static plane bisection_plane(unsigned n, point o[])
{
point com = center_of_mass(n, o);
basis im = inertia_matrix(n, o, com);
point axis = min_eigenvec(im);
return median_plane(n, o, axis);
}
static int private_add_shape (
LIPhyShape* self,
btConvexShape* shape,
const LIMatTransform* transform)
{
btVector3 p(0.0f, 0.0f, 0.0f);
btQuaternion r(0.0f, 0.0f, 0.0f, 1.0f);
btTransform center_of_mass(r, btVector3 (
self->center_of_mass.x, self->center_of_mass.y, self->center_of_mass.z));
if (transform != NULL)
{
p = btVector3 (transform->position.x, transform->position.y,
transform->position.z);
r = btQuaternion(transform->rotation.x, transform->rotation.y,
transform->rotation.z, transform->rotation.w);
}
try
{
self->shape->addChildShape (center_of_mass.inverse() * btTransform (r, p), shape);
}
catch (...)
{
return 0;
}
/* Update the bounding box. */
btVector3 min;
btVector3 max;
self->shape->getAabb(btTransform::getIdentity (), min, max);
self->bounds.min = limat_vector_init (min[0], min[1], min[2]);
self->bounds.max = limat_vector_init (max[0], max[1], max[2]);
return 1;
}
void map_fragment::center_by_mass()
{
shift(center_of_mass().vector_negation());
area_.clear();
for (tile_info& ti : items_) {
area_.insert(ti.offset);
}
}
static void compute_vectors(SegmentArray* segments,
SkPoint* fanPt,
SkPath::Direction dir,
int* vCount,
int* iCount) {
center_of_mass(*segments, fanPt);
int count = segments->count();
// Make the normals point towards the outside
SkPoint::Side normSide;
if (dir == SkPath::kCCW_Direction) {
normSide = SkPoint::kRight_Side;
} else {
normSide = SkPoint::kLeft_Side;
}
*vCount = 0;
*iCount = 0;
// compute normals at all points
for (int a = 0; a < count; ++a) {
Segment& sega = (*segments)[a];
int b = (a + 1) % count;
Segment& segb = (*segments)[b];
const SkPoint* prevPt = &sega.endPt();
int n = segb.countPoints();
for (int p = 0; p < n; ++p) {
segb.fNorms[p] = segb.fPts[p] - *prevPt;
segb.fNorms[p].normalize();
segb.fNorms[p].setOrthog(segb.fNorms[p], normSide);
prevPt = &segb.fPts[p];
}
if (Segment::kLine == segb.fType) {
*vCount += 5;
*iCount += 9;
} else {
*vCount += 6;
*iCount += 12;
}
}
// compute mid-vectors where segments meet. TODO: Detect shallow corners
// and leave out the wedges and close gaps by stitching segments together.
