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Quite a simple question but just couldn't find the answer online... I want to visualise a point cloud gathered from a lidar. I can plot the individual frames but wanted to loop them to create a "animation". I know how to do it for normal plots with drawnow but can't get it working with a scatter3. If I simply call scatter3 again like I have done in the commented code then the frame that I am viewing in the scatter plot jumps around with every update (Very uncomfortable). How do i get the scatter3 plot to update to the new points without changing the UI of the scatter ie. Still be able to pan and zoom around the visualised point cloud while it loops through.
EDIT: The file is a rosbag file, I cannot attach it because it is 170MB. The problem doesn't happen when using scatter3 in a loop with a normal array seems to be something with using scatter3 to call a PointCloud2 type file using frame = readMessages(rawBag, i).
EDIT: The problem does not seem to be with the axis limits but rather with the view of the axis within the figure window. When the scatter is initialised it is viewed with the positive x to the right side, positive y out of the screen and positive z upwards, as shown in view 1. Then after a short while it jumps to the second view, where the axis have changed, positive x is now out of the screen, positive y to the right and positive z upwards (both views shown in figures). This makes it not possible to view in a loop as it is constantly switching. So basically how to update the plot without calling scatter3(pointCloudData)?
rawBag = rosbag('jackwalking.bag');
frame = readMessages(rawBag, 1);
scatter3(frame{1});
hold on
for i = 1:length(readMessages(rawBag))
disp(i)
frame = readMessages(rawBag, i);
% UPDATE the 3D Scatter %
% drawnow does not work?
% Currently using:
scatter3(frame{1})
pause(.01)
end
The trick is to not use functions such as scatter or plot in an animation, but instead modify the data in the plot that is already there. These functions always reset axes properties, which is why you see the view reset. When modifying the existing plot, the axes are not affected.
The function scatter3 (as do all plotting functions) returns a handle to the graphics object that renders the plot. In the case of scatter3, this handle has three properties of interest here: XData, YData, and ZData. You can update these properties to change the location of the points:
N = 100;
data = randn(N,3) * 40;
h = scatter3(data(:,1),data(:,2),data(:,3));
for ii = 1:500
data = data + randn(N,3);
set(h,'XData',data(:,1),'YData',data(:,2),'ZData',data(:,3));
drawnow
pause(1/5)
end
The new data can be totally different too, it doesn't even need to contain the same number of points.
But when modifying these three properties, you will see the XLim, YLim and ZLim properties of the axes change. That is, the axes will rescale to accommodate all the data. If you need to prevent this, set the axes' XLimMode, YLimMode and ZLimMode to 'manual':
set(gca,'XLimMode','manual','YLimMode','manual','ZLimMode','manual')
When manually setting the limits, the limit mode is always set to manual.
As far as I understood what you describe as "plots jumpying around", the reason for this are the automatically adjusted x,y,z limits of the scatter3 plot. You can change the XLimMode, YLimMode, ZLimMode behaviour to manual to force the axis to stay fixed. You have to provide initial axes limits, though.
% Mock data, since you haven't provided a data sample
x = randn(200,50);
y = randn(200,50);
z = randn(200,50);
% Plot first frame before loop
HS = scatter3(x(:,1), y(:,1), z(:,1));
hold on
% Provide initial axes limits (adjust to your data)
xlim([-5,5])
ylim([-5,5])
zlim([-5,5])
% Set 'LimModes' to 'manual' to prevent auto resaling of the plot
set(gca, 'XLimMode', 'manual', 'YLimMode', 'manual', 'ZLimMode', 'manual')
for i=2:len(x,2)
scatter3(x(:,i), y(:,i), z(:,i))
pause(1)
end
This yields an "animation" of plots, where you can pan and zoom into the data while continuous points are added in the loop
If I run
plot(1:1001)
Matlab automatically sets the x range to be 1:1200. I am aware that xlim([1,1001]) exists, but I don't want to add this line every single time I use plot.
Is there a way to change Matlab's behavior so that plot sets the x-limits equal to the range of the data by default instead of having to do it manually every time? (For example with a flag I can set at the top of my script).
Or a parameter I can pass to plot to make this happen?
You could set your default XlimSpec property for Axes.
set(0,'defaultAxesXLimSpec', 'tight')
Then when you plot it will use X axes tight setting for every new plot.
This will revert back to normal after you close & restart Matlab. However, you could add that to your startup script to always apply it.
