Know slice number? - vtk

I have a DICOM series, with following origin, spacing and extent:
int nExtent[6];
double dSpacing[3];
double dOrigin[3];
m_pReader->GetOutputInformation(0)->Get(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(), nExtent);
m_pReader->GetOutput()->GetSpacing(dSpacing);
m_pReader->GetOutput()->GetOrigin(dOrigin);
where m_pReader is vtkDICOMReader object ...
dOrigin is 0, 0, 0;
dSpacing id 0.447266, 0.447266, 3.998718;
nExtent is 0, 511, 0, 511, 0, 43;
the series is AXIAL.
Now, if I slice the series through AXIAL plan, I could slice the series by 44 slices, like that:
double deltaY = 0.0;
delta += 1.0;
pReslice->Update();
double dSliceSpacing = pReslice->GetOutput()->GetSpacing()[2];
vtkMatrix4x4* pMatrix = pReslice->GetResliceAxes();
// move the dCenter dPoint that we are slicing through
double dPoint[4];
double dCenter[4];
dPoint[0] = 0.0;
dPoint[1] = 0.0;
dPoint[2] = dSliceSpacing * deltaY;
dPoint[3] = 1.0;
pMatrix->MultiplyPoint(dPoint, dCenter);
pMatrix->SetElement(0, 3, dCenter[0]);
pMatrix->SetElement(1, 3, dCenter[1]);
pMatrix->SetElement(2, 3, dCenter[2]);
Everything is allright ...
The problem: if I slice the series through CORONAL plan, the slices number are not 44 !! But how many ? How can I know the slice number if the plan is CORONAL or SAGITTAL ?

On Coronal and Sagittal slicing its more about position instead of slice index.
You need to calculate your min/max origin for each axis (x,y,z)
e.g.
myOriginMax.X = myOrigin.X + ((ImageDimension.SizeX - 1) * mySpacing.X);
You can compute your new origin in your slicing Event, where _positionDelta is your inc/dec value. (more or less pseudo code)
e.g.
double[] _origin = myImageReslice.GetResliceAxesOrigin();
if(_view == "SAGITTAL")
{
_origin[0] = Math.Min(_origin[0] + _positionDelta * mySpacing.X, myOriginMax.X);
}
else if(_view == "CORONAL")
{
_origin[1] = Math.Min(_origin[1] + _positionDelta * mySpacing.Y, myOriginMax.Y);
}
else //AXIAL
{
_origin[2] = Math.Min(_origin[2] + _positionDelta * mySpacing.Z, myOriginMax.Z);
}
myImageReslice.SetReliceAxesOrigin(_origin[0], _origin[1], _origin[2]);
Render();

Yes, it is another compute method ... in my case I have m_pReslice for axial plan, m_pReslice2 for coronal plan, and m_pReslice3 for sagittal plan ... I don't know if is the proper architecture, but applying your algorithm I arrive in the same place :)
m_pReslice->GetResliceAxesOrigin(dOrigin);
int nSizeX = nExtent[0] + nExtent[1];
int nSizeY = nExtent[2] + nExtent[3];
int nSizeZ = nExtent[4] + nExtent[5];
double dOriginMax[3];
dOriginMax[0] = dOrigin[0] + ((nSizeX - 1) * dSpacing[0]);
dOriginMax[1] = dOrigin[1] + ((nSizeY - 1) * dSpacing[1]);
dOriginMax[2] = dOrigin[2] + ((nSizeZ - 1) * dSpacing[2]);
dOrigin[0] = min(dOrigin[0] + 1.0 * dSpacing[0], dOriginMax[0]);
dOrigin[1] = min(dOrigin[1] + 1.0 * dSpacing[1], dOriginMax[1]);
dOrigin[2] = min(dOrigin[2] + 1.0 * dSpacing[2], dOriginMax[2]);
m_pReslice->SetResliceAxesOrigin(dOrigin);
this is the case for m_pReslice (axial plan) ... if I apply the algorithm for m_pReslice2 (coronal) and for m_pReslice3 (sagittal), I still don't know how may slices I have in coronal case (or sagittal) ...

