From 49dbdd4940aa78021f4ba516f4edb632058262bf Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Wed, 25 Jun 2014 09:44:48 +0000
Subject: [PATCH] Fixes bugs in creating IsakPrograms compatible image
---
src/cross-section.c | 127 ++++++++++++++++++++++++++++++++++++++----
1 files changed, 115 insertions(+), 12 deletions(-)
diff --git a/src/cross-section.c b/src/cross-section.c
index 1b0930e..d4da81c 100644
--- a/src/cross-section.c
+++ b/src/cross-section.c
@@ -1,7 +1,8 @@
#include<general.h>
#include<cross-section.h>
#include<coord.h>
-
+#include<cairo/cairo.h>
+#include<stdint.h>
/** @brief Calculates cross-section of vesicle with plane.
*
* Function returns points of cross-section of vesicle with plane. Plane is described with equation $ax+by+cz+d=0$. Algorithm extracts coordinates of each vertex of a vesicle and then:
@@ -12,12 +13,12 @@
ts_coord_list *get_crossection_with_plane(ts_vesicle *vesicle,ts_double a,ts_double b,ts_double c, ts_double d){
- ts_uint i, j;
+ ts_uint i, j,k,l;
ts_double pp,Dsq; // distance from the plane squared
- ts_double ppn; // distance from the plane squared of a neighbor
- ts_double u; //factor to scale vector from first vector to the second to get intersection
+ ts_double ppn1; // distance from the plane squared of a neighbor
ts_vertex *vtx;
-
+ ts_uint ntria=0; // number triangles
+ ts_triangle *tria[2]; // list of triangles
ts_coord_list *pts=init_coord_list();
for(i=0;i<vesicle->vlist->n;i++){
vtx=vesicle->vlist->vtx[i];
@@ -26,13 +27,26 @@
Dsq=pp*pp/(a*a+b*b+c*c);
if(Dsq<vesicle->dmax){
for(j=0;j<vtx->neigh_no;j++){
- ppn=vtx->neigh[j]->x*a+vtx->neigh[j]->y*b+vtx->neigh[j]->z*c+d;
- if(pp*ppn<0){ //the combination of vertices are good candidates for a crossection
- u=pp/(a*(vtx->x-vtx->neigh[j]->x)+b*(vtx->y-vtx->neigh[j]->y)+c*(vtx->z-vtx->neigh[j]->z));
- add_coord(pts, vtx->x+u*(vtx->neigh[j]->x - vtx->x),
- vtx->y+u*(vtx->neigh[j]->y - vtx->y),
- vtx->z+u*(vtx->neigh[j]->z - vtx->z),
- TS_COORD_CARTESIAN);
+ ppn1=vtx->neigh[j]->x*a+vtx->neigh[j]->y*b+vtx->neigh[j]->z*c+d;
+ if(pp*ppn1<=0.0){ //the combination of vertices are good candidates for a crossection
+ //find triangle that belongs to the two vertices
+ ntria=0;
+ for(k=0;k<vtx->tristar_no;k++){
+ if(vtx->tristar[k]->vertex[0]==vtx && ( vtx->tristar[k]->vertex[1]==vtx->neigh[j] || vtx->tristar[k]->vertex[2]==vtx->neigh[j]) ){
+ //triangle found.
+ tria[ntria]=vtx->tristar[k];
+ ntria++;
+ }
+ }
+ if(ntria==0) continue; // no need to continue
+ //find the two intersections (in general) to form a intersection line
+ for(l=0;l<ntria;l++){
+ //we add intersection line between two points for each of the triangles found above.
