vtkColorCodedDepthVolume

vtkColorCodedDepthVolume is a sample application that demonstrates animating a sequence of NRRD volumes with custom blend modes in VTK.

Features

• Switch between different volume rendering modes
  • Composite blending (stock volume rendering)
  • Average intensity projection
  • Maximum intensity projection
  • Color coding the depth of first non-transparent voxel along the ray. (Think of this as a colored depth map).
  • Color coding based on the depth of individual voxels (yellow-brown-blue color function).
• Demonstrates use of custom shaders in VTK volume rendering
• Read and animate a sequence of NRRD volumes in VTK
• Licensed under Apache version 2.0

Compile

Use CMake to configure the build system for the platform of choice. Build the configured system using the generator selected in CMake. For more details, take a look at the Running CMake tutorial.

Usage

$ ./vtkColorCodedDepthVolume <Nrrd files directory>

The argument should point to the directory containing the time sequence of NRRD volumes as individual files.

Note Take a look at Preparing Data to convert a single NRRD sequence file into multiple files.

Once the above command is run, the application starts reading each file in the directory as a time series and instantiates a volume pipeline for each dataset. A default color and scalar opacity transfer function are applied for the composite blend mode. One can now use the mouse to interact with the rendered data. Use the custom keymappings below to interact with the whole series:

Key	Mapping
Space	Play / Loop through sequence
n	Next volume
p	Previous volume
a	Average Intensity Projection
m	Maximum Intensity Projection
c	Composite Blend (default)
d	Color coded depth map (First non-transparent voxel)
o	Color coded depth

Preparing Data

For converting a single *.seq.nrrd (4D NRRD volume) into individual 3D NRRD volumes, one can use teem-unu.

$ unu dice -a 0 -i <input 4D file> -o <output basename> -ff %03.nrrd

Description

The source for vtkColorCodedDepthVolume consists of:

• vtkColorCodedDepthVolume.cxx: This file provides the main() function for the application that sets up the rendering pipeline as well as defines relevant callbacks for the different key-mappings as described in Usage.
• vtkNrrdSequenceReader.h(cxx): This is a VTK reader that reads in multiple NRRD files from a single directory as individual time steps. The output of the reader is a vtkImageData object of the first timestep by default. The reader provides API for specifying a particular timestep as well as convenience API like Next() and Previous().
• ColorCodedDepthFragmentShader.glsl: This is a custom fragment shader that is used for color coding the depth of first non-transparent voxel along the ray. To simplify consumption of the shader code in the C++ application, it is converted to a C string using vtkEncodeString.cmake.

Custom shaders

This application also serves as an example for using custom GLSL shading code in VTK's volume rendering framework. There are two types of customizations available to the user - partial replacements or full shader replacements.

The application uses vtkOpenGLGPUVolumeRayCastMapper::AddShaderReplacement() to modify final color computation in the fragment shader. The final image is a composite representing depth of individual voxels in a yellow - brown - blue color transfer function.

The application uses vtkOpenGLGPUVolumeRayCastMapper::SetFragmentShaderCode() to replace the whole shader code with the code provided by ColorCodedDepthFragmentShader.glsl. This code terminates the ray at the first non-transparent voxel and registers its depth. The final color of the rendered fragment is decided based on the depth value registered for the fragment. In this case, the color transfer function is defined over the Z-range i.e. (0, depth) range of the volume. We set vtkGPUVolumeRayCastMapper::SetColorRangeType to NATIVE to avoid re-scaling the transfer function over the scalar range in the mapper.