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In a given domain, I need to represent mathematical plane in 3D space, so I intend to create a Plane3D class.
I would also have Point3D, Vector3D, Ray3D, and so on. Main use case would be to test/find line-plane intersections, line-plane angles, and other geometric operations.
Question is:
Which would be a good, canonical, computation-friendly way to implement plane definition in a class?
Most obvious candidates would be "point-normal" form, with six numeric parameters (three coordinates for the point, three for the vector) and "general (algebraic) form", with four numeric parameters (one coefficient per coordinate and one constant). Is one of them computationally preferrable?
Also, is there any open source, high level 3D Geometry library already implementing this class, which would be worth taking a look for inspiration?
OBS: Since .NET has System.Windows.Media.Media3D library with some useful classes, most probably I'll implement this in C#, taking advantage of Point3D and Vector3D structs, but I think the question is language-agnostic.
I'd go for what you call algebraic form. A point (x,y,z) is on a plane (a,b,c,d) if a*x+b*y+c*z+d=0.
To intersect that plane with a line spanned by (x1,y1,z1) and (x2,y2,z2), compute s1=a*x1+b*y1+c*z1+d and s2=a*x2+b*y2+c*z2+d. Then your point of intersection is defined by
x=(s1*x2-s2*x1)/(s1-s2)
y=(s1*y2-s2*y1)/(s1-s2)
z=(s1*z2-s2*z1)/(s1-s2)
To compute the angle between a line and a plane, simply compute
sin(α)=(a*x+b*y+c*z)/sqrt((a*a+b*b+c*c)*(x*x+y*y+z*z))
where (a,b,c) represents the normal vector in this representation of the plane, and (x,y,z) is the direction vector of the line, i.e. (x2-x1,y2-y1,z2-z1). The equation is essentially a normalized dot product, and as such is equivalent to the cosine between the two vectors. And since the normal vector is perpendicular to the plane, and sine and cosine differ by 90°, this means that you get the sine of the angle between the line and the plane itself.
I want to detect the best rototraslation matrix between two set of points.
The second set of points is the same of the first, but rotated, traslated and affecteb by noise.
I tried to use least squared method by obviously the solution is usually similar to a rotation matrix, but with incompatible structure (for example, where i should get a value that represents the cosine of an angle i could get a value >1).
I've searched for the Constrained Least Squared method but it seems to me that the constrains of a rototraslation matrix cannot be expressed in this form.
In this PDF i've stated the problem more formally:
http://dl.dropbox.com/u/3185608/minquad_en.pdf
Thank you for the help.
The short answer: What you will need here is "Principal Component Analysis".
Apply this to both sets of points centered at their respective centers of mass. The PCA will effectively give you a rotation matrix for each aligned to the data set principal components. Multiplying the inverse matrix of the original set by the new rotation will give you a matrix that takes the old (centered) set to the new. Inverse translations and translations can similarly be applied to the rotation to create a homogeneous matrix that maps the one set to the other.
The book PRINCE, Simon JD. Computer vision: models, learning, and inference. Cambridge University Press, 2012.
gives, in Appendix "B.4 Reparameterization", some info about how to constrain a matrix to be a rotation matrix.
It seems to me that your problem has also a solution based on SVD: see the Kabsch algorithm also described by Olga Sorkine-Hornung and Michael Rabinovich in
Least-Squares Rigid Motion Using SVD and, more practically, by Nghia Kien Ho in FINDING OPTIMAL ROTATION AND TRANSLATION BETWEEN CORRESPONDING 3D POINTS.
Suppose you have a list of 2D points with an orientation assigned to them. Let the set S be defined as:
S={ (x,y,a) | (x,y) is a 2D point, a is an orientation (an angle) }.
Given an element s of S, we will indicate with s_p the point part and with s_a the angle part. I would like to know if there exist an efficient data structure such that, given a query point q, is able to return all the elements s in S such that
(dist(q_p, s_p) < threshold_1) AND (angle_diff(q_a, s_a) < threshold_2) (1)
where dist(p1,p2), with p1,p2 2D points, is the euclidean distance, and angle_diff(a1,a2), with a1,a2 angles, is the difference between angles (taken to be the smallest one). The data structure should be efficient w.r.t. insertion/deletion of elements and the search as defined above. The number of vectors can grow up to 10.000 and more, but take this with a grain of salt.
Now suppose to change the above requirement: instead of using the condition (1), let's request all the elements of S such that, given a distance function d, we want all elements of S such that d(q,s) < threshold. If i remember well, this last setup is called range-search. I don't know if the first case can be transformed in the second.
For the distance search I believe the accepted best method is a Binary Space Partition tree. This can be stored as a series of bits. Each two bits (for a 2D tree) or three bits (for a 3D tree) subdivides the space one more level, increasing resolution.
Using a BSP, locating a set of objects to compare distances with is pretty easy. Just find the smallest set of squares or cubes which contain the edges of your distance box.
For the angle, I don't know of anything. I suppose that you could store each object in a second list or tree sorted by its angle. Then you would find every object at the proper distance using the BSP, every object at the proper angles using the angle tree, then do a set intersection.
You have effectively described a "three dimensional cyclindrical space", ie. a space that is locally three dimensional but where one dimension is topologically cyclic. In other words, it is locally flat and may be modeled as the boundary of a four-dimensional object C4 in (x, y, z, w) defined by
z^2 + w^2 = 1
where
a = arctan(w/z)
With this model, the space defined by your constraints is a 2-dimensional cylinder wrapped "lengthwise" around a cross section wedge, where the wedge wraps around the 4-d cylindrical space with an angle of 2 * threshold_2. This can be modeled using a "modified k-d tree" approach (modified 3-d tree), where the data structure is not a tree but actually a graph (it has cycles). You can still partition this space into cells with hyperplane separation, but traveling along the curve defined by (z, w) in the positive direction may encounter a point encountered in the negative direction. The tree should be modified to actually lead to these nodes from both directions, so that the edges are bidirectional (in the z-w curve direction - the others are obviously still unidirectional).
