I am trying to take numbers from two intervals in Julia. The problem is the following,
I am trying to create concentric spheres and I need to generate vectors of dimension equal to 15 filled with numbers taken from each circle. The code is:
rmax = 5
ra = fill(0.0,1,rmax)
for i=1:rmax-1
ra[:,i].=rad/i
ra[:,rmax].= 0
end
for i=1:3
ptset = Any[]
for j=1:200
yt= 0
yt= rand(Truncated(Normal(0, 1), -ra[i], ra[i] ))
if -ra[(i+1)] < yt <= -ra[i] || ra[(i+1)] <= yt < ra[i]
push!(ptset,yt)
if length(ptset) == 15
break
end
end
end
end
Here, I am trying to generate spheres with uniform random numbers inside of each one; In this case, yt is only part of the construction of the numbers inside the sphere.
I would like to generate points in a sphere with radius r0 (ra[:,4] for this case), then points distributed from the edge of the first sphere to the second one wit radius r1 (here ra[:,3]) and so on.
In order to do that, I try to take elements that fulfill one of the two conditions -ra[(i+1)] < yt <= -ra[i]
or ra[(i+1)] <= yt < ra[i], i.e. I would like to generate a vector with positive and negative numbers. I used the operator || but it seems to take only the positive part. I am new in Julia and I am not sure how to take the elements from both parts of the interval. Does anyone has a hit on how to do it?. Thanks in advance
I hope I understood you correctly. First, we need to be able to sample uniformly from an N-dimensional shell with radii r0 and r1:
using Random
using LinearAlgebra: normalize
struct Shell{N}
r0::Float64
r1::Float64
end
Base.eltype(::Type{<:Shell}) = Vector{Float64}
function Random.rand(rng::Random.AbstractRNG, d::Random.SamplerTrivial{Shell{N}}) where {N}
shell = d[]
Δ = shell.r1 - shell.r0
θ = normalize(randn(N)) # uniformly distributed N-dimensional direction of length 1
r = shell.r0 .* θ # scale to a point on the interior of the shell
return r .+ Δ .* θ .* .√rand(N) # add a uniformly random segment between r0 and r1
end
(See here for more info about hooking into Random. You could equally implement a new Distribution, but that's not really necessary.)
Most importantly, a truncated normal will not result in a uniform distribution, but neither will adding a uniform scaling into the right direction: see here for why the square root is necessary (and I hope I got it right; you should check the math once more).
Then we can just create a sequence of shell samples with nested radii:
rmax = 5
rad = 10.0
ra = range(0, rad, length=rmax)
ptset = [rand(Shell{2}(ra[i], ra[i+1]), 15) for i = 1:(rmax - 1)]
(This part I wasn't really sure about, but the point should be clear.)
Related
i am trying to learn matlab.
I am trying to make a program that draw these imaginary numbers: ("," = decimal number)
and determine what of the 500 numbers that is closest the real axis.
And i need a little guidance.
What do i have to do to solve this task?
I was thinking about making a loop where all the "values" get stored in a array:
[code]
n= 1
while n < 500
value=1+0.1^n;
disp(value)
n=n+1[/code]
(seems like value is printing wrong values? and how to store in a array?)
And then somehow determine what number that is nearest the real axis and then display the value.
would be really grateful if someone could help me.
thanks in advance.
MATLAB creates imaginary numbers by appending an i or j term with the number. For example, if you wanted to create an imaginary number such that the real component was 1 and the imaginary component was 1, you would simply do:
>> A = 1 + i
A =
1.0000 + 1.0000i
You can see that there is a distinct real component as well as an imaginary component and is stored in A. Similarly, if you want to make the imaginary component have anything other than 1, you would need to add a constant in front of the i (or j). Something like:
>> A = 3 + 6i
A =
3.0000 + 6.0000i
Therefore, for your task, you simply need to create a vector of n between 1 to 500, input this into the above equation, then plot the resulting imaginary numbers. In this case, you would plot the real component on the x axis and the imaginary component on the y axis. Something like:
>> n = 1 : 500;
>> A = (1 + 0.1i).^n;
>> plot(real(A), imag(A));
real and imag are functions in MATLAB that access the real and imaginary components of complex numbers stored in arrays, matrices or single values. As noted by knedlsepp, you can simply plot the array itself as plot can handle complex-valued arrays:
>> plot(A);
Nice picture btw! Be mindful of the . operator appended with the ^ operator. The . means an element-wise operation. This means that we wish to apply the power operation for each value of n from 1 to 500 with 1 + 0.1i as the base. The result would be a 500 element array with the resulting calculations. If we did ^ by itself, we would be expecting to perform a matrix power operation, when this is not the case.
