Print specific Error message for missing ROI

nathansteenbuck commented 1 year ago

I am analysing a mcd with multiple ROIs and stumbled upon this error:

2023-05-15 15:11:13,563 WARNING steinbock.preprocessing.imc - Error reading acquisition 72 from file /tmp/tmp63oinnto/6483_Immune/6483_Immune.mcd: MCD file '6483_Immune.mcd' corrupted: invalid acquisition image data offsets

However, instead of issues with the image offsets, the .txt-file of ROI 72 doesn`t exist.

My suggestion would be to print a more specific error message catching that exception :)

jwindhager commented 1 year ago

Hi @nathansteenbuck ! Transferring this to the steinbock repo, as the recovery-from-txt functionality is implemented there

jwindhager commented 1 year ago

I understand that the message is not informative in your case, however:

steinbock uses mcd files as primary input
if the mcd file is broken AND a matching txt file is available, it will try to recover the data
if not, the error message giving details why the mcd file is broken is logged (which seems to be the case here)

One could of course think of being more verbose and add a message to the log saying that the mcd file is broken AND that no matching txt file has been found for recovery (basically add an else branch to https://github.com/BodenmillerGroup/steinbock/blob/bc10207a5a690254bb4e65089c06004fe3f19b05/steinbock/preprocessing/imc.py#L369C53-L404). I think this would be a good addition @Milad4849

BodenmillerGroup / steinbock

Print specific Error message for missing ROI #184