I have two contour plots and I want to be able to fill from one contour in one image to the same height contour in the other.
In the plot you can see two lines of each color - these are the lines I want to fill between, with the same color as the lines (though preferably translucent). The code for these are as follows
test = repmat(repelem(0:6,2),10,1);
test1 = test(:,2:end-1);
test2 = test(:,1:end-2);
contour(test1,1:5);
hold on;
contour(test2,1:5);
I did think that maybe I could create another image that has the desired height at each bin and do some kind of contourf, but that could be a problem if in future the lines cross over, which they may well do. In that case, I'd like the area they cross to be a combination of the colors that are crossing over.
Have you try using ```fill``?
% test values
col = 'g';
x1=[6 6 6];y1=[1 5 10]; x2= [7 7 7];
x2 = [x1, fliplr(x2)];
inBetween = [y1, fliplr(y1)];
fill(x2, inBetween, col);
Related
I want to make a figure in MATLAB as described in the following image
What I did is the following:
x = [1 2 3];
y = [2 2 4];
radius = [1 1.2 2.2];
theta = [-pi 0 pi];
figure;
scatter(x,y,radius)
How do I add an angle theta to the plot to represent a complex number z = radius.*exp(1j*theta) at every spacial coordinates?
Technically speaking, those are only circles if x and y axes are scaled equally. That is because scatter always plots circles, independently of the scales (and they remain circles if you zoom in nonuniformly. + you have the problem with the line, which should indicate the angle...
You can solve both issues by drawing the circles:
function plotCirc(x,y,r,theta)
% calculate "points" where you want to draw approximate a circle
ang = 0:0.01:2*pi+.01;
xp = r*cos(ang);
yp = r*sin(ang);
% calculate start and end point to indicate the angle (starting at math=0, i.e. right, horizontal)
xt = x + [0 r*sin(theta)];
yt = y + [0 r*cos(theta)];
% plot with color: b-blue
plot(x+xp,y+yp,'b', xt,yt,'b');
end
having this little function, you can call it to draw as many circles as you want
x = [1 2 3];
y = [2 2 4];
radius = [1 1.2 2.2];
theta = [-pi 0 pi];
figure
hold on
for i = 1:length(x)
plotCirc(x(i),y(i),radius(i),theta(i))
end
I went back over scatter again, and it looks like you can't get that directly from the function. Hopefully there's a clean built-in way to do this, and someone else will chime in with it, but as a backup plan, you can just add the lines yourself.
You'd want a number of lines that's the same as the length of your coordinate set, from the center point to the edge at the target angle, and fortunately 'line' does multiple lines if you feed it a matrix.
You could just tack this on to the end of your code to get the angled line:
x_lines = [x; x + radius.*cos(theta)];
y_lines = [y; y + radius.*sin(theta)];
line(x_lines, y_lines, 'Color', 'b')
I had to assign the color specifically, since otherwise 'line' makes each new line cycle through the default colors, but that also means you could easily change the line color to stand out more. There's also no center dot, but that'd just be a second scatter plot with tiny radius. Should plot most of what you're looking for, at least.
(My version of Matlab is old enough that scatter behaves differently, so I can only check the line part, but they have the right length and location.)
Edit: Other answer makes a good point on whether scatter is appropriate here. Probably better to draw the circle too.
Say that I have a matrix Z with some values, and I want to illustrate it by a plotting the values in Z by height. The first solution comes to mind is a surface, but using surf and similar functions with small matrices doesn't look good.
So I thought about using something like a 3D bar plot with bar3. But the problem is that this function always sets the color by the group and not by height, and I can't get it to do so.
Here is an example:
Z = peaks(5);
subplot 121
surf(Z)
title('Surface look bad')
subplot 122
bar3(Z)
title('The color is not by height')
I tried to look for the color properties in the handles returned by bar3 (like CData and FaceColor) but got lost with all the values and how they relate to the bars themselves.
Ultimately, I would like to have a general solution that for 2 matrices Z and C I can create a 3D bar plot with bars in height given by Z and color given by C.
