Data visualization

Plot traces of single node

For quick visualization of results, traces extracted from the center of the tissue can be plotted with the command

$ python3 -m simcardems postprocess "path_to_results" --plot-state-traces

The path_to_results directs to the folder containing the results.h5 file. A figure is generated showing traces of membrane potential (\(V\)), intracellular calcium concentration (\(Ca\)), stress (\(\lambda\)) and active tension (\(T_a\)). This figure is saved in the folder containing the original data. By the default trace is extracted by averaging over the domain. For a slab geometry you can also get the value at the center of the slab using the command

$ python3 -m simcardems postprocess "path_to_results" --plot-state-traces --reduction="center"

Create XDMF-files

The results of a simulation with simcardems are stored in a single file called results.h5. These results can be visualized in ParaView, but require 1 step in between: Creation of XDMF-files from results.h5. Execute

$ python3 -m simcardems postprocess "path_to_results" --make-xdmf

to create XMDF-files of all stored variables. Each XDMF-file is named after the variable, and has a h5-file with the corresponding name.

Visualization in ParaView

The XDMF-files can be opened in ParaView using XDMF3ReaderS or XDMF3ReaderT, but require the corresponding h5-file to be present in the same folder.