vrgrouprwth / pli_view Goto Github PK

Building:

• Go to the project root directory.
• Run "source utility/load_modules.sh".
• Then make a directory for the build, go into it.
• Run "ccmake ..". Most dependencies should pick up automatically (you might need to set HDF5 by hand).
• Configure and generate. Ignore the warnings.
• Run "make".

Preparation:

• Add an HDF5 attribute called "VectorSpacing" to the Vervet1818.h5 dataset. This attribute is a 3-value array which tells the distance in the XY-plane and the distance in the Z-direction:
• Note that the MSA0309.h5 has an attribute like this already, called "Voxelsize" as seen below:

Running:

• Copy "utility/run.sh" to the directory where the executable is and run it:
• If you want to display Vervet1818.h5-like data (where each slice is a separate dataset) toggle "Slice by slice". If you want to display MSA0309.h5-like data (where all slices are stored in a single volume, indexed as ZVXY) toggle "Volume".
• Click browse and select the dataset.
• Click the "Selector" plugin:
• Select a region of the dataset and click "Update Viewer". The retardation and fiber orientation maps will appear:
• For ODFs: Ensure the selection is a power of two (e.g. 2048x2048x1) and click the "Fiber Distribution Maps" plugin, adjust the parameters as you like, and click "Calculate".

Examples:

• The following are example visualizations extracted from the application.

Limitations:

• For the hierarchical ODF tree to work correctly, one must use power-of-2 selections.