Related

Optimize quadratic curve tracing using numeric methods

I am trying to trace quadratic bezier curves, placing "markers" at a given step length distance. Tried to do it a naive way:
const p = toPoint(map, points[section + 1]);
const p2 = toPoint(map, points[section]);
const {x: cx, y: cy} = toPoint(map, cp);
const ll1 = toLatLng(map, p),
ll2 = toLatLng(map, p2),
llc = toLatLng(map, { x: cx, y: cy });
const lineLength = quadraticBezierLength(
ll1.lat,
ll1.lng,
llc.lat,
llc.lng,
ll2.lat,
ll2.lng
);
for (let index = 0; index < Math.floor(lineLength / distance); index++) {
const t = distance / lineLength;
const markerPoint = getQuadraticPoint(
t * index,
p.x,
p.y,
cx,
cy,
p2.x,
p2.y
);
const markerLatLng = toLatLng(map, markerPoint);
markers.push(markerLatLng);
}
This approach does not work since the correlation of a quadratic curve between t and L is not linear. I could not find a formula, that would give me a good approximation, so looking at solving this problem using numeric methods [Newton]. One simple option that I am considering is to split the curve into x [for instance 10] times more pieces than needed. After that, using the same quadraticBezierLength() function calculate the distance to each of those points. After this, chose the point so that the length is closest to the distance * index.
This however would be a huge overkill in terms of algorithm complexity. I could probably start comparing points for index + 1 from the subset after/without the point I selected already, thus skipping the beginning of the set. This would lower the complexity some, yet still very inefficient.
Any ideas and/or suggestions?
Ideally, I want a function that would take d - distance along the curve, p0, cp, p1 - three points defining a quadratic bezier curve and return an array of coordinates, implemented with the least complexity possible.
OK I found analytic formula for 2D quadratic bezier curve in here:
Calculate the length of a segment of a quadratic bezier
So the idea is simply binary search the parameter t until analytically obtained arclength matches wanted length...
C++ code:
//---------------------------------------------------------------------------
float x0,x1,x2,y0,y1,y2; // control points
float ax[3],ay[3]; // coefficients
//---------------------------------------------------------------------------
void get_xy(float &x,float &y,float t) // get point on curve from parameter t=<0,1>
{
float tt=t*t;
x=ax[0]+(ax[1]*t)+(ax[2]*tt);
y=ay[0]+(ay[1]*t)+(ay[2]*tt);
}
//---------------------------------------------------------------------------
float get_l_naive(float t) // get arclength from parameter t=<0,1>
{
// naive iteration
float x0,x1,y0,y1,dx,dy,l=0.0,dt=0.001;
get_xy(x1,y1,t);
for (int e=1;e;)
{
t-=dt; if (t<0.0){ e=0; t=0.0; }
x0=x1; y0=y1; get_xy(x1,y1,t);
dx=x1-x0; dy=y1-y0;
l+=sqrt((dx*dx)+(dy*dy));
}
return l;
}
//---------------------------------------------------------------------------
float get_l(float t) // get arclength from parameter t=<0,1>
{
// analytic fomula from: https://stackoverflow.com/a/11857788/2521214
float ax,ay,bx,by,A,B,C,b,c,u,k,cu,cb;
ax=x0-x1-x1+x2;
ay=y0-y1-y1+y2;
bx=x1+x1-x0-x0;
by=y1+y1-y0-y0;
A=4.0*((ax*ax)+(ay*ay));
B=4.0*((ax*bx)+(ay*by));
C= (bx*bx)+(by*by);
b=B/(2.0*A);
c=C/A;
u=t+b;
k=c-(b*b);
cu=sqrt((u*u)+k);
cb=sqrt((b*b)+k);
return 0.5*sqrt(A)*((u*cu)-(b*cb)+(k*log(fabs((u+cu))/(b+cb))));
}
//---------------------------------------------------------------------------
float get_t(float l0) // get parameter t=<0,1> from arclength
{
float t0,t,dt,l;
for (t=0.0,dt=0.5;dt>1e-10;dt*=0.5)
{
t0=t; t+=dt;
l=get_l(t);
if (l>l0) t=t0;
}
return t;
}
//---------------------------------------------------------------------------
