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Suppose I have a series of (imperfect) azimuth readouts, giving me vague angles between a number of points. Lines projected from points A, B, C obviously [-don't-always-] never converge in a single point to define the location of point D. Hence, angles as viewed from A, B and C need to be adjusted.
To make it more fun, I might be more certain of the relative positions of specific points (suppose I locate them on a satellite image, or I know for a fact they are oriented perfectly north-south), so I might want to use that certainty in my calculations and NOT adjust certain angles at all.
By what technique should I average the resulting coordinates, to achieve a "mostly accurate" overall shape?
I considered treating the difference between non-adjusted and adjusted angles as "tension" and trying to "relieve" it in subsequent passes, but that approach gives priority to points calculated earlier.
Another approach could be to calculate the total "tension" in the set, then shake all angles by a random amount, see if that resulted in less tension, and repeat for possibly improved results, trying to evolve a possibly better solution.
As I understand it you have a bunch of unknown points (p[] say) and a number of measurements of azimuths, say Az[i,j] of p[j] from p[i]. You want to find the coordinates of the points.
You'll need to fix one point. This is because if the values of p[] is a solution -- i.e. gave the measured azimuths -- so too is q[] where for some fixed x,
q[i] = p[i] + x
I'll suppose you fix p[0].
You'll also need to fix a distance. This is because if p[] is a solution, so too is q[] where now for some fixed s,
q[i] = p[0] + s*(p[i] - p[0])
I'll suppose you fix dist(p[0], p[1]), and that there is and azimuth Az[1,2]. You'd be best to choose p[0] p[1] so that there is a reliable azimuth between them. Then we can compute p[1].
The usual way to approach such problems is least squares. That is we seek p[] to minimise
Sum square( (Az[i,j] - Azimuth( p[i], p[j]))/S[i,j])
where Az[i,j] is your measurement data
Azimuth( r, s) is the function that gives the azimuth of the point s from the point r
S[i,j] is the 'sd' of the measurement A[i,j] -- the higher the sd of a particular observation is, relative to the others, the less it affects the final result.
The above is a non linear least squares problem. There are many solvers available for this, but generally speaking as well as providing the data -- the Az[] and the S[] -- and the observation model -- the Azimuth function -- you need to provide an initial estimate of the state -- the values sought, in your case p[2] ..
It is highly likely that if your initial estimate is wrong the solver will fail.
One way to find this estimate would be to start with a set K of known point indices and seek to expand it. You would start with K being {0,1}. Then look for points that have as many azimuths as possible to points in K, and for such points estimate geometrically their position from the known points and the azimuths, and add them to K. If at the end you have all the points in K, then you can go on to the least squares. If it isn't its possible that a different pair of initial fixed points might do better, or maybe you are stuck.
The latter case is a real possibility. For example suppose you had points p[0],p[1],p[2],p[3] and azimuths A[0,1], A[1,2], A[1,3], A[2,3].
As above we fix the positions of p[0] and p[1]. But we can't compute positions of p[2] and p[3] because we do not know the distances of 2 or 3 from 1. The 1,2,3 triangle could be scaled arbitrarily and still give the same azimuths.
I am running into problems when computing the relative risk estimation (relrisk.ppp) of two point patterns: One with four marks in a rectangular region and the other with two marks in a circular region.
For the first pattern with four marks, I am able to get the relative risk and the resulting object in a large imlist with 4 elements corresponding to each mark.
However, for the second pattern, it gives a list of 10 elements, of which the first matrix v is empty with NA entries. I am breaking my head on what possibly could be wrong when the created point pattern objects seems to be identical. Any help will be appreciated. Thanks.
For your first dataset, the result is a list of image objects (a list of four objects of class im). For your second dataset, the result of relrisk.ppp is a single image (object of class im). This is the default behaviour when there are only two possible types of points (two possible mark values). See help(relrisk.ppp).
In all cases, you should just be able to plot and print the resulting object. You don't need to examine the internal data of the image.
More explanation: when there are only two possible types of points, the default behaviour of relrisk.ppp is to treat them as case-control data, where the points belonging to the first type are treated as controls (e.g. non-infected people), and the points of the second type are treated as cases (e.g. infected people). The ratio of intensities (cases divided by controls) is estimated as an image.
