I am trying to make a plot with an intensity that varies over time:
[X,Y] = meshgrid(-30:.1:30);
figure;
colormap(bone);
for t = 0:0.1:2*pi
R = sqrt(X.^2 + Y.^2);
Z = cos(t)*abs(besselj(2,R));
surf(Z,'EdgeColor','None');
view(90,90);
axis([0 600 0 600 -0.5 0.5])
pause(0.1);
end
I want to look at this from the top, such that as the Z value changes, the color changes. The problem is that rather than having an absolute scale (black = -0.5, white = 0.5), the color scale is relative to the maximum and minimum values, such that the colors only change when the sign flips change. How can I set an absolute scale for the color map?
Thank you.
You have to use scaled colour mapping mode and set the limits of the scaling by using the caxis command.
Now the problem with your current code is that you call surf at each iteration of the loop, essentially destroying the current plot and generating a new plot each time. This will reset a lot of properties, including the caxis limits to auto. To overcome that, simply create your plot only once before the loop, then in the loop you only change the properties which are modified (the Z values in this case). This way everything else stays the same in the figure.
So you code becomes:
%% // Prepare and initialize the surface plot
[X,Y] = meshgrid(-30:.1:30);
R = sqrt(X.^2 + Y.^2) ; %// this doesn't need to be in the loop
Z = cos(0)*abs(besselj(2,R)) ; %// calculate initial value to create the surface
surfHandle = surf( Z , 'EdgeColor','None' ) ; %// create a first surface, and save the handle to the surface object
colormap(bone);
colorbar %// this is optional, just to make sure the colorbar does not vary
caxis([-5 5 ] ) ; %// this is what sets the color scaling to what you want
view(90,90);
axis([0 600 0 600 -0.5 0.5]) ; %// this doesn't need to be in the loop anymore
%% // Modify and update the surface plot
for t = 0:pi/100:2*pi
Z = cos(t)*abs(besselj(2,R));
set( surfHandle , 'ZData' , Z )
drawnow
pause(0.01);
end
Read coloring-mesh-and-surface-plots for more info on how surfaces can be colored.
If you just want white for values less than 0 and black for values greater than 0, you ca simply do:
surf(Z,sign(Z),'EdgeColor','None');
which uses the optional C argument to surf, telling Matlab to colour the plot depending on the values of C, not Z. sign(Z) is a matrix that has 1's where Z>0, 0's where Z=0, and -1's where Z<0.
Related
z is 200*200 array and I have a surf plot using Matlab surf(x,y,z). I am trying to plot the surf plot so that when z<10 it will be blue and when z>10 it will be red. At the moment the surf plot is like this. Can someone please suggest a way to do this in Matlab?
One way to achieve that (there are several ways) is to use a custom colormap:
Build a colormap with only the color you want to appear in your graph, then just adjust the levels so the midpoint is for Z=10.
The first part of the code shows how to create your custom colormap and apply it:
Zt = 10 ; % threshold level for Z
z = peaks+Zt ; % dummy test data
% build a colormap with your 2 custom color
% [%Red %green %blue]
cmap = [0.79 0.22 0.81 ; % some kind of purple
0 0 1 ] ; % pure blue
surf(z) ; % plot the surface
colormap(cmap) ; % apply the custom colormap
hcb = colorbar ;
This produces a surface with your two chosen colors:
But wait! The separation is not exactly at the Z=10 level. No problem, if we adjust the boundaries of the colormap so your threshold level is bang in the middle, Matlab will take care of adjusting the coloring for us:
%% Now center the colormap boundaries around your threshold level
% get the minimum and maximum
zmax = ceil( max(max(z)) ) ;
zmin = floor( min(min(z)) ) ;
span = max( [zmax-Zt, Zt-zmin] ) ; % calculate the span each side of [Zt]
caxis([Zt-span , Zt+span]) ; % center the colormap around [Zt]
The last bit of code above allow to define an equal span around your chosen threshold level and take the content of the Z data into account. If you know in advance the limits of your data you don't need to do the calculations. On the example above I could also have simply use the last line with some hard coded values:
caxis([0 , 20]) ;
As long as the interval you specify for caxis is centered around your threshold level it will work.
