Newer
Older
#include <iostream>
#include <fstream>
#include <map>
#include <i3d/draw.h>
#include <i3d/morphology.h>
#include <i3d/DistanceTransform.h>
#include <i3d/filters.h>
#include "../cmath3d_v/TriangleMesh_v.h"
#include "../src/rnd_generators.h"
#include "../src/texture/texture.h"
#undef min
#undef max
Vladimír Ulman
committed
//some debug-code enabling triggers
//#define SAVE_INTERMEDIATE_IMAGES
Vladimír Ulman
committed
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
//'multiple' should be ideally 10^desired_decimal_accuracy
int inline RoundTo(const float val, const float multiple=1000.f)
{
return ( int(floorf(val*multiple)) );
}
//puts v1 into Pos, with mPos being a helper structure preventing having
//v1 multiple times inside the Pos
long unsigned int Enlist(
const Vector3FC& v1,
std::vector<Vector3FC>& Pos,
std::map< int,std::map< int,std::map< int,long unsigned int > > >& mPos)
{
long unsigned int o1; //ret val
std::map< int,std::map< int,long unsigned int > >& mY=mPos[RoundTo(v1.x)];
if (mY.empty())
{
Pos.push_back(v1);
o1=Pos.size();
//add reference to this vertex in the mPos structure
std::map< int,long unsigned int > mZ;
mZ[RoundTo(v1.z)]=o1;
std::map< int,std::map< int,long unsigned int > > my;
my[RoundTo(v1.y)]=mZ;
mPos[RoundTo(v1.x)]=my;
}
else
{
std::map< int,long unsigned int >& mZ=mY[RoundTo(v1.y)];
if (mZ.empty())
{
Pos.push_back(v1);
o1=Pos.size();
//add reference to this vertex in the mPos structure
std::map< int,long unsigned int > mZ;
mZ[RoundTo(v1.z)]=o1;
mY[RoundTo(v1.y)]=mZ;
}
else
{
if (mZ[RoundTo(v1.z)] == 0)
{
Pos.push_back(v1);
o1=Pos.size();
//add reference to this vertex in the mPos structure
mZ[RoundTo(v1.z)]=o1;
}
else
{
o1=mZ[RoundTo(v1.z)];
}
}
}
return o1;
}
int ActiveMesh::ImportSTL(const char *filename)
{
Pos.clear();
ID.clear();
norm.clear();
//a helper map to (efficiently) search for already stored vertices inside Pos
std::map< int,std::map< int,std::map< int,long unsigned int > > > mPos;
// x y z offset+1 in Pos
//try to open the file
std::ifstream file(filename);
if (!file.is_open()) return 1;
//read the "header" line
char tmp[1024];
file >> tmp; //dangerous...
//check tmp for "solid" or complain
if (tmp[0] != 's'
|| tmp[1] != 'o'
|| tmp[2] != 'l'
|| tmp[3] != 'i'
|| tmp[4] != 'd') { file.close(); return(2); }
//read (and skip) the rest of the header line
file.ignore(10240,'\n');
//read facet by facet
while (file >> tmp)
{
//check tmp for "facet" or "endsolid" or complain
if (tmp[0] != 'f'
|| tmp[1] != 'a'
|| tmp[2] != 'c'
|| tmp[3] != 'e'
|| tmp[4] != 't')
{
//no new face starting, end of file then?
if (tmp[0] != 'e'
|| tmp[1] != 'n'
|| tmp[2] != 'd'
|| tmp[3] != 's'
|| tmp[4] != 'o') { file.close(); return(3); }
else break;
}
//read normal
file >> tmp; //"normal" keyword
float x,y,z;
file >> x >> y >> z;
Vector3F normal(x,y,z);
//read triangle vertices
file >> tmp;
//check tmp for "outer" or complain
if (tmp[0] != 'o'
|| tmp[1] != 'u'
|| tmp[2] != 't'
|| tmp[3] != 'e'
|| tmp[4] != 'r') { file.close(); return(4); }
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
file >> tmp; //"loop" keyword
file >> tmp; //"vertex" keyword
file >> x >> y >> z;
Vector3FC v1(x,y,z);
file >> tmp;
file >> x >> y >> z;
Vector3FC v2(x,y,z);
file >> tmp;
file >> x >> y >> z;
Vector3FC v3(x,y,z);
file >> tmp; //"endloop" keyword
file >> tmp; //"endfacet" keyword
//add this triangle to the ActiveMesh data structures
//we need to:
// scale, round and use this for comparison against already
// discovered vertices to avoid for having the same vertex saved twice
long unsigned int o1,o2,o3;
o1=Enlist(v1,Pos,mPos);
o2=Enlist(v2,Pos,mPos);
o3=Enlist(v3,Pos,mPos);
//
// three offsets to the Pos array should be output
// add them to the ID array
ID.push_back(o1-1);
ID.push_back(o2-1);
ID.push_back(o3-1);
// add normal to the norm array
norm.push_back(normal);
/*
std::cout << "v1: " << v1.x << "," << v1.y << "," << v1.z << " -- o1=" << o1 << "\n";
std::cout << "v2: " << v2.x << "," << v2.y << "," << v2.z << " -- o2=" << o2 << "\n";
std::cout << "v3: " << v3.x << "," << v3.y << "," << v3.z << " -- o3=" << o3 << "\n";
std::cout << "normal: " << normal.x << "," << normal.y << "," << normal.z << "\n\n";
*/
}
file.close();
return(0);
}
int ActiveMesh::ExportSTL(const char *filename)
{
//try to open the file
std::ofstream file(filename);
if (!file.is_open()) return(1);
file << "solid Vladimir Ulman - meshSurface testing app\n";
for (unsigned int i=0; i < ID.size(); i+=3)
{
file << "facet normal " << norm[i/3].x << " " << norm[i/3].y << " " << norm[i/3].z << "\n";
file << "outer loop\n";
file << "vertex " << Pos[ID[i+0]].x << " " << Pos[ID[i+0]].y << " " << Pos[ID[i+0]].z << "\n";
file << "vertex " << Pos[ID[i+1]].x << " " << Pos[ID[i+1]].y << " " << Pos[ID[i+1]].z << "\n";
file << "vertex " << Pos[ID[i+2]].x << " " << Pos[ID[i+2]].y << " " << Pos[ID[i+2]].z << "\n";
file << "endloop\nendfacet\n";
}
file.close();
return(0);
}
int ActiveMesh::ImportVTK(const char *filename) //surface version
{
Pos.clear();
ID.clear();
norm.clear();
//try to open the file
std::ifstream file(filename);
if (!file.is_open()) return 1;
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
//read the "header" line
char tmp[1024];
file >> tmp >> tmp; //dangerous...