How can I do so?
The function bar3 returns a surface object, one for each group (i.e. one for each color), so all the bars in one group are essentially plotted as one 'broken' surface. This is explained very good in this answer, so I won't repeat it here.
Instead, I'll get to the solution for this specific problem. The relevant property of the surface is CData. When we create the bar plot, each surface's CData is assigned with a matrix in some size (we'll get to this) that is all equal one value. A different value for each surface. This is how the figure as a whole translates its color map to the color of the groups.
As written above (and elaborated in the linked answer), each group represented by a surface, so it takes a whole matrix to define the color at each point of the surface. The first thing we want to do is to get this matrix size:
Z = peaks(5);
bar_h = bar3(Z);
% we take only the first one, but they are all the same size:
cdata_sz = size(bar_h(1).CData)
cdata_sz =
30 4
CData has always 4 columns (see here why), and the number of rows is always 6*number of groups. This is because it takes 5 vertices to create one closed rectangle with an area object (the last vertex is like the first one) and one line is for spacing between the bars with NaNs, so they will look separated.
Next, we need to enlarge our original colormap (which is the same size of Z) to fit CData in the right way. Essentially, we just want to repeat the same value for all vertices that belong to the same bar. Assuming Z is also our color data (i.e. we color by height) we do:
z_color = repelem(Z,6,4)
Now we need to split our z_color to different cells in the number of our groups. Each cell will contain the coloring data for one surface object:
z_color = mat2cell(z_color,cdata_sz(1),ones(1,size(Z,2))*cdata_sz(2));
And finally, we apply the new color data to the bar plot:
set(bar_h,{'CData'},z_color.')
As a bonus, if we want to remove all zero values from our bar, it can be done easily by setting them to NaN:
Z(abs(Z)<eps) = nan;
C(isnan(Z)) = nan; % if we use a colormap C different from Z
All the above could be boiled down to this handy function:
function bar_h = Cbar3(Z,C,b,y)
% Z - The data
% C - CData (if other then Z values)
% b - Minimum absolute value to keep colored
% y - y-axis values to order the data by
if nargin<2, C = Z; end
if nargin<3 || isempty(b), b = 0; end
Z(abs(Z)<b) = nan;
C(isnan(Z)) = nan;
if nargin<4
bar_h = bar3(Z);
else
bar_h = bar3(y,Z);
end
cdata_sz = size(bar_h(1).CData);
z_color = repelem(C,6,4);
z_color = mat2cell(z_color,...
cdata_sz(1),ones(1,size(Z,2))*cdata_sz(2));
set(bar_h,{'CData'},z_color.')
end
Example of usage:
subplot 121
Z = peaks(30);
Cbar3(Z,Z,0.5);
pbaspect auto
shading flat % just to get a cleaner look
title('Cbar3 using height as color')
subplot 122
Cbar3(Z,rand(size(Z)),0.5);
pbaspect auto
shading flat % just to get a cleaner look
title('Cbar3 using random as color')
Result:
This is a partial answer.
The case of using the bar height as color is covered by the official MATLAB documentation. Essentially the example code boils down to:
function q45423394
hB = bar3(peaks(25)); colorbar;
for indE = 1:numel(hB)
hB(indE).CData = hB(indE).ZData;
end
All you need to do afterwards is make sure that the colormap is the one you want.
While I find EBH's solution aesthetically more pleasing, here there is a simpler solution: interpolation
z = peaks(5);
[x,y]=meshgrid(1:0.1:size(z,1),1:0.1:size(z,2));
zn=interp2(z,x,y,'nearest');
% plot it
surf(zn,'edgecolor','none','facecolor','interp')
I'm plotting a changing number of line trajectories on a sequence of images. I want the lines to be of different colors (as much as possible), and I want the colors to be retained throughout the sequence.