void set_coef() // compute coefficients from control points
{
ax[0]= ( x0);
ax[1]= +(2.0*x1)-(2.0*x0);
ax[2]=( x2)-(2.0*x1)+( x0);
ay[0]= ( y0);
ay[1]= +(2.0*y1)-(2.0*y0);
ay[2]=( y2)-(2.0*y1)+( y0);
}
//---------------------------------------------------------------------------
Usage:
set control points x0,y0,...
then you can use t=get_t(wanted_arclength) freely
In case you want to use get_t_naive and or get_xy you have to call set_coef first
In case you want to tweak speed/accuracy you can play with the target accuracy of binsearch currently set to1e-10
Here optimized (merged get_l,get_t functions) version:
//---------------------------------------------------------------------------
float get_t(float l0) // get parameter t=<0,1> from arclength
{
float t0,t,dt,l;
float ax,ay,bx,by,A,B,C,b,c,u,k,cu,cb,cA;
// precompute get_l(t) constants
ax=x0-x1-x1+x2;
ay=y0-y1-y1+y2;
bx=x1+x1-x0-x0;
by=y1+y1-y0-y0;
A=4.0*((ax*ax)+(ay*ay));
B=4.0*((ax*bx)+(ay*by));
C= (bx*bx)+(by*by);
b=B/(2.0*A);
c=C/A;
k=c-(b*b);
cb=sqrt((b*b)+k);
cA=0.5*sqrt(A);
// bin search t so get_l == l0
for (t=0.0,dt=0.5;dt>1e-10;dt*=0.5)
{
t0=t; t+=dt;
// l=get_l(t);
u=t+b; cu=sqrt((u*u)+k);
l=cA*((u*cu)-(b*cb)+(k*log(fabs((u+cu))/(b+cb))));
if (l>l0) t=t0;
}
return t;
}
//---------------------------------------------------------------------------
For now, I came up with the below:
for (let index = 0; index < Math.floor(numFloat * times); index++) {
const t = distance / lineLength / times;
const l1 = toLatLng(map, p), lcp = toLatLng(map, new L.Point(cx, cy));
const lutPoint = getQuadraticPoint(
t * index,
p.x,
p.y,
cx,
cy,
p2.x,
p2.y
);
const lutLatLng = toLatLng(map, lutPoint);
const length = quadraticBezierLength(l1.lat, l1.lng, lcp.lat, lcp.lng, lutLatLng.lat, lutLatLng.lng);
lut.push({t: t * index, length});
}
const lut1 = lut.filter(({length}) => !isNaN(length));
console.log('lookup table:', lut1);
for (let index = 0; index < Math.floor(numFloat); index++) {
const t = distance / lineLength;
// find t closest to distance * index
const markerT = lut1.reduce((a, b) => {
return a.t && Math.abs(b.length - distance * index) < Math.abs(a.length - distance * index) ? b.t : a.t || 0;
});
const markerPoint = getQuadraticPoint(
markerT,
p.x,
p.y,
cx,
cy,
p2.x,
p2.y
);
const markerLatLng = toLatLng(map, markerPoint);
}
I think only that my Bezier curve length is not working as I expected.
function quadraticBezierLength(x1, y1, x2, y2, x3, y3) {
let a, b, c, d, e, u, a1, e1, c1, d1, u1, v1x, v1y;
v1x = x2 * 2;
v1y = y2 * 2;
d = x1 - v1x + x3;
d1 = y1 - v1y + y3;
e = v1x - 2 * x1;
e1 = v1y - 2 * y1;
c1 = a = 4 * (d * d + d1 * d1);
c1 += b = 4 * (d * e + d1 * e1);
c1 += c = e * e + e1 * e1;
c1 = 2 * Math.sqrt(c1);
a1 = 2 * a * (u = Math.sqrt(a));
u1 = b / u;
a = 4 * c * a - b * b;
c = 2 * Math.sqrt(c);
return (
(a1 * c1 + u * b * (c1 - c) + a * Math.log((2 * u + u1 + c1) / (u1 + c))) /
(4 * a1)
);
}
I believe that the full curve length is correct, but the partial length that is being calculated for the lookup table is wrong.
If I am right, you want points at equally spaced points in terms of curvilinear abscissa (rather than in terms of constant Euclidean distance, which would be a very different problem).
Computing the curvilinear abscissa s as a function of the curve parameter t is indeed an option, but that leads you to the resolution of the equation s(t) = Sk/n for integer k, where S is the total length (or s(t) = kd if a step is imposed). This is not convenient because s(t) is not available as a simple function and is transcendental.
A better method is to solve the differential equation
dt/ds = 1/(ds/dt) = 1/√(dx/dt)²+(dy/dt)²
using your preferred ODE solver (RK4). This lets you impose your fixed step on s and is computationally efficient.