If you don't want this to happen, set the argument casecontrol=FALSE and then relrisk.ppp will always return a list of images, with one image for each possible mark. Each image gives the spatially-varying probability of that type of point.
It's all explained in help(relrisk.ppp) or in the book.
I have three arrays of points:
A=[[5,2],[1,0],[5,1]]
B=[[3,3],[5,3],[1,1]]
C=[[4,2],[9,0],[0,0]]
I need the most efficient way to find the three points (one for each array) that are closest to each other (within one pixel in each axis).
What I'm doing right now is taking one point as reference, let's say A[0], and cycling all other B and C points looking for a solution. If A[0] gives me no result I'll move the reference to A[1] and so on. This approach as a huge problem because if I increase the number of points for each array and/or the number of arrays it requires too much time to converge some times, especially if the solution is in the last members of the arrays. So I'm wondering if there is any way to do this without maybe using a reference, or any quicker way than just looping all over the elements.
The rules that I must follow are the following:
the final solution has to be made by only one element from each array like: S=[A[n],B[m],C[j]]
each selected element has to be within 1 pixel in X and Y from ALL the other members of the solution (so Xi-Xj<=1 and Yi-Yj<=1 for each member of the solution).
For example in this simplified case the solution would be: S=[A[1],B[2],C[1]]
To clarify further the problem: what I wrote above it's just a simplify example to explain what I need. In my real case I don't know a priori the length of the lists nor the number of lists I have to work with, could be A,B,C, or A,B,C,D,E... (each of one with different number of points) etc. So I also need to find a way to make it as general as possible.
This requirement:
each selected element has to be within 1 pixel in X and Y from ALL the other members of the solution (so Xi-Xj<=1 and Yi-Yj<=1 for each member of the solution).
massively simplifies the problem, because it means that for any given (xi, yi), there are only nine possible choices of (xj, yj).
So I think the best approach is as follows:
Copy B and C into sets of tuples.
Iterate over A. For each point (xi, yi):
Iterate over the values of x from xi−1 to xi+1 and the values of y from yi−1 to yi+1. For each resulting point (xj, yj):
Check if (xj, yj) is in B. If so:
Iterate over the values of x from max(xi, xj)−1 to min(xi, xj)+1 and the values of y from max(yi, yj)−1 to min(yi, yj)+1. For each resulting point (xk, yk):
Check if (xk, yk) is in C. If so, we're done!
If we get to the end without having a match, that means there isn't one.
This requires roughly O(len(A) + len(B) + len(C)) time and O(len(B) + len(C) extra space.
Edited to add (due to a follow-up question in the comments): if you have N lists instead of just 3, then instead of nesting N loops deep (which gives time exponential in N), you'll want to do something more like this:
Copy B, C, etc., into sets of tuples, as above.
Iterate over A. For each point (xi, yi):
Create a set containing (xi, yi) and its eight neighbors.
For each of the lists B, C, etc.:
For each element in the set of nine points, see if it's in the current list.
Update the set to remove any points that aren't in the current list and don't have any neighbors in the current list.
If the set still has at least one element, then — great, each list contained a point that's within one pixel of that element (with all of those points also being within one pixel of each other). So, we're done!
If we get to the end without having a match, that means there isn't one.
which is much more complicated to implement, but is linear in N instead of exponential in N.
Currently, you are finding the solution with a bruteforce algorithm which has a O(n2) complexity. If your lists contains 1000 items, your algo will need 1000000 iterations to run... (It's even O(n3) as tobias_k pointed out)
Like you can see there: https://en.wikipedia.org/wiki/Closest_pair_of_points_problem, you could improve it by using a divide and conquer algorithm, which would run in a O(n log n) time.
You should search for Delaunay triangulation and/or Voronoi diagram implementations.
NB: if you can use external libs, you should also consider taking a look at the scipy lib: https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.spatial.Delaunay.html
How do I compute the generalized mean for extreme values of p (very close to 0, or very large) with reasonable computational error?
As per your link, the limit for p going to 0 is the geometric mean, for which bounds are derived.
The limit for p going to infinity is the maximum.
I have been struggling with the same problem. Here is how I handled this:
Let gmean_p(x1,...,xn) be the generalized mean where p is real but not 0, and x1, ..xn nonnegative. For M>0, we have gmean_p(x1,...,xn) = M*gmean_p(x1/M,...,xn/M) of which the latter form can be exploited to reduce the computational error. For large p, I use M=max(x1,...,xn) and for p close to 0, I use M=mean(x1,..xn). In case M=0, just add a small positive constant to it. This did the job for me.
