3.9.0:
  Users: Add new protocol for cropping tomograms.
  Developers: Small fixes and updates.
3.8.1: deploy test.
3.8.0:
  Users:
   - IMOD binary installed by default was updated to imod_5.1.3_RHEL8-64_CUDA12.0.
   - Interpolated tilt-series was removed excepting for apply transform protocol.
   - Add protocol for automatic erasing of gold beads in tilt-series.
   - More protocols streamified:
        * CTF estimation (auto).
        * Dose filter.
        * Fiducial alignment.
        * Fiducial eraser.
        * Generate fiducial model.
        * Coarse pre-alignment.
        * X-Rays eraser.
   - IMOD_VIEWER_BINNING removed, by default it is targeting the closest binning to 10A resolution.
   - Imod viewer shows the interpolated tilt series if tilt series has alignment info
   - eTomo protocol fixed
   - Tomo projection protocol creates dummy CTF set too.
   - If a protocol creates new binary files, the sampling rate is properly set in the header of each file.
  Development:
   - Adapted to the updated TiltSeries model from scipion-em-tomo 3.10.1.
   - Decentralization of the output creation.
   - Refactor the base protocol and the utils, making them lighter. Create a convert and a data import.
   - Fix streaming condition to insert the closing step. Now it uses collections.Counter when comparing
     the tsId lists instead of direct comparison, which is order-sensitive.
   - Streaming: add a decorator to manage the possible db locks.
3.7.0:
  Users:
   - Add protocol for automatic tilt-series alignment using IMOD's batchruntomo wrapper made by Team Tomo. Streamified.
   - As a consequence, the installer was updated and a conda environment is generated.
   - Parallelization of most of the protocols.
   - Streamify the protocols tilt-series preprocess and tomograms reconstruction.
   - Deprecating some density scaling options in tomo and ts preprocess.
   - Fix viewer call from the file browser.
   - Protocol batchruntomo -> fix bug: all the tilt-images were considered when calculating the alignment even if they
     had been excluded. Fix some expansion of these changes in both fiducial alignment and model as a consequence.
  Developers:
   - Replace the setup.py by the corresponding pyproject.toml.
   - Add preventing lock in the call to loadAllProperties of the stepsGeneratorStep of the streamified protocols.
   - Improve robustness in streaming: check the tilt-series size before inserting the steps.
   - Update the Github actions file, which was in an obsolete format.
3.6.1:
 Users:
  - bugfix for o/e tomo reconstruction, see #271
 Developers:
  - Calls to TiltSeries method for exclusions of views updated.
  - Calls to TiltSeries clone method updated as it is a literal clone now.
3.6.0:
 Users:
  - fix default params (close check default values #281 )
  - change several form params from Enum to Boolean and from Float to Int, change default values from wrong str to int/float
  - Protocol Import transformation matrix admits {TS} pattern
 Developers:
  - move constants to a dedicated file
  - remove BETA status
  - unify runProgram , use params dict
  - unify close outputs step
  - add possible outputs to all protocols
  - reduce number of get() queries
  - change several form params from Enum to Boolean and from Float to Int, change default values from wrong str to int/float
  - do convert to float and normalize stacks in preXcorr
  - fix newstack options: tapering, antialias etc.
  - unify failed output set creation
  - remove try/except decorator
  - refactor tests code
  - remove redundant store/write, getDim and other calls
  - use indirect pointers
  - use copyItems analog for creating outputs and updating their attrs
  - implemented parallel steps for many protocols
  - add a new batch of tests based TCL.
  - some fixes from errors detected with the new tests.
  - protocol excluded views: remove the in file option.
3.5.1:
  - CTF correction: get rid of the decorator. Manage the failed TS in the createOutputStep.
  - Fix a bug in the base class for the generation of alignment files when there input TS are not aligned and there
    aren't excluded views.
  - Fix a bug in the generation of defocus files.
3.5.0:
 Users:
  - Protocols' help added.
  - Help of the parameters was enhanced.
  - New feature: patch tracking alignment added.
  - Trimming options in fiducial model added
  - The order of the parameters in the forms was slightly modified according to the user actions.
  - Protocol CTF correction:
    * Now it can deal with excluded views in the CTF and/or in the TS.
    * The same when entering with interpolated or not aligned TS.
    * The xf, defocus, and tlt files are generated inside each TS extra sub-directory.
 Developers:
  - Update the acquisition order in the CTFTomo objects (field added to that class in scipion-em-tomo v3.7.0).
  - Refactorization: avoid the excessive usage of getFirstItem.
  - File generation methods (most of them in utils) adapted to the CTF-TS intersection functionality.