for (int a = 0; a < count; ++a) {
const Segment& sega = (*segments)[a];
int b = (a + 1) % count;
Segment& segb = (*segments)[b];
segb.fMid = segb.fNorms[0] + sega.endNorm();
segb.fMid.normalize();
// corner wedges
*vCount += 4;
*iCount += 6;
}
}
struct tvector* negative_center_of_mass (struct atomgrp* ag)
{
struct tvector* tvec = center_of_mass (ag);
// negate the tvec
tvec->X = -tvec->X;
tvec->Y = -tvec->Y;
tvec->Z = -tvec->Z;
return tvec;
}
template <> complex_number Graph<Circle>::direction_from_center_of_mass(const unsigned int &index) const
{
if (index > vertices_.size())
{
std::cout << "ERROR in Graph<Point>::direction_from_center_of_mass: bad index" << std::endl;
throw(QString("ERROR in Graph<Point>::direction_from_center_of_mass: bad index"));
}
complex_number u = get_affix_by_index(index) - center_of_mass().get_affix();
return u/abs(u);
}
int main(int argc, char *argv[]) {
int dims = 2;
int nr_particles = 5;
if (argc > 1)
dims = atoi(argv[1]);
if (argc > 2)
nr_particles = atoi(argv[2]);
System *system = init_system(nr_particles, dims);
print_system(system);
printf("total mass = %lf\n", total_mass(system));
double cms[dims];
center_of_mass(system, cms);
print_position(cms, dims);
free_system(system);
return EXIT_SUCCESS;
}
float* moment_of_inertia (struct atomgrp* ag)
{
struct tvector* com = center_of_mass (ag);
float sq_x_com = powf (com->X, 2.0);
float sq_y_com = powf (com->Y, 2.0);
float sq_z_com = powf (com->Z, 2.0);
float sum_sq_x = 0;
float sum_sq_y = 0;
float sum_sq_z = 0;
float sum_mult_xy = 0;
float sum_mult_xz = 0;
float sum_mult_yz = 0;
int i;
for (i = 0; i < ag->natoms; i++)
{
sum_sq_x += powf (ag->atoms[i].X, 2.0);
sum_sq_y += powf (ag->atoms[i].Y, 2.0);
sum_sq_z += powf (ag->atoms[i].Z, 2.0);
sum_mult_xy += ag->atoms[i].X * ag->atoms[i].Y;
sum_mult_xz += ag->atoms[i].X * ag->atoms[i].Z;
sum_mult_yz += ag->atoms[i].Y * ag->atoms[i].Z;
}
float* moi_matrix = (float*) _mol_malloc (sizeof (float) * 9);
moi_matrix[0] = sum_sq_y + sum_sq_z - (sq_y_com + sq_z_com) * ag->natoms;
moi_matrix[1] = -sum_mult_xy + com->X * com->Y * ag->natoms;
moi_matrix[2] = -sum_mult_xz + com->X * com->Z * ag->natoms;
moi_matrix[3] = -sum_mult_xy + com->X * com->Y * ag->natoms;
moi_matrix[4] = sum_sq_x + sum_sq_z - (sq_x_com + sq_z_com) * ag->natoms;
moi_matrix[5] = -sum_mult_yz + com->Y * com->Z * ag->natoms;
moi_matrix[6] = -sum_mult_xz + com->X * com->Z * ag->natoms;
moi_matrix[7] = -sum_mult_yz + com->Y * com->Z * ag->natoms;
moi_matrix[8] = sum_sq_x + sum_sq_y - (sq_x_com + sq_y_com) * ag->natoms;
free (com);
return moi_matrix;
}
int main(int argc, char **argv)
{
Ics_Error icserr;
ICS* ics;
size_t dims[ICS_MAXDIM];
int ndims;
int i,j;
Ics_DataType dt;
char fname[32];
char cmdlin[256];
/* TODO */
pix_type *prev; /* previous frame */
unsigned char *buf; /* 8-bit buffer */
int startframe,endframe;
int *tmp;
int *probb;
int *prob;
int *imsob;
FILE *f;
int w,h;
int err;
/* unsigned char *wsh; */
int markx[2],marky[2];
unsigned char *wsh;
if(argc < 2){
printf(" usage: edgeprob <filename>.ics <prob.pgm> [startframe [endframe]] [-e cutoff]\n");
