AMILab Volume rendering

Volume rendering is a technique used to display a 2D projection of a 3D discretely sampled data set. A typical 3D data set is a group of 2D slice images acquired by a CT, MRI, or MicroCT scanner. Usually these are acquired in a regular pattern (e.g., one slice every millimeter) and usually have a regular number of image pixels in a regular pattern. AMILab uses an implementation of the volume ray casting algorithm powered by VTK, we have chosen this method for two reasons, it is one of the methods with highest resolution and widely used by all expert community and VTK includes a fast GPU implementation of the algorithm.

AMILab included the Volume Rendering Interface since the version 3.1.0. The first implementation of the method could work with several volumes on a scene and set configurations in real time on the volume. Right now, in the last development release version ( 3.1.1 ), AMILab has a new friendly and powerfull UI for the Volume Rendering. Among the new enhancements are:

  • A toolbar, with the more used and common operations.
  • A new configuration system for represent the volume and scene.
  • Previewer system, for choice a preset configurations.
  • Severals little change in the UI.

The new architecture of AMILab is much more powerful, thank to include the multi-inherit in its desing, allowing to do scripts more simple and decoupled. The new UI keeps the older options and something new.

Demo

How to use Volume Rendering in AMILab (Version 3.0)

Once AMILab is running, Figure 2, you can work with volume rendering easily, you can start from Menubar→Scripts→Visualization→Volume Rendering or from its icon in the right tool bar, with both options AMILab will show the Volume Rendering Interface. The interface is organized in three basic parts, the VTK viewer(1), the histogram window(2) and the user interface panel(3). The VTK viewer is a 3D viewer optimized for work with several volumes, the histogram window is an auxiliary windows that let you know information about the volume, in this windows we can interact with the volume's curve and in the user interface panel we can find all of the operator of the Volume Rendering interface.

Figure 2 - AMILab user interface

The first step is load at least one volume from the user interface panel, as an example, you can:

  • Before loading, we can create a synthetic volume (It can be possible execute any options from the Menubar→Scripts→ 3D Synthetic Image )
  • Load a DICOM (Digital Imaging and Communication in Medicine) from your computer (Its interface can be found in the Menubar→ITK→IO→DICOM ).

The second step is to select the volume loaded, you can do this operation in the tab IO of the Volume Rendering interface, option Input. To display the volume, you have to press the button “Starts rendering” (Eye figure). Sometimes, if you don't have enough memory in your graphic card, you may need to resize the volume, you can do this operation with the command:

AUX_OBJ = Resize(IMG_OBJ, IMG_OBJ.tx/2, IMG_OBJ.ty/2, IMG_OBJ.tz/2,1) 

from the console of AMILab, or using the Resize option of IO tab of the user interface panel.

If you want to load a second volume, you have to repeat the step two with the second volume option.

Right now, you can view and work with the volume represented. The user interface panel has three tabs, Figure 3, in these ones you can find the IO operations, the manager volumes and the scene configuration options.

  • In the first one, you have the input volume options and the histogram manager for show or hide it.
  • In the second one, you have several tools for change the appearance the volume, Blend, Clip, Shade and, some GPU and Render options.
  • In the third one, you have the options for change the color of the background, take a snapshot or change the figure rotation.
Figure 3 -VolRen User interface

Also you can configure the points and the curves of the histogram as you wish, Figure 6. For example, is possible:

  • Move the curve, you have to press SHIFT+LEFT MOUSE BUTTON over one curve's point.
  • Move a point, you have to press LEFT MOUSE BUTTON over one point.
  • Show pop-up menu, you have to press RIGHT BUTTON on the item.
    • Add/Remove grid
    • Change the reference color of the figure
    • Add/Remove point
    • Add/Remove curve

Figure 4 - Menus of histogram window

Volume Rendering in AMILab (Version 3.1.1)

The steps to work with the VRI still remaining the same in the new version, so for load and use the volume you have to follow How to use Volume Rendering in AMILab chapter. As we said before, we have introduced several little change in the new version:

  • Now is possible work with “n” volumes in the same scene (but nowadays is limited from the UI).
  • Also is possible choice the mapper that best suits your graphic configuration.
  • We included a toolbar with the most common and useful operations:
    • Show/Hide Histogram.
    • Show the Preview of the current volume.
    • Get a SnapShot
    • Save the curve of the current volume
  • Structure curve representation
  • Preview

The new VRI is shown in the figure 5 and in the figure 6 its new toolbar:

  • In the first tab, we will return to show only IO functions.
  • In the second tab, we still having several settings for change the volume options, Blend, Clip, Shade and, some GPU and Render options.
  • In the third tab, you have the options for change the background color and the camera interface (these are absolute to the current position)

FIGURA 5

This toolbar is available as long as the VolRen UI. FIGURA 6

Preview

The preview is a collection of presets to speed up the configurations settings of the volumes. It is one of the most important change added because it modifies the actual work style. With its incorporation some blend options have disappeared from the main interface, however we did not lose features because the preview has the ability to load settings file with information of the curve and scene. This files can be finding in SCRIPTS/VISUALIZATION/VOLREN/CURVES directory where you can add new categories creating a new folder and puting settings files inside it. From the toolbar if possible save the settings of the current volume (You can choice the volume selection its tab in the UI).

How it works… The first step is choice one of the preload volume and after click in the toolbar button. This operation show the preview interface, it has several volume viewers that can be configured dynamically according to the number of presets. These viewers show us several representations of the chosen volume with different configurations in their opacity and color curves and another scene properties. In the figure 7, we can view the interface, in the top of the window we have the differents categorys of presets, if we choose another its configurations files will present us. For select one of the configuration just click on the volume whose we want, and his description will change to red colour. If we wish applied the selected configuration we have to click in Apply button (In the bottom of the window).

FIGURA 7

tutorial-volumerendering.txt · Last modified: 2018/01/23 17:38 (external edit)
 
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
Recent changes RSS feed Donate Powered by PHP Valid XHTML 1.0 Valid CSS Run by Debian Driven by DokuWiki