Imod tilt-series normalization is introducing some error in the alignment matrix

[fede-pe]

When binning a tilt series with a transformation matrix associated, it is necessary to correct the scale of the shifts in order to keep the alignment consistent.

[azazellochg]

I think this is already done : https://github.com/scipion-em/scipion-em-imod/blob/devel/imod/protocols/protocol_tsNormalization.py#L258

[fede-pe]

You are right. Let me check why it is failing to me then. The behavior I am experiencing is that when applying ts normalization before reconstruction the final tomogram appears artifacted. This only happens when taking the TS with the associated alignment info (if taking the interpolated tilt series for normalization then the tomogram seems to be correct).

[pconesa]

I think what is happening is that is applying the transformation matrix, but not removing it from the set.

I'd suggest to add a parameter to do it or not...and clear the matrix if apply?