printf(" example: edgeprob livecell.ics livecell1.pgm 30 35 e\n");
printf(" center of cell should be marked with single dot of intensity 128\n");
printf(" does all frames if start frame not specified\n");
return 0;
}
/* Open file */
icserr = IcsOpen(&ics, argv[1], "r");
ICS_CHECK(icserr);
#ifdef DEBUG_PRINT
printf("ics file loaded.\n");
#endif
/* Sniff out file; make sure it is compatible with our prog */
icserr = IcsGetLayout(ics, &dt, &ndims, dims);
ICS_CHECK(icserr);
if(dt != Ics_uint16){
printf("Sorry, image modes other than 16-bit (unsigned) ");
printf("not supported at the moment.\n");
return 0;
}
/* number of frames specified */
startframe = 0;
endframe = dims[3];
if(argc >= 4){
startframe = strtol(argv[3],NULL,0);
if(startframe > dims[3]) startframe = dims[3];
if(startframe < 0){
printf("Start frame number must be non-negative.\n");
return 1;
}
if(argc >= 5){
endframe = strtol(argv[4],NULL,0);
if(endframe < startframe){
printf("End frame number must be greater than start.\n");
return 2;
}
if(endframe > dims[3]) endframe = dims[3];
}
}
#ifdef DEBUG_PRINT
printf("dimensions: ");
for(i=0;i<ndims;i++)
printf("%ld ", dims[i]);
printf("data type: %d \n", dt);
#endif
/* TODO: warning if dimensions look non-standard */
/* allocate space before reading */
/* Only allocate for one frame; allows images with many frames
* to be loaded without much memory, unlike some programs
* (I'm looking at you, ics_opener/ImageJ ! */
prev = (pix_type *) malloc(dims[1]*dims[2]*sizeof(pix_type));
buf = (unsigned char *)malloc(dims[1]*dims[2]*sizeof(unsigned char));
tmp = (int *) malloc(dims[1]*dims[2]*sizeof(int));
probb = (int *) malloc(dims[1]*dims[2]*sizeof(int));
prob = (int *) malloc(dims[1]*dims[2]*sizeof(int));
imsob = (int *) malloc(dims[1]*dims[2]*sizeof(int));
wsh = (unsigned char *)malloc(dims[1]*dims[2]*sizeof(unsigned char));
if((!prev)||(!buf)||(!tmp)||(!probb)||(!prob)||(!imsob)||(!wsh))
{
printf("Couldn't allocate enough memory.\n");
return 1;
}
/* load probabilities */
f = fopen(argv[2],"r");
if(!f){
printf("Error: could not open file %s\n",argv[2]);
return 10;
}
if((err = load_data(f, &prob, &w, &h))){
printf("Error: %s: incorrect or corrupt pgm file.\n",argv[2]);
return 11;
}
if((w!=dims[1])||(h!=dims[2])){
printf("Error: Size mismatch. ICS data are %ldx%ld but probability data are %dx%d\n",
dims[1],dims[2],w,h);
return 9;
}
fclose(f);
/* obtain marker from prob image */
markx[0]=10; marky[0]=10;
markx[1]=markx[0]; marky[1]=marky[0];
for(j=0;j<dims[2];j++){
for(i=0;i<dims[1];i++){
if(prob[j*dims[1] + i]==128){
markx[1]=i;
marky[1]=j;
}
}
}
if((markx[0]==markx[1])&&(marky[1]==marky[0])){
printf("Error: marker not found in prob image.\n");
printf("(should be single pixel with intensity 128)\n");
return 8;
}
printf("tracking...\n");
/* read sequentially from file. */
/* Each call to IcsGetDataBlock proceeds from the end of the last */
for(i=0;i<endframe;i++){
icserr = IcsGetDataBlock(ics, prev, dims[1]*dims[2]*2);
ICS_CHECK(icserr);
if(i>=startframe){
/* blur probabilities */
memcpy(probb, prob, sizeof(int)*dims[1]*dims[2]);