//check tmp for "vtk" or complain
if (tmp[0] != 'v'
|| tmp[1] != 't'
|| tmp[2] != 'k') { file.close(); return(2); }
//read (and skip) the rest of the header line
file.ignore(10240,'\n');
//ignore "vtk output"
file.ignore(10240,'\n');
//read "ASCII"
file >> tmp;
if (tmp[0] != 'A'
|| tmp[1] != 'S'
|| tmp[2] != 'C'
|| tmp[3] != 'I'
|| tmp[4] != 'I') { file.close(); return(3); }
file.ignore(10240,'\n');
//ignore "DATASET POLYDATA"
file.ignore(10240,'\n');
//read points header
int itemCount;
file >> tmp >> itemCount;;
if (tmp[0] != 'P'
|| tmp[1] != 'O'
|| tmp[2] != 'I'
|| tmp[3] != 'N'
|| tmp[4] != 'T'
|| tmp[5] != 'S') { file.close(); return(4); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " point coordinates\n";
Pos.reserve(itemCount);
//read all points...
float x,y,z;
while (itemCount > 0 && file >> x)
{
file >> y >> z;
//... and save them
Vector3FC v1(x,y,z);
v1*=100.f;
Pos.push_back(v1);
--itemCount;
}
std::cout << "last coordinate was: " << x << "," << y << "," << z << "\n";
//prepare "information about faces normals"
Vector3F fictiveNormal(1.f,0.f,0.f);
//read polyhedra header
file >> tmp >> itemCount;
if (tmp[0] != 'P'
|| tmp[1] != 'O'
|| tmp[2] != 'L'
|| tmp[3] != 'Y'
|| tmp[4] != 'G'
|| tmp[5] != 'O'
|| tmp[6] != 'N'
|| tmp[7] != 'S') { file.close(); return(5); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " triangles\n";
ID.reserve(3*itemCount);
norm.reserve(itemCount);
//read all polyhedra vertices
int ignore,v1,v2,v3;
while (itemCount > 0 && file >> ignore && ignore == 3)
{
file >> v1 >> v2 >> v3;
//save v1,v2,v3 (TODO: if not already saved...)
//make triangles use CW winding order
ID.push_back(v1);
ID.push_back(v3);
ID.push_back(v2);
norm.push_back(fictiveNormal);
--itemCount;
}
std::cout << "last triangle was: " << v1 << "," << v2 << "," << v3 << "\n";
file.close();
return(0);
}
int ActiveMesh::ImportVTK_Volumetric(const char *filename,bool saveAlsoTetrahedra)
{
Pos.clear();
ID.clear();
norm.clear();
if (saveAlsoTetrahedra) VolID.clear();
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
//try to open the file
std::ifstream file(filename);
if (!file.is_open()) return 1;
//read the "header" line
char tmp[1024];
file >> tmp >> tmp; //dangerous...
//check tmp for "vtk" or complain
if (tmp[0] != 'v'
|| tmp[1] != 't'
|| tmp[2] != 'k') { file.close(); return(2); }
//read (and skip) the rest of the header line
file.ignore(10240,'\n');
//ignore "vtk output"
file.ignore(10240,'\n');
//read "ASCII"
file >> tmp;
if (tmp[0] != 'A'
|| tmp[1] != 'S'
|| tmp[2] != 'C'
|| tmp[3] != 'I'
|| tmp[4] != 'I') { file.close(); return(3); }
file.ignore(10240,'\n');
//ignore "DATASET UNSTRUCTURED GRID"
file.ignore(10240,'\n');
//read points header
int itemCount;
file >> tmp >> itemCount;;
if (tmp[0] != 'P'
|| tmp[1] != 'O'
|| tmp[2] != 'I'
|| tmp[3] != 'N'
|| tmp[4] != 'T'
|| tmp[5] != 'S') { file.close(); return(4); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " point coordinates\n";
Pos.reserve(itemCount);
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
//read all points...
float x,y,z;
while (itemCount > 0 && file >> x)
{
file >> y >> z;
//... and save them
Vector3FC v1(x,y,z);
v1*=100.f;
Pos.push_back(v1);
--itemCount;
}
std::cout << "last coordinate was: " << x << "," << y << "," << z << "\n";
//prepare "information about faces normals"
Vector3F fictiveNormal(1.f,0.f,0.f);
//read polyhedra header
file >> tmp >> itemCount;
if (tmp[0] != 'C'
|| tmp[1] != 'E'
|| tmp[2] != 'L'
|| tmp[3] != 'L'
|| tmp[4] != 'S') { file.close(); return(5); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " polyhedra\n";
ID.reserve(3*itemCount);
norm.reserve(itemCount);
//read all polyhedra vertices
int ignore,v1,v2,v3,v4;
while (itemCount > 0 && file >> ignore && ignore == 4)
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
{
file >> v1 >> v2 >> v3 >> v4;
//save v1,v2,v3 (TODO: if not already saved...)
ID.push_back(v1);
ID.push_back(v2);
ID.push_back(v3);
norm.push_back(fictiveNormal);
//save v1,v2,v4 (TODO: if not already saved...)
ID.push_back(v1);
ID.push_back(v2);
ID.push_back(v4);
norm.push_back(fictiveNormal);
//save v1,v4,v3 (TODO: if not already saved...)
ID.push_back(v1);
ID.push_back(v4);
ID.push_back(v3);
norm.push_back(fictiveNormal);
//save v4,v2,v3 (TODO: if not already saved...)
ID.push_back(v4);
ID.push_back(v2);
ID.push_back(v3);
norm.push_back(fictiveNormal);
if (saveAlsoTetrahedra)
{
VolID.push_back(v1);
VolID.push_back(v2);
VolID.push_back(v3);
VolID.push_back(v4);
}
--itemCount;
}
std::cout << "last polyhedron was: " << v1 << "," << v2 << "," << v3 << "," << v4 << "\n";
file.close();
return(0);
}
int ActiveMesh::ImportVTK_Ftree(const char *filename,bool resetMesh)
{
const int PointsOnRadiusPeriphery=10;
const float radiusCorrection=0.1f;
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
if (resetMesh)
{
Pos.clear();
ID.clear();
norm.clear();
}
//local/temporary list of vertices of segments that make up the f-tree
//later, we convert these to triangles and save these guys instead
fPoints.clear();
segFromPoint.clear();
segToPoint.clear();
segFromRadius.clear();
//try to open the file
std::ifstream file(filename);
if (!file.is_open()) return 1;
//read the "header" line
char tmp[1024];
file >> tmp >> tmp; //dangerous...
//check tmp for "vtk" or complain
if (tmp[0] != 'v'
|| tmp[1] != 't'
|| tmp[2] != 'k') { file.close(); return(2); }
//read (and skip) the rest of the header line
file.ignore(10240,'\n');
//ignore "vtk output"
file.ignore(10240,'\n');
//read "ASCII"
file >> tmp;
if (tmp[0] != 'A'
|| tmp[1] != 'S'
|| tmp[2] != 'C'
|| tmp[3] != 'I'
|| tmp[4] != 'I') { file.close(); return(3); }
file.ignore(10240,'\n');
//ignore "DATASET UNSTRUCTURED GRID"
file.ignore(10240,'\n');
//read points header
int itemCount;
file >> tmp >> itemCount;;
if (tmp[0] != 'P'
|| tmp[1] != 'O'
|| tmp[2] != 'I'
|| tmp[3] != 'N'
|| tmp[4] != 'T'
|| tmp[5] != 'S') { file.close(); return(4); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " point coordinates\n";
fPoints.reserve(itemCount);
//read all points...
