Volumetric Data Explorer

App for exploring higher dimensional data using volumetric visualizations and animation.

Description

This app provides an interactive environment to explore four and five dimensional data using some of MATLAB's abilities for volumetric visualization and animation. It was designed for data that was measured in a 3D grid of data points, for example temperature or wind speed taken at each point in a 3D space. If this data is taken over time, it can also be animated. Any data that fits the form v = f(x,y,z) or v = f(x,y,z,t) can be used.

If you have any ideas for enhancements or find any bugs, please let me know below. I'm open to adding more options/features if people find this useful.

Please use the 'Watch this file' option on this page to get auto updates when I add/fix things in the app.

Acknowledgements

Screen Capture Get A Screen Capture Of A Figure Frame Or Component, Gui Layout Toolbox, and Uigetvariables: Dialog To Pass Variables From Workspace Into Gui inspired this file.

• Required Products: MATLAB
• MATLAB release: MATLAB 8.1 (R2013a)

[Adam Filion]

Updated version is on its way, hopefully posted today or tomorrow, that incorporates some of the feedback from this forum. Try out V 1.5.0 when it's available and let me know if you have any further feedback!

[Adam Filion]

Thanks for the feedback Matt! I'm surprised you had to change the renderer manually. My default rendered is painters, and I've never had any problems with the transparency. Likewise I haven't heard of anyone else needing to change the renderer manually. Still, I see your point and will update the app. As for the sliders, that's on my to-do list for the app, so keep an eye out for updates. Thanks!

[Matt Smith]

Adam, this is a great start.

My defaultfigurerenderer was NOT 'opengl' and thus the transparency didn't render. There was no option within the app to fix this. I closed the app, and in the command line, did

>> set(0,'DefaultFigureRenderer','opengl')

and then reran the app and it worked. Consider setting the figure's renderer manually to opengl when you create it so you don't have to rely on user's potentially different default settings.

Another suggestion, have the sliders update the slices dynamically as you slide them. This can be done and there's material online to do this. I think I've used addListener to check for changes in the slider value, which will be changing as it slides.

Great functionality so far and a nice interface. Great job!

[Swati Tiwari]

 

[Martin Lechner]

Thanks, for the fast respones. It works good.
Martin

[Adam Filion]

Thanks for the feedback Martin. I've uploaded a new version that will hopefully get posted today (since I work for MathWorks there's a separate process that can take some time). It includes the isosurface sliders and an option for coloring that you suggested. I plan to add some of your other feedback when I have the time. Let me know if you have any other comments on it.

Thanks, Adam

[Martin Lechner]

Hi Adam,

nice to hear, that you are continue to improve this great tool.

In the options menue (Options/Set Axes Names) I can change the x-, y- and z-axis labels but the description for the actual Level is for example always X Slice At.
I would suggest include the axis labels below the text X Slice At and so on. The area for displaying the value is high enough.
Minor Hint the dialog title for changing the axes label is wrong (Set Font ...).

Normaly the color value has a physical meaning, so i would like to have the possibility to add also a description to the colorbar. This description should also be shown below ISO Level 1 and 2.

If I missuse the time axis for a fifth dimension (other physical meaning than time), i want to change the description 'Current time:' for example to 'speed [km/h]:'.

I suggest to include this 2 labels in the menue for changing the axes labels.

Thanks, Martin

[Adam Filion]

Thanks for trying out the app Martin, that's a lot of great feedback! To address your points:

- I'll check the dimension order and update doc where appropriate
- The warning you get when not importing a time vector stems from simplified (aka lazy) programming on my part that categorized missing and incorrectly sized time inputs the same. It's on my to-do list to separate those when I have the time so you can avoid the unnecessary warning.
- Animations for scrolling slices and rotations is a great idea, I'll see if I can find an easy-to-use way to implement it
- The colors and sliders for isosurfaces is another thing that's been on my to-do list, so keep an eye out for it in an update
- The colorbar is off by default because it slows down animation (I'm not sure why). You can use the Options menu -> Save/Load Options to turn it on then set the current options configuration to the default to it is always on when loading in data.
- Where else would you like to change the x/y/z/time/colorbar label?

Thanks, Adam

[Martin Lechner]

Hi Adam,
the tool works really greate.
I had an issue with my own data:
From the documentation I thought that the 1st dimension is x (size(data,1)), 2nd is y and 3rd is z. Debugging of the code showed me that:
1st Dimension is y
2nd x
3rd z

Please improve the documentation or change the order.

Further suggestions for improvement:
Making a plot with 4D-Data and not provideing a time vector (like: DataExplorer(y,x,z,count) count is a 3D matrix) should not bring the following warning:
Warning: Invalid or missing time data, using defaults

My main purpose is the visualization of 3D Data, so I would like to have the possibility to create animations like:
* automatic scrolling the slices
* or rotate the orientation

Because my data often represents not x,y and z coordinates I would like to have the possibility to give custom x,y,z, time and colorbar value labels (not only the labels of the axis).

