Scipion-em-tomo

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

- Compose tilt series: Allowing tilt series with gaps
- New protocol: "meshes from tomoMask"
- Tomoviewer: Can sort by acquisition order too.
- Sampling rate in Coordinates3D rounded to 2 decimal places upon visualization.
- HIV STA template divided into 2: Dynamo STA and Relion4 STA
- Picking template tutorial (cryolo, eman, deepfinder) changed
Developers:
- TestBaseCentralizedLayer: New test class to make more precise assertions on outputs.
- Adding a method for extracting odd-even filenames
- Fix schedule execution in protocol for importing coords from Scipion

- Tomo metadata viewer increase contrast when left clicking on the preview image.
- Import tilt series movies using a pattern instead of from mdoc files was improved and admits brackets [] in the
basename of the files.
- Import tilt series from mdoc now admits numeric base names or base names beginning by a numeric character
- New config var: NAPARI_ENV_ACTIVATION, used by other plugins. Napari binary installation is centralized here.

Developers:
- Coordinates 3D object have a new attribute _score to store the coordinates score, when necessary.
- SetOfSubTomograms append method now manages the align attribute of the set.

- New protocol: "Landmarks to 2D coordinates". To jump to SPA from 3d info.
- Tolerate empty lines in tlt files
- Motion correction outputs renamed and fixed for odd/even and dose weighted
- Tilt series can be sent to Xmipp metadata viewer for subsetting/inspection
- TomoMetadataViewer shows the preview of the slice and some metadata (tiltAxisAngle)
- Fix: Imod not needed for importing coordinates, unless imod mode is selected
- Compose tilt series: Added "exclusion words" to filter out mdocs

Developers:
- angleAxis1 and angleAxis2 removed from the TomoAcquisition class

- Reconstruction template fixed.
- Relion 4 /dynamo template tweaked. Specifically dynamo alignment
- HIV template tweaked: one 3d classification removed. Mapback uses the 3d class.
- OddEven functionality reviewed: Tilt Series set and Tomograms set have oddeven attributes/flags and
there is no need for separate sets anymore. odd and even are internally referenced.
- Added a new ctf tomo viewer (CtfConsensusTomoViewer)
- ComposeTS: allowNull control added, removed validation and added _possibleOutputs

Developers:
- SubTomogram.getVolName() uses Coordinate3D.getTomoId()