These cycles do not change the effectiveness of the data structure in locating nearby points or allowing your constraint search. In fact, for the most part, those algorithms are only slightly modified (the simplest approach being to hold a visited node data structure to prevent cycles in the search - you test the next neighbors about to be searched).
This will work especially well for your criteria, since the region you define is effectively bounded by these axis-defined hyperplane-bounded cells of a k-d tree, and so the search termination will leave a region on average populated around pi / 4 percent of the area.
I have a set of vectors in multidimensional space (may be several thousands of dimensions). In this space, I can calculate distance between 2 vectors (as a cosine of the angle between them, if it matters). What I want is to visualize these vectors keeping the distance. That is, if vector a is closer to vector b than to vector c in multidimensional space, it also must be closer to it on 2-dimensional plot. Is there any kind of diagram that can clearly depict it?
I don't think so. Imagine any twodimensional picture of a tetrahedron. There is no way of depicting the four vertices in two dimensions with equal distances from each other. So you will have a hard time trying to depict more than three n-dimensional vectors in 2 dimensions conserving their mutual distances.
(But right now I can't think of a rigorous proof.)
Update:
Ok, second idea, maybe it's dumb: If you try and find clusters of closer associated objects/texts, then calculate the center or mean vector of each cluster. Then you can reduce the problem space. At first find a 2D composition of the clusters that preserves their relative distances. Then insert the primary vectors, only accounting for their relative distances within a cluster and their distance to the center of to two or three closest clusters.
This approach will be ok for a large number of vectors. But it will not be accurate in that there always will be somewhat similar vectors ending up at distant places.
I have a 3D datacube, with two spatial dimensions and the third being a multi-band spectrum at each point of the 2D image.
H[x, y, bands]
Given a wavelength (or band number), I would like to extract the 2D image corresponding to that wavelength. This would be simply an array slice like H[:,:,bnd]. Similarly, given a spatial location (i,j) the spectrum at that location is H[i,j].
I would also like to 'smooth' the image spectrally, to counter low-light noise in the spectra. That is for band bnd, I choose a window of size wind and fit a n-degree polynomial to the spectrum in that window. With polyfit and polyval I can find the fitted spectral value at that point for band bnd.
Now, if I want the whole image of bnd from the fitted value, then I have to perform this windowed-fitting at each (i,j) of the image. I also want the 2nd-derivative image of bnd, that is, the value of the 2nd-derivative of the fitted spectrum at each point.
Running over the points, I could polyfit-polyval-polyder each of the x*y spectra. While this works, this is a point-wise operation. Is there some pytho-numponic way to do this faster?
If you do least-squares polynomial fitting to points (x+dx[i],y[i]) for a fixed set of dx and then evaluate the resulting polynomial at x, the result is a (fixed) linear combination of the y[i]. The same is true for the derivatives of the polynomial. So you just need a linear combination of the slices. Look up "Savitzky-Golay filters".
EDITED to add a brief example of how S-G filters work. I haven't checked any of the details and you should therefore not rely on it to be correct.
So, suppose you take a filter of width 5 and degree 2. That is, for each band (ignoring, for the moment, ones at the start and end) we'll take that one and the two on either side, fit a quadratic curve, and look at its value in the middle.
So, if f(x) ~= ax^2+bx+c and f(-2),f(-1),f(0),f(1),f(2) = p,q,r,s,t then we want 4a-2b+c ~= p, a-b+c ~= q, etc. Least-squares fitting means minimizing (4a-2b+c-p)^2 + (a-b+c-q)^2 + (c-r)^2 + (a+b+c-s)^2 + (4a+2b+c-t)^2, which means (taking partial derivatives w.r.t. a,b,c):
4(4a-2b+c-p)+(a-b+c-q)+(a+b+c-s)+4(4a+2b+c-t)=0
-2(4a-2b+c-p)-(a-b+c-q)+(a+b+c-s)+2(4a+2b+c-t)=0
(4a-2b+c-p)+(a-b+c-q)+(c-r)+(a+b+c-s)+(4a+2b+c-t)=0
or, simplifying,
22a+10c = 4p+q+s+4t
10b = -2p-q+s+2t
10a+5c = p+q+r+s+t
so a,b,c = p-q/2-r-s/2+t, (2(t-p)+(s-q))/10, (p+q+r+s+t)/5-(2p-q-2r-s+2t).
And of course c is the value of the fitted polynomial at 0, and therefore is the smoothed value we want. So for each spatial position, we have a vector of input spectral data, from which we compute the smoothed spectral data by multiplying by a matrix whose rows (apart from the first and last couple) look like [0 ... 0 -9/5 4/5 11/5 4/5 -9/5 0 ... 0], with the central 11/5 on the main diagonal of the matrix.
So you could do a matrix multiplication for each spatial position; but since it's the same matrix everywhere you can do it with a single call to tensordot. So if S contains the matrix I just described (er, wait, no, the transpose of the matrix I just described) and A is your 3-dimensional data cube, your spectrally-smoothed data cube would be numpy.tensordot(A,S).
This would be a good point at which to repeat my warning: I haven't checked any of the details in the few paragraphs above, which are just meant to give an indication of how it all works and why you can do the whole thing in a single linear-algebra operation.