Modified etomo protocol to enhance usability of outputs downstream

[rdrighetto]

The major changes are the following:

1) We now save the original tilt series (unbinned, non-interpolated) as an output, with the difference that it will have the associated transformation matrix determined in Etomo and excluded views taken into account, so downstream protocols (for example imod - apply transformation and imod - tomo reconstruction) will work correctly, including for the odd/even stacks if they are associated. (a minor caveat is that this output TS is now possibly corrected for dead/hot pixels in the X-ray filtering procedure, the first step of Etomo. I think this is healthy, honestly).

2) Outputs are renamed for clarity: PrealignedTiltSeries, AlignedTiltSeries and TiltSeriesWithAli TiltSeriesWithAli is the output I'm talking about in 1). Suggestions to enhance clarity are appreciated.

3) I explicitly enforce PrealignedTiltSeries, AlignedTiltSeries to not have odd/even associated, because they don't.

Albeit indirectly, this fixes #262.

[sonarcloud[bot]]

Quality Gate failed

Failed conditions
16.2% Duplication on New Code (required ≤ 3%)

See analysis details on SonarCloud

[azazellochg]

If someone else could review it as well, it would be great!

[rdrighetto]

Hi @pconesa - yes, that's exactly it

[azazellochg]

2 - yes, AlignedTS is the "final interpolated" one just before the reconstruction.