Is there a way to prevent quaternions from misbehaving?

I am working on a game engine, and I ran into this problem when creating a position rotation scale component. The position and scale work just fine, but when I recalculate the rotation quaternion it will invert itself (i.e. point in the opposite direction). What we do is simple -
Whenever the parent quaternion is changed:
We rotate the parent accordingly - Fine
We calculate the child's local rotation (relative to parent) - Fine
We multiply the parent rotation by the child's local rotation - Not fine.
What we are doing is literally (q2/q1)*q2 -> q2*q1^-1*q2
I am using the http://www.technologicalutopia.com/sourcecode/xnageometry/quaternion.cs.htm implementation, where multiplying quaternions will rotate the first by the second, and dividing does the inverse.
I have spent weeks on this problem, so any help is appreciated. :)
There appears to be an error in the CreateFromRotationMatrix method code in the link you posted. My calculations show that all of the difference calculations have the wrong sign. The corrected code would be this, changes where annotated:
public static Quaternion CreateFromRotationMatrix(Matrix matrix)
{
double num8 = (matrix.M11 + matrix.M22) + matrix.M33;
Quaternion quaternion;
if (num8 > 0.0)
{
double num = (double)sqrt((double)(num8 + 1.0));
quaternion.W = num * 0.5;
num = 0.5 / num;
quaternion.X =-(matrix.M23 - matrix.M32) * num; // -
quaternion.Y =-(matrix.M31 - matrix.M13) * num; // -
quaternion.Z =-(matrix.M12 - matrix.M21) * num; // -
return quaternion;
}
if ((matrix.M11 >= matrix.M22) && (matrix.M11 >= matrix.M33))
{
double num7 = (double)sqrt((double)(((1.0 + matrix.M11) - matrix.M22) - matrix.M33));
double num4 = 0.5 / num7;
quaternion.X = 0.5 * num7;
quaternion.Y = (matrix.M12 + matrix.M21) * num4;
quaternion.Z = (matrix.M13 + matrix.M31) * num4;
quaternion.W =-(matrix.M23 - matrix.M32) * num4; // -
return quaternion;
}
if (matrix.M22 > matrix.M33)
{
double num6 = (double)sqrt((double)(((1.0 + matrix.M22) - matrix.M11) - matrix.M33));
double num3 = 0.5 / num6;
quaternion.X = (matrix.M21 + matrix.M12) * num3;
quaternion.Y = 0.5 * num6;
quaternion.Z = (matrix.M32 + matrix.M23) * num3;
quaternion.W =-(matrix.M31 - matrix.M13) * num3; // -
return quaternion;
}
double num5 = (double)sqrt((double)(((1.0 + matrix.M33) - matrix.M11) - matrix.M22));
double num2 = 0.5 / num5;
quaternion.X = (matrix.M31 + matrix.M13) * num2;
quaternion.Y = (matrix.M32 + matrix.M23) * num2;
quaternion.Z = 0.5 * num5;
quaternion.W =-(matrix.M12 - matrix.M21) * num2; // -
return quaternion;
}
A sample run with a MATLAB mex file (qstuff) as a driver:
>> q2
q2 =
0.531932290454131 -0.391764141068189 0.538459173155997 0.523097137240767
>> qstuff('CreateFromRotationMatrix',qstuff('ToMatrix',q2))
ans =
0.531932290454131 0.391764141068189 -0.538459173155998 -0.523097137240767
>> qstuff('CreateFromRotationMatrixNew',qstuff('ToMatrix',q2))
ans =
0.531932290454131 -0.391764141068189 0.538459173155998 0.523097137240767
The original code doesn't reproduce the quaternion, but the corrected code does.