blur_diffuse(probb, tmp, dims[1], dims[2]);
blur_diffuse(tmp, probb, dims[1], dims[2]);
blur_cusp(probb, tmp, dims[1], dims[2], 210);
blur_diffuse(probb, tmp, dims[1], dims[2]);
blur_diffuse(tmp, probb, dims[1], dims[2]);
/* come up with new probabilities */
im2int(prev, tmp, dims[1], dims[2]);
sobel(tmp, imsob, dims[1], dims[2]);
/* convert to probability */
for(j=0;j<dims[1]*dims[2];j++){
imsob[j] >>= 4;
if(imsob[j]>255) imsob[j]=255;
}
/* mix them up */
combine_prob(probb, imsob, prob, dims[1], dims[2]);
normalize_prob(prob, dims[1], dims[2]);
/* watershed to 'collapse' probabilities */
/*watershed(prob, wsh, tmp, dims[1], dims[2], markx, marky, 2);
for(j=0;j<dims[1]*dims[2];j++){
wsh[j] = (wsh[j]==2 ? 8 : 0);
}*/
watershed_rep(prob, buf, tmp, dims[1], dims[2], markx, marky, 2, wsh, 8, 24.0);
center_of_mass(wsh, dims[1], dims[2], 8, markx, marky);
hardedge(wsh, buf, dims[1], dims[2]);
/* now combine the existing probabilities with the ones from hardedge */
for(j=0;j<dims[1]*dims[2];j++){
if(buf[j]==255) prob[j]=(3*255+prob[j])/4;
}
for(j=0;j<dims[1]*dims[2];j++)
buf[j]=prob[j];
printf("frame %d\n", i);
sprintf(fname, "prob_%04d.png", i);
export_8bit_pgm(buf, dims[1], dims[2], "tmp.pgm");
sprintf(cmdlin, "pnmtopng -compression 1 < tmp.pgm > %s", fname);
system(cmdlin);
}
}
virtual void init(Voxel& voxel)
{
if(voxel.vs[0] == 0.0 ||
voxel.vs[1] == 0.0 ||
voxel.vs[2] == 0.0)
throw std::runtime_error("No spatial information found in src file. Recreate src file or contact developer for assistance");
begin_prog("normalization");
VG = fa_template_imp.I;
VF = voxel.fa_map;
image::filter::gaussian(voxel.fa_map);
image::filter::gaussian(voxel.fa_map);
image::filter::gaussian(voxel.qa_map);
image::filter::gaussian(voxel.qa_map);
image::normalize(voxel.fa_map,1.0);
image::normalize(voxel.qa_map,1.0);
for(unsigned int index = 0;index < voxel.qa_map.size();++index)
if(voxel.qa_map[index] == 0.0 || voxel.fa_map[index]/voxel.qa_map[index] > 2.5)
VF[index] = 0.0;
image::filter::gaussian(VF);
src_geo = VF.geometry();
image::normalize(VF,1.0);
//VF.save_to_file<image::io::nifti<> >("VF.nii");
image::normalize(VG,1.0);
// get rid of the gray matters
image::minus_constant(VF.begin(),VF.end(),0.3);
image::lower_threshold(VF.begin(),VF.end(),0.00);
image::normalize(VF,1.0);
image::minus_constant(VG.begin(),VG.end(),0.3);
image::lower_threshold(VG.begin(),VG.end(),0.00);
image::normalize(VG,1.0);
VGvs[0] = std::fabs(fa_template_imp.tran[0]);
VGvs[1] = std::fabs(fa_template_imp.tran[5]);
VGvs[2] = std::fabs(fa_template_imp.tran[10]);
image::affine_transform<3,double> arg_min;
// VG: FA TEMPLATE
// VF: SUBJECT QA
arg_min.scaling[0] = voxel.vs[0] / VGvs[0];
arg_min.scaling[1] = voxel.vs[1] / VGvs[1];
arg_min.scaling[2] = voxel.vs[2] / VGvs[2];
voxel_volume_scale = arg_min.scaling[0]*arg_min.scaling[1]*arg_min.scaling[2];
// calculate center of mass
image::vector<3,double> mF = center_of_mass(VF);
image::vector<3,double> mG = center_of_mass(VG);
arg_min.translocation[0] = mG[0]-mF[0]*arg_min.scaling[0];
arg_min.translocation[1] = mG[1]-mF[1]*arg_min.scaling[1];