Edit:
To control the labels of the colorbar, I usually set the Ticks and TickLabels after the colorbar (or axes) is created. For this you need the handle of the colorbar object.
Note that in the code above I modified the last line of the first code block. I changed colorbar, to hcb=colorbar;. This way we have the handle of the colorbar, which allow us to set any arbitrary tick and associated label.
The most straightforward way to get your result for this specific example is:
hcb.Ticks = [ 5 , 10 , 15 ] ;
hcb.TickLabels = {'<10','10','>10'} ;
However if you want a more generic solution which can work with any threshold Zt then you can use:
%% adjust colorbar labels
zl = caxis ; % get the limits of the color scale
Zstr = num2str(Zt) ; % get a string representing the threshold
hcb.Ticks = [ (Zt+zl(1))/2 , Zt , (zl(2)+Zt)/2 ] ;
hcb.TickLabels = { ['<' Zstr] , Zstr , ['>' Zstr] } ;
For your example, both options produce:
Adapted from MATLAB Answers
z = peaks+10; % sample data generated between 3.4 and 18.1
% Make colors be red above 10, and blue below 10.
redChannel = z > 10;
greenChannel = 0*z;
blueChannel = z < 10;
% Make the RGB image.
colors = double(cat(3, redChannel, greenChannel, blueChannel));
% Plot the surface with those colors.
surf(z, colors);
try this
surf(x,y,z)
map = [0.0 0.0 1.0
1.0 0.0 0.0];
colormap(map);
caxis([0 20]);
I find that data points that lie on or near the axes are difficult to see. The obvious fix, of course, is to simply change the plot area using axis([xmin xmax ymin ymax]), but this is not preferable in all cases; for example, if the x axis is time, then moving the minimum x value to -1 to show activity at 0 does not make sense.
Instead, I was hoping to simply move the x and y axes away from the plot area, like I have done here:
left: MATLAB generated, right: desired (image editing software)
Is there a way to automatically do this in MATLAB? I thought there might be a way to do it by using the outerposition axes property (i.e., set it to [0 0 0.9 0.9] and drawing new axes where they originally were?), but I didn't get anywhere with that strategy.
The answers here already show you most of the way - here is the last step to separate the x and y axle as per the example you put together.
f = figure ( 'color', 'white' );
% create the axes and set some properties
ax = axes ( 'parent', f, 'box', 'off', 'nextplot', 'add', 'XMinorTick', 'on', 'YMinorTick', 'on' );
% plot some data
plot ( ax, 0:10, [0:10].^2, 'rx-' )
% modify the x and y limits to below the data (by a small amount)
ax.XLim(1) = ax.XLim(1)-(ax.XTick(2)-ax.XTick(1))/4;
ax.YLim(1) = ax.YLim(1)-(ax.YTick(2)-ax.YTick(1))/4;
% Set the tick direction
ax.TickDir = 'out';
% draw the plot to generate the undocumented vertex data var
drawnow()
%% R2015a
% X, Y and Z row of the start and end of the individual axle.
ax.XRuler.Axle.VertexData(1,1) = 0;
ax.YRuler.Axle.VertexData(2,1) = 0;
%% R2015b
% extract the x axis vertext data
% X, Y and Z row of the start and end of the individual axle.
vd = get(ax.XAxis.Axle,'VertexData');
% reset the zero value
vd(1,1) = 0;
% Update the vertex data
set(ax.XAxis.Axle,'VertexData',vd);
% repeat for Y (set 2nd row)
vd = get(ax.YAxis.Axle,'VertexData');
vd(2,1) = 0;
set(ax.YAxis.Axle,'VertexData',vd);
Edit: The vertex is something that Matlab recreates whenever the axes/figure changes size or if you zoom or pan for example.