I suspect if you're interested in very large or small values of p, it may be best to do some form of algebraic manipulation of the generalized-mean formula before putting in numerical values.
For example, in the small-p limit, one can show that the generalized mean tends to the n'th root of the product x_1*x_2*...x_n. The higher order terms in p involve sums and products of log(x_i), which should also be relatively numerically stable to compute. In fact, I believe the first-order expansion in p has a simple relationship to the variance of log(x_i):
If one applies this formula to a set of 100 random numbers drawn uniformly from the range [0.2, 2], one gets a trend like this:
which here shows the asymptotic formula becoming pretty accurate for p less than about 0.3, and the simple formula only failing when p is less than about 1e-10.
The case of large p, is dominated by that x_i which has the largest magnitude (lets call that index i_max). One can rearrange the generalized mean formula to take the following form, which has less pathological behaviour for large p:
If this is applied (using standard numpy routines including numpy.log1p) to another 100 uniformly distributed samples over [0.2, 2.0], one finds that the rearranged formula agrees essentially exactly with the simple formula, but remains valid for much larger values of p for which the simple formula overflows when computing powers of x_i.
(Note that the left-hand plot has the blue curve for the simple formula shifted up by 0.1 so that one can see where it ends due to overflows. For p less than about 1000, the two curves would otherwise be indistinguishable.)
I think the answer here should be to use a recursive solution. In the same way that mean(1,2,3,4)=mean(mean(1,2),mean(3,4)), you can do this kind of recursion for generalized means. What this buys you is that you won't need to do as many sums of really large numbers and you decrease the likelihood of creating an overflow. Also, the other danger when working with floating point numbers is when adding numbers of very different magnitudes (or subtracting numbers of very similar magnitudes). So to avoid these kinds of rounding errors it might help to sort your data before you try and calculate the generalized mean.
Here's a hunch:
First convert all your numbers into a representation in base p. Now to raise to a power of 1/p or p, you just have to shift them --- so you can very easily do all powers without losing precision.
Work out your mean in base p, then convert the result back to base two.
If that doesn't work, an even less practical hunch:
Try working out the discrete Fourier transform, and relating that to the discrete Fourier transform of the input vector.
I would like to sort a one-dimensional list of colors so that colors that a typical human would perceive as "like" each other are near each other.
Obviously this is a difficult or perhaps impossible problem to get "perfectly", since colors are typically described with three dimensions, but that doesn't mean that there aren't some sorting methods that look obviously more natural than others.
For example, sorting by RGB doesn't work very well, as it will sort in the following order, for example:
(1) R=254 G=0 B=0
(2) R=254 G=255 B=0
(3) R=255 G=0 B=0
(4) R=255 G=255 B=0
That is, it will alternate those colors red, yellow, red, yellow, with the two "reds" being essentially imperceivably different than each other, and the two yellows also being imperceivably different from each other.
But sorting by HLS works much better, generally speaking, and I think HSL even better than that; with either, the reds will be next to each other, and the yellows will be next to each other.
But HLS/HSL has some problems, too; things that people would perceive as "black" could be split far apart from each other, as could things that people would perceive as "white".
Again, I understand that I pretty much have to accept that there will be some splits like this; I'm just wondering if anyone has found a better way than HLS/HSL. And I'm aware that "better" is somewhat arbitrary; I mean "more natural to a typical human".
For example, a vague thought I've had, but have not yet tried, is perhaps "L is the most important thing if it is very high or very low", but otherwise it is the least important. Has anyone tried this? Has it worked well? What specifically did you decide "very low" and "very high" meant? And so on. Or has anyone found anything else that would improve upon HSL?
I should also note that I am aware that I can define a space-filling curve through the cube of colors, and order them one-dimensionally as they would be encountered while travelling along that curve. That would eliminate perceived discontinuities. However, it's not really what I want; I want decent overall large-scale groupings more than I want perfect small-scale groupings.
Thanks in advance for any help.
If you want to sort a list of colors in one dimension you first have to decide by what metrics you are going to sort them. The most sense to me is the perceived brightness (related question).
I have came across 4 algorithms to sort colors by brightness and compared them. Here is the result.
