Translating 2D image with RGB colours along axes - matlab

I am trying to create my own voronoi diagram. I have an arbitrary shape defined by their x and y coordinates stored in separate vectors. Inside this shape are some points of interest (with known coordinates) that belong to two different groups and act as seeds to the voronoi diagram. As an example, the whole diagram ranges from x=-10 to x=90 and y=-20 to y=60. The boundary shape is not rectangular but falls within the axes range above.
What I have done so far is to create a 3D matrix (100 X 80 X 3), C, with all ones so that the default colour will be white. I then looped through from i=1:100, j=1:80, testing individual pixels to see if they fall within the shape using inpolygon. If they do, I then find out which point is the pixel closest to and assign it a colour based on whether the closest point belongs to group 1 or 2.
All is good so far. I then used imagesc to display the image with a custom axis range. The problem is that the voronoi diagram has the general shape but it is off in terms of position as the pixel coordinates are different from the actual world coordinates.
I tried to map it using imref2d but I do not know how it really works or how to display the image after using imref2d. Please help me on this.
I am open to other methods too!
Thank you!
Edit:
As requested, let me give a more detailed example and explanation of my problem.
Let us assume a simple diamond shape boundary with the following vectors and 4 points with the following coordinate vectors:
%Boundary vectors
Boundary_X = [-5 40 85 40 -5];
Boundary_Y = [20 50 20 -10 20];
%Point vectors
Group_One_X = [20 30];
Group_One_Y = [10 40];
Group_Two_X = [50 70];
Group_Two_Y = [5 20];
Next I plot all of them, with different groups having different colours.
%Plot boundary and points
hold on
plot(Boundary_X,Boundary_Y)
scatter(Group_One_X,Group_One_Y,10,'MarkerFaceColor','Black',...
'MarkerEdgeColor','Black')
scatter(Group_Two_X,Group_Two_Y,10,'MarkerFaceColor','Red',...
'MarkerEdgeColor','Red')
hold off
axis([-10, 90, -20, 60])
This is the result:
Boundary with points
Next I test the whole graph area pixel by pixel, and colour them either cyan or yellow depending on whether they are closer to group 1 or 2 points.
%Create pixel vector with default white colour
C=ones(100,80,3);
Colour_One = [0 1 1];
Colour_Two = [1 1 0];
%Loop through whole diagram
for i=1:100
for j=1:80
x=i;
y=j
if inpolygon(x,y,Boundary_X,Boundary_Y)
%Code for testing which point is pixel closest to
%If closest to group 1, assign group 1 colour, else group 2
%colour
end
end
end
%Display image
hold on
imagesc(C)
hold off
This is the result
Failed Voronoi Diagram
The shape is somewhat correct for the right side but not for the others. I understand that this because my world coordinates start from negative values but the pixel coordinates start from 1.
Hence I am at a lost as to how can I solve this problem.
Thank you!