My code right now uses one plot command (plot(traj_to_plot{:})) using a cell array containing alternating x and y coordinates for each trajectory (meaning traj_to_plot={[traj1_x_coor] [traj1_y_coor] [traj2_x_coor] [traj2_y_coor] ...}). The order of the trajectories between each cycle of the loop is not always retained, and the number of the trajectories can change, as mentioned before.I need some way of relating between the trajectory drawn in one frame to the same trajectory drawn in a consecutive frame, and if it stopped, I need the following trajectories to stay in the same color (not simply change according to the ColorOrder cycle).
Here's two consecutive images where a change occurs:
the problem is evident in these sample photos. Because ant number 2 wasn't recognized in the second frame, the color order cycle changed the color of most of the trajectories.
Any ideas?
You could manually assign colours to each plot as so:
figure();
hold on;
plot(traj_to_plot{1},'red')
plot(traj_to_plot{2},'blue')
and so on.
If this a repetitive task, you could use something along the lines of:
colours = {'blue', 'green', 'red', 'cyan', 'magenta', 'yellow', 'black'};
figure();
hold on;
traj_to_plot1{1} = [1 2 3];
traj_to_plot1{2} = [0 2 4];
for ii=1:numel(traj_to_plot1)
plot(traj_to_plot1{ii},colours{mod(ii,numel(colours))});
end
traj_to_plot2{1} = [0.5 2 3.5];
traj_to_plot2{2} = [-0.5 2 4.5];
traj_to_plot2{3} = [-1.0 2 5];
for ii=1:numel(traj_to_plot2)
plot(traj_to_plot2{ii},colours{mod(ii-1,numel(colours))+1}); %Thanks to #wakjah.
end
I have a question about using the area function; or perhaps another function is in order...
I created this plot from a large text file:
The green and the blue represent two different files. What I want to do is fill in the area between the red line and each run, respectively. I can create an area plot with a similar idea, but when I plot them on the same figure, they do not overlap correctly. Essentially, 4 plots would be on one figure.
I hope this makes sense.
Building off of #gnovice's answer, you can actually create filled plots with shading only in the area between the two curves. Just use fill in conjunction with fliplr.
Example:
x=0:0.01:2*pi; %#initialize x array
y1=sin(x); %#create first curve
y2=sin(x)+.5; %#create second curve
X=[x,fliplr(x)]; %#create continuous x value array for plotting
Y=[y1,fliplr(y2)]; %#create y values for out and then back
fill(X,Y,'b'); %#plot filled area
By flipping the x array and concatenating it with the original, you're going out, down, back, and then up to close both arrays in a complete, many-many-many-sided polygon.
Personally, I find it both elegant and convenient to wrap the fill function.
To fill between two equally sized row vectors Y1 and Y2 that share the support X (and color C):
fill_between_lines = #(X,Y1,Y2,C) fill( [X fliplr(X)], [Y1 fliplr(Y2)], C );
You can accomplish this using the function FILL to create filled polygons under the sections of your plots. You will want to plot the lines and polygons in the order you want them to be stacked on the screen, starting with the bottom-most one. Here's an example with some sample data:
x = 1:100; %# X range
y1 = rand(1,100)+1.5; %# One set of data ranging from 1.5 to 2.5
y2 = rand(1,100)+0.5; %# Another set of data ranging from 0.5 to 1.5
baseLine = 0.2; %# Baseline value for filling under the curves
index = 30:70; %# Indices of points to fill under
plot(x,y1,'b'); %# Plot the first line
hold on; %# Add to the plot
h1 = fill(x(index([1 1:end end])),... %# Plot the first filled polygon
[baseLine y1(index) baseLine],...
'b','EdgeColor','none');
plot(x,y2,'g'); %# Plot the second line
h2 = fill(x(index([1 1:end end])),... %# Plot the second filled polygon
[baseLine y2(index) baseLine],...