It would be great when the color of the isosurface would be the same as in the left plot on the colorbar (possibility to link the color).

A slider for the isosurface levels would be nice. The levels could be markers in the colorbar which can be moved throw the colorbar. The colorbar should be shown as default.

Nevertheless, a very good and useful tool.

Thanks, Martin

[Adam Filion]

Hi jp,
Sorry to hear it still isn't working. I tried this out on a Debian install and everything worked fine, very stable. I don't have access to Ubuntu at the moment. I think you're right, it's some compatibility issue between your java and/or Ubuntu version and R2013a.

The only other thing I can suggest is to make sure your java and Ubuntu are up to date and supported by R2013a.

Thanks, Adam

[jp]

Hi Adam,

I made the tests you suggested. The behaviour is very erratic, sometimes works fine but in the majority of the attempts the java error still appears, freezing the whole GUI... I'm sorry that I can't provide more details... It's probably some issue between matlab/java/ubuntu. Let me point out that such instabilities are indeed very common when running more complex 3D graphics under Linux.
cheers !
JP

[Adam Filion]

Hi jp,

The error you are getting could be the result of loading in data that is not of type double or single, which are the only types supported by the built-in SLICE command used in the GUI. I thought I had added a check so that incorrect data types couldn't be imported form the workspace, but I guess I imagined that because I just did it myself.

Could you try:
- Opening the app, and checking that it looks like the screenshot on this page, minus the plotted data. If not, we need to sort that out first.
- If it's good, load one of the example data sets and see if that works
- Then try importing double or single precision data from workspace with a fresh startup of the app

While the beginning of the error is expected for an incorrect data type, the java error is not. I'm going to try this on a linux install and see if I can reproduce it.

Thanks, Adam

[jp]

Hi Adam, thanks for your swift reply. I've reinstalled it using a different directory and managed to launch the app, but I'm still receiving lots of error msgs... I'm already runing as administrator.
Path gives me: /home/jpn12/Documents/MATLAB/Apps/DataExplorer - 2
/home/jpn12/Documents/MATLAB/Apps/DataExplorer - 2/Patch
/home/jpn12/Documents/MATLAB/Apps/DataExplorer - 2/html
/home/jpn12/Documents/MATLAB/Apps/DataExplorer - 2/metadata

and when loading some data (or trying the built-in examples) into the app I got:
Error using griddedInterpolant
Sample values must be a single or double array.
Error in interp3 (line 141)
F = griddedInterpolant(X, Y, Z, V, method,extrap);
Error in slicemod (line 100)
vi = interp3(x,y,z,v,xi,yi,zi,method);
Error in DataExplorer/RedrawSlice (line 984)
app.SliceHandle =
slicemod(app.SliceAxis,app.DimValues{1},app.DimValues{2},app.DimValues{3},app.Data(:,:,:,app.CurrentSample),SliceLoc(1),SliceLoc(2),SliceLoc(3));
Error in DataExplorer>@(varargin)app.RedrawSlice(varargin{:})
(line 178)
app.GridComp{1,2} =
uicontrol('Parent',app.SliceGrid,'Style','slider','Callback',@app.RedrawSlice);
Error while evaluating uicontrol Callback

java.lang.IllegalArgumentException: adding a container to a container on a different GraphicsDevice
at java.awt.Component.checkGD(Unknown Source)
at java.awt.Container.addImpl(Unknown Source)
at java.awt.Container.add(Unknown Source)
at com.mathworks.hg.peer.FigurePanel.doAdd(FigurePanel.java:215)
at com.mathworks.hg.peer.FigurePanel.assembleFigurePanel(FigurePanel.java:203)
at com.mathworks.hg.peer.FigurePanel.reconstructFigurePanel(FigurePanel.java:131)
at com.mathworks.hg.peer.FigurePanel.handleNotification(FigurePanel.java:88)
at com.mathworks.hg.peer.FigureNotificationHandlerImpl.forwardNotification(FigureNotificationHandlerImpl.java:62)
at com.mathworks.hg.peer.FigureNotificationHandlerImpl.handleNotification(FigureNotificationHandlerImpl.java:29)
at com.mathworks.hg.peer.FigureAxisComponentProxy.construct(FigureAxisComponentProxy.java:89)
at com.mathworks.hg.peer.FigureAxisComponentProxy.setVisual(FigureAxisComponentProxy.java:112)
at com.mathworks.hg.peer.FigureHG1Mediator.setClientVisual(FigureHG1Mediator.java:119)
at com.mathworks.hg.peer.HG1FigurePeer.setVisualImpl(HG1FigurePeer.java:169)
at com.mathworks.hg.peer.FigurePeer$25.run(FigurePeer.java:2552)
at com.mathworks.hg.util.HGPeerQueue$HGPeerRunnablesRunner.runit(HGPeerQueue.java:262)
at com.mathworks.hg.util.HGPeerQueue$HGPeerRunnablesRunner.runNotThese(HGPeerQueue.java:294)
at com.mathworks.hg.util.HGPeerQueue$HGPeerRunnablesRunner.run(HGPeerQueue.java:310)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

BTW: I'm using dual monitors, and I know Matlab doesn't behave well with this configuration sometimes...

tks, jp

[Adam Filion]

Hi jp, thanks for trying out the app. I haven't seen that error before with the app. I only tested on win7 but I don't think that should be an issue.