  - Fixing sorted dictionary in ctf correction. How to access the defocus list in utils.py
3.3.0:
  - bugfix for import ctf, set missing defocus flag
  - move plugin-specific import CTF protocol to the core
  - add IMOD 4.11.25 version
  - Prevent viewers from locking the screen focus.
  - tilt series normalization: defines possible outputs
  - tomo preprocess: always outputs mrc file
3.2.4: bug fixed in odd-even management in CTF correction
3.2.3: declare requirements.txt in manifest
3.2.2:
  - Add requirements
3.2.1:
  - Fixing a bug with odd even in tomogram reconstruction
  - Tolerating errors in alignment
  - Making tomogram reconstruction error tolerant
  - Making tilt series alignment error tolerant
  - Adding possible outputs in xray eraser
  - Removing visible parameters with the intepolation is not applied
3.2.0:
  - add more possible outputs
  - fixing ctf after aretomo
  - make ctf auomatic estimation tolerant to errors
  - odd/even processing implemented
  - update FiducialModel
  - changes in protocols to save if landmark model has residual information
  - fix: interpolated flag is no set when correcting the CTFs
  - user-controllable binning for display in 3dmod: plugin variable -> IMOD_VIEWER_BINNING = 1
3.1.10:
  - fix DefocusTol param type for CTF correction protocol: must be integer
  - fix binning for other protocols
3.1.9:
  - fix binning for normalization protocols
  - fix excluded views parsing
3.1.8:
  - Reconstruction:
     - tomoWidth added to specify a width when reconstructing
     - Shift in Z is registered in tomogram origin

  - Ctf correction: Allows different size of ctf set and ts set. Only paired (TS-CTF) ones will be processed
3.1.7:
  - Validate input alignment for TS preprocess protocol
  - Fix: Xray eraser when there is alignment.
3.1.6:
  icon added
  template added for automatic tilt series alignment
3.1.5: fix xf file reading, add IMOD 4.11.24, remove previous binaries as they are gone fron the website
3.1.4: set tilt axis to 0 if TS is aligned (reported by Bram Koster)
3.1.3: fix installation: remove libjpeg62 check
3.1.2:
  - Flag ts as interpolated in some cases
  - Imod protocols do not work, for now in streaming
3.1:
  - remove displayAll button from set viewer as it seems to be not practical to open all items at once (close #141)
  - change etomo naming style to mrc (close #153)
  - output xtilt file from fid alignment
  - rename fid alignment output to align.log and parse it with imod tools
  - add beadtrack step  with current model as seed (close #160)
  - refactor viewers:
     - remove ImodSetOfLandmarkModelsView, ImodSetOfTomogramsView, ImodSetView
     - remove displayAllButton
     - update etomoviewer for new naming style
     - show tilt angles in 3dmod viewer (close #161 )
     - fix saved3DCoord etomo output display
  - fix rotation angle calculation for newstack operation
  - remove transformation step from imod ctf estimation (ctf is estimated on raw ts stack)
  - fix rotation angle range for swapping x/y for newstack
  - do not copy objId for apply TM protocol when excluding views
  - fix output size in apply TM protocol
  - fix wrong output file index numbers in the exclude views protocol
  - fix gold erasing option in the fid. alignment protocol
  - fix generating ctf output; hide some params from manual ctf protocol; do not run autofit for manual protocol
  - added xform file to ctfphaseflip to rotate astigmatism estimation and adjust for x  -shifts for the image center
  - fix excluded views parsing from com files
  - rename "normalization" to "preprocess" protocols
  - handle excluded views properly (closes #137 , closes #147)
  - ctfplotter handles excluded views properly, output ctfs for such views have 0 values
  - fix failed ts generation in fid.alignment protocol
  - pep8 fixes, add pip  -related files
  - mtffilter was missing pixelsize param, causing wrong filter being applied (always with 1A/px)
  - add antialias param to ts norm protocol
  - fix wrong default naming style for etomo
  - enable robust fitting for beadtracker
  - remove redundant updateDim calls
  - get acquisition from ts when creating a tomo
  - fix pixsize and dims for etomo outputs (closes #139)
  - fix beadtrack args to match copytomocoms script
  - always use antialias when binning a stack
  - two surfaces search is off in both protocols for consistency
  - bead radius default is 18px (good range for bin 4 and 10nm beads)
  - use sobel filter for bead centering for most cryo data
  - use lowpass for bead tracking
  - use adjustbeadsizes
  - trimvol -yz replaced by -rx, the first one flips the hand
  - add expandcircles to eraser
  - replace wrong dose file format for mtffilter
  - set output 3D coord size based on bead diameter
  - fix betterradius param in gold eraser tab of the fid alignment
  - add missing pix size in fid align
  - fix minpacing in gold picker
  - add missing taper arg for newstack