arg_min.translocation[2] = mG[2]-mF[2]*arg_min.scaling[2];
bool terminated = false;
set_title("linear registration");
begin_prog("conducting registration");
check_prog(0,2);
image::reg::linear(VF,VG,arg_min,image::reg::affine,image::reg::square_error(),terminated,0.25);
check_prog(1,2);
// create VFF the affine transformed VF
image::basic_image<float,3> VFF(VG.geometry());
{
affine = arg_min;
image::reg::linear_get_trans(VF.geometry(),VG.geometry(),affine);
{
std::vector<double> T(16);
affine.save_to_transform(T.begin());
T[15] = 1.0;
math::matrix_inverse(T.begin(),math::dim<4,4>());
affine.load_from_transform(T.begin());
}
image::resample(VF,VFF,affine);
//VFF.save_to_file<image::io::nifti<> >("VFF.nii");
//VG.save_to_file<image::io::nifti<> >("VG.nii");
}
{
switch(voxel.reg_method)
{
case 0:
mni.normalize(VG,VFF);
break;
case 1:
mni.normalize(VG,VFF,12,14,12,4,8);
break;
}
//calculate the goodness of fit
std::vector<float> x,y;
x.reserve(VG.size());
y.reserve(VG.size());
image::interpolation<image::linear_weighting,3> trilinear_interpolation;
for(image::pixel_index<3> index;VG.geometry().is_valid(index);
index.next(VG.geometry()))
if(VG[index.index()] != 0)
{
image::vector<3,double> pos;
mni.warp_coordinate(index,pos);
double value = 0.0;
if(!trilinear_interpolation.estimate(VFF,pos,value))
continue;
x.push_back(VG[index.index()]);
y.push_back(value);
}
R2 = x.empty() ? 0.0 : image::correlation(x.begin(),x.end(),y.begin());
R2 *= R2;
std::cout << "R2 = " << R2 << std::endl;
}
check_prog(2,2);
// setup output bounding box
{
//setBoundingBox(-78,-112,-50,78,76,85,1.0);
float voxel_size = voxel.param[1];
bounding_box_lower[0] = std::floor(-78.0/voxel_size+0.5)*voxel_size;
bounding_box_lower[1] = std::floor(-112.0/voxel_size+0.5)*voxel_size;
bounding_box_lower[2] = std::floor(-50.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[0] = std::floor(78.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[1] = std::floor(76.0/voxel_size+0.5)*voxel_size;
bounding_box_upper[2] = std::floor(85.0/voxel_size+0.5)*voxel_size;
des_geo[0] = (bounding_box_upper[0]-bounding_box_lower[0])/voxel_size+1;//79
des_geo[1] = (bounding_box_upper[1]-bounding_box_lower[1])/voxel_size+1;//95
des_geo[2] = (bounding_box_upper[2]-bounding_box_lower[2])/voxel_size+1;//69
des_offset[0] = bounding_box_lower[0]/VGvs[0]-fa_template_imp.tran[3]/fa_template_imp.tran[0];
des_offset[1] = bounding_box_lower[1]/VGvs[1]-fa_template_imp.tran[7]/fa_template_imp.tran[5];
des_offset[2] = bounding_box_lower[2]/VGvs[2]-fa_template_imp.tran[11]/fa_template_imp.tran[10];
scale[0] = voxel_size/VGvs[0];
scale[1] = voxel_size/VGvs[1];
scale[2] = voxel_size/VGvs[2];
}
begin_prog("q-space diffeomorphic reconstruction");
float sigma = voxel.param[0]; //diffusion sampling length ratio, optimal 1.24
// setup mask
{
// set the current mask to template space
voxel.image_model->set_dimension(des_geo[0],des_geo[1],des_geo[2]);
for(image::pixel_index<3> index;des_geo.is_valid(index);index.next(des_geo))
{
image::vector<3,int> mni_pos(index);
mni_pos *= voxel.param[1];
mni_pos[0] /= VGvs[0];
mni_pos[1] /= VGvs[1];
