Scipion-em-tomo

- Tilt order inferred from dose when tlt file has dose
- Fix: subtomograms with coordinates work in absence of volId
- HIV-HTA template: removes coords extraction and reconstruction since mapback can be done without them
- Import Tilt series or Import tilt series movies do not work in streaming anymore
- Import tomograms outputs "Tomograms" and defines possible outputs. Templates and tests adapted
- Pyseg workflow template fixed (extra graphs removed)
- HIV Reconstruction workflow template fixed (tomograms origin taken from mrc)
- Protocols "fit vesicles" brought here from xmipptomo. Test added with filter by normals.
Developers:
- __init__ uses logger now
- test_transformation fixed
- SetOfCoordinates refactored internally to deal better with tomograms.
- SetOfSubtomograms.iterCoordinates --> Mimics SetOfCoordinates behavior

developers: hot fix, invalid import in test centralized layer

users:
- cbox format from cryolo implemented to import 3d coordinates
- hide transform matrix column for TS movies
- fix CTF viewer help (close 253)
- change TS flags
- Added an option to import the dose accumulation using a tlt file as second column
- Fix: uses subsets of representatives are more accurate and not always SetOfVolumes
- Fix: Single import of a numeric tilt series
- Template for HIV STA improved
developers:
- Subtomogram has a constant for its tomoid attribute name: Subtomogram.VOL_NAME_FIELD = "_volName"
- Add test centralization layer (not finished, but quite advanced and operative for coordinates and subtomograms)

users:
- Tutorials templates renamed
- LandMarkModel shows Å not pixels in its description
developers:
- Subtomogram getTransform returns its contained transform if non convention is passed
- Transformation subtomo test labels improved
- tomo-em dataset definition: 3 trams added
- TestImportTomoMasks: output names fixed
- Fixes in import coordinates from Scipion (sqlite)

- HIV STA Template not using 16 bit mrc

- Templates folder added for packaging