Trouble with tumorcode supplementary material tutorials

[Romain-Enjalbert]

Hello,

I am currently going through the supplementary material from the publication on tumorcode introducing the framework.

I can generate the vessel network and generate the tumour, but from there I am having three problems.

1 & 2. When I run submitDetailedO2 default_o2 tumBulk-default-typeI-sample00-defaultconfig_bulktissue.h5 out0005 I immediately come up with an error and similarly when I run submitIff iff_default tumBulk-default-typeI-sample00-defaultconfig_bulktissue.h5 out0005 (picture attached for both)

3. when I use the hdf2vtk.py and parse the tumBulk file with out0005 I have an output with the vessels, but not with the fields, which the supplementary material suggests I should also have.

Would you be able to provide help to solve the above ?

Kind Regards,

Romain

[thierry3000]

Dear Romain,
finally I found some time to check on your issue.
1)
I think the culprit is at commit 5f8d616
when I introduced a "smart" parameter handling relevant for some other parts of the code. Unfortunaltelly there is no fast fix for this. It is a deeper python <-> c++ thing. See "struct DetailedO2ParamsFromPy" in python-oxygen2.cpp.
2) probably similar to 1)
3) use the syntax:
python2 -d /localdisk/tc_install/py/krebs/hdf2vtk.py tumBulk-default-typeI-sample00-defaultconfig_bulktissue.h5 out0001 --writeFields out0001/fieldGf
to get additional fields from the hdf5 to the vtk format
(this was a new an undokumented feature of tumorcode)

Once I find more time I will get back to 1). Thanks for pointing that out.

[Romain-Enjalbert]

Thank you for your quick response. I have tried the syntax you suggested for the hdf2vtk.py and it worked, thank you. When do you think you will be able to get back to the IFF and detailedo2?

Kind Regards,

Romain

[thierry3000]

Dear Romain,

unfortunately some project I am currently doing for money run behind schedule. At the moment there is not much time left. However I try to remember the issue.

Best, Thierry

[Romain-Enjalbert]

Dear Thierry,

I hope you are well. Have you had some time recently to have a look at the issue related to the IFF and detailedo2 ?

Kind Regards,

Romain

[thierry3000]

Dear Romain,

finally I found the time to look at the issues you described. Indeed there were some problems. I hope I could fix them with the three commits: 1eb3e18, c4e7c42 and 2aae71b.

Please let me know whether it worked for you.

Kind regards, Thierry

[Romain-Enjalbert]

Dear Thierry,

I gave it a go with the changes you made. The submitIff now works and generates an output. However while trying to process it with the plotIff.py (plotDrug.py gives the same result) I have this error

I tried finding the module in the scripts and was unable to find it.

I also tried converting it to vtk as per the syntax in the supplementary material and the one you provided above and was unable to make it work.

The subitDetailedO2 continues to have an error, similar to the previous one although slightly different, see below.

Thank you for taking the time to look at this.

Kind Regards,

Romain

[thierry3000]

Hi,
I found some time to look into the tedious boost numpy interface changes. With c13f81d, 1cc4278, b2e2ef4 and 3ff28f3 I attempted to restore a working configuration. Unfortunately there were not only changes in boost::numpy, but also in the c++ support for HDF5 (H5Cpp). I try to deal with this also in 5b37852. Maybe you can make sense out of theses commits and identify the culprit further.
Best, Thierry