The values that you want to analyze for each value of n being applied to the equation in your post are stored in A. We then plot the real and imaginary components on the graph. Now if you want to find which numbers are closest to the real axis, you simply need to find the smallest absolute imaginary component of the numbers stored in A, then search for all of those numbers that share this number.
>> min_dist = min(abs(imag(A)));
>> vals = A(abs(imag(A)) == min_dist)
vals =
1.3681 - 0.0056i
This means that the value of 1.3681 - 0.0056i is the closest to the real axis.
This question is related to matlab: find the index of common values at the same entry from two arrays.
Suppose that I have an 1000 by 10000 matrix that contains value 0,1,and 2. Each row are treated as a sample. I want to calculate the pairwise distance between those samples according to the formula d = 1-1/(2p)sum(a/c+b/d) where a,b,c,d can treated as as the row vector of length 10000 according to some definition and p=10000. c and d are probabilities such that c+d=1.
An example of how to find the values of a,b,c,d: suppose we want to find d between sample i and bj, then I look at row i and j.
If kth entry of row i and j has value 2 and 2, then a=2,b=0,c=1,d=0 (I guess I will assign 0/0=0 in this case).
If kth entry of row i and j has value 2 and 1 or vice versa, then a=1,b=0,c=3/4,d=1/4.
The similar assignment will give to the case for 2,0(a=0,b=0,c=1/2,d=1/2),1,1(a=1,b=1,c=1/2,d=1/2),1,0(a=0,b=1,c=1/4,d=3/4),0,0(a=0,b=2,c=0,d=1).
The matlab code I have so far is using for loops for i and j, then find the cases above by using find, then create two arrays for a/c and b/d. This is extremely slow, is there a way that I can improve the efficiency?
Edit: the distance d is the formula given in this paper on page 13.
Provided those coefficients are fixed, then I think I've successfully vectorised the distance function. Figuring out the formulae was fun. I flipped things around a bit to minimise division, and since I wasn't aware of pdist until #horchler's comment, you get it wrapped in loops with the constants factored out:
% m is the data
[n p] = size(m, 1);
distance = zeros(n);
for ii=1:n
for jj=ii+1:n
a = min(m(ii,:), m(jj,:));
b = 2 - max(m(ii,:), m(jj,:));
c = 4 ./ (m(ii,:) + m(jj,:));
c(c == Inf) = 0;
d = 1 - c;
distance(ii,jj) = sum(a.*c + b.*d);
% distance(jj,ii) = distance(ii,jj); % optional for the full matrix
end
end
distance = 1 - (1 / (2 * p)) * distance;
I have a large data set with two arrays, say x and y. The arrays have over 1 million data points in size. Is there a simple way to do a scatter plot of only 2000 of these points but have it be representative of the entire set?
I'm thinking along the lines of creating another array r ; r = max(x)*rand(2000,1) to get a random sample of the x array. Is there a way to then find where a value in r is equal to, or close to a value in x ? They wouldn't have to be in the same indexed location but just throughout the whole matrix. We could then plot the y values associated with those found x values against r
I'm just not sure how to code this. Is there a better way than doing this?
I'm not sure how representative this procedure will be of your data, because it depends on what your data looks like, but you can certainly code up something like that. The easiest way to find the closest value is to take the min of the abs of the difference between your test vector and your desired value.
r = max(x)*rand(2000,1);
for i = 1:length(r)
[~,z(i)] = min(abs(x-r(i)));
end
plot(x(z),y(z),'.')
Note that the [~,z(i)] in the min line means we want to store the index of the minimum value in vector z.