I generated colors in cycle where only about every 400th color was used. Each color is represented by 2x2 pixels, colors are sorted from darkest to lightest (left to right, top to bottom).
1st picture - Luminance (relative)
0.2126 * R + 0.7152 * G + 0.0722 * B
2nd picture - http://www.w3.org/TR/AERT#color-contrast
0.299 * R + 0.587 * G + 0.114 * B
3rd picture - HSP Color Model
sqrt(0.299 * R^2 + 0.587 * G^2 + 0.114 * B^2)
4td picture - WCAG 2.0 SC 1.4.3 relative luminance and contrast ratio formula
Pattern can be sometimes spotted on 1st and 2nd picture depending on the number of colors in one row. I never spotted any pattern on picture from 3rd or 4th algorithm.
If i had to choose i would go with algorithm number 3 since its much easier to implement and its about 33% faster than the 4th
You cannot do this without reducing the 3 color dimensions to a single measurement. There are many (infinite) ways of reducing this information, but it is not mathematically possible to do this in a way that ensures that two data points near each other on the reduced continuum will also be near each other in all three of their component color values. As a result, any formula of this type will potentially end up grouping dissimilar colors.
As you mentioned in your question, one way to sort of do this would be to fit a complex curve through the three-dimensional color space occupied by the data points you're trying to sort, and then reduce each data point to its nearest location on the curve and then to that point's distance along the curve. This would work, but in each case it would be a solution custom-tailored to a particular set of data points (rather than a generally applicable solution). It would also be relatively expensive (maybe), and simply wouldn't work on a data set that was not nicely distributed in a curved-line sort of way.
A simpler alternative (that would not work perfectly) would be to choose two "endpoint" colors, preferably on opposite sides of the color wheel. So, for example, you could choose Red as one endpoint color and Blue as the other. You would then convert each color data point to a value on a scale from 0 to 1, where a color that is highly Reddish would get a score near 0 and a color that is highly Bluish would get a score near 1. A score of .5 would indicate a color that either has no Red or Blue in it (a.k.a. Green) or else has equal amounts of Red and Blue (a.k.a. Purple). This approach isn't perfect, but it's the best you can do with this problem.
There are several standard techniques for reducing multiple dimensions to a single dimension with some notion of "proximity".
I think you should in particular check out the z-order transform.
You can implement a quick version of this by interleaving the bits of your three colour components, and sorting the colours based on this transformed value.
The following Java code should help you get started:
public static int zValue(int r, int g, int b) {
return split(r) + (split(g)<<1) + (split(b)<<2);
}
public static int split(int a) {
// split out the lowest 10 bits to lowest 30 bits
a=(a|(a<<12))&00014000377;
a=(a|(a<<8)) &00014170017;
a=(a|(a<<4)) &00303030303;
a=(a|(a<<2)) &01111111111;
return a;
}
There are two approaches you could take. The simple approach is to distil each colour into a single value, and the list of values can then be sorted. The complex approach would depend on all of the colours you have to sort; perhaps it would be an iterative solution that repeatedly shuffles the colours around trying to minimise the "energy" of the entire sequence.
My guess is that you want something simple and fast that looks "nice enough" (rather than trying to figure out the "optimum" aesthetic colour sort), so the simple approach is enough for you.
I'd say HSL is the way to go. Something like
sortValue = L * 5 + S * 2 + H
assuming that H, S and L are each in the range [0, 1].
Here's an idea I came up with after a couple of minutes' thought. It might be crap, or it might not even work at all, but I'll spit it out anyway.
Define a distance function on the space of colours, d(x, y) (where the inputs x and y are colours and the output is perhaps a floating-point number). The distance function you choose may not be terribly important. It might be the sum of the squares of the differences in R, G and B components, say, or it might be a polynomial in the differences in H, L and S components (with the components differently weighted according to how important you feel they are).
Then you calculate the "distance" of each colour in your list from each other, which effectively gives you a graph. Next you calculate the minimum spanning tree of your graph. Then you identify the longest path (with no backtracking) that exists in your MST. The endpoints of this path will be the endpoints of the final list. Next you try to "flatten" the tree into a line by bringing points in the "branches" off your path into the path itself.
Hmm. This might not work all that well if your MST ends up in the shape of a near-loop in colour space. But maybe any approach would have that problem.