basic fractal coloring problems

I am trying to get more comfortable with the math behind fractal coloring and understanding the coloring algorithms much better. I am the following paper:
http://jussiharkonen.com/files/on_fractal_coloring_techniques%28lo-res%29.pdf
The paper gives specific parameters to each of the functions, however when I use the same, my results are not quite right. I have no idea what could be going on though.
I am using the iteration count coloring algorithm to start and using the following julia set:
c = 0.5 + 0.25i and p = 2
with the coloring algorithm:
The coloring function simply returns the number of
elements in the truncated orbit divided by 20
And the palette function:
I(u) = k(u − u0),
where k = 2.5 and u0 = 0, was used.
And with a palette being white at 0 and 1, and interpolating to black in-between.
and following this algorithm:
Set z0 to correspond to the position of the pixel in the complex plane.
Calculate the truncated orbit by iterating the formula zn = f(zn−1) starting
from z0 until either
• |zn| > M, or
• n = Nmax,
where Nmax is the maximum number of iterations.
Using the coloring and color index functions, map the resulting truncated
orbit to a color index value.
Determine an RGB color of the pixel by using the palette function
Using this my code looks like the following:
float izoom = pow(1.001, zoom );
vec2 z = focusPoint + (uv * 4.0 - 2.0) * 1.0 / izoom;
vec2 c = vec2(0.5f, 0.25f) ;
const float B = 2.0;
float l;
for( int i=0; i<100; i++ )
{
z = vec2( z.x*z.x - z.y*z.y, 2.0*z.x*z.y ) + c;
if( length(z)>10.0) break;
l++;
}
float ind = basicindex(l);
vec4 col = color(ind);
and have the following index and coloring functions:
float basicindex(float val){
return val / 20.0;
}
vec4 color(float index){
float r = 2.5 * index;
float g = r;
float b = g;
vec3 v = 0.5 - 0.5 * sin(3.14/2.0 + 3.14 * vec3(r, g, b));
return vec4(1.0 - v, 1.0) ;
}
The paper provides the following image:
https://imgur.com/YIZMhaa
While my code produces:
https://imgur.com/OrxdMsN
I get the correct results by using k = 1.0 instead of 2.5, however I would prefer to understand why my results are incorrect. When extending this to the smooth coloring algorithms, my results are still incorrect so I would like to figure this out first.
Let me know if this isn't the correct place for this kind of question and I can move it to the math stack exchange. I wasn't sure which place was more appropriate.
Your image is perfectly implemented for Figure 3.3 in the paper. The other image you posted uses a different routine.
Your figure seems to have that bit of perspective code there at top, but remove that and they should be the same.
If your objection is the color extremes you set that with the "0.5 - 0.5 * ..." part of your code. This makes the darkest black originally 0.5 when in the example image you're trying to duplicate the darkest black should be 1 and the lightest white should be 0.
You're making the whiteness equal to the distance from 0.5
If you ignore the fractal all together you are getting a bunch of values that can be normalized between 0 and 1 and you're coloring those in some particular ways. Clearly the image you are duplicating is linear between 0 and 1 so putting black as 0.5 cannot be correct.
o = {
length : 500,
width : 500,
c : [.5, .25], // c = x + iy will be [x, y]
maxIterate : 100,
canvas : null
}
function point(pos, color){
var c = 255 - Math.round((1 + Math.log(color)/Math.log(o.maxIterate)) * 255);
c = c.toString(16);
if (c.length == 1) c = '0'+c;
o.canvas.fillStyle="#"+c+c+c;
o.canvas.fillRect(pos[0], pos[1], 1, 1);
}
function conversion(x, y, R){
var m = R / o.width;
var x1 = m * (2 * x - o.width);
var y2 = m * (o.width - 2 * y);
return [x1, y2];
}
function f(z, c){
return [z[0]*z[0] - z[1] * z[1] + c[0], 2 * z[0] * z[1] + c[1]];
}
function abs(z){
return Math.sqrt(z[0]*z[0] + z[1]*z[1]);
}
function init(){
var R = (1 + Math.sqrt(1+4*abs(o.c))) / 2,
z, x, y, i;
o.canvas = document.getElementById('a').getContext("2d");
for (x = 0; x < o.width; x++){
for (y = 0; y < o.length; y++){
i = 0;
z = conversion(x, y, R);
while (i < o.maxIterate && abs(z) < R){
z = f(z, o.c);
if (abs(z) > R) break;
i++;
}
if (i) point([x, y], i / o.maxIterate);
}
}
}
init();
<canvas id="a" width="500" height="500"></canvas>
via: http://jsfiddle.net/3fnB6/29/