float x,y,z;
while (itemCount > 0 && file >> x)
{
file >> y >> z;
//... and save them
Vector3FC v1(x,y,z);
v1*=100.f;
fPoints.push_back(v1);
--itemCount;
}
std::cout << "last coordinate was: " << x << "," << y << "," << z << "\n";
//read segments header
file >> tmp >> itemCount;
if (tmp[0] != 'C'
|| tmp[1] != 'E'
|| tmp[2] != 'L'
|| tmp[3] != 'L'
|| tmp[4] != 'S') { file.close(); return(5); }
file.ignore(10240,'\n');
std::cout << "reading " << itemCount << " segments\n";
segFromPoint.reserve(itemCount);
segToPoint.reserve(itemCount);
segFromRadius.reserve(itemCount);
//read all segments vertices
int ignore,v1,v2;
while (itemCount > 0 && file >> ignore && ignore == 2)
{
file >> v1 >> v2;
segFromPoint.push_back(v1);
segToPoint.push_back(v2);
--itemCount;
}
std::cout << "last segment was: " << v1 << "," << v2 << "\n";
//"ignore" cell types header, body
file >> tmp >> itemCount;
if (tmp[0] != 'C'
|| tmp[1] != 'E'
|| tmp[2] != 'L'
|| tmp[3] != 'L'
|| tmp[4] != '_'
|| tmp[5] != 'T'
|| tmp[6] != 'Y') { file.close(); return(6); }
file.ignore(10240,'\n');
while (itemCount > 0)
{
file.ignore(10240,'\n');
--itemCount;
}
//read radii, i.e. CELL_DATA header
file >> tmp >> itemCount;
if (tmp[0] != 'C'
|| tmp[1] != 'E'
|| tmp[2] != 'L'
|| tmp[3] != 'L'
|| tmp[4] != '_'
|| tmp[5] != 'D'
|| tmp[6] != 'A') { file.close(); return(7); }
file.ignore(10240,'\n');
file.ignore(10240,'\n'); //ignore SCALARS..
file.ignore(10240,'\n'); //ignore LOOKUP_TABLE
//read the radii
v1=0;
while (itemCount > 0 && file >> x)
{
segFromRadius.push_back(x*radiusCorrection);
--itemCount;
++v1;
}
file.close();
//now widen segments and save triangles...
//prepare "information about faces normals"
Vector3F fictiveNormal(1.f,0.f,0.f);
size_t firstRadiusPoint=Pos.size();
PointsFirstOffset=firstRadiusPoint;
//for all bending points except the last one (tip)
for (unsigned int i=0; i < segFromPoint.size(); ++i)
{
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
//we need to construct rotation matrix that would
//rotate points on a circle which lays in the XZ plane
//(Y axis is normal to it then) such that the points
//would lay in the plane to which this new Y axis
//would be normal
//
//new Y axis
Vector3F nYaxis=fPoints[segToPoint[i]];
if (i == 0) nYaxis-=fPoints[segFromPoint[i]];
else
{
nYaxis-=fPoints[segFromPoint[i-1]];
nYaxis/=2.f; //unnecessary scaling
}
Vector3F nZaxis(0.f,1.f,0.f); //in fact it is original Yaxis _for now_
Vector3F nXaxis;
//new X axis is perpendicular to the original and new Y axis
Mul(nYaxis,nZaxis,nXaxis);
//new Z axis is perpendicular to the new X and Y axes
Mul(nYaxis,nXaxis,nZaxis);
//normalize...
nXaxis/=nXaxis.Len();
nZaxis/=nZaxis.Len();
//now render the points on the circle and project them into the scene
for (int p=0; p < PointsOnRadiusPeriphery; ++p)
{
//the point in its original position
float x=segFromRadius[i]*cosf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
float z=segFromRadius[i]*sinf(6.28f*float(p)/float(PointsOnRadiusPeriphery));
//rotate
Vector3FC V(x*nXaxis);
V+=z*nZaxis;
//shift to the centre and save
V+=fPoints[segFromPoint[i]];
Pos.push_back(V);
}
}
//finally, add the tip point
Pos.push_back(fPoints[segToPoint.back()]);
//now create triangles for all segment strips
//except the last one (that leads to the tip)
for (unsigned int i=1; i < segFromPoint.size(); ++i)
{
int p=0;
for (; p < PointsOnRadiusPeriphery-1; ++p)
{
ID.push_back(firstRadiusPoint+p);
ID.push_back(firstRadiusPoint+p+1);
ID.push_back(firstRadiusPoint+p+PointsOnRadiusPeriphery);
norm.push_back(fictiveNormal);
ID.push_back(firstRadiusPoint+p+PointsOnRadiusPeriphery+1);
ID.push_back(firstRadiusPoint+p+PointsOnRadiusPeriphery);
ID.push_back(firstRadiusPoint+p+1);
norm.push_back(fictiveNormal);
}
ID.push_back(firstRadiusPoint+p);
ID.push_back(firstRadiusPoint);
ID.push_back(firstRadiusPoint+p+PointsOnRadiusPeriphery);
norm.push_back(fictiveNormal);
ID.push_back(firstRadiusPoint +PointsOnRadiusPeriphery);
ID.push_back(firstRadiusPoint+p+PointsOnRadiusPeriphery);
ID.push_back(firstRadiusPoint);
norm.push_back(fictiveNormal);
firstRadiusPoint+=PointsOnRadiusPeriphery;
}
//the last segment...
