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CHANGES.txt
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v4.0.2:
Users:
- RelionSubtomograms do not longer have an index in the path. Just the file name. This allows for correct visualization
of the subtomograms in the metadata viewers.
v4.0.1:
Users:
- Ensure that the pseudo-subtomograms of the initial model protocol have even dimensions.
- Post-process: the FSC generated contain the path to the postprocess.star file.
- CTF refinement and bayesian polishing: form adapted to admit FSC as input and get the postprocess.star
file from it.
Developers:
- Fix in the convert transformation matrix for negative rotation angles.
- Add binThreads and needsGpu to the protocols.
- Replace the setup.py + requirements.txt files by the new pyproject.toml.
v4.0.0:
Users:
- Relion 5.0.
- Adapted to scipion-em-relion deprecation of relion3.
- Add warning preventing to set the box size and the cropped box size to the same value as it may cause an
internal error in relion (Thanks to DSheperd).
Developers:
- Fix inspect in buildbot: Tkagg not set in wizard module.
- Protocols CTF refine and Bayesian polising get the postprocess.star the introduced post-processed volume, as an
extended attribute.
- Fix convert for 3D particles in Relion 5.
- Improve the validations in protocols autorefine and classify 3d.
v3.4.0:
Note: this was supposed to be 3.3.0, but was published as 3.4.0
Users:
- After having performed a refine or classification of particles, fields _rlnLogLikeliContribution,
_rlnMaxValueProbDistribution and _rlnNrOfSignificantSamples are registered, so they can be plotted versus the
no. particles using the data viewer and used as quality control metrics.
- Add extra params to some more protocols apart from refine subtomograms.
- Fix some initial MPI/Threads combinations (Thanks to Bram Koster).
- Rename the protocols the same as in native Relion.
- Enhancing the helps and use of RelionTomo4 (Thanks to J. L. Vilas).
- Validation conditions have been release and checked (Thanks to J. L. Vilas).
Developers:
- Tests rewritten using the test dataset relion40_sta_tutorial_data, using the Test Centralization Layer (TCL), and
decoupled in independent tests.
- Remove BETA status
v3.2.2:
Users:
- Hotfix: the protocol visualization on the left panel was fixed.
- Call the tlt file generation method considering the excluded views.
- Fix the 3d classification Scipion Classes objects generation (previous bad particle assignment).
Developers:
- Fix: the coordinates generated in the convert input step of the prepare data protocol are now float instead of
integer.
v3.2.1:
- Installation requirements better managed.
- Fix: Relion output now copies the acquisition.
- Fix: The sampling rate displayed for the initial volume was incorrect.
- Fix: FSC object stored unused data for the FSC viewer. That data was removed.
- Tests updated.
v3.2.0:
- Wizard to apply operation in relion particles
- 3D Classification defines its possible outputs
- An initio fixed (not using optimization set)
- Other FSCs are plotted in the refine and postprocess protocols
v3.1.6:
- 3D Classification more completed/standard
- 3D classes can be fed to mapback or others
- Refine and 3D classification use and register optimisation_set.star files
v3.1.5:
- Prepare more robust and optimized to subsets of coordinates and Tilt series. Still ctf could be added to the ecuation.
v3.1.4:
- GroupId is not lost through reliontomo processing
- Fix shifts conversion in subsets: Scipion-Relion and viceversa
- Export pseudo to coordinates removed completely
- Apply operation works on non extracted pseudo subtomograms
- Dataviewer shows Pseudosubtomograms better.
- Import coordinates from star: fix scheduling (indirect pointer to precedents)
- Prepare data:
Fix scheduling (indirect pointer to ts from fiducials)
Shifts in z and x are now taken from tomogram origin and into imod files
Tilt series input is now mandatory until we manage to get the right one though the other inputs.
- Fix refine: uses now the latest star file and priors are produced without a subset
v3.1.3:
- Fix: Use one of the halves map in auto-refine if it exists
- Fix: LandMark model generation in prepare when a join coordinates has happened. Sorting issue.
- Reconstruct does not generate PseudoSubtomograms.
- Option to "consider angles as priors" in refine and 3d classification
- Takes into account tomogram shift (X, Z) in prepare
v3.1.2:
- Fix: Fiducial size in prepare is now correct (in Å)
- Make pseudo subtomograms: float 16 is False by default and hidden. Prevents manual subsets.
v3.1.0:
- First plugin release