'g','EdgeColor','none');
plot(x(index),baseLine.*ones(size(index)),'r'); %# Plot the red line
And here's the resulting figure:
You can also change the stacking order of the objects in the figure after you've plotted them by modifying the order of handles in the 'Children' property of the axes object. For example, this code reverses the stacking order, hiding the green polygon behind the blue polygon:
kids = get(gca,'Children'); %# Get the child object handles
set(gca,'Children',flipud(kids)); %# Set them to the reverse order
Finally, if you don't know exactly what order you want to stack your polygons ahead of time (i.e. either one could be the smaller polygon, which you probably want on top), then you could adjust the 'FaceAlpha' property so that one or both polygons will appear partially transparent and show the other beneath it. For example, the following will make the green polygon partially transparent:
set(h2,'FaceAlpha',0.5);
You want to look at the patch() function, and sneak in points for the start and end of the horizontal line:
x = 0:.1:2*pi;
y = sin(x)+rand(size(x))/2;
x2 = [0 x 2*pi];
y2 = [.1 y .1];
patch(x2, y2, [.8 .8 .1]);
If you only want the filled in area for a part of the data, you'll need to truncate the x and y vectors to only include the points you need.
Let's say I have 9 MxN black and white images that are in some way related to one another (i.e. time lapse of some event). What is a way that I can display all of these images on one surface plot?
Assume the MxN matrices only contain 0's and 1's. Assume the images simply contain white lines on a black background (i.e. pixel value == 1 if that pixel is part of a line, 0 otherwise). Assume images are ordered in such a way as to suggest movement progression of line(s) in subsequent images. I want to be able to see a "side-view" (or volumetric representation) of these images which will show the surface that a particular line "carves out" in its movement across the images.
Coding is done in MATLAB. I have looked at plot (but it only does 2D plots) and surf, which does 3D plots but doesn't work for my MxNx9 matrix of images. I have also tried to experiment with contourslice, but not sure what parameters to pass it.
Thanks!
Mariya
Are these images black and white with simple features on a "blank" field, or greyscale, with more dense information?
I can see a couple of approaches.
You can use movie() to display a sequence of images as an animation.
For a static view of sparse, simple data, you could plot each image as a separate layer in a single figure, giving each layer a different color for the foreground, and using AlphaData to make the background transparent so all the steps in the sequenc show through. The gradient of colors corresponds to position in the image sequence. Here's an example.
function plotImageSequence
% Made-up test data
nLayers = 9;
x = zeros(100,100,nLayers);
for i = 1:nLayers
x(20+(3*i),:,i) = 1;
end
% Plot each image as a "layer", indicated by color
figure;
hold on;
for i = 1:nLayers
layerData = x(:,:,i);
alphaMask = layerData == 1;
layerData(logical(layerData)) = i; % So each layer gets its own color
image('CData',layerData,...
'AlphaData',alphaMask,...
'CDataMapping','scaled');
end
hold off
Directly showing the path of movement a "line" carves out is hard with raster data, because Matlab won't know which "moved" pixels in two subsequent images are associated with each other. Don't suppose you have underlying vector data for the geometric features in the images? Plot3() might allow you to show their movement, with time as the z axis. Or you could use the regular plot() and some manual fiddling to plot the paths of all the control points or vertexes in the geometric features.
EDIT: Here's a variation that uses patch() to draw each pixel as a little polygon floating in space at the Z level of its index in the image sequence. I think this will look more like the "surface" style plots you are asking for. You could fiddle with the FaceAlpha property to make dense plots more legible.
function plotImageSequencePatch
% Made-up test data
nLayers = 6;
sz = [50 50];
img = zeros(sz(1),sz(2),nLayers);
for i = 1:nLayers
img(20+(3*i),:,i) = 1;
end
% Plot each image as a "layer", indicated by color
% With each "pixel" as a separate patch
figure;
set(gca, 'XLim', [0 sz(1)]);
set(gca, 'YLim', [0 sz(2)]);
hold on;
for i = 1:nLayers
layerData = img(:,:,i);
[x,y] = find(layerData); % X,Y of all pixels
% Reshape in to patch outline
x = x';
y = y';
patch_x = [x; x+1; x+1; x];
patch_y = [y; y; y+1; y+1];
patch_z = repmat(i, size(patch_x));
patch(patch_x, patch_y, patch_z, i);
end
hold off