You might also try something like a moving average, see this video: http://blogs.mathworks.com/videos/2012/04/17/using-convolution-to-smooth-data-with-a-moving-average-in-matlab/
Or you can plot every n points, something like (I haven't tested this, so no guarantees):
n = 1000;
plot(x(1:n:end),y(1:n:end))
Or, if you know the number of points you want (again, untested):
npoints = 2000;
interval = round(length(x)/npoints);
plot(x(1:interval:end),y(1:interval:end))
Perhaps the easiest way is to use round function and convert things to integers, then they can be compared. For example, if you want to find points that are within 0.1 of the values of r, multiply the values by 10 first, then round:
r = max(x) * round(2000,1);
rr = round(r / 0.1);
xx = round(x / 0.1);
inRR = ismember(xx, rr)
plot(x(inRR), y(inRR));
By dividing by 0.1, any values that have the same integer value are within 0.1 of each other.
ismember returns a 1 for each value of xx if that value is in rr, otherwise a 0. These can be used to select entries to plot.
I've been trying to find solution to my problem for more than a week and I couldn't find out anything better than a milion iterations prog, so I think it's time to ask someone to help me.
I've got a 3D array. Let's say, we're talking about the ground and the first layer is a surface.
Another layers are floors below the ground. I have to find deepest path's length, count of isolated caves underground and the size of the biggest cave.
Here's the visualisation of my problem.
Input:
5 5 5 // x, y, z
xxxxx
oxxxx
xxxxx
xoxxo
ooxxx
xxxxx
xxoxx
and so...
Output:
5 // deepest path - starting from the surface
22 // size of the biggest cave
3 // number of izolated caves (red ones) (izolated - cave that doesn't reach the surface)
Note, that even though red cell on the 2nd floor is placed next to green one, It's not the same cave because it's placed diagonally and that doesn't count.
I've been told that the best way to do this, might be using recursive algorithm "divide and rule" however I don't really know how could it look like.
I think you should be able to do it in O(N).
When you parse your input, assign each node a 'caveNumber' initialized to 0. Set it to a valid number whenever you visit a cave:
CaveCount = 0, IsolatedCaveCount=0
AllSizes = new Vector.
For each node,
ProcessNode(size:0,depth:0);
ProcessNode(size,depth):
If node.isCave and !node.caveNumber
if (size==0) ++CaveCount
if (size==0 and depth!=0) IsolatedCaveCount++
node.caveNumber = CaveCount
AllSizes[CaveCount]++
For each neighbor of node,
if (goingDeeper) depth++
ProcessNode(size+1, depth).
You will visit each node 7 times at worst case: once from the outer loop, and possibly once from each of its six neighbors. But you'll only work on each one once, since after that the caveNumber is set, and you ignore it.
You can do the depth tracking by adding a depth parameter to the recursive ProcessNode call, and only incrementing it when visiting a lower neighbor.
The solution shown below (as a python program) runs in time O(n lg*(n)), where lg*(n) is the nearly-constant iterated-log function often associated with union operations in disjoint-set forests.
In the first pass through all cells, the program creates a disjoint-set forest, using routines called makeset(), findset(), link(), and union(), just as explained in section 22.3 (Disjoint-set forests) of edition 1 of Cormen/Leiserson/Rivest. In later passes through the cells, it counts the number of members of each disjoint forest, checks the depth, etc. The first pass runs in time O(n lg*(n)) and later passes run in time O(n) but by simple program changes some of the passes could run in O(c) or O(b) for c caves with a total of b cells.
Note that the code shown below is not subject to the error contained in a previous answer, where the previous answer's pseudo-code contains the line
if (size==0 and depth!=0) IsolatedCaveCount++
The error in that line is that a cave with a connection to the surface might have underground rising branches, which the other answer would erroneously add to its total of isolated caves.