int p=0;
for (; p < PointsOnRadiusPeriphery-1; ++p)
{
ID.push_back(firstRadiusPoint+p);
ID.push_back(firstRadiusPoint+p+1);
ID.push_back(firstRadiusPoint+PointsOnRadiusPeriphery);
norm.push_back(fictiveNormal);
}
ID.push_back(firstRadiusPoint+p);
ID.push_back(firstRadiusPoint);
ID.push_back(firstRadiusPoint+PointsOnRadiusPeriphery);
norm.push_back(fictiveNormal);
void ActiveMesh::RenderMask(i3d::Image3d<i3d::GRAY16>& mask,const bool showTriangles)
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
{
//time savers: resolution
const float xRes=mask.GetResolution().GetX();
const float yRes=mask.GetResolution().GetY();
const float zRes=mask.GetResolution().GetZ();
//time savers: offset
const float xOff=mask.GetOffset().x;
const float yOff=mask.GetOffset().y;
const float zOff=mask.GetOffset().z;
//over all triangles
for (unsigned int i=0; i < ID.size()/3; ++i)
//for (unsigned int i=0; i < 15; ++i)
{
const Vector3F& v1=Pos[ID[3*i+0]];
const Vector3F& v2=Pos[ID[3*i+1]];
const Vector3F& v3=Pos[ID[3*i+2]];
//sweeping (and rendering) the triangle
for (float c=0.f; c <= 1.0f; c += 0.1f)
for (float b=0.f; b <= (1.0f-c); b += 0.1f)
{
float a=1.0f -b -c;
Vector3F v=a*v1;
v+=b*v2;
v+=c*v3;
//std::cout << "ID #" << i << ": v=(" << v.x << "," << v.y << "," << v.z << ")\n";
//nearest neighbor pixel coordinate
const int x=(int)roundf( (v.x-xOff) *xRes);
const int y=(int)roundf( (v.y-yOff) *yRes);
const int z=(int)roundf( (v.z-zOff) *zRes);
short val=(showTriangles)? short(i%5 *30 +100) : 100;
if (mask.Include(x,y,z)) mask.SetVoxel(x,y,z,val);
}
}
//this floods cell exterior from the image corner
i3d::Image3d<i3d::GRAY16> tmpMask(mask);
i3d::Dilation(tmpMask,mask,i3d::nb3D_o18);
i3d::FloodFill(mask,(i3d::GRAY16)50,0);
//this removes the flooding while filling
//everything else (and closing holes in this was)
i3d::GRAY16* p=mask.GetFirstVoxelAddr();
i3d::GRAY16* const pL=p+mask.GetImageSize();
while (p != pL)
{
*p=(*p != 50)? std::max(*p,i3d::GRAY16(100)) : 0;
++p;
}
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
}
void ActiveMesh::RenderMaskB(i3d::Image3d<i3d::GRAY16>& mask)
{
//time savers: resolution
const float xRes=mask.GetResolution().GetX();
const float yRes=mask.GetResolution().GetY();
const float zRes=mask.GetResolution().GetZ();
//time savers: offset
const float xOff=mask.GetOffset().x;
const float yOff=mask.GetOffset().y;
const float zOff=mask.GetOffset().z;
//over all triangles
//for (unsigned int i=0; i < ID.size()/3; ++i)
for (unsigned int i=0; i < 15; ++i)
{
const Vector3F& v1=Pos[ID[3*i+0]];
const Vector3F& v2=Pos[ID[3*i+1]];
const Vector3F& v3=Pos[ID[3*i+2]];
//Vector3F e12=v2-v1; //ID=0
//Vector3F e13=v3-v1; //ID=1
//Vector3F e23=v3-v2; //ID=2
Vector3F edges[3]={v2-v1,v3-v1,v3-v2};
short order[3]={0,1,2};
if (edges[1].LenQ() < edges[0].LenQ()) { order[0]=1; order[1]=0; }
if (edges[2].LenQ() < edges[order[1]].LenQ())
{
order[2]=order[1];
order[1]=2;
if (edges[2].LenQ() < edges[order[0]].LenQ())
{
order[1]=order[0];
order[0]=2;
}
}
//point within a triangle will of the form: vv + b*vb + c*vc
//vb is the shortest edge, vc is the longest edge
//vv is their common vertex
//vb,vc are oriented outward from this vertex
Vector3F vv,vb,vc;
if (order[0]==0 && order[2]==1)
{
//order[0] "points" at shortest edge
vv=v1;
vb=edges[0];
vc=edges[1];
}
else
if (order[0]==0 && order[2]==2)
{
vv=v2;
vb=-edges[0];
vc=edges[2];
}
else
if (order[0]==1 && order[2]==0)
{
vv=v1;
vb=edges[1];
vc=edges[0];
}
else
if (order[0]==1 && order[2]==2)
{
vv=v3;
vb=-edges[1];
vc=-edges[2];
}
else
if (order[0]==2 && order[2]==0)
{
vv=v2;
vb=edges[2];
vc=-edges[0];
}
else
if (order[0]==2 && order[2]==1)
{
vv=v3;
vb=-edges[2];
vc=-edges[1];
}
//optimal increment for the short and long edge, respectively
float db=(vb.x*xRes > vb.y*yRes)? vb.x*xRes : vb.y*yRes;
db=(vb.z*zRes > db)? vb.z*zRes : db;
db=1.f/db;
float dc=(vc.x*xRes > vc.y*yRes)? vc.x*xRes : vc.y*yRes;
dc=(vc.z*zRes > dc)? vc.z*zRes : dc;
dc=1.f/dc;
std::cout << "\nID #" << i << ": v1=(" << v1.x << "," << v1.y << "," << v1.z << ")\n";
std::cout << "ID #" << i << ": v2=(" << v2.x << "," << v2.y << "," << v2.z << ")\n";
std::cout << "ID #" << i << ": v3=(" << v3.x << "," << v3.y << "," << v3.z << ")\n";
//sweeping (and rendering) the triangle
for (float c=0.f; c <= 1.0f; c += dc)
for (float b=0.f; b <= (1.0f-c); b += db)
{
Vector3F v=vv;
v+=b*vb;
v+=c*vc;
std::cout << "ID #" << i << ": v=(" << v.x << "," << v.y << "," << v.z << ")\n";
//nearest neighbor pixel coordinate
const int x=(int)roundf( (v.x-xOff) *xRes);
const int y=(int)roundf( (v.y-yOff) *yRes);
const int z=(int)roundf( (v.z-zOff) *zRes);
if (mask.Include(x,y,z)) mask.SetVoxel(x,y,z,short(i));
}
}
}
void ActiveMesh::RenderOneTimeTexture(const i3d::Image3d<i3d::GRAY16>& mask,
i3d::Image3d<i3d::GRAY16>& texture)
{
i3d::Image3d<float> dt;
i3d::GrayToFloat(mask,dt);
#ifdef SAVE_INTERMEDIATE_IMAGES
i3d::Image3d<float> perlinInner,perlinOutside;
perlinInner.CopyMetaData(mask);
DoPerlin3D(perlinInner,5.0,0.8*1.5,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinInner.SaveImage("2_PerlinAlone_Inner.ics");
perlinOutside.CopyMetaData(mask);
DoPerlin3D(perlinOutside,2.,0.8*1.5,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinOutside.SaveImage("2_PerlinAlone_Outside.ics");
i3d::Image3d<i3d::GRAY16> erroded;
i3d::ErosionO(mask,erroded,1);
//initial object intensity levels
float* p=dt.GetFirstVoxelAddr();
float* const pL=p+dt.GetImageSize();
const float* pI=perlinInner.GetFirstVoxelAddr();
const float* pO=perlinOutside.GetFirstVoxelAddr();
const i3d::GRAY16* er=erroded.GetFirstVoxelAddr();
//are we within the mask?
