Viewer3D

MIP, Color, Slice and Shaded 3D (shearwarp) Volume Rendering, interactive 3D view/measurement GUI

Description

This function(s) can be used to interactively view any kind of 3D image volumes like CT and MRI, and for distance measurements or ROI selection in 2D slices.

It includes Maximum intensity projections (MIP), Volume Rendering (VR) , Slice render, and colored and Phong shaded Volume rendering.

Voxel opacity and color tables can be changed on the fly allowing also iso surface kind of renders.

The fast render algorithm which renders a 3D volume to a 2D image, is based on a Matlab coded implementation of the Shear-Warp transform, in which instead of rotating the viewer rays the slices are sheared.

There are two major Matlab files:
- viewer3d.m : The interactive GUI
- render.m : The function which renders volume data with the shear-warp transform to an 2D image.
 
Note:
This version is 100% Matlab code, but to make it faster you can run "compile_c_files.m" to use c-coded multi-threaded image warp (only windows). I also included an older version with the shearwarp algorithm in c-code / mex-code

New in this version ( 7 ) :
- Slice view, with ROI selection and distance measurements.
- Faster, with new multi-threaded warp c-code.

Please report bugs, successes and if you know some possible code speedups.

• Required Products: Image Processing Toolbox
• MATLAB release: MATLAB 7.8 (R2009a)
• HTML Files: Viewer3D Help

Other Files

affine_transform_2d_double.c,
affine_transform_2d_double.m,
compile_c_files.m,
default_config.mat,
help/help001.png,
help/help002.png,
help/help003.png,
help/help004.png,
help/help005.png,
help/help006.png,
help/help007.png,
help/help008.png,
help/help009.png,
icon_mouse_pan.png,
icon_mouse_rotate1.png,
icon_mouse_rotate2.png,
icon_mouse_zoom.png,
license.txt,
makeViewMatrix.m,
render.m,
TestData.mat,
TestVolume.mat,
viewer3d.fig,
viewer3d.m,
viewer3d_about.fig,
viewer3d_about.m,
viewer3d_console.fig,
viewer3d_console.m,
viewer3d_contrast.fig,
viewer3d_contrast.m,
viewer3d_dicom.m,
viewer3d_error.fig,
viewer3d_error.m,
viewer3d_histogram.fig,
viewer3d_histogram.m,
viewer3d_lightvector.fig,
viewer3d_lightvector.m,
viewer3d_qualityspeed.fig,
viewer3d_qualityspeed.m,
viewer3d_version5_with_mex_code.zip,
viewer3d_voxelsize.fig,
viewer3d_voxelsize.m,
viewer3d_workspacevars.fig,
viewer3d_workspacevars.m

[Joaquim Luis]

Dirk,
There is absolutely no help on how to use this. When I try to "Load view" than an endless number of errors occur.

[Joaquim Luis]

OK
Sorry, I found a little help on the function's help section.

[Dirk-Jan Kroon]

*Joaquim
Load View only works with Matlab files created by Save View. Some help can be found in menu -> help, and with help function.m in the console window.

[Jean-Yves Tinevez]

Tested successfully on MacOSX-Tiger, MATLAB 2008b & a.

Worked absolutely fine with matrices entered from command line (e.g. viewer3d(I)).

I had plenty of errors when trying to load a .mat file (e.g. the 2 ones given in demo), and putting tyhe mouse over the window. Here is the 1st one

??? Reference to non-existent field 'histogram_positions'.

Error in ==> viewer3d>createAlphaColorTable at 154
        if (i<data.histogram_positions(1)), alpha=0; color=data.histogram_colors(1,:);

Error in ==> viewer3d>menu_load_view_Callback at 542
createAlphaColorTable();

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> viewer3d at 50
    gui_mainfcn(gui_State, varargin{:});

Error in ==>
guidemfile>@(hObject,eventdata)viewer3d('menu_load_view_Callback',hObject,eventdata,guidata(hObject))

 

[Dirk-Jan Kroon]

Tommorow (06-2008) a version with extended HTML help will be online

* Jean-Yves Tinevez
The TestVolume.mat example:
load TestVolume;
viewer3d(V);

[Cris Luengo]

Very nice! But it's not very fast. I will try the old MEX-file code next, to see if that speeds it up or not. I tried it with an image 1000x500x250 pixels and found the rendering took 30 s or more.

Some suggestions:

- Don't update the display every time a node is moved in the alpha colors window. Instead, have a button "preview" to update the rendered image.

- Add checkmarks next to the menu items of the activated modes (render and config menus).

- Add an option to enter pixel spacing for non-isotropically sampled images (common in 3D imaging)

- Put the support M-files either within the main M-file or into a private/ subdirectory. That would make it easier to get started...

Great tool! Thanks!

[Dirk-Jan Kroon]

*Cris Luengo
Thanks for your Feedback, I will use it in my nex file update.
(non-isotropically display, can done by viewer3d(Image, [2 1 1]) with [2 1 1] the scaling)

[Shi vera]

Fantastic

[jichao zhao]

it is very cool staffs. many thanks

[Wenyuan]

Must it be run in the matlab 7.8 version? My matlab version is 7.0, will it be OK? I can't even run the sample: load TestVolume;viewer3d(V). Is it because of the lower matlab version?? Thanks..

[Dirk-Jan Kroon]

*Wenyuan
It runs on most Matlab versions, but not on the very old ones because Matlab figure file format changed in time, and saving to an older figure-file-format doesn't work that well.

[Siyi Deng]

awesome!

[Aaron Schurger]

Outstanding! Sometimes has an error when I switch to a different rendering mode. Thanks for this application.

[Ted Teng]

excellent work. thanks for sharing!