mni_pos[2] /= VGvs[2];
mni_pos += des_offset;
voxel.image_model->mask[index.index()] =
fa_template_imp.I.at(mni_pos[0],mni_pos[1],mni_pos[2]) > 0.0? 1: 0;
}
}
q_vectors_time.resize(voxel.bvalues.size());
for (unsigned int index = 0; index < voxel.bvalues.size(); ++index)
{
q_vectors_time[index] = voxel.bvectors[index];
q_vectors_time[index] *= std::sqrt(voxel.bvalues[index]*0.01506);// get q in (mm) -1
q_vectors_time[index] *= sigma;
}
b0_index = -1;
if(voxel.half_sphere)
for(unsigned int index = 0;index < voxel.bvalues.size();++index)
if(voxel.bvalues[index] == 0)
b0_index = index;
ptr_images.clear();
for (unsigned int index = 0; index < voxel.image_model->dwi_data.size(); ++index)
ptr_images.push_back(point_image_type((const unsigned short*)voxel.image_model->dwi_data[index],src_geo));
voxel.qa_scaling = voxel.reponse_function_scaling/voxel.vs[0]/voxel.vs[1]/voxel.vs[2];
max_accumulated_qa = 0;
std::fill(voxel.vs.begin(),voxel.vs.end(),voxel.param[1]);
jdet.resize(des_geo.size());
if (voxel.odf_deconvolusion)
{
gqi.init(voxel);
deconvolution.init(voxel);
}
if (voxel.odf_decomposition)
{
gqi.init(voxel);
decomposition.init(voxel);
}
angle_variance = 8; //degress;
angle_variance *= M_PI/180;
angle_variance *= angle_variance;
angle_variance *= 2.0;
}
// EVT_SNAPSHOT
std::ostream& record_output_1(std::ostream &out, gpulog::logrecord &lr, swarm::body_range_t &body_range)
{
double time;
int nbod, sys, flags;
const body *bodies;
lr >> time >> sys >> flags >> nbod >> bodies;
body center;
const swarm::body &star = bodies[0];
switch(planets_coordinate_system)
{
case astrocentric:
center = star;
break;
case barycentric:
center = center_of_mass( bodies, nbod );
break;
case jacobi:
center = star;
break;
case origin:
center.x = center.y = center.z = center.vx = center.vy = center.vz = 0.; center.mass = star.mass;
break;
};
if((time<=0.) && false) // was used for debugging at some point
{
if (keplerian_output)
{ std::cerr << "# Output in Keplerian coordinates "; }
else { std::cerr << "# Output in Cartesian coordinates "; }
switch(planets_coordinate_system)
{
case astrocentric:
std::cerr << "(astrocentric) " << center.x << ' ' << center.y << ' '<< center.z << " " << center.vx << ' ' << center.vy << ' ' << center.vz;
break;
case barycentric:
std::cerr << "(barycentric) "<< center.x << ' ' << center.y << ' '<< center.z << " " << center.vx << ' ' << center.vy << ' ' << center.vz;
break;
case jacobi:
std::cerr << "(jacobi) " << center.x << ' ' << center.y << ' '<< center.z << " " << center.vx << ' ' << center.vy << ' ' << center.vz;
break;
case origin:
std::cerr << "(origin) " << center.x << ' ' << center.y << ' '<< center.z << " " << center.vx << ' ' << center.vy << ' ' << center.vz;
break;
}
std::cerr << "\n";
}
size_t bufsize = 1000;
char buf[bufsize];
for(int bod = 0; bod < nbod; bod++)
{
if(!body_range.in(bod)) { continue; }
const swarm::body &b = bodies[bod];
if( keplerian_output && (bod==0) ) { continue; }
if( (planets_coordinate_system==jacobi) && (bod==0) ) { continue; }
if( ( !keplerian_output && (planets_coordinate_system!=jacobi) && (bod> 0) ) ||