You can try to counteract this (remember you are using undocumented features here) by adding a listener to attempt to capture this. We can use the MarkedClean event which is called quite a lot of times.
addlistener ( ax, 'MarkedClean', #(obj,event)resetVertex(ax) );
Where you resetVertex function is something like: (R2015b shown only)
Edit 2 added the code to turn off the minor ticks below 0.
function resetVertex ( ax )
% extract the x axis vertext data
% X, Y and Z row of the start and end of the individual axle.
ax.XAxis.Axle.VertexData(1,1) = 0;
% repeat for Y (set 2nd row)
ax.YAxis.Axle.VertexData(2,1) = 0;
% You can modify the minor Tick values by modifying the vertex data
% for them, e.g. remove any minor ticks below 0
ax.XAxis.MinorTickChild.VertexData(:,ax.XAxis.MinorTickChild.VertexData(1,:)<0) = [];
ax.YAxis.MinorTickChild.VertexData(:,ax.YAxis.MinorTickChild.VertexData(2,:)<0) = [];
end
Note: this uses undocumented features -> so may only work in certain versions of Matlab (I have added the code for r2015a & r2015b) and Matlab may recreate the vertex data depending on what you do with the plots..
Here is a simple way for achieving that:
% some data:
x = 1:100;
f=#(x) 5.*x;
y=f(x)+rand(1,length(x))*50;
close all
% plotting:
f1 = figure('Color','white');
ax = axes;
plot(ax,x,y,'o');
% 'clean' the data area a little bit:
box off
ax.TickDir = 'out';
% pushing the axis a bit forward:
lims = axis;
pos = ax.Position;
axis([lims(1)-ax.XTick(2)/5 lims(2)+0.1 lims(3)-ax.YTick(2)/5 lims(4)+0.1])
% Create lines
firstXtick = 0.013; %this value need to be adjusted only once per figure
firstYtick = 0.023; %this value need to be adjusted only once per figure
lx = annotation(f1,'line',[pos(1) pos(1)+firstXtick],...
[pos(2) pos(2)],'Color',[1 1 1],'LineWidth',1);
ly = annotation(f1,'line',[pos(1) pos(1)],...
[pos(2) pos(2)+firstYtick],'Color',[1 1 1],'LineWidth',1);
Which yields this figure:
The only thing to adjust here, once per type of figure, is firstXtick and firstYtick values, that have to be fine tuned to the specific axis. After setting them to the correct value the figure can be resized with no problem. Zoom and pan require a little fixes.
You can start your axes from less than zero and then remove the less than zero ticks from your plot. e.g.
plot(0:3:30,0:3:30); %Some random data for plotting
h = gca;
axis([-1 30 -1 30]); %Setting the axis from less than zero
box off; %Removing box
h.TickDir = 'out'; %Setting Direction of ticks to outwards
h.XTickLabel(1)= {' '}; %Removing the first tick of X-axis
h.YTickLabel(1)= {' '}; %Removing the first tick of Y-axis
With this code, you'll get this result:
This may have a drawback, sometimes, that zero ticks may also get removed (as you can see in above figure). This is because the plot had set the first ticks of axes equal to zero. This can be avoided using if condition. So, the code can be modified as below:
plot(0:3:30,0:3:30);
h = gca;
axis([-1 30 -1 30]);
box off;
h.TickDir = 'out';
if str2num(cell2mat(h.XTickLabel(1))) <0
h.XTickLabel(1)= {' '};
end
if str2num(cell2mat(h.YTickLabel(1))) <0
h.YTickLabel(1)= {' '};
end
The above code will yield the following result:-
Also note that, for your case, since your axes ticks are very less, -1 may not be much suitable for the starting value of axes and you may need to use -0.1 instead i.e. axis([-0.1 30 -0.1 30]);
With a slight modification of #matlabgui's answer you can track the (major) tick limits:
ax = gca();
% Set the tick direction
ax.TickDir = 'out';
% Make sure this stays when saving, zooming, etc
addlistener ( ax, 'MarkedClean', #(obj,event) change_ticks(ax) );
% Draw the plot to generate the undocumented vertex data variable
% and call callback for the first time
drawnow();
The callback
function change_ticks( ax )
% Modify ruler
ax.XRuler.Axle.VertexData(1,1) = ax.XTick(1);
ax.XRuler.Axle.VertexData(1,2) = ax.XTick(end);
ax.YRuler.Axle.VertexData(2,1) = ax.YTick(1);
ax.YRuler.Axle.VertexData(2,2) = ax.YTick(end);
end
I haven't test extensively but seems to work for custom ticks too. This nicely cuts the rulers not only on zero but beyond the fist and last tick. This was tested in Matlab 2019a on Windows and ax.XRuler.Axle.VertexData works just fine. Note this is only for major ticks!
