JanaLipkova
commented
3 years ago Hi Andy,
thank you for the mail. And my apology for the late reply. I didn’t notice that my github account is linked with my former e-mail account.
To your question. You can save the tumor cell density at uniform grid using _dumpUQoutput() function (see https://github.com/JanaLipkova/GliomaSolver/blob/20fffcaaf816ad163d8499e116573ac03f57b165/Glioma/Glioma_ReactionDiffusion.cpp#L208 )
This function maps the tumor cell density into uniform grid (even when using adaptive part of the solver) and save it in the .dat format. To save the tumor cell density at the end of the simulation, you can just modify line 342 of the same file from:
if(bUQ) _dumpUQoutput();
to _dumpUQoutput();
But this will save only the final tumor state. If you want to save the data over time, same as the .vtu data dumper, you would need to modify the function _dumpUQoutput() such that it takes as input integer argument (e.g. number of iteration) and change the name of the output file from “HGG_data.dat” to a name including this unique integer (as not to overwrite the output each iteration). Then instead of calling _dump() you will call _dumpUQoutput( iteration_count)
Also, you can look at this file: https://github.com/JanaLipkova/GliomaSolver/blob/master/tools/DataProcessing/lib/Matlab2C/matrixMatlab2Cpp/matlab/loadMatrix.m which reads the .dat data from the solver into Matlab.
I hope it helped. If you have more questions let me know. Best regards, Jana Lipkova
azhu529 @.**@.>> Thu, 3 Jun, 15:51 (11 days ago) to JanaLipkova/GliomaSolver, JanaLipkova, Mention [https://mail.google.com/mail/u/0/images/cleardot.gif]
Hi @JanaLipkovahttps://github.com/JanaLipkova,
Thank you for the solver. In the documentation, I noticed it said "The GliomaSolver outputs data in two formats: .dat and .vtu."
However, when I tried the first example in the tutorial "Tumor Growth Modeling," I could not find an option to dump the output data as a .dat file. It only accepted a boolean vtk that determined if .vtu data was dumped.
Is there some way to make the solver yield a .dat file that has uniform resolution of the tumor density?
Thanks, Andy
Jana Lipkova
Pathology Department Harvard Medical School Brigham and Women's Hospital Lab: https://faisal.ai/
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andyxzhu
Hi @JanaLipkova,
Thank you for the solver. In the documentation, I noticed it said "The GliomaSolver outputs data in two formats: .dat and .vtu."
However, when I tried the first example in the tutorial "Tumor Growth Modeling," I could not find an option to dump the output data as a .dat file. It only accepted a boolean
vtkthat determined if .vtu data was dumped.Is there some way to make the solver yield a .dat file that has uniform resolution of the tumor density?
Thanks, Andy