This meets some of your requirements I saw you mentioned in the comments about not using a wrapper and trying to minimize running extra commands after call plot
Matlab uses an internal algorithm to determine the best interval of axis ticks. I doubt you can manipulate it and, even if it was possible, I recommend you not to do it. Such operation would change the behavior of your own Matlab installation, but everybody else using your code would stumble upon a different axis labelling probably not well fitting with your purposes.
Keep on defining your ticks manually or implement your own generalized logics into a separate function that you can release together with your scripts. This code shows how to implement one, and can represent a good starting point for you.
If you want to make things simpler, create a wrapper of the plot function as follows:
h = plot_wrapper(true,1:101,1:101);
function varargout = plot_wrapper(fix_limits,varargin)
han = plot(varargin{:});
if (fix_limits)
x = get(han,'XData');
xlim(gca,[min(x) max(x)]);
y = get(han,'YData');
ylim(gca,[min(y) max(y)]);
end
if (nargout)
varargout{1} = han;
end
end
You want the x-axis limits to tightly fit your data. If you don't mind the y-axis also having that behaviour, you can simply use
plot(1:1001)
axis tight
From the documentation,
axis tight sets the axis limits to the range of the data
If you want only the x-axis to be tight, you can do it manually as follows:
h = plot(1:1001); % h is a line object
h.Parent.XLim = [min(h.XData) max(h.XData)]; % set x-axis limits as per the line data
Note that the second line uses dot notation, which is available since R2014b. For older Matlab versions use set/get .
Or you can do it automatically by setting the seemingly undocumented 'XLimSpec' property of the axis to 'tight':
plot(1:1001)
set(gca, 'XLimSpec', 'tight')
which is what axis tight internally does (for the x-, y- and z-axis), at least in R2017a.
I would really appreciate some help.
I have to independent datasets. Each dataset contains two variables: dates (as datenumber) and corresponding data. I need to plot both datasets on one scatter plot with dates on x-axis and two y-axes. I have been trying with the following code:
figure(1);
scatter(x1,y1,'g');
set(gca);
ax1=gca;
set(ax1,'YColor','g');
ax2 = axes('Position',get(gca,'Position'),'YAxisLocation','right', XTick'[],'Color','none','YColor','r');
hold on; scatter(x2,y2,'r');
Now, this gives correct y-axis on the right side, however on the right side I end up with two overlapping y-axes.
Also, I need to change x-axis so that it displays dates as opposed to datenumbers. I've tried to incorporate datetick into the code but it again gives me two overlapping x-axes.
Does anyone know how to go about it?
thank you
I tried your script with your sample input and found no problems. Anyway, here's a solution which uses the matlab function plotyy, which is suited to simple plots like this:
%generate input
x1=[732490 732509 732512 732513 732521 732528];
y1=[7.828 7.609 22.422 14.758 26.258 1.477];
x2=[732402 732403 732404 732404 732433];
y2=[0.693 0.645 0.668 0.669 0.668];
figure(1);
[ax, h1,h2]=plotyy(x1,y1,x2,y2,'scatter');
%set colors manually
green=[0 1 0];
red=[1 0 0];
set(h1,'cdata',green);
set(h2,'cdata',red);
set(ax(1),'ycolor',green);
set(ax(2),'ycolor',red);
%note the 'keepticks' and 'keeplimits' options
datetick(ax(1),'x','yyyy-mm-dd','keepticks','keeplimits');
datetick(ax(2),'x','yyyy-mm-dd','keepticks','keeplimits');
Without the datetick call the plotyy function synchronizes the xticks in the plot. When you call datetick, it recalculates the ticks, unless you explicitly tell it not to, see the option keepticks, and this is seen as two sets of x axes (even though the x coordinates are the same, the ticks are located at different positions). The keeplimits option is needed to preserve the original xlim. It obviously needs some more manual work to get plots like this sufficiently pretty.
Also note that I set the axes and data colors manually: there might be a way to do this more elegantly.
Update: keeplimits originally missing
Update2: changed sample data to correspond to updated question comment
If f is the figure handle, I wanted to use plot3(..) on it just like I would use plot(..), but this didn't work:
>> plot3(f, t, real(Y), imag(Y))
Error using plot3
Vectors must be the same lengths.
Then I figured out that the way to do this is to:
First make the relevant figure current.
Then use the plot3(..) function.
I can find what the current figure is using gcf, but how do I make a figure current (via its handle)?
This method has my personal preference:
set(0, 'currentfigure', f); %# for figures
set(f, 'currentaxes', axs); %# for axes with handle axs on figure f
because these commands are their own documentation. I find
figure(f)
and the like confusing on first read -- do you create a new figure? or merely make an existing one active? -> more reading of the context is required.