I am having trouble plotting a histogram of the x-values of my data points together with a line showing the relationship between x and y, mainly because the scale in the y direction of the histogram is not of the same magnitude as the scale in the line plot. For example:
% generate data
rng(1, 'twister')
x = randn(10000,1);
y = x.^2
% plot line, histogram, then histogram and line.
subplot(3,1,1)
scatter(x, y, 1, 'filled')
ax = gca;
maxlim = max(ax.XLim); % store maximum y-value to rescale histogram to this value
subplot(3,1,2)
h = histogram(x, 'FaceAlpha', 0.2)
subplot(3,1,3)
scatter(x, y, 1, 'filled')
hold on
h = histogram(x, 'FaceAlpha', 0.2)
Produces the following:
where the line chart is completely obscured by the histogram.
Now, one might naively try to rescale the histogram using:
h.Values = h.Values/max(h.Values) * maxlim;
which gives
You cannot set the read-only property 'Values' of Histogram.
Alternatively one can get the bin counts using histcounts, but as far as I can tell, the bar function does not allow one to set the face alpha or have other configurability as per the call to histogram.
As discussed in the comments there are several solutions that depend on the version of Matlab you are using. To restate the problem, the histogram function allows you to control many graphics properties like transparency, but only gives you a limited number of options to change the height of the bars. With histcounts you can get the bar heights and rescale them however you want, but you must plot the bars yourself.
First option: use histogram
As you cannot rescale the histogram heights, you must plot them on separate axis.
From release 2016a and onwards, you can use yyaxis left for the scatter plot and yyaxis right for the histogram, see Matlab documentation:
Prior to this one must manually create and set separate y-axis. Although I have not found a good simple example of this, this is perhaps the most relevant answer here: plot two histograms (using the same y-axis) and a line plot (using a different y-axis) on the same figure
Using histcounts and manually creating a bar chart
Using my example, we can get counts as follows:
[Values, Edges] = histcounts(x);
And rescaling:
Values = Values / max(Values) * maxlim;
and finding centres of bars:
bar_centres = 0.5*(Edges(1:end-1) + Edges(2:end));
Up to release 2014a, bar charts had a 'children' property for the patches that allows transparency to be controlled, e.g.:
% plot histogram
b1 = bar(bar_centres,Values);
% change transparency
set(get(b1,'Children'),'FaceAlpha',0.3)
After 2014a bar charts no longer have this property, and to get around it I plot the patches myself using the code from this mathworks q&a, replicated here:
function ptchs = createPatches(x,y,offset,c,FaceAlpha)
%createPatches.m
% This file will create a bar plot with the option for changing the
% FaceAlpha property. It is meant to be able to recreate the functionality
% of bar plots in versions prior to 2014b. It will create the rectangular
% patches with a base centered at the locations in x with a bar width of
% 2*offset and a height of y.
% Ensure x and y are numeric vectors
validateattributes(x,{'numeric'},{'vector'});
validateattributes(y,{'numeric'},{'vector'});
validateattributes(c,{'char'},{'scalar'});
%#TODO Allow use of vector c
% Check size(x) is same as size(y)
assert(all(size(x) == size(y)),'x and y must be same size');
% Default FaceAlpha = 1
if nargin < 5
FaceAlpha = 1;
end
if FaceAlpha > 1 || FaceAlpha <= 0
warning('FaceAlpha has been set to 1, valid range is (0,1]');
FaceAlpha = 1;
end
ptchs = cell(size(x)); % For storing the patch objects
for k = 1:length(x)
leftX = x(k) - offset; % Left Boundary of x
rightX = x(k) + offset; % Right Boundary of x
ptchs{k} = patch([leftX rightX rightX leftX],...
