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CHANGES.txt
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3.10.