if (*p > 0.f)
if (*p < 0.3f || *er == 0) *p=2000.f + 5000.f*(*pO); //corona
else *p=500.f + 600.f*(*pI); //inside
if (*er == 0) *p=2000.f; //std::max(*p,2000.f); //corona
if (*p < 0.f) *p=0.f;
#ifdef SAVE_INTERMEDIATE_IMAGES
perlinInner.DisposeData();
perlinOutside.DisposeData();
erroded.DisposeData();
i3d::GaussIIR(dt,2.f,2.f,2.0f);
#ifdef SAVE_INTERMEDIATE_IMAGES
dt.SaveImage("4_texture_filtered.ics");
//downsample now:
float factor[3]={1.f,1.f,0.125f};
i3d::Image3d<float>* tmp=NULL;
i3d::lanczos_resample(&dt,tmp,factor,2);
#ifdef SAVE_INTERMEDIATE_IMAGES
tmp->SaveImage("5_texture_filtered_resampled.ics");
#endif
for (int z=0; z < (signed)dt.GetSizeZ(); ++z)
for (int y=0; y < (signed)dt.GetSizeY(); ++y)
for (int x=0; x < (signed)dt.GetSizeX(); ++x, ++p)
//background signal:
float distSq=((float)x-110.f)*((float)x-110.f) + ((float)y-110.f)*((float)y-110.f);
*p+=100.f*expf(-0.5f * distSq / 900.f);
//uncertainty in the number of incoming photons
const float noiseMean = sqrtf(*p), // from statistics: shot noise = sqrt(signal)
noiseVar = noiseMean; // for Poisson distribution E(X) = D(X)
*p+=30.f*((float)GetRandomPoisson(noiseMean) - noiseVar);
//constants are parameters of Andor iXon camera provided from vendor:
//photon shot noise: dark current
*p+=(float)GetRandomPoisson(0.06f);
//read-out noise:
// variance up to 25.f (old camera on ILBIT)
// variance about 1.f (for the new camera on ILBIT)
*p+=GetRandomGauss(480.f,20.f);
//*p+=530.f;
#ifdef SAVE_INTERMEDIATE_IMAGES
dt.SaveImage("6_texture_filtered_resampled_finalized.ics");
#endif
i3d::FloatToGrayNoWeight(dt,texture);
}
void ActiveMesh::CenterMesh(const Vector3F& newCentre)
{
//calc geom. centre
double x=0.,y=0.,z=0.;
for (unsigned int i=0; i < Pos.size(); ++i)
{
x+=Pos[i].x;
y+=Pos[i].y;
z+=Pos[i].z;
}
x/=double(Pos.size());
y/=double(Pos.size());
z/=double(Pos.size());
//std::cout << "mesh centre is: " << x << "," << y << "," << z << "\n";
x-=newCentre.x;
y-=newCentre.y;
z-=newCentre.z;
//shift the centre to point (0,0,0)
for (unsigned int i=0; i < Pos.size(); ++i)
{
Pos[i].x-=float(x);
Pos[i].y-=float(y);
Pos[i].z-=float(z);
}
for (unsigned int i=0; i < fPoints.size(); ++i)
{
fPoints[i].x-=float(x);
fPoints[i].y-=float(y);
fPoints[i].z-=float(z);
}
}
void ActiveMesh::ScaleMesh(const Vector3F& scale)
{
for (unsigned int i=0; i < Pos.size(); ++i)
{
Pos[i].x*=scale.x;
Pos[i].y*=scale.y;
Pos[i].z*=scale.z;
}
}
void ActiveMesh::TranslateMesh(const Vector3F& shift)
{
for (unsigned int i=0; i < Pos.size(); ++i)
{
Pos[i].x+=shift.x;
Pos[i].y+=shift.y;
Pos[i].z+=shift.z;
}
}
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
// ============== surface fitting ==============
int ActiveMesh::CalcQuadricSurface_Taubin(const int vertexID,
float (&coeffs)[10])
{
//determine some reasonable number of nearest neighbors
std::vector< std::vector<size_t> > neigsLeveled;
ulm::getVertexNeighbours(*this,vertexID,2,neigsLeveled);
//make it flat...
std::vector<size_t> neigs;
for (unsigned int l=0; l < neigsLeveled.size(); ++l)
for (unsigned int i=0; i < neigsLeveled[l].size(); ++i)
neigs.push_back(neigsLeveled[l][i]);
neigsLeveled.clear();
//V be the vector of [x,y,z] combinations, a counterpart to coeffs
float V[10],V1[10],V2[10],V3[10];
//M be the matrix holding initially sum of (square matrices) V*V'
//N is similar, just a sum of three different Vs is used
float M[100],N[100];
for (int i=0; i < 100; ++i) M[i]=N[i]=0.f;
//over all neighbors (including the centre vertex itself),
//
//this order garuantees that array V will be relevant for input
//vertexID after the cycles are over -- will become handy later
for (signed int n=(int)neigs.size()-1; n >= 0; --n)
{
//shortcut to the current point
const Vector3FC& v=Pos[neigs[n]];
//get Vs for the given point 'v'
V[0]=1.f; V1[0]=0.f; V2[0]=0.f; V3[0]=0.f;
V[1]=v.x; V1[1]=1.f; V2[1]=0.f; V3[1]=0.f;
V[2]=v.y; V1[2]=0.f; V2[2]=1.f; V3[2]=0.f;
V[3]=v.z; V1[3]=0.f; V2[3]=0.f; V3[3]=1.f;
V[4]=v.x*v.y; V1[4]=v.y; V2[4]=v.x; V3[4]=0.f;
V[5]=v.x*v.z; V1[5]=v.z; V2[5]=0.f; V3[5]=v.x;
V[6]=v.y*v.z; V1[6]=0.f; V2[6]=v.z; V3[6]=v.y;
V[7]=v.x*v.x; V1[7]=2.f*v.x; V2[7]=0.f; V3[7]=0.f;
V[8]=v.y*v.y; V1[8]=0.f; V2[8]=2.f*v.y; V3[8]=0.f;
V[9]=v.z*v.z; V1[9]=0.f; V2[9]=0.f; V3[9]=2.f*v.z;
//construct V*V' and add it to M and N
for (int j=0; j < 9; ++j) //for column
for (int i=0; i < 9; ++i) //for row; note the order optimal for Fortran
{
//C order (row-major): M_i,j -> M[i][j] -> &M +i*STRIDE +j
//Lapack/Fortran order (column-major): M_i,j -> M[i][j] -> &M +j*STRIDE +i
//const int off=i*10 +j; //C
const int off=j*9 +i; //Fortran
M[off]+= V[j+1]* V[i+1];
N[off]+=V1[j+1]*V1[i+1];
N[off]+=V2[j+1]*V2[i+1];
N[off]+=V3[j+1]*V3[i+1];
}
}
//now, solve the generalized eigenvector of the matrix pair (M,N):
//MC = nNC
//
//M,N are (reduced) 9x9 matrices constructed above,
//C is vector (infact, the coeff), n is scalar Lagrange multiplier
//
//if M,N were (full-size) 10x10 matrices, the N would be singular
//as the 1st row would contain only zeros,
//it is therefore reduced to 9x9 sacrifing the first row
//
//according to netlib (Lapack) docs, http://www.netlib.org/lapack/lug/node34.html
//type 1, Az=lBz -- A=M, B=N, z=C
//function: SSYGV
lapack_int itype=1;
char jobz='V';
char uplo='U';
lapack_int n=9;
float w[10];
float work[512];
lapack_int lwork=512;
lapack_int info;
LAPACK_ssygv(&itype,&jobz,&uplo,&n,M,&n,N,&n,w,work,&lwork,&info);
std::cout << "vertices considered: " << neigs.size() << "\n";
std::cout << "info=" << info << " (0 is OK)\n";
std::cout << "work(1)=" << work[0] << " (should be below 512)\n";
//if some error, report it to the caller
if (info != 0) return info;
//M is now matrix of eigenvectors
//it should hold (according to Lapack docs):
//Z^T N Z = I where Z is one eigenvector, I is identity matrix
//
//w holds eigenvalues in ascending order
//our result c[1]...c[9] is the eigenvector
Vladimír Ulman
committed
//corresponding to the smallest non-negative eigenvalue, so the j-th eigenvector
int j=0;
while (j < 9 && w[j] < 0.f) ++j;
//have we found some non-negative eigenvalue?