+ add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[0], tria[l]->vertex[1]);
+ add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[0], tria[l]->vertex[2]);
+ add_crosssection_point(pts,a,b,c,d,tria[l]->vertex[1], tria[l]->vertex[2]);
+
+ }
}
}
}
@@ -41,3 +55,92 @@
}
+
+ts_bool add_crosssection_point(ts_coord_list *pts, ts_double a, ts_double b, ts_double c, ts_double d, ts_vertex *vtx1, ts_vertex *vtx2){
+ ts_double pp=vtx1->x*a+vtx1->y*b+vtx1->z*c+d;
+ ts_double pp2=vtx2->x*a+vtx1->y*b+vtx2->z*c+d;
+ if(pp*pp2<=0.0){
+ ts_double u=pp/(a*(vtx1->x-vtx2->x)+b*(vtx1->y-vtx2->y)+c*(vtx1->z-vtx2->z));
+ add_coord(pts, vtx1->x+u*(vtx2->x - vtx1->x),
+ vtx1->y+u*(vtx2->y - vtx1->y),
+ vtx1->z+u*(vtx2->z - vtx1->z),
+ TS_COORD_CARTESIAN);
+
+ return TS_SUCCESS;
+ } else {
+ return TS_FAIL;
+ }
+}
+
+/** Saves calculated crossection as a png image */
+ts_bool crossection_to_png(ts_coord_list *pts, char *filename){
+
+ cairo_surface_t *surface;
+ cairo_t *cr;
+ ts_uint i;
+ surface = cairo_image_surface_create (CAIRO_FORMAT_ARGB32, 768, 576);
+ cr = cairo_create (surface);
+ cairo_rectangle(cr, 0.0, 0.0, 768,576);
+ cairo_set_source_rgb(cr, 1.0, 1.0, 1.0);
+ cairo_fill(cr);
+ cairo_set_line_width (cr, 2.0/8.0);
+ cairo_set_line_cap(cr, CAIRO_LINE_CAP_ROUND);
+ cairo_set_line_join(cr, CAIRO_LINE_JOIN_ROUND);
+ cairo_translate(cr, 380,250);
+ cairo_scale (cr, 8.0, 8.0);
+ cairo_set_source_rgb (cr, 0.3, 0.3, 0.3);
+
+ for(i=0;i<pts->n;i+=2){
+ cairo_move_to(cr, pts->coord[i]->e1, pts->coord[i]->e2);
+ cairo_line_to(cr, pts->coord[i+1]->e1, pts->coord[i+1]->e2);
+ }
+ cairo_stroke(cr);
+ cairo_surface_write_to_png (surface,filename);
+ append_to_isak_program_raw(surface,"experimental.img");
+ cairo_surface_finish (surface);
+ return TS_SUCCESS;
+}
+
+
+ts_bool save_crossection_snapshot(ts_coord_list *pts, ts_uint timestepno){
+ char filename[255];
+ sprintf(filename,"timestep_%.6u.png",timestepno);
+ crossection_to_png(pts,filename);
+ return TS_SUCCESS;
+}
+
+ts_bool append_to_isak_program_raw(cairo_surface_t *surface, char *filename){
+
+ unsigned char *d=cairo_image_surface_get_data(surface);
+ int w=cairo_image_surface_get_width(surface);
+ int h=cairo_image_surface_get_height(surface);
+ int s=cairo_image_surface_get_stride(surface);
+ int i,j;
+ FILE *fd=fopen(filename, "a+");
+
+ uint32_t *pixelptr;
+ uint32_t my_pixel;
+ uint8_t pixel_channel;
+// red = (pixel[8] >> 16) & 0xFF;
+
+
+
+ fwrite (&w,sizeof(uint32_t),1,fd);
+ fwrite (&h,sizeof(uint32_t),1,fd);
+ fwrite (&w,sizeof(uint32_t),1,fd);//time!
+ for(i=0;i<h;i++){
+ for(j=0;j<w;j++){
+ pixelptr=(uint32_t *)(d + i * s);
+ my_pixel = pixelptr[j];
+ pixel_channel=(my_pixel>>16)&0xFF;
+ fwrite(&pixel_channel,sizeof(uint8_t), 1,fd);
+ }
+ }
+ fclose(fd);
+ return TS_SUCCESS;
+}
+
+/*ts_bool init_isak_program_raw_output_file(ts_uint w, ts_uint h, char *filename){
+
+
+}*/
--
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