( !keplerian_output && (planets_coordinate_system==jacobi) && (bod> 1) ) ||
( keplerian_output && (bod> 1 ) ) ){ out << "\n"; }
if( planets_coordinate_system == jacobi )
{ center = center_of_mass ( bodies, bod); }
if( keplerian_output && bod > 0)
{
if(planets_coordinate_system==barycentric) center.mass -= b.mass;
keplerian_t orbit = keplerian_for_cartesian( b, center );
if(planets_coordinate_system==barycentric) center.mass += b.mass;
const double rad2deg = 180./M_PI;
snprintf(buf, bufsize, "%10d %lg %6d %6d %lg % 9.5lg % 9.5lg % 9.5lg % 9.5lg % 9.5lg % 9.5lg %d", lr.msgid(), time, sys, bod, b.mass, orbit.a, orbit.e , orbit.i*rad2deg, orbit.O*rad2deg, orbit.w *rad2deg, orbit.M*rad2deg, flags);
}
if(!keplerian_output)
{
double x = b.x - center.x;
double y = b.y - center.y;
double z = b.z - center.z;
double vx= b.vx- center.vx;
double vy= b.vy- center.vy;
double vz= b.vz- center.vz;
snprintf(buf, bufsize, "%10d %lg %6d %6d %lg %9.5lg %9.5lg %9.5lg %9.5lg %9.5lg %9.5lg %d", lr.msgid(), time, sys, bod, b.mass, x, y, z, vx, vy, vz, flags);
}
out << buf; // << "\n";
}
return out;
}
int main(int argc, char **argv)
{
Ics_Error icserr;
ICS* ics;
size_t dims[ICS_MAXDIM];
int ndims;
int i,j;
Ics_DataType dt;
/* TODO */
pix_type *prev; /* previous frame */
unsigned char *buf; /* 8-bit buffer */
int startframe,endframe;
int *tmp1,*tmp2,*var,*sob;
int xmark[2],ymark[2];
unsigned char *wsh;
FILE *comf;
char fname[64],cmdlin[128];
if(argc < 4){
printf("usage: nucfollow <filename>.ics <x> <y> [startframe [endframe]] [-e cutoff]\n");
printf("(x,y) is the coordinate of the nucleus at first iteration.\n");
printf("example: nucfollow livecell.ics 400 300 30\n");
printf("extracts all frames if start frame not specified\n");
return 0;
}
/* Open file */
icserr = IcsOpen(&ics, argv[1], "r");
ICS_CHECK(icserr);
#ifdef DEBUG_PRINT
printf("ics file loaded.\n");
#endif
/* Sniff out file; make sure it is compatible with our prog */
icserr = IcsGetLayout(ics, &dt, &ndims, dims);
ICS_CHECK(icserr);
if(dt != Ics_uint16){
printf("Sorry, image modes other than 16-bit (unsigned) ");
printf("not supported at the moment.\n");
return 0;
}
/* marker */
xmark[0] = 10;
ymark[0] = 10;
xmark[1] = strtol(argv[2],NULL,0);
ymark[1] = strtol(argv[3],NULL,0);
/* number of frames specified */
startframe = 0;
endframe = 1;
if(argc >= 5){
startframe = strtol(argv[4],NULL,0);
if(startframe > dims[3]) startframe = dims[3];
if(startframe < 0){
printf("Start frame number must be non-negative.\n");
return 1;
}
if(argc >= 6){
endframe = strtol(argv[5],NULL,0);
if(endframe < startframe){
printf("End frame number must be greater than start.\n");
return 2;
}
if(endframe > dims[3]) endframe = dims[3];
} else {
endframe = startframe+1;
}
}
#ifdef DEBUG_PRINT
printf("dimensions: ");
for(i=0;i<ndims;i++)
printf("%ld ", dims[i]);
printf("data type: %d \n", dt);
#endif
/* TODO: warning if dimensions look non-standard */
/* allocate space before reading */
/* Only allocate for one frame; allows images with many frames
* to be loaded without much memory, unlike some programs
* (I'm looking at you, ics_opener/ImageJ ! */