if (j == 9) return(-9999);
//also:
//the last missing coefficient c[0] we will determine by submitting
//the given input vertex to the algebraic expresion of the surface
//(given with coeffs) and equating it to zero:
coeffs[0]=0.f;
for (int i=0; i < 9; ++i)
{
Vladimír Ulman
committed
coeffs[i+1]=M[j*9 +i]; //copy eigenvector
coeffs[0]-=coeffs[i+1]*V[i+1]; //determine c[0]
Vladimír Ulman
committed
std::cout << "w(j)=" << w[j] << ", j=" << j << "\n";
bool ActiveMesh::GetPointOnQuadricSurface(const float x,const float y,
float &z1, float &z2,
const float (&coeffs)[10])
{
const float a=coeffs[9];
const float b=coeffs[3] +coeffs[5]*x +coeffs[6]*y;
const float c=coeffs[0] +coeffs[1]*x +coeffs[2]*y
+coeffs[4]*x*y +coeffs[7]*x*x +coeffs[8]*y*y;
const float sqArg=b*b - 4*a*c;
if (sqArg < 0.f) return false;
if (a == 0.f) return false;
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
z1=(-b + sqrtf(sqArg)) / (2.f*a);
z2=(-b - sqrtf(sqArg)) / (2.f*a);
return true;
}
float ActiveMesh::GetClosestPointOnQuadricSurface(Vector3F& point,
const float (&coeffs)[10])
{
//backup original input coordinate
const float x=point.x;
const float y=point.y;
const float z=point.z;
float tmp1,tmp2;
//list of possible coordinates
std::vector<Vector3F> pointAdepts;
//took a pair of coordinates, calculate the third one
//and make it an adept...
if (GetPointOnQuadricSurface(x,y,tmp1,tmp2,coeffs))
{
pointAdepts.push_back(Vector3F(x,y,tmp1));
pointAdepts.push_back(Vector3F(x,y,tmp2));
}
if (GetPointOnQuadricSurface(x,z,tmp1,tmp2,coeffs))
{
pointAdepts.push_back(Vector3F(x,tmp1,z));
pointAdepts.push_back(Vector3F(x,tmp2,z));
}
if (GetPointOnQuadricSurface(y,z,tmp1,tmp2,coeffs))
{
pointAdepts.push_back(Vector3F(tmp1,y,z));
pointAdepts.push_back(Vector3F(tmp2,y,z));
}
//are we doomed?
if (pointAdepts.size() == 0)
return (-999999.f);
//find the closest
int closestIndex=ChooseClosestPoint(pointAdepts,point);
//calc distance to it
point-=pointAdepts[closestIndex];
tmp1=point.Len();
//adjust the input/output point
point=pointAdepts[closestIndex];
return (tmp1);
}
int ActiveMesh::ChooseClosestPoint(const std::vector<Vector3F>& points,
const Vector3F& point)
{
int minIndex=-1;
float minSqDist=9999999999999.f;
Vector3F p;
for (unsigned int i=0; i < points.size(); ++i)
{
p=point;
p-=points[i];
if (p.LenQ() < minSqDist)
{
minIndex=i;
minSqDist=p.LenQ();
}
}
return minIndex;
}
Vladimír Ulman
committed
void ActiveMesh::InitDots(const i3d::Image3d<i3d::GRAY16>& mask)
{
i3d::Image3d<float> dt;
i3d::GrayToFloat(mask,dt);
i3d::EDM(dt,0,100.f,false);
#ifdef SAVE_INTERMEDIATE_IMAGES
dt.SaveImage("1_DTAlone.ics");
#endif
i3d::Image3d<float> perlinInner,perlinOutside;
perlinInner.CopyMetaData(mask);
DoPerlin3D(perlinInner,5.0,0.8*1.5,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinInner.SaveImage("2_PerlinAlone_Inner.ics");
Vladimír Ulman
committed
#endif
perlinOutside.CopyMetaData(mask);
DoPerlin3D(perlinOutside,2.,0.8*1.5,0.7*1.5,6);
#ifdef SAVE_INTERMEDIATE_IMAGES
//perlinOutside.SaveImage("2_PerlinAlone_Outside.ics");
Vladimír Ulman
committed
#endif
i3d::Image3d<i3d::GRAY16> erroded;
i3d::ErosionO(mask,erroded,1);
//initial object intensity levels
float* p=dt.GetFirstVoxelAddr();
float* const pL=p+dt.GetImageSize();
const float* pI=perlinInner.GetFirstVoxelAddr();
const float* pO=perlinOutside.GetFirstVoxelAddr();
const i3d::GRAY16* er=erroded.GetFirstVoxelAddr();
while (p != pL)
{
//are we within the mask?
if (*p > 0.f)
{
//close to the surface?
if (*p < 0.3f || *er == 0) *p=2000.f + 5000.f*(*pO); //corona
else *p=500.f + 600.f*(*pI); //inside
Vladimír Ulman
committed
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
if (*er == 0) *p=2000.f; //std::max(*p,2000.f); //corona
if (*p < 0.f) *p=0.f;
}
++p; ++pI; ++pO; ++er;
}
#ifdef SAVE_INTERMEDIATE_IMAGES
dt.SaveImage("3_texture.ics");
#endif
perlinInner.DisposeData();
perlinOutside.DisposeData();
erroded.DisposeData();
//now, read the "molecules"
dots.clear();
dots.reserve(1<<23);
//time savers...
const float xRes=mask.GetResolution().GetX();
const float yRes=mask.GetResolution().GetY();
const float zRes=mask.GetResolution().GetZ();
const float xOff=mask.GetOffset().x;
const float yOff=mask.GetOffset().y;
const float zOff=mask.GetOffset().z;
p=dt.GetFirstVoxelAddr();
for (int z=0; z < (signed)dt.GetSizeZ(); ++z)
for (int y=0; y < (signed)dt.GetSizeY(); ++y)
for (int x=0; x < (signed)dt.GetSizeX(); ++x, ++p)
for (int v=0; v < *p; v+=50)
{
//convert px coords into um
const float X=(float)x/xRes + xOff;
const float Y=(float)y/yRes + yOff;
const float Z=(float)z/zRes + zOff;
dots.push_back(Vector3F(X,Y,Z));
/*
if (dots.size() == dots.capacity())
{
std::cout << "reserving more at position: " << x << "," << y << "," << z << "\n";
dots.reserve(dots.size()+(1<<20));
}
*/
}
//#ifdef SAVE_INTERMEDIATE_IMAGES
Vladimír Ulman
committed
std::cout << "intiated " << dots.size() << " fl. molecules (capacity is for "
<< dots.capacity() << ")\n";
Vladimír Ulman
committed
}
void ActiveMesh::BrownDots(const i3d::Image3d<i3d::GRAY16>& mask)
{
//TODO REMOVE ME
for (size_t i=0; i < dots.size(); ++i)
dots[i].x+=1.0f;
}
template <class VT>
VT GetPixel(i3d::Image3d<VT> const &img,const float x,const float y,const float z)
Vladimír Ulman
committed
{
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
/*
//nearest neighbor:
int X=static_cast<int>(roundf(x));
int Y=static_cast<int>(roundf(y));
int Z=static_cast<int>(roundf(z));
if (img.Include(X,Y,Z)) return(img.GetVoxel(X,Y,Z));
else return(0);
*/
//nearest not-greater integer coordinate, "o" in the picture in docs
//X,Y,Z will be coordinate of the voxel no. 2
const int X=static_cast<int>(floorf(x));
const int Y=static_cast<int>(floorf(y));
const int Z=static_cast<int>(floorf(z));
//now we can write only to pixels at [X or X+1,Y or Y+1,Z or Z+1]
//quit if too far from the "left" borders of the image
//as we wouldn't be able to draw into the image anyway
if ((X < -1) || (Y < -1) || (Z < -1)) return (0);
//residual fraction of the input coordinate
const float Xfrac=x - static_cast<float>(X);
const float Yfrac=y - static_cast<float>(Y);
const float Zfrac=z - static_cast<float>(Z);
//the weights
float A=0.0f,B=0.0f,C=0.0f,D=0.0f; //for 2D
//x axis:
A=D=Xfrac;
B=C=1.0f - Xfrac;
//y axis:
A*=1.0f - Yfrac;
B*=1.0f - Yfrac;
C*=Yfrac;
D*=Yfrac;
//z axis:
float A_=A,B_=B,C_=C,D_=D;
A*=1.0f - Zfrac;
B*=1.0f - Zfrac;
C*=1.0f - Zfrac;
D*=1.0f - Zfrac;
A_*=Zfrac;
B_*=Zfrac;
C_*=Zfrac;
D_*=Zfrac;
//portions of the value in a bit more organized form, w[z][y][x]
const float w[2][2][2]={{{B ,A },{C ,D }},
{{B_,A_},{C_,D_}}};
//the return value
float v=0;
//reading from the input image,
//for (int zi=0; zi < 2; ++zi) if (Z+zi < (signed)img.GetSizeZ()) { //shortcut for 2D cases to avoid some computations...
