Formalize data format - Githubissues

tjsego / PersistentCell

A project to compare persistent random walk models

MIT License

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Formalize data format #5

Open tjsego opened 2 months ago

tjsego commented 2 months ago

@ingewortel proposed the following csv format:

Column 1: time
Column 2: cell ID (or simulation seed)
Columns 3-4: x and y coordinates

I proposed adding a header following the labels in the data schema, with appropriate additions.

[x] Settle on the format.
[ ] Document the format.
[ ] Update the Artistoo implementation.
[x] Update the CC3D implementation.
[ ] Update the Morpheus implementation.
[ ] Update the PhysiCell implementation.
[x] Update the Tissue Forge implementation.
[x] Update the comparison module.

starboerg commented 2 months ago

I am fine with a csv scheme update. Imho the json format should also be adapted accordingly (com1/2 can be arrays of arrays).

tjsego commented 2 months ago

Discussion outcome: format supports additional data beyond column 4. Headers will not be included. Otherwise, proposed format as noted here is how we will proceed.

ingewortel commented 2 months ago

@tjsego just to clarify: what do you mean with "headers will not be included" - just that we don't specify the required header in the schema, right? Because I currently still assume the csv to have some header, I just don't use the column names internally.

tjsego commented 2 months ago

@tjsego just to clarify: what do you mean with "headers will not be included" - just that we don't specify the required header in the schema, right? Because I currently still assume the csv to have some header, I just don't use the column names internally.

I was originally envisioning starting the data with something like the following:

time,id,com_1,com_2,other_data_entry
...

Each column label would correspond to an entry in our data schema and "other_data_entry" would be optional additional data (e.g., cell area).

tjsego commented 4 weeks ago

comparison module updated in https://github.com/tjsego/PersistentCell/commit/c7b943df7da8eb79460cabbcb7b6a0de689cb094.

tjsego commented 4 weeks ago

CC3D implementation updated in https://github.com/tjsego/PersistentCell/commit/e5d3bfa957492322ac79b1ec829970c298974b44.

tjsego commented 4 weeks ago

Tissue Forge implementation updated in https://github.com/tjsego/PersistentCell/commit/77524ae0892ff3c05d4a9326907bef364e9aff2d.