One thing to notice is that you have to convert between image and plot coordinates. The plot coordinates are (x,y) where x goes to the right, and y goes up. The matrix coordinates are (i,j) where i goes down, and j to the right. An easy way to do this is with the use of vec_X,vec_Y as shown below.
Another solution for the newer Matlab versions would be - as you said - using imref2d but unfortunately I have no experience with that command.
%Boundary vectors
Boundary_X = [-5 40 85 40 -5];
Boundary_Y = [20 50 20 -10 20];
%Point vectors
Group_One_X = [20 30];
Group_One_Y = [10 40];
Group_Two_X = [50 70];
Group_Two_Y = [5 20];
%Coordinate system
min_X = -10;
max_X = 90;
min_Y = -20;
max_Y = 60;
axis([min_X, max_X, min_Y, max_Y])
%Create pixel vector with default white colour
rows_N = 100;
columns_N = 80;
C=ones(rows_N,columns_N,3);
%These vectors say where each of the pixels is in the plot coordinate
%system
vec_X = linspace(min_X,max_X,columns_N);
vec_Y = linspace(min_Y,max_Y,rows_N);
Colour_One = [0 1 1];
Colour_Two = [1 1 0];
%Loop through whole diagram
for i=1:100
for j=1:80
if inpolygon(vec_X(j),vec_Y(i),Boundary_X,Boundary_Y)
%calculate distance to each point
Distances_One = zeros(size(Group_One_X));
Distances_Two = zeros(size(Group_Two_X));
for k=1:numel(Group_One_X);
Distances_One(k) = norm([Group_One_X(k),Group_One_Y(k)]-[vec_X(j),vec_Y(i)]);%assuming euclidean norm, but can be adjusted to whatever norm you need
end
for k=1:numel(Group_Two_X);
Distances_Two(k) = norm([Group_Two_X(k),Group_Two_Y(k)]-[vec_X(j),vec_Y(i)]);%assuming euclidean norm, but can be adjusted to whatever norm you need
end
if min(Distances_One) < min(Distances_Two);
C(i,j,:) = Colour_One;
else
C(i,j,:) = Colour_Two;
end
end
end
end
%Display image
imagesc(vec_X,vec_Y,C) %lets you draw the image according to vec_X and vec_Y
%Plot boundary and points
hold on
plot(Boundary_X,Boundary_Y)
scatter(Group_One_X,Group_One_Y,10,'MarkerFaceColor','Black',...
'MarkerEdgeColor','Black')
scatter(Group_Two_X,Group_Two_Y,10,'MarkerFaceColor','Red',...
'MarkerEdgeColor','Red')
hold off

Related

How to plot a Diagonal Histogram in Matlab

Given scatter data, or a matrix, I would like to generate a nice plot such as the one shown below, with all 3 histograms and a colored matrix. I'm specifically interested in the diagonal histogram, which ideally, would correspond to the diagonals of a matrix:
Source figure: www.med.upenn.edu/mulab/jpst.html
The existing command scatterhist is not that powerful to generate this type of graph. Any ideas?
Thanks!
EDIT:
Following #Cris Luengo's hints, I came up with the following code which does some first work at the inclined histogram: WORK IN PROGRESS (HELP WELCOME)!!
b = [0 1 2 3 4 5 6 7 8 9 10];
h = [0.33477 0.40166 0.20134 0.053451 0.008112 0.000643 2.7e-05 0 0 0 0];
wid = 0.25; bb = sort([b-wid b-wid b+wid b+wid]);
kk = [zeros(numel(h),1) h(:) h(:) zeros(numel(h),1)];
kk = reshape(kk',[1,numel(kk)]);
pp=patch(bb,kk,'b');axis([-.5 5 0 .5])
set(gca,'CameraUpVector',[-1,.08,0]);axis square
EDIT 2: Using rotation
phi = pi/4;
R = [cos(phi),-sin(phi);sin(phi),cos(phi)];
rr = [bb' kk'] * R;
bb = rr(:,1); kk = rr(:,2);
patch(bb,kk,'b'); axis([-.5 3 -4 .5])
Here is a recipe to plot the diagonal histogram, if you can do that I’m sure you can figure out the rest too.
Compute the histogram, the bin counts are h, the bin centers are b.
Build a coordinate matrix, attaching the coordinates of a point on the x-axis at the left and right ends of the histogram:
coords = [b(:),h(:)];
coords = [coord;b(end),0;b(1),0];
Using patch you can now plot the histogram as follows:
patch(coords(1,:),coords(2,:));
To plot a rotated histogram you can simply multiply the coords matrix with a rotation matrix, before using patch:
phi = pi/4;
R = [cos(phi),-sin(phi);sin(phi),cos(phi)];
coords = R * coords;
You might need to shift the plot to place it at the right location w.r.t. the other elements.
I recommend that you place all these graphic elements in the same axes object; you can set the axes’ visibility to 'off' so that it works only as a canvas for the other elements.
It will be a bit of work to get everything placed as in the plot you show, but none of it is difficult. Use the low-level image, line,patch and text to place those types of elements, don’t try to use the higher-level plotting functions such as plot, they don’t provide any benefits over the low-level ones in this case.

Matlab: Why is the fill function not filling the area between two circles?