It is actually as simple as feeding the f back into the figure(..) command:
figure(f) %Makes the figure current.
Also, if I did something like this:
f = figure('IntegerHandle','off'); % With unique, non-reusable handle.
top = subplot(2, 1, 1);
bot = subplot(2, 1, 2);
Then I can make the axes top or bottom current by issuing a command like this:
subplot(top);
This also works:
axes(top);
But the two types of handles cannot be intermixed: axes(..) and subplot(..) work on axes handles, while figure(..) works on figure handles.
While others have provided you exactly what you've asked for (how to make an axes or figure the current one). My preferred way for dealing with this, is to explicitly specify the parent of your plot in the call to plot3.
If you look at the documentation, you will see that you can specify the parent axes as the first parameter to the function. If looks like you attempted to do this in your example, but you provided a handle to a figure rather than an axes.
f = figure()
ax = axes('Parent', f)
im = plot3(ax, X, Y, Z);
Alternately, I prefer the explicit solution
im = plot3(X, Y, Z, 'Parent', ax)
The nice thing about this explicit parameter/value specification of the parent is that it is accepted by all graphics objects. Functions like plot and plot3 are actually helper functions that wrap the functionality of line and allow for the convention of passing the parent first. The parameter/value approach is widely accepted regardless of whether you're working with a higher level function (plot, plot3, imshow) or the lower level objects (line, image, etc.)
The two benefits here are that you remove the overhead of MATLAB trying to figure out where to put your plot and also, it prevents MATLAB from having to change which figure is currently displayed, forcing a re-rendering which is one of MATLAB's slowest tasks.
give handle name to figure, give you a little example
f1 = figure;
imshow(image1);
f2 = figure;
imshow(image2);
% edit image 1
figure(f1);
text(2,3,'done');
I am writing two small psychoacoustic testing applications in MATLAB. The first one works without problems but the second one doesn't, and I just can't figure out why.
Here is the problem: the axes object is created, but it is empty.
failed_axis http://dl.getdropbox.com/u/98854/help.png
Here is the code that creates this figure and axes:
hFig = figure('dockcontrols','off','menubar','none', ...
'name','choose the better sounding file', ...
'numbertitle','off','position',[0,0,700,500], ...
'resize','off','toolbar','none','units','normalized', ...
'color',[.8,.8,.8]);
progress_idc = axes('position',[.1,.8,.8,.05],'box','on','parent',hFig,...
'xlim',[-.03,1.03],'xtickmode','manual','xtick',[], ...
'xticklabelmode','manual','xticklabel',[], ...
'ylim',[-1,1],'ytickmode','manual','ytick',[], ...
'yticklabelmode','manual','yticklabel',[], ...
'nextplot','add');
And here is the code that plots in this axes (the function is called regularly by a timer):
function replot(varargin) % this is a nested function
cla;
% plot start_indicator
plot([x_start,x_start],[-.7,.7],'k','linewidth',2);
fill([x_start,x_start-.02,x_start-.02],[0,-.7,.7],[0,0,0]);
% plot stop_indicator
plot([x_stop,x_stop],[-.7,.7],'k','linewidth',2);
fill([x_stop,x_stop+.02,x_stop+.02],[0,-.7,.7],[0,0,0]);
% plot play_position
plot([x_play,x_play],[-1,1],'r');
drawnow;
end
This is what it looks like if it works:
proper_axis http://dl.getdropbox.com/u/98854/help2.png
Do you have any idea what is going wrong here?
I ran the code you included above and got the correct output.
If I had to take a wild guess as to what the problem is, I'd guess that you may be creating other axes in your application that you are not listing above, or that you may have other axes not related to the application open at the time the application is running. When you plot your objects in the function replot, you are by default plotting them to the currently active axes. If you have multiple axes open, the plotting may therefore be going on in the wrong set of axes.
One suggestion I would make is to explicitly specify what the parent axes object should be in your calls to PLOT and FILL. If you add the arguments ...,'Parent',progress_idc); to your plotting calls, it will ensure that the correct axes is always used. I make a habit of always specifying the parent axes object instead of assuming that the currently active axes will always be the one I need it to be.
I finally found the (dumb) answer. The title accidentally had the same position as the plot axis. Due to some rendering-details of Matlab, it obscures the whole axis except for the rightmost and bottommost line of pixels, which makes the axis look "empty".
Oh, what a dumb error.