prev = malloc(dims[1]*dims[2]*sizeof(pix_type));
buf = malloc(dims[1]*dims[2]*sizeof(unsigned char));
tmp1 = (int *)malloc(dims[1]*dims[2]*sizeof(int));
tmp2 = (int *)malloc(dims[1]*dims[2]*sizeof(int));
var = (int *)malloc(dims[1]*dims[2]*sizeof(int));
sob = (int *)malloc(dims[1]*dims[2]*sizeof(int));
wsh = (unsigned char*)malloc(dims[1]*dims[2]*sizeof(int));
if((!prev)||(!buf)||(!tmp1)||(!tmp2)||(!var)||(!sob)||(!wsh))
{
printf("Couldn't allocate enough memory.\n");
return 1;
}
/* open CoM file for output */
comf = fopen("comf.txt","w");
if(!comf){
printf("error: couldn't open comf.txt to write center of mass data!\n");
return 22;
}
fprintf(comf,"frame x y\n"); /* legend */
printf("tracking...\n");
/* read sequentially from file. */
/* Each call to IcsGetDataBlock proceeds from the end of the last */
for(i=0;i<endframe;i++){
icserr = IcsGetDataBlock(ics, prev, dims[1]*dims[2]*2);
ICS_CHECK(icserr);
if(i <startframe) continue;
/* we are at the desired frame sequence. */
/* variance filter */
printf("frame %d\n", i);
printf(" Variance filter...\n");
#if 0
if(variance(prev,var,tmp1,tmp2,dims[1],dims[2],1.0,4.0,12))
printf("Variance filter error!\n");
#endif
fast_variance(prev, var, tmp1, dims[1], dims[2]);
printf(" Cusp blur...\n");
blur_cusp(var,tmp1,dims[1],dims[2],230);
/*printf("Diffusion blur...\n");
blur_diffuse(var,tmp2,dims[1],dims[2]);
blur_diffuse(tmp2,var,dims[1],dims[2]);
*/
int maxo;
maxo=0;
for(j=0;j<dims[1]*dims[2];j++) if(var[j]>maxo) maxo=var[j];
printf(" maxo: %d\n", maxo);
printf(" Sobel edge detection...\n");
sobel(var, sob, dims[1], dims[2]);
/* reduce the output of sobel before watershed;
* this greatly reduces processing time */
/* TODO: infer this from the actual histographic data */
for(j=0;j<dims[1]*dims[2];j++) sob[j] /= 10;
for(j=0;j<dims[1]*dims[2];j++) if(sob[j]>255) sob[j]=255;
printf(" watershed assembly...\n");
if(watershed_rep(sob, wsh, tmp1, dims[1], dims[2], xmark, ymark, 2, buf, 8, 8.0)){
printf(" error during watershed!\n");
return 1;
}
/* print center of mass to file */
fprintf(comf,"%d %d %d\n", i, xmark[1], ymark[1]);
/* modify mark */
if(center_of_mass(buf, dims[1], dims[2], 8, xmark+1, ymark+1)){
printf(" zero identified regions!\n aborting.\n");
break; /* abort so we can at least see the results */
}
/* output superimposed image */
for(j=0;j<dims[1]*dims[2];j++)
wsh[j] = prev[j] >> 4;
hardedge(buf, wsh, dims[1], dims[2]);
sprintf(fname,"vesw_sup_%04d.pgm",i);
export_8bit_pgm(wsh, dims[1], dims[2], fname);
sprintf(cmdlin,"pnmtopng < %s > vesw_sup_%04d.png\nrm %s\n", fname, i, fname);
if(system(cmdlin)){
printf("Error during NetPbm invoke!\n");
return 55;
}
}
buf[ymark[1]*dims[1] + xmark[1]]=255-buf[ymark[1]*dims[1] + xmark[1]]; /* mark next CoM */
export_8bit_pgm(buf, dims[1], dims[2], "vesw.pgm");
for(j=0;j<dims[1]*dims[2];j++) buf[j] = var[j]/64;
export_8bit_pgm(buf, dims[1], dims[2], "ve.pgm");
for(j=0;j<dims[1]*dims[2];j++) buf[j] = sob[j]/8;
export_8bit_pgm(buf, dims[1], dims[2], "ves.pgm");
fclose(comf);
/* no need to free memory; that's just silly */
IcsClose(ics);
return 0;
}
