Code covered by the BSD License  

Highlights from
vol3d v2

4.94118

4.9 | 17 ratings Rate this file 171 Downloads (last 30 days) File Size: 3.4 KB File ID: #22940
image thumbnail

vol3d v2

by

 

10 Feb 2009 (Updated )

3-d volume (voxel) rendering

Editor's Notes:

This file was selected as MATLAB Central Pick of the Week

| Watch this File

File Information
Description

An update to Joe Conti's popular vol3d function, allowing voxel colors and alpha values to be defined explicitly. Functionality is increased, but the function is entirely backwards compatible.

In cases where voxels can be any RGB color, use:
   vol3d('CData', cdata);
where cdata is an MxNxPx3 array, with RGB color along the 4th dimension. In cases where color and alpha values are highly independent, specify an MxNxP alphamatte as follows:
   vol3d('CData', cdata, 'Alpha', alpha);

This function amends the original (as little as possible) with the full permission of Joe Conti. The original function comes with some additional tools for editing colormaps and alphamaps which are not included in this version. See:
http://www.mathworks.com/matlabcentral/fileexchange/4927

Acknowledgements

This file inspired Tactics Toolbox.

MATLAB release MATLAB 7.5 (R2007b)
Tags for This File   Please login to tag files.
Please login to add a comment or rating.
Comments and Ratings (32)
29 Sep 2014 Ander Biguri  
21 Aug 2014 Javier Montoya

Hi Oliver, nice visualization tool! Was wondering which is the best way to add labels on the axes? By using xlabel/ylabel/zlabel, the labels aren't displayed, especially if one rotates the 3d volume.

25 Jun 2014 Darren Price

Wow! It has just made an almost impossible job very easy. Thanks! I will certainly be inspecting this code to learn a thing or two :)

06 Jun 2014 Alexandros Iliopoulos  
25 May 2014 Yu  
11 Mar 2014 Zoidberg  
29 Jan 2014 Ben

Great contribution!

29 Dec 2013 Xiaoyin  
24 Oct 2013 Hg  
18 Oct 2013 Jun Hao

Oliver, this is really brilliant!

I have another question. Is it possible to include interpolation while carrying out the 3D rendering if there is a certain element spacing between each slice?

28 Aug 2013 Emmanuel Farhi

An excellent contribution for 3D rendering. However, the initial vol3d is not available anymore.

18 Aug 2013 William Warriner

Absolutely wonderful code. Very useful for visualizing voxel representations of part models for analysis of casting properties.

I made a slight change to the code on my own machine that has made some models a bit prettier. Specifically, at lines 204, 222, and 239, (drawing individual surface patches for x,y,z slices), I added a second line that adds 1 to the relevant dimension to draw the back surface of each voxel as well. While this obviously doubles the quantity of objects that need to be rendered, it makes very thin voxel sections (1 voxel thickness) more aesthetically appealing.

Perhaps an option to draw back surface patches? Just a suggestion.

Thank you for this code, I wouldn't be moving nearly as fast on my own work without it.

03 Apr 2013 Oliver Woodford

Naomi - The help text clearly states:
vol3d(...,'XData',x) 1x2 x-axis bounds. Default: [0 size(data, 2)].
vol3d(...,'YData',y) 1x2 y-axis bounds. Default: [0 size(data, 1)].
vol3d(...,'ZData',z) 1x2 z-axis bounds. Default: [0 size(data, 3)].
I have nothing more to add.

03 Apr 2013 Naomi

How can I specify the location (x,y,z) of my cData?

28 Feb 2013 Raz Shimoni

Great 3D visualization tool.

15 Jan 2013 Irvin

Excellent tool, works well for 3D probability density functions. Thanks.

08 Apr 2012 edward kabanyas

Oliver, it is possible to use vol3d for 3D map ? I have 3D data (latitude x longitude x time). I want to produce a volumetric plot, how to use vol3d for this ?

03 Feb 2012 Mohamed Nassar

Oliver, Thank you so much, it works fine with me

03 Feb 2012 Oliver Woodford

Mohamed: If you run the demo you should discover that mri.mat is included with MATLAB. The 3D data is displayed using textured-mapped 2D planes, as described in the help. Call
view(3)
to see a 3D view of the data.

03 Feb 2012 Mohamed Nassar

Hello oliver, I used your code to display a 3D volume raw data, using this command "H= vol3d('cdata',datafile); it just displayed the 2D images on top of each other, looks like only a one 2d image, the datafile format is (x,y,z), where x is the number of frames, y *z is the 2d image's size, also at the end of the module, you load a mat file "mri.mat" which is not included, could you please advise me with that? thank you so much, you reply is highly appreciated

20 Dec 2011 Jean-Philippe

This script works great to display MRI-like 3d images.

In the case that I have a logical 3d array (ie: a segmentation mask of an anatomical structure from an MRI), how can I use vold3d to only show the resulting mask? I am able to display my MRI model, but when I just want to display the mask I get a blank plot.

I = a [MxNxP] matrix for my MRI [grayscale values 0-255]
J = a [MxNxP] matrix for my mask [logical 0 or 1]

figure;
vol3d('cdata',I, 'texture','3D'); %this works
vol3d('cdata',J, 'texture','3D'); %this is blank
view(3);

Thank you for your help.

05 Dec 2011 Wilson

The hgsave command works, many thanks

05 Dec 2011 Oliver Woodford

Wilson: saveas requires a figure handle. vol3d returns a structure, hence the first error. The second error is due to the figure being too large. Try:
hgsave(gcf, 'Image3D.fig', '-v7.3');

05 Dec 2011 Wilson

Nice code, but in my case, I can only render a 3D image but can not save the image.

When I use command:
h = vol3d('CData',Y); saveas(h,'Image3D.fig');
Matlab displays it's a 'Invalid handle'

If I save the image directly from figure, it displays:

Warning: Variable 'hgS_070000' cannot be saved to a MAT-file
whose version is older than 7.3.
To save this variable, use the -v7.3 switch.
Skipping...
> In hgsave at 93
In general\private\saveasfig at 7
In saveas at 126
In filemenufcn>localSaveExportHelper at 203
In filemenufcn>localSaveExport at 316
In filemenufcn at 56

And only a figure frame is saved instead of the actual image.

any ideas?

15 Aug 2011 Oliver Woodford

The rendering method does stress MATLAB's rendering pipeline, so large volumes can slow down your machine significantly. Good graphics hardware helps a bit. Smaller datasets do too.

14 Aug 2011 harish raj

matlab collapses if i run vol3d code

24 May 2011 Maxwell  
18 Apr 2011 Oliver Woodford

Matthias: The latest version allows you to set axis limits.

10 May 2010 Oliver Woodford

Matthias: Unfortunately specifying different axis values isn't currently possible using this function. It is straightforward to implement though. You just need to change lines 121, 124 and 127 to achieve the desired results.

08 May 2010 Matthias Pospiech

Wonderful script to generate 3D Volume plots.

However I need to set the axis values other than just the sizes of the data matrix.

How can one specifiy the axis (in x,y and z) for this plot?

31 Dec 2009 Greg Siegle

Marvelous! Gorgeous 3d renderings of MRIs. Esp. in bone colormap.

09 Jul 2009 Jan Van den Bulcke

Wonderful!

Updates
16 Apr 2011

Avoid destroying other vol3d objects when rerendering. Added a demo.

Contact us