for (int zi=0; zi < 2; ++zi)
for (int yi=0; yi < 2; ++yi)
for (int xi=0; xi < 2; ++xi)
if (img.Include(X+xi,Y+yi,Z+zi)) {
//if we got here then we can safely change coordinate types
v+=(float)img.GetVoxel((size_t)X+xi,(size_t)Y+yi,(size_t)Z+zi) * w[zi][yi][xi];
}
//}
return ( static_cast<VT>(v) );
}
void ActiveMesh::FFDots(const i3d::Image3d<i3d::GRAY16>& mask,
const FlowField<float> &FF)
{
//TODO: tests: FF consistency, same size as mask?
//time savers...
const float xRes=mask.GetResolution().GetX();
const float yRes=mask.GetResolution().GetY();
const float zRes=mask.GetResolution().GetZ();
const float xOff=mask.GetOffset().x;
const float yOff=mask.GetOffset().y;
const float zOff=mask.GetOffset().z;
//apply FF on the this->dots (no boundary checking)
Vladimír Ulman
committed
for (size_t i=0; i < dots.size(); ++i)
{
//turn micron position into pixel one
const float X=(dots[i].x -xOff) *xRes;
const float Y=(dots[i].y -yOff) *yRes;
const float Z=(dots[i].z -zOff) *zRes;
//note: GetPixel() returns 0 in case we ask for value outside the image
//TODO: check against mask
dots[i].x += GetPixel(*FF.x, X,Y,Z);
dots[i].y += GetPixel(*FF.y, X,Y,Z);
dots[i].z += GetPixel(*FF.z, X,Y,Z);
}
Vladimír Ulman
committed
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
}
void ActiveMesh::RenderDots(const i3d::Image3d<i3d::GRAY16>& mask,
i3d::Image3d<i3d::GRAY16>& texture)
{
texture.CopyMetaData(mask);
texture.GetVoxelData()=0;
//time savers...
const float xRes=texture.GetResolution().GetX();
const float yRes=texture.GetResolution().GetY();
const float zRes=texture.GetResolution().GetZ();
const float xOff=texture.GetOffset().x;
const float yOff=texture.GetOffset().y;
const float zOff=texture.GetOffset().z;
//time-savers for boundary checking...
const int maxX=(int)texture.GetSizeX()-1;
const int maxY=(int)texture.GetSizeY()-1;
const int maxZ=(int)texture.GetSizeZ()-1;
//time-savers for accessing neigbors...
const size_t xLine=texture.GetSizeX();
const size_t Slice=texture.GetSizeY() *xLine;
i3d::GRAY16* const T=texture.GetFirstVoxelAddr();
//render the points into the texture image
for (size_t i=0; i < dots.size(); ++i)
{
const int x=(int)roundf( (dots[i].x-xOff) *xRes);
const int y=(int)roundf( (dots[i].y-yOff) *yRes);
const int z=(int)roundf( (dots[i].z-zOff) *zRes);
if ((x > 0) && (y > 0) && (z > 0)
&& (x < maxX) && (y < maxY) && (z < maxZ)) T[z*Slice +y*xLine +x]+=i3d::GRAY16(50);
Vladimír Ulman
committed
}
Vladimír Ulman
committed
}
Vladimír Ulman
committed
Vladimír Ulman
committed
void ActiveMesh::PhaseII(const i3d::Image3d<i3d::GRAY16>& texture,
i3d::Image3d<float>& intermediate)
{
i3d::GrayToFloat(texture,intermediate);
Vladimír Ulman
committed
Vladimír Ulman
committed
i3d::GaussIIR(intermediate,2.f,2.f,2.0f);
Vladimír Ulman
committed
#ifdef SAVE_INTERMEDIATE_IMAGES
Vladimír Ulman
committed
intermediate.SaveImage("4_texture_filtered.ics");
Vladimír Ulman
committed
#endif
Vladimír Ulman
committed
}
Vladimír Ulman
committed
Vladimír Ulman
committed
void ActiveMesh::PhaseIII(i3d::Image3d<float>& intermediate,
i3d::Image3d<i3d::GRAY16>& texture)
{
Vladimír Ulman
committed
#ifdef SAVE_INTERMEDIATE_IMAGES
Vladimír Ulman
committed
intermediate->SaveImage("5_texture_filtered_resampled.ics");
Vladimír Ulman
committed
#endif
Vladimír Ulman
committed
float* p=intermediate.GetFirstVoxelAddr();
for (int z=0; z < (signed)intermediate.GetSizeZ(); ++z)
for (int y=0; y < (signed)intermediate.GetSizeY(); ++y)
for (int x=0; x < (signed)intermediate.GetSizeX(); ++x, ++p)
Vladimír Ulman
committed
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
{
//background signal:
float distSq=((float)x-110.f)*((float)x-110.f) + ((float)y-110.f)*((float)y-110.f);
*p+=100.f*expf(-0.5f * distSq / 900.f);
//uncertainty in the number of incoming photons
const float noiseMean = sqrtf(*p), // from statistics: shot noise = sqrt(signal)
noiseVar = noiseMean; // for Poisson distribution E(X) = D(X)
*p+=30.f*((float)GetRandomPoisson(noiseMean) - noiseVar);
//constants are parameters of Andor iXon camera provided from vendor:
//photon shot noise: dark current
*p+=(float)GetRandomPoisson(0.06f);
//read-out noise:
// variance up to 25.f (old camera on ILBIT)
// variance about 1.f (for the new camera on ILBIT)
*p+=GetRandomGauss(480.f,20.f);
//*p+=530.f;
}
#ifdef SAVE_INTERMEDIATE_IMAGES
Vladimír Ulman
committed
intermediate.SaveImage("6_texture_filtered_resampled_finalized.ics");
Vladimír Ulman
committed
#endif
//obtain final GRAY16 image
Vladimír Ulman
committed
i3d::FloatToGrayNoWeight(intermediate,texture);
Vladimír Ulman
committed
}
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
void ActiveMesh::ConstructFF(FlowField<float> &FF)
{
//erase the flow field
//iterate:
// put displacement vectors
// smooth
//tests: TODO
//FF must be consistent
//oldVolPos and newVolPos must be of the same length
//erase
FF.x->GetVoxelData()=0;
FF.y->GetVoxelData()=0;
FF.z->GetVoxelData()=0;
//time savers...
