->size1*m->size2, sizeof(int)); + size = 32; + n = 0; + p = gsl_matrix_calloc(2, size); + //printf("ff: starting loop\n"); - for (i=0;i<m->size1;i++) { - for (j=0;j<m->size2;j++) { - if (gsl_matrix_get(m,i,j)>threshold) { - if (mask[i+j*m->size1]==0) { + for ( i=0; i<m->size1; i++ ) { + for ( j=0; j<m->size2; j++ ) { + if ( gsl_matrix_get(m, i, j) > threshold ) { + if ( mask[i+j*m->size1] == 0 ) { + //printf("ff: found starting point (%d,%d)\n",i,j); - com_size=32; - com_n=0; + com_size = 32; + com_n = 0; com_x = com_y = 0.; - com = gsl_matrix_calloc(2,com_size); //this is going to hold the points found for this location + com = gsl_matrix_calloc(2, com_size); //this is going to hold the points found for this location //printf("ff: starting floodfill stack\n"); com = itrans_peaksearch_stat_do_ff(i, j, mask, threshold, m, com, &com_n, &com_size); //printf("ff: ended floodfill stack\n"); - for (k=0;k<com_n;k++) { - com_x += gsl_matrix_get(com,0,k); - com_y += gsl_matrix_get(com,1,k); + for ( k=0; k<com_n; k++ ) { + com_x += gsl_matrix_get(com, 0, k); + com_y += gsl_matrix_get(com, 1, k); } com_x /= com_n; com_y /= com_n; //printf("ff: point CoM (%lf,%lf)\n",com_x,com_y); - gsl_matrix_set(p,0,n,com_x); - gsl_matrix_set(p,1,n,com_y); + gsl_matrix_set(p, 0, n, com_x); + gsl_matrix_set(p, 1, n, com_y); n++; - if (n==size) { - p = itrans_peaksearch_stat_matrix_expand(p,size,size*2); + if ( n == size ) { + p = itrans_peaksearch_stat_matrix_expand(p, size, size*2); size *= 2; } + } } } } //printf("ff: ending loop, found %d\n",n); + *count = n; //printf("pcheck s1=%d s2=%d\n",p->size1,p->size2); - p = itrans_peaksearch_stat_matrix_expand(p,size,n); + p = itrans_peaksearch_stat_matrix_expand(p, size, n); //printf("pcheck s1=%d s2=%d\n",p->size1,p->size2); + return p; + } - - /* Implements the iteration based automatic method * returns a gsl_matrix formatted as described in flood-fill */ static gsl_matrix *itrans_peaksearch_stat_iterate(gsl_matrix *m, unsigned int *count) { - int old = m->size1*m->size2; + int old; int cur; double k; double mean,sigma; gsl_matrix *p; gsl_matrix *kernel; - printf("Iterate: starting\n"); + old = m->size1*m->size2; + + //printf("Iterate: starting\n"); //printf("Iterate: generating kernel\n"); kernel = itrans_peaksearch_stat_generate_flat_kernel(1); - printf("Iterate: performing local_sigma_filter\n"); - itrans_peaksearch_stat_local_sigma_filter(m,10,1.); + //printf("Iterate: performing local_sigma_filter\n"); + itrans_peaksearch_stat_local_sigma_filter(m, 10, 1.); //printf("Iterate: starting loop\n"); - while (1) { + while ( 1 ) { + //printf("Iterate: smoothing"); - itrans_peaksearch_stat_apply_kernel(m,kernel); + itrans_peaksearch_stat_apply_kernel(m, kernel); //printf(" (1)"); - itrans_peaksearch_stat_apply_kernel(m,kernel); + itrans_peaksearch_stat_apply_kernel(m, kernel); //printf(" (2)\n"); mean = itrans_peaksearch_stat_image_mean(m); sigma = itrans_peaksearch_stat_image_sigma(m,mean); @@ -421,15 +473,19 @@ static gsl_matrix *itrans_peaksearch_stat_iterate(gsl_matrix *m, unsigned int *c //printf("Iterate: applying sigma_filter(%lf)\n",k); itrans_peaksearch_stat_sigma_filter(m,k); //printf("Iterate: floodfilling\n"); - p = itrans_peaksearch_stat_floodfill(m,0,&cur); - printf("Iterate: %d points found\n",cur); - if (old < 1.05*cur) break; + p = itrans_peaksearch_stat_floodfill(m, 0, &cur); + //printf("Iterate: %d points found\n", cur); + if ( old < 1.05*cur ) break; old = cur; + } + gsl_matrix_free(kernel); - printf("Iterate: finished\n"); + //printf("Iterate: finished\n"); *count = cur; + return p; + } unsigned int itrans_peaksearch_stat(int16_t *image, ControlContext *ctx, double tilt_degrees, ImageDisplay *imagedisplay) { |