New cords for larger line

I have a class representing lines on two-dimensional space:
class Line {
Point start;
Point end;
Float length; // calculated property, something like sqrt(pow(end.x - start.x, 2) + pow(end.y - start.y, 2))
}
I want a method to make a line bigger from the center.
For example, if I create some parallel to X:
Point start = Point(1, 3)
Point end = Point(1, 10)
Line newLine = Line(start, end) // newLine.length here is 7
and then call method makeBigger:
newLine.makeBigger(4); // pass number of points here
I want to receive new line (or modify old's start / end properties) with start = (1,1) / end = (1, 12), so its length becomes 11.
Please note, that I want to consider angles as well.
As far as I understand, makeBigger(4) denotes than you want to increase length by 4. So use simple proportionality
newlength = length + increasevalue
dx = (end.x - start.x) / 2
mx = (end.x + start.x) / 2
newstart.x = mx - dx * newlength / length
newend.x = mx + dx * newlength / length
and similar for y

maximum volume of a box with perimeter and area given

Here's the link to the question..
http://www.codechef.com/problems/J7
I figured out that 2 edges have to be equal in order to give the maximum volume, and then used x, x, a*x as the lengths of the three edges to write the equations -
4*x + 4*x + 4*a*x = P (perimeter) and,
2*x^2 + 4*(a*x *x) = S (total area of the box)
so from the first equation I got x in terms of P and a, and then substituted it in the second equation and then got a quadratic equation with the unknown being a. and then I used the greater root of a and got x.
But this method seems to be giving the wrong answer! :|
I know that there isn't any logical error in this. Maybe some formatting error?
Here's the main code that I've written :
{
public static void main(String[] args)
{
TheBestBox box = new TheBestBox();
reader = box.new InputReader(System.in);
writer = box.new OutputWriter(System.out);
getAttributes();
writer.flush();
reader.close();
writer.close();
}
public static void getAttributes()
{
t = reader.nextInt(); // t is the number of test cases in the question
for (int i = 0; i < t; i++)
{
p = reader.nextInt(); // p is the perimeter given as input
area = reader.nextInt(); // area of the whole sheet, given as input
a = findRoot(); // the fraction by which the third side differs by the first two
side = (double) p / (4 * (2 + a)); // length of the first and the second sides (equal)
height = a * side; // assuming that the base is a square, the height has to be the side which differs from the other two
// writer.println(side * side * height);
// System.out.printf("%.2f\n", (side * side * height));
writer.println(String.format("%.2f", (side * side * height))); // just printing out the final answer
}
}
public static double findRoot() // the method to find the 2 possible fractions by which the height can differ from the other two sides and return the bigger one of them
{
double a32, b, discriminant, root1, root2;
a32 = 32 * area - p * p;
b = 32 * area - 2 * p * p;
discriminant = Math.sqrt(b * b - 4 * 8 * area * a32);
double temp;
temp = 2 * 8 * area;
root1 = (- b + discriminant) / temp;
root2 = (- b - discriminant) / temp;
return Math.max(root1, root2);
}
}
could someone please help me out with this? Thank You. :)
I also got stuck in this question and realized that can be done by making equation of V(volume) in terms of one side say 'l' and using differentiation to find maximum volume in terms of any one side 'l'.
So, equations are like this :-
P = 4(l+b+h);
S = 2(l*b+b*h+l*h);
V = l*b*h;
so equation in l for V = (l^3) - (l^2)P/4 + lS/2 -------equ(1)
After differentiation we get:-
d(V)/d(l) = 3*(l^2) - l*P/2 + S/2;
to get max V we need to equate above equation to zero(0) and get the value of l.
So, solutions to a quadratic equation will be:-
l = ( P + sqrt((P^2)-24S) ) / 24;
so substitute this l in equation(1) to get max volume.

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