[0 0 y(k) y(k)],c,'FaceAlpha',FaceAlpha, ...
'EdgeColor', 'none');
end
end
I made one change: that is, imposed the no edge condition. Then, it is perfectly fine to use:
createPatches(bin_centres, Values, 1,'k', 0.2)
to create the bars.
I read in an image in MATLAB and display it using imagesc. I then set the colormap to grey.
On top of this image, I plot points with the jet colour scheme. How do I then display the jet colorbar, to correspond to the colours of the points plotted on top of the original image? I tried redefining the colorbar after all of the plots, but this changes the original grey scale image back to colours, which isn't desired.
Code:
%Create Figure with handle.
h5=figure('units','normalized','outerposition',[0 0 1 1]);
whitebg(h5,[0 0 0]);
subplot(2,5,1);
k=1;
for i=16:25
subplot(2,5,k);
imagesc(squeeze(ana(:,:,i)));
title(['Z=',num2str(i)]);
colormap gray
axis equal
k=k+1;
colorbar
end
%Adapt colour values so that they are between 0 and 1. We want to scale
%both data sets equally, so we find the smallest value across Ix and Iy. We
%also find what will be the new largest value across Ix and Iy, after we
%add the magnitude of the smallest value to make all numbers greater than
%or equal to 0.
absolutemin=min(min(Ix(:,1)),min(Iy(:,1)));
absolutemax=max(abs(absolutemin)+(max(Ix(:,1))),abs(absolutemin)+max(Iy(:,1)));
%Add the smallest value, and divide by the largest maximum value for both Ix
%and Iy.
ixcolours=uint8(((Ix(:,1)+abs(absolutemin))/absolutemax).*255)+1;
iycolours=uint8(((Iy(:,1)+abs(absolutemin))/absolutemax).*255)+1;
mycolours=jet(256);
o=1;
for k=16:25; %For all 3D slices
for i=1:471; %and for all x and y seed slices
if k==seed_locs(i,3);
subplot(2,5,o);
hold all%go to the corresponding z subplot
plot(seed_locs(i,1),seed_locs(i,2),'MarkerFaceColor',mycolours(ixcolours(i),:),'MarkerEdgeColor',mycolours(ixcolours(i),:),'MarkerSize',10,'Marker','s') %plot the x and y seedlocs
%hold on
end
end
for i=1:486;
if k==test_locs(i,3);
subplot(2,5,o);
hold all
plot(test_locs(i,1),test_locs(i,2),'MarkerFaceColor',mycolours(iycolours(i),:),'MarkerEdgeColor',mycolours(iycolours(i),:),'MarkerSize',10,'Marker','s') %plot the x and y seedlocs
% hold on
end
end
o=o+1; %go to the next z subplot
end
colormap jet
colorbar
I think the following example can help you to improve your code. You firstly need to define two colormaps:
colormap([cool(64);gray(64)]);
Then let's say we have two different sets of datapoints to plot:
[X,Y,Z] = peaks(25);
h(1) = surf(X,Y,Z);hold on
h(2) = pcolor(X,Y,Z);
So the data is defined with two different handles. Now we need to make the CData using the minimum and maximum values.
cmin = min(Z(:));
cmax = max(Z(:));
C1 = min(64,round((64-1)*(Z-cmin)/(cmax-cmin))+1); % CData for the first datapoints
C2 = 64+C1; % CData for the second datapoints
Now we update the CDatas for each object.
set(h(1),'CData',C1);
set(h(2),'CData',C2);
Now you can set the CLim property of axes:
caxis([min(C1(:)) max(C2(:))])
colorbar;
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