Run output is placed under
Some of the output data is stored as
.cpicklefiles. To observe those files, you need the original Python classes, and therefore you have to be inside Docker, from the host it won't work.
We can list all the plots that have been produced under
Plots are also available in SVG and PDF formats, e.g.:
find -name '*.png'
The output directory has a hierarchical structure of type:
wildtype_000000: variant conditions.
wildtypeis a human readable label, and
000000is an index amongst the possible
wildtypeconditions. For example, we can have different simulations with different nutrients, or different DNA sequences. An example of this is shown at run variants.
000000: initial random seed for the initial cell, likely fed to NumPy's
genereation_000000: this will increase with generations if we simulate multiple cells, which is supported by the model
000000: this will presumably contain the cell index within a generation
We also understand that some of the top level directories contain summaries over all cells, e.g. the
massFractionSummary.pdfplot exists at several levels of the hierarchy:
./out/manual/plotOut/massFractionSummary.pdf ./out/manual/wildtype_000000/plotOut/massFractionSummary.pdf ./out/manual/wildtype_000000/000000/plotOut/massFractionSummary.pdf ./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/massFractionSummary.pdf
Each of thoes four levels of
plotOutis generated by a different one of the analysis scripts:
./out/manual/plotOut: generated by
python runscripts/manual/analysisVariant.py. Contains comparisons of different variant conditions. We confirm this by looking at the results of run variants.
./out/manual/wildtype_000000/plotOut: generated by
python runscripts/manual/analysisCohort.py --variant_index 0. TODO not sure how to differentiate between two different labels e.g.
-vis not given, a it just picks the first one alphabetically. TODO not sure how to automatically generate all of those plots without inspecting the directories.
./out/manual/wildtype_000000/000000/plotOut: generated by
python runscripts/manual/analysisMultigen.py --variant_index 0 --seed 0
./out/manual/wildtype_000000/000000/generation_000000/000000/plotOut: generated by
python runscripts/manual/analysisSingle.py --variant_index 0 --seed 0 --generation 0 --daughter 0. Contains information about a single specific cell.