My first guess is that this is a path issue. After loading the app, when you get the error, can you check the state of the MATLAB path? You can do so by entering >>path or using the Set Path utility in the home tab.

After loading the app, four folders should now be at the top of your path:
<approot>\DataExplorer
<approot>\DataExplorer\GUILayout-v1p12
<approot>\DataExplorer\GUILayout-v1p12\Patch
<approot>\DataExplorer\html

Where <approot> is the app install location, which you can set through the MATLAB Preferences -> Apps section.

The only other possibility I can think of is maybe some kind of permissions issue, though I kinda doubt it. In any case, can you try running MATLAB in administrator mode and use the app to see if that changes things?

Please confirm if your path is correct after loading the app, and I'll try thinking of some other possibilities in the meantime.

Thanks, Adam

[jp]

Dear Adam,

it doesn't work for me... runing R2013a under ubuntu... Tks

Warning: Function /home/jpn12/rotinas matlab/dataexplorer/%2Buiextras/get.m has
the same name as a MATLAB builtin. We suggest you rename the function to avoid a
potential name conflict.
> In path at 110
In addpath at 87
In runapp at 10
Warning: Function /home/jpn12/rotinas matlab/dataexplorer/%2Buiextras/set.m has
the same name as a MATLAB builtin. We suggest you rename the function to avoid a
potential name conflict.
> In path at 110
In addpath at 87
In runapp at 10
Error using get (line 40)
Property name must begin with 'Default'.
Error in DataExplorer (line 100)
screensize = get(0,'ScreenSize');
Error in DataExplorer0x2D1App/startApp (line 60)
obj.AppHandle = eval('DataExplorer');
Error in DataExplorer0x2D1App (line 37)
startApp(obj)
Error in appinstall.internal.runapp>execute (line 69)
out = evalin('caller', [script ';']);
Error in appinstall.internal.runapp>runapp13a (line 51)
outobj = execute(fullfile(appinstalldir, [wrapperfile 'App.m']));
Error in appinstall.internal.runapp>runcorrectversion (line 35)
appobj = runapp13a(appinstalldir);
Error in appinstall.internal.runapp (line 17)
out = runcorrectversion(appmetadata, appentrypoint, appinstalldir);
>>

[Paul Andrews]

 

[Warwick]

Terrific. Going to be very useful for my work in meteorology and climatology.

[Adam Filion]

Thanks for the comment Matthew, I think that's a good suggestion. As you use it, let me know if there are any additional options/features that would be useful.

[Matthew]

I really like:
* The GUI layout
* The documentation and help in first rate.
* The code style is pretty good.

I would suggest that name change would be appropriate. Maybe "Volumetric Data Explorer" would better suggest the applicability of your tool.

[Adam Filion]

Bug fix is in, app has been updated to V 1.0.1

[Adam Filion]

Hi Warwick,

Thanks for trying out the app. That's a bug I hadn't caught in testing. I'm updating the file, but since I work for MathWorks there's a separate submission process and I'm not sure when it will go through. Please use the 'Watch this file' link at the top of the page to get auto updates when the file changes.

Thanks, Adam

[Warwick]

This is potentially a very useful app of 5 stars for my work. The demo data works well. However, after I put in a sample array of v = f(x,y,z) data, then any attempt to "Import from workspace" gives me errors as "Undefined function 'isdouble' for input arguments of type 'double'.
Error in
DataExplorer/ImportWorkspaceCB/@(in)(ndims(in)==4||ndims(in)==3)&&(isdouble(in)||issingle(in))

Error in uigetvariables (line 309)
t(jj) = evalin('base',['validationfunction_(' varnames{jj} ');']);
Error in DataExplorer/ImportWorkspaceCB (line 450)
data =
uigetvariables(text,'ValidationFcn',checkvars,'Introduction',intro);
Error in
DataExplorer>@(varargin)app.ImportWorkspaceCB(varargin{:})
(line 117)
app.Menu(2) = uimenu(app.Menu(1),'Label','Import from
Workspace','Callback',@app.ImportWorkspaceCB);
Error while evaluating uimenu Callback ".

Maybe a simple example at the Description would help me.