The code shown below produces the following output:
Deepest: 5 Largest: 22 Isolated: 3
(Note that the count of 24 shown in your diagram should be 22, from 4+9+9.)
v=[0b0000010000000000100111000, # Cave map
0b0000000100000110001100000,
0b0000000000000001100111000,
0b0000000000111001110111100,
0b0000100000111001110111101]
nx, ny, nz = 5, 5, 5
inlay, ncells = (nx+1) * ny, (nx+1) * ny * nz
masks = []
for r in range(ny):
masks += [2**j for j in range(nx*ny)][nx*r:nx*r+nx] + [0]
p = [-1 for i in range(ncells)] # parent links
r = [ 0 for i in range(ncells)] # rank
c = [ 0 for i in range(ncells)] # forest-size counts
d = [-1 for i in range(ncells)] # depths
def makeset(x): # Ref: CLR 22.3, Disjoint-set forests
p[x] = x
r[x] = 0
def findset(x):
if x != p[x]:
p[x] = findset(p[x])
return p[x]
def link(x,y):
if r[x] > r[y]:
p[y] = x
else:
p[x] = y
if r[x] == r[y]:
r[y] += 1
def union(x,y):
link(findset(x), findset(y))
fa = 0 # fa = floor above
bc = 0 # bc = floor's base cell #
for f in v: # f = current-floor map
cn = bc-1 # cn = cell#
ml = 0
for m in masks:
cn += 1
if m & f:
makeset(cn)
if ml & f:
union(cn, cn-1)
mr = m>>nx
if mr and mr & f:
union(cn, cn-nx-1)
if m & fa:
union(cn, cn-inlay)
ml = m
bc += inlay
fa = f
for i in range(inlay):
findset(i)
if p[i] > -1:
d[p[i]] = 0
for i in range(ncells):
if p[i] > -1:
c[findset(i)] += 1
if d[p[i]] > -1:
d[p[i]] = max(d[p[i]], i//inlay)
isola = len([i for i in range(ncells) if c[i] > 0 and d[p[i]] < 0])
print "Deepest:", 1+max(d), " Largest:", max(c), " Isolated:", isola
It sounds like you're solving a "connected components" problem. If your 3D array can be converted to a bit array (e.g. 0 = bedrock, 1 = cave, or vice versa) then you can apply a technique used in image processing to find the number and dimensions of either the foreground or background.
Typically this algorithm is applied in 2D images to find "connected components" or "blobs" of the same color. If possible, find a "single pass" algorithm:
http://en.wikipedia.org/wiki/Connected-component_labeling
The same technique can be applied to 3D data. Googling "connected components 3D" will yield links like this one:
http://www.ecse.rpi.edu/Homepages/wrf/pmwiki/pmwiki.php/Research/ConnectedComponents
Once the algorithm has finished processing your 3D array, you'll have a list of labeled, connected regions, and each region will be a list of voxels (volume elements analogous to image pixels). You can then analyze each labeled region to determine volume, closeness to the surface, height, etc.
Implementing these algorithms can be a little tricky, and you might want to try a 2D implementation first. Thought it might not be as efficient as you like, you could create a 3D connected component labeling algorithm by applying a 2D algorithm iteratively to each layer and then relabeling the connected regions from the top layer to the bottom layer:
For layer 0, find all connected regions using the 2D connected component algorithm
For layer 1, find all connected regions.
If any labeled pixel in layer 0 sits directly over a labeled pixel in layer 1, change all the labels in layer 1 to the label in layer 0.
Apply this labeling technique iteratively through the stack until you reach layer N.
One important considering in connected component labeling is how one considers regions to be connected. In a 2D image (or 2D array) of bits, we can consider either the "4-connected" region of neighbor elements
X 1 X
1 C 1
X 1 X
where "C" is the center element, "1" indicates neighbors that would be considered connected, and "X" are adjacent neighbors that we do not consider connected. Another option is to consider "8-connected neighbors":
1 1 1
1 C 1
1 1 1
That is, every element adjacent to a central pixel is considered connected. At first this may sound like the better option. In real-world 2D image data a chessboard pattern of noise or diagonal string of single noise pixels will be detected as a connected region, so we typically test for 4-connectivity.
For 3D data you can consider either 6-connectivity or 26-connectivity: 6-connectivity considers only the neighbor pixels that share a full cube face with the center voxel, and 26-connectivity considers every adjacent pixel around the center voxel. You mention that "diagonally placed" doesn't count, so 6-connectivity should suffice.