I'm trying to fill the intersecting area between two circles in Matlab. I've quite literally copied and pasted this piece of code from this article on Matlab Central.
t = linspace(0, 2*pi, 100);
cir = #(r,ctr) [r*cos(t)+ctr(1); r*sin(t)+ctr(2)]; % Circle Function
c1 = cir(1.0, [0; 0]);
c2 = cir(1.5, [1; 1]);
in1 = find(inpolygon(c1(1,:), c1(2,:), c2(1,:), c2(2,:))); % Circle #1 Points Inside Circle #2
in2 = find(inpolygon(c2(1,:), c2(2,:), c1(1,:), c1(2,:))); % Circle #2 Points Inside Circle #1
[fillx,ix] = sort([c1(1,in1) c2(1,in2)]); % Sort Points
filly = [c1(2,in1) (c2(2,in2))];
filly = filly(ix);
figure(1)
plot(c1(1,:), c1(2,:))
hold on
plot(c2(1,:), c2(2,:))
fill([fillx fliplr(fillx)], [filly fliplr(filly)], 'g', 'EdgeColor','none')
hold off
axis square
What I end up with is the following image:
However, it should appear as this image:
Why is the area not being filled as it is in the example article?
If you have Mapping Toolbox you can use polybool to find the intersection between to polygones, and than patch (which dosen't require Mapping Toolbox, and is better than fill) to draw it. The folowing code works even without the first 2 lines that use poly2cw, but it issues some warnings. This can be solved with the poly2cw trasfomation:
[c1(1,:), c1(2,:)] = poly2cw(c1(1,:), c1(2,:)); % clock-wise transform
[c2(1,:), c2(2,:)] = poly2cw(c2(1,:), c2(2,:)); % clock-wise transform
[xb, yb] = polybool('intersection',c1(1,:),c1(2,:),c2(1,:), c2(2,:));
plot(c1(1,:), c1(2,:))
hold on
plot(c2(1,:), c2(2,:))
patch(xb, yb, 1, 'FaceColor', 'g','EdgeColor','none')
axis equal
The code in the question does not work because it has some mistake in the order of the points in fillx and filly. We can see that if we set the 'EdgeColor' to be visible, and follow the peripheral line of the patch (see below, here reduced to 20 points, for the illustration). We can clearly see that the point of the polygon to be filled are ordered in a 'zig-zag' between the circles, so it has no area at all. I have numbered the vertices of the polygon taken from each circle to demonstrate in what order the fill function read them.
In order to fill with color all the intersection between the circles, we need to define the 'polygon' by the points on the circles that intersect (in1 and in2) in the right order. This means we want them to make a closed shape if an imaginary pencil is drawing a line between them in the same order they are given. Like this:
We start with 1 in one of the circles and continue until the numbers on that circle are ended, and then move to 1 on the other circle, and when we reach the end in the second circle we close the polygon by connecting the last point to the first one. As you can see in both figure above, the starting point and the end point of the circles are really close, so we get 2 numbers above each other.
How can we order the points correctly?
We start by getting in1 and in2 as described in the question. Let's take a look at in1:
in1 =
1 2 3 4 5 6 7 19 20
Those are the indices of the points from c1 to be taken, they appear to be in order, but contains a gap. This gap is because inpolygon checks the points by the order in c1, and the starting point of c1 is within the intersection region. So we get the first 7 points, then we are out of the intersection, and we go back in as we reach points 19 and 20. However, for our polygon, we need this points to start from the closest point to one of that places where the circle intersect and to go around the circle until we reach the second point of intersection.
To do that, we look for the 'gap' in the points order:
gap = find(diff(in1)>1);
and reorder them correctly:
X1 = [c1(1,in1(gap+1:end)) c1(1,in1(1:gap))];
Y1 = [c1(2,in1(gap+1:end)) c1(2,in1(1:gap))];
But, there may be no 'gap', as we see in in2:
in2 =
11 12 13 14
So we need to wrap this within an if to check if the points need to be reordered:
if ~isempty(gap)
X1 = [c1(1,in1(gap+1:end)) c1(1,in1(1:gap))];
Y1 = [c1(2,in1(gap+1:end)) c1(2,in1(1:gap))];
else
X1 = c1(1,in1);
Y1 = c1(2,in1);
end
Now all we need to do it to concatenate X1 and X2 (for circle 2), and the same for the Ys, and use patch (which is like fill, but better) to draw it:
patch([X1 X2],[Y1 Y2],'g','EdgeColor','none')
With 20 points the circle is not really a circle and the intersection is partially colored, so here is the full code and the result with 200 points:
t = linspace(0, 2*pi, 200);
cir = #(r,ctr) [r*cos(t)+ctr(1); r*sin(t)+ctr(2)]; % Circle Function
c1 = cir(1.0, [0; 0]);
c2 = cir(1.5, [1; 1]);
plot(c1(1,:), c1(2,:))
hold on
plot(c2(1,:), c2(2,:))
axis equal
in1 = find(inpolygon(c1(1,:), c1(2,:), c2(1,:), c2(2,:)));
in2 = find(inpolygon(c2(1,:), c2(2,:), c1(1,:), c1(2,:)));
gap = find(diff(in1)>1);
if ~isempty(gap)
X1 = [c1(1,in1(gap+1:end)) c1(1,in1(1:gap))];
Y1 = [c1(2,in1(gap+1:end)) c1(2,in1(1:gap))];
else
X1 = c1(1,in1);
Y1 = c1(2,in1);
end
gap = find(diff(in2)>1);
if ~isempty(gap)
X2 = [c2(1,in2(gap+1:end)) c2(1,in2(1:gap))];
Y2 = [c2(2,in2(gap+1:end)) c2(2,in2(1:gap))];
else
X2 = c2(1,in2);
Y2 = c2(2,in2);
end
patch([X1 X2],[Y1 Y2],'g','EdgeColor','none')
hold off
All mentioned above could be replace with the use of convhull on the vertices that intersect and give the same result:
x = [c1(1,in1) c2(1,in2)]; % all x's for intersecting vertices
y = [c1(2,in1) c2(2,in2)]; % all y's for intersecting vertices
k = convhull(x,y); % calculate the convex polygon
patch(x(k),y(k),'g','EdgeColor','none')