const float xRes=FF.x->GetResolution().GetX();
const float yRes=FF.x->GetResolution().GetY();
const float zRes=FF.x->GetResolution().GetZ();
const float xOff=FF.x->GetOffset().x;
const float yOff=FF.x->GetOffset().y;
const float zOff=FF.x->GetOffset().z;
//time-savers for boundary checking...
const int maxX=(int)FF.x->GetSizeX()-1;
const int maxY=(int)FF.x->GetSizeY()-1;
const int maxZ=(int)FF.x->GetSizeZ()-1;
//time-savers for accessing neigbors...
const size_t xLine=FF.x->GetSizeX();
const size_t Slice=FF.x->GetSizeY() *xLine;
float* const ffx=FF.x->GetFirstVoxelAddr();
float* const ffy=FF.y->GetFirstVoxelAddr();
float* const ffz=FF.z->GetFirstVoxelAddr();
//inject displacements
for (size_t i=0; i < oldVolPos.size(); ++i)
const int x=(int)roundf( (oldVolPos[i].x-xOff) *xRes);
const int y=(int)roundf( (oldVolPos[i].y-yOff) *yRes);
const int z=(int)roundf( (oldVolPos[i].z-zOff) *zRes);
const float dx=newVolPos[i].x - oldVolPos[i].x;
const float dy=newVolPos[i].y - oldVolPos[i].y;
const float dz=newVolPos[i].z - oldVolPos[i].z;
if ((x > 0) && (y > 0) && (z > 0)
&& (x < maxX) && (y < maxY) && (z < maxZ))
{
ffx[z*Slice +y*xLine +x]=dx;
ffy[z*Slice +y*xLine +x]=dy;
ffz[z*Slice +y*xLine +x]=dz;
//smooth
i3d::GaussIIR(*FF.x,15.0f);
i3d::GaussIIR(*FF.y,15.0f);
i3d::GaussIIR(*FF.z,15.0f);
//multiply (to "correct" after normalized smoothing)
FF.x->GetVoxelData()*=1240.f;
FF.y->GetVoxelData()*=1240.f;
FF.z->GetVoxelData()*=1240.f;
Vladimír Ulman
committed
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
1640
1641
1642
1643
1644
1645
1646
1647
1648
1649
1650
1651
1652
1653
1654
1655
1656
1657
1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
1668
1669
1670
1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
1714
1715
1716
void ActiveMesh::ConstructFF_T(FlowField<float> &FF)
{
//erase the flow field
//add displacement vectors by "rendering" displacement tetrahedra
//smooth
//tests: TODO
//FF must be consistent
//oldVolPos and newVolPos must be of the same length
//length of oldVolPos*4 and length of VolID must be the same
//erase
FF.x->GetVoxelData()=0;
FF.y->GetVoxelData()=0;
FF.z->GetVoxelData()=0;
i3d::Image3d<i3d::GRAY16> imgCounts;
imgCounts.CopyMetaData(*FF.x);
imgCounts.GetVoxelData()=0;
//time savers...
const float xRes=FF.x->GetResolution().GetX();
const float yRes=FF.x->GetResolution().GetY();
const float zRes=FF.x->GetResolution().GetZ();
const float xOff=FF.x->GetOffset().x;
const float yOff=FF.x->GetOffset().y;
const float zOff=FF.x->GetOffset().z;
//time-savers for boundary checking...
const int maxX=(int)FF.x->GetSizeX()-1;
const int maxY=(int)FF.x->GetSizeY()-1;
const int maxZ=(int)FF.x->GetSizeZ()-1;
//time-savers for accessing neigbors...
const size_t xLine=FF.x->GetSizeX();
const size_t Slice=FF.x->GetSizeY() *xLine;
float* const ffx=FF.x->GetFirstVoxelAddr();
float* const ffy=FF.y->GetFirstVoxelAddr();
float* const ffz=FF.z->GetFirstVoxelAddr();
i3d::GRAY16* const ffC=imgCounts.GetFirstVoxelAddr();
//over all tetrahedra
for (size_t i=0; i < VolID.size(); i+=4)
{
//tetrahedron to drive positions in the FF
//(positions tetrahedron)
const Vector3F& v1=oldVolPos[VolID[i+0]];
const Vector3F& v2=oldVolPos[VolID[i+1]];
const Vector3F& v3=oldVolPos[VolID[i+2]];
const Vector3F& v4=oldVolPos[VolID[i+3]];
//now iterate over the tetrahedra:
for (float d=0.f; d <= 1.0f; d += 0.04f)
for (float c=0.f; c <= (1.0f-d); c += 0.04f)
for (float b=0.f; b <= (1.0f-d-c); b += 0.04f)
{
float a=1.0f -b -c -d;
//float-point coordinate:
Vector3F tmp;
tmp =a*v1;
tmp+=b*v2;
tmp+=c*v3;
tmp+=d*v4;
//pixel (integer) coordinate:
const int x=(int)roundf( (tmp.x-xOff) *xRes);
const int y=(int)roundf( (tmp.y-yOff) *yRes);
const int z=(int)roundf( (tmp.z-zOff) *zRes);
if ((x > 0) && (y > 0) && (z > 0)
&& (x < maxX) && (y < maxY) && (z < maxZ))
{
//tetrahedron to drive values to place at these positions
//(values tetrahedron)
const Vector3F dv1=newVolPos[VolID[i+0]] - v1;
const Vector3F dv2=newVolPos[VolID[i+1]] - v2;
const Vector3F dv3=newVolPos[VolID[i+2]] - v3;
const Vector3F dv4=newVolPos[VolID[i+3]] - v4;
//value
tmp =a*dv1;
tmp+=b*dv2;
tmp+=c*dv3;
tmp+=d*dv4;
ffx[z*Slice +y*xLine +x]+=tmp.x;
ffy[z*Slice +y*xLine +x]+=tmp.y;
ffz[z*Slice +y*xLine +x]+=tmp.z;
ffC[z*Slice +y*xLine +x]+=1;
}
}
}
//finish the averaging of FF
for (size_t i=0; i < imgCounts.GetImageSize(); ++i)
if (*(ffC+i))
{
*(ffx+i)/=float(*(ffC+i));
*(ffy+i)/=float(*(ffC+i));
*(ffz+i)/=float(*(ffC+i));
}
//imgCounts.SaveImage("counts.ics"); //TODO REMOVE
}