You can observe it as a graph where (non-diagonal) adjacent elements are connected if they both empty (part of a cave). Note that you don't have to convert it to a graph, you can use normal 3d array representation.
Finding caves is the same task as finding the connected components in a graph (O(N)) and the size of a cave is the number of nodes of that component.
Given the vector size N, I want to generate a vector <s1,s2, ..., sn> that s1+s2+...+sn = S.
Known 0<S<1 and si < S. Also such vectors generated should be uniformly distributed.
Any code in C that helps explain would be great!
The code here seems to do the trick, though it's rather complex.
I would probably settle for a simpler rejection-based algorithm, namely: pick an orthonormal basis in n-dimensional space starting with the hyperplane's normal vector. Transform each of the points (S,0,0,0..0), (0,S,0,0..0) into that basis and store the minimum and maximum along each of the basis vectors. Sample uniformly each component in the new basis, except for the first one (the normal vector), which is always S, then transform back to the original space and check if the constraints are satisfied. If they are not, sample again.
P.S. I think this is more of a maths question, actually, could be a good idea to ask at http://maths.stackexchange.com or http://stats.stackexchange.com
[I'll skip "hyper-" prefix for simplicity]
One of possible ideas: generate many uniformly distributed points in some enclosing volume and project them on the target part of plane.
To get uniform distribution the volume must be shaped like the part of plane but with added margins along plane normal.
To uniformly generate points in such volumewe can enclose it in a cube and reject everything outside of the volume.
select margin, let's take margin=S for simplicity (once margin is positive it affects only performance)
generate a point in cube [-M,S+M]x[-M,S+M]x[-M,S+M]
if distance to the plane is more than M, reject the point and go to #2
project the point on the plane
check that projection falls into [0,S]x[0,S]x[0,S], if not - reject and go to #2
add this point to the resulting set and go to #2 is you need more points
The problem can be mapped to that of sampling on linear polytopes for which the common approaches are Monte Carlo methods, Random Walks, and hit-and-run methods (see https://www.jmlr.org/papers/volume19/18-158/18-158.pdf for examples a short comparison). It is related to linear programming, and can be extended to manifolds.
There is also the analysis of polytopes in compositional data analysis, e.g. https://link.springer.com/content/pdf/10.1023/A:1023818214614.pdf, which provide an invertible transformation between the plane and the polytope that can be used for sampling.
If you are working on low dimensions, you can use also rejection sampling. This means you first sample on the plane containing the polytope (defined by your inequalities). This later method is easy to implement (and wasteful, of course), the GNU Octave (I let the author of the question re-implement in C) code below is an example.
The first requirement is to get vector orthogonal to the hyperplane. For a sum of N variables this is n = (1,...,1). The second requirement is a point on the plane. For your example that could be p = (S,...,S)/N.
Now any point on the plane satisfies n^T * (x - p) = 0
we assume also that x_i >= 0
With these given you compute an orthonormal basis on the plane (the nullity of the vector n) and then create random combination on that bases. Finally you map back to the original space and apply your constraints on the generated samples.
# Example in 3D
dim = 3;
S = 1;
n = ones(dim, 1); # perpendicular vector
p = S * ones(dim, 1) / dim;
# null-space of the perpendicular vector (transposed, i.e. row vector)
# this generates a basis in the plane
V = null (n.');
# These steps are just to reduce the amount of samples that are rejected
# we build a tight bounding box
bb = S * eye(dim); # each column is a corner of the constrained region
# project on the null-space
w_bb = V \ (bb - repmat(p, 1, dim));
wmin = min (w_bb(:));
wmax = max (w_bb(:));
# random combinations and map back
nsamples = 1e3;
w = wmin + (wmax - wmin) * rand(dim - 1, nsamples);
x = V * w + p;
# mask the points inside the polytope
msk = true(1, nsamples);
for i = 1:dim
msk &= (x(i,:) >= 0);
endfor
x_in = x(:, msk); # inside the polytope (your samples)
x_out = x(:, !msk); # outside the polytope
# plot the results
scatter3 (x(1,:), x(2,:), x(3,:), 8, double(msk), 'filled');
hold on
plot3(bb(1,:), bb(2,:), bb(3,:), 'xr')
axis image