How do I create a polar plot with concentric colored rings corresponding to single values in Matlab?

I am trying to create a plot that looks like this with rings of constant values (colors) extending from 0 to 100 in 10 unit increments.
Rings of single values extending outward from center
However, my code is not producing this, and I do not know where it has gone wrong.
% values representing the colors that each ring should be
% starting from the center and moving outwards in 10 unit increments.
values = [364,358,354,348,339,335,330,325,320,310];
xCoord = linspace(0,2*pi,10);
yCoord = linspace(0,100,10);
[TH,R] = meshgrid(xCoord,yCoord);
[X,Y] = pol2cart(TH,R);
[Z] = meshgrid(values);
contour_ticks = 300:5:375;
figure
hold on
contourf(X,Y,Z,contour_ticks);
a=gca; cb=colorbar; colormap('jet'); caxis([300 375]);
This produces a plot resembling this:
Incorrect plot
Any ideas what I'm doing wrong? Any help is greatly appreciated. Thanks.
If you just want to plot circles, you can use the following approach:
radii = 100:-10:10; %// descending order, so that bigger circles don't cover small ones
colors = parula(numel(radii)); %// or use some other colormap
for n = 1:numel(radii)
r = radii(n);
rectangle('Position', [-r -r 2*r 2*r], 'Curvature', [1 1], 'FaceColor', colors(n,:),...
'EdgeColor', 'none') %// plot each circle using sequential colors, no edge
hold on
end
axis equal
axis([-1 1 -1 1]*max(radii))

