v3.11.4: Hotfix - Fix an error generating subsets from the ctftomo-viewer
v3.11.3: Deploy test.
v3.11.2:
 Users:
    - Update the templates of STA (Apoferritin, Chlamidomones, HIV) and removing old ones
v3.11.1:
 Users:
    - Skipping failed tiltseries or tiltimages in the tomography viewer
v3.11.0:
 Users:
    - Fixing an error sorting in the CTF viewer.
    - Improve the fail tolerance when importing tilt-series / tilt-series movies.
    - New protocols added:
        * Invert tilt angles on tilt-series.
        * Apply tomomasks to tomograms.
        * Get tilt-series from tomograms.
    - Tomo Viewer applies orientation to the images.
    - Tomo viewer is capable of managing tomograms.
    - Improve the matching method in protocol tilt-series assign alignment.
    - Deprecate unused and obsolete protocols.
 Developers:
    - Changes in the TiltSeries data model.
    - Expand the TCL:
        * For non-deterministic protocols that generates coordinates.
        * To add a tolerance to the checking of oriented coordinates of particles allowing some percentage with
          the identity matrix.
        * Checks set properties.
        * Check the sampling rate in the header of the binary files created.
        * Add tolerance in position and shift for coordinates.
    - Adding delimiter parameter to generate xf files.
    - SetOfLandmarkMOdels.getBinning() to be used in viewers.
    - SetOfSubtomogramsBase available to inherit from it in RelionPseudoSubtomograms.
    - For parallel processing, ensure that the file is completely written and persists on disk
v3.10.0:
 Users:
  - Removing unused and old templates
  - sort items in the TS viewer by tsId
 Developers:
  - Update TiltSeries data model to manage properly the even/odd tilt-series as metadata instead of
    independent objects.
  - Update TCL and some test data description.
  - Replace setup.py by the corresponding pyproject.toml

v3.9.2: add tomo course 2024 template --> HIV processing workflow.
v3.9.1:
 Users:
  - Import TomoMasks: it now admits {TS} pattern.
  - Import TS: Improve TS accumulated dose determination when using mdoc.
  - Import Tomograms: exclusion words fixed in import tomograms when not using a pattern.
  - Scipion metadata viewer for SetOfTomograms and SetOfTomoMasks: updated the visible fields and order.
 Developers:
  - Tilt Series class:
     * Fix the clone method --> now it is a literal clone is expected by default instead
       of ignoring some attributes.
     * Fix TS reStack method.
     * Methods applyTSTransform and generateTltFile updated to work with presentAcqOrders.
  - Import TomoMasks refactored.
  - Fixing an error in the compose_TS protocol creating the TS
  - Using the getSize method to get the anglesCount
  - Fix TS motioncor viewer
v3.9.0:
 Users: 
  - Add a protocol for filtering coordinates based on a mask.
  - TS viewer: Adding angles and the transformation matrix information
  - Update napari to v0.4.19
  - Steps more precise in GPU usage. Improved execution
  - add export coordinates 3D protocol
 Developers:
  - Execution mode at class level
  - Protocol assign transformation to TS: fix a bug in the assignment of the tilt angle to each new tilt image.
v3.8.0:
 Users:
  - Import tomograms, CTFs and Transformation matrices (IMOD): added import functionality using the pattern {TS} to
    select the substring that will be considered as tsId.
  - Import TS:
    * Fix the heterogeneous set of TS validation using a range of angles.
    * Multiple TS can be imported without the label {TS}.
  - Join heterogeneous sets are possible for tomography objects TS and tomograms.
  - New protocol correct tilt offset: It allows to correct the tilt offset of a tilt series
  - Fix the protocol tomograms to micrographs. Helps enhanced. ImageHandler replaced by mrcfile.
  - Import from Mdoc: more precise error when calculating the dose. GUI log with more information.
  - TS viewer: Deleting excluded views and creating a new TS stack.
  - Fixing an error creating new outputs through the tiltserie viewer and import error in absence of metadataviewer.
  - Fixing an error plotting the defocus values in the ctfEstimation viewer
  - Import TS with mdoc: fix in the assignment of the initial dose.
  - Assign Transformation Matrix: combine alignments removed. Some fixes at metadata level.
Developers:
  - Attribute _acquisition is initialized as None in TSBase, so the coppyAttributes callen in protocol for joining.
    sets work properly. The same whith the attribute _origin.
  - Method hasAcquisition re-defined in TSBase for the same reason exposed in the previous line.
  - Attribute _isHetereogeneous and accessors added to SetOfTomograms and SetOfTiltSeries. Used in the string
    representation of both objects.
  - TiltSeries: method reStack added and applyTransforma refactored. Both related to the management of the excluded
    views.
  - Fix update method in Set of Tomos and Set of TS: It does not turn homogeneous sets into heterogeneous ones, nor
    does it look at the X and Y dimensions because they are considered heterogeneous under the criteria used before.
    Only the third dimension is checked for the heterogeneous set check.
  - CTFTomoSeries: method setNumberOfEstimationsInRangeFromDefocusList can handle now the excluded views.
  - TCL:
    * Attribute _isHetereogeneous checked in the corresponding sets.
    * Method checktomograms now is able to check the acquisition.
    * Method checkTsOriginMatrix added.
  - TS viewer:
    * Fix the list of tilt-series viewers
    * Using ScipionImageReader to read tiltseries
v3.7.2:
 Users:
   - Handling the matching in the ctf import(generalizing without the need to set patterns such as {TS}).
   - Refactoring the tiltserie viewer
  - Import TS, TSM and tomos: remove double underscore from both the linked filenames and the tsIds.
  - Import TS: add a validation for the case of heterogeneous sets of TS in the number of tilt images and providing the
    angular data using a range. The cases avoided with this validation prevents erratic behavior in the subsequent
    protocols.
 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).
v3.7.0:
 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.

v3.6.1:
 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.

v3.6.0:

 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.

v3.5.0:
 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.
v3.4.1:
  - Update HIV-tiltseries-alignment-reconstruction.json template
  - Update Picking template II
  - Update Relion4 template
v3.4:
  - 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
v3.3:
  - 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.

v3.2:
  - 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

v3.1.9:
  - 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()

v3.1.8:
  - SetOfSubtomoClasses improved: sampling rate set, coordinates injected

v3.1.7:
  - Templates tweaked: title and some mpi values

  Developers:
  - SetOfCoordinates and SetOfTiltSeries have a getTSIds method to return TS is contained (+ test)

v3.1.6:
  - 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

v3.1.5:
 developers: hot fix, invalid import in test centralized layer
v3.1.4:
 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)


v3.1.3:
 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)

V3.1.2:
  - HIV STA Template not using 16 bit mrc
V3.1.1:
  - Templates folder added for packaging
v3.1.0:
  - First plugin release.See README.rst for more details
  - Tomography 2022 course: 5 templates added. Need You'll need to download its dataset -> scipion3 testdata --download tomo-tutorial
