Scipion-em-tomo

Users:
- Import TS, TSM and tomos: remove double underscore from both the linked filenames and the tsIds.
Developers:
- Add to Tomogram and SetOfTomograms the attribute _ctfcorrected, the same way it was added to the tilt-series.
- Update the TCL based on the previous point.
v3.7.1: HOTFIX - join TS bug solved (Thanks to Doulin Sheperd).

Developers:
- Add acquistion order attribute to the CTFTomo to provide a robust matching between tilt-images and CTFTomos.
- Add method getTsIds to SetOfTomograms (useful when importing coordinates).
- CTFTomoSeries: add method getCtfTomoFromTi.
- CTFTomo: add acqOrder to the attributes list used on its copy method.
- TiltSeriesBase - method generateTltFile expanded: optional input presentAcqOrders to manage the view exclusion.
- Utils - add method getCommonTsAndCtfElements to intersect tilt images and CTFs based on the value of the
attribute acquisition order, or index in case it's not present or empty (backwards compatibility)
- SetOfCTFTomoSeries: add method getTSIds, just the same as for SetOfTiltSeries and SetOfCoordinates3D.
- Method getTSIds methods simplified. They call now getUniqueValues instead of aggregate.

Users:
- Collapse the tilt-series tree by default in the tomo data viewer
- Fix in protocol import TS: when providing mdoc files, label DividedBy2 is now only applied in the case of
calculating it from fields MinMaxMean, PixelSpacing and CountsPerElectron (case 4).

Developers:
- Fix: class Tomogram method getDim removed as it did not manage heterogeneous sets correctly when iterating (read the
header once, stored it and reused). The Volume method is used now instead, as it reads the size from the file
header for each file.
- use setFramesFrange when importing TS movies
- Class Tomogram method getDim removed as it did not manage heterogeneous sets correctly when iterating (read the
header once, stored it and reused). The Volume method is used now instead, as it reads the size from the file
header for each file.

Users:
- Tilt series subsets and CTFTomoseries clone the enable flag
- Acquisition data storage fixed when importing tilt series and tilt series movies (min angle, max angle, and step)

Developers:
- Test dataset relion40_sta_tutorial_data expanded.
- TCL: methods dor checking sets of TS and TsM improved.

Users:
- Improve the TiltSeries viewer. Allowing to exclude TiltImages
- New protocol to import tilt-series CTF from different plugins
- The CTF tomo series viewer now only plots the Enabled tilt images/ctfs.
- Template HIV- STA with reliontomo: update the CTF importing method to the new centralized located in em-tomo.
- Prevent viewers from locking the screen focus.
- Improve SetOfCoordinates3D str method.
- Fit vesicles prot nos requesting the tomograms. Refactored.
- Fix accum dose in TS import without mdoc.
- Napari 0.4.17 is the default version. boxmanager and tomotwin are now independent

Developers:
- Improve the Test Centralization layer.
- Tests for AreTomo2 CTF import added.
- Expand the method checkTomograms from the Test Centralization Layer.
- Import tomograms: the acquisition is now copied to both the set and the items.
- Some refactor in protocol_ts_estimate_ctf.py required for the new CTF code design prots approach.
- TiltSeries object: expand the method to generate the imod tlt file allowing to consider the excluded views.
- TS movies not hiding any acquisition parameter to prevent accidental override.

- Update HIV-tiltseries-alignment-reconstruction.json template
- Update Picking template II
- Update Relion4 template