Rotating a Plot About the Y Axis

I have a vector of values that I want to plot as brightness on a circle through the radius of it (I.e. If it was 0 3 1 5 I'd want a circle that was dark at the centre, then a bright ring around it, then a slightly darker ring, then a brighter ring).
To do this I've attempted to rotate my radial vector (E) around the y axis, as such
[X,Y,Z] = cylinder(E);
h = surf(X,Y,Z),
However I'm clearly not doing it right, as this appears to be rotating my curve around the x axis. I've tried just swapping X and Y, but it still rotates it around the x axis. Any help would be greatly appreciated.
One way would be to rotate your vector and create a surface. The Z data of the surface (your rotated vector) will be color coded according to the colormap you choose, if you display the surface from the top you get your circles at the different brightness.
If you are really only interested from the "top view" of this surface, then no need to create a full surface, a simple pcolor will do the job.
example:
%% // input data (and assumptions)
E=[0 3 1 5 2 7];
nBrightness = 10 ; %// number of brightness levels
r = (0:numel(E)) ; %// radius step=1 by default for consecutive circles
%// otherwise define different thickness for each circle
So if I use stairs([E 0]) you get your different brightness levels:
I had to add a last 0 to the vector to "close" the last level, we'll have to do that again in the solution below.
Now to rotate/replicate that around Y, color code the height, and look at it from the top:
%% // replicate profile around axis
ntt = 50 ; %// define how many angular division for the plot
theta = linspace(0,2*pi,ntt) ; %// create all the angular divisions
[rr,tt]=meshgrid(r,theta) ; %// generate a grid
z = repmat( [E 0] , ntt , 1 ) ; %// replicate our "E" vector to match the grid
[xx,yy,zz] = pol2cart(tt,rr,z) ; %// convert everything to cartesian coordinates
pcolor(xx,yy,zz) %// plot everything
colormap(gray(nBrightness)) %// make sure we use only "nBrightness" colors (Shades of gray)
caxis([0 nBrightness])
shading flat ; axis equal %// refine the view (axis ratio and "spokes" not visible) etc...
colorbar
axis off
will yield the following :
Note that your problem was not fully defined, I had to take assumptions on:
What radius each brightness circle should have ? (I made them all the same but you can modify that)
How many brightness levels you want ? (You can also modify that easily though).
Have you tried the rotate function?
direction = [0 1 0];
rotate(h,direction,90);
In this example a 90 degree rotation is performed around the y axis.
Using this library http://www.mathworks.com/matlabcentral/fileexchange/45952-circle-plotter
%http://www.mathworks.com/matlabcentral/fileexchange/45952-circle-plotter
x0 = 0;
y0 = 0;
colors = [0 3 1 5];
maxC = max(colors);
sz = numel(colors);
for i=fliplr(1:sz)
c = colors(i);
circles(x0,y0,i,'facecolor',[c/maxC c/maxC 0]) % http://au.mathworks.com/help/matlab/ref/colorspec.html
end

creating exponentially decaying beams on a matlab plot

I am having some trouble figuring out how to create these beams in my plot in matlab.
I have created this graphic that I need to use before the beams are added, but I am not sure how to proceed.
The beams should decay (or attenuate) exponentially from the surface with a decay constant of 15 cm. So, if a surface tile has energy energy value 1, at depth i, where i represents the depth in centimeters, the value should be exp(-i/15). Note that the beams should cover the entire extent of the middle square.
the graphic:
My code for this graphic:
Rows = 30;
Cols = 40;
body = zeros(Rows, Cols);
clims = [-1 1];
imagesc(body, clims);
hold on
x = 0:5:40;
y = 0:5:30;
imagesc(x, y, body)
axis([0 40 0 30])
axis xy
shading flat
colorbar
hold on
plot([18, 22],[13, 13],'k')
hold on
plot([18, 18],[13, 17],'k')
hold on
plot([18, 22],[17, 17],'k')
hold on
plot([22, 22],[13, 17],'k')
Any help would be so much appreciated!
There's a few ways to do this. Basically, you want to set the values in your body before you plot them. Here's one example of a similar curve, I'll let you figure out how to extrapolate it to your exact needs.
Rows = 30;
Cols = 40;
body = zeros(Rows, Cols);
xsize=size(body,1);
ysize=size(body,2);
for x=1:xsize
for y=1:ysize
body(x,y)=exp((y-ysize/2)*(x-xsize/2));
end
end
x = 0:5:40;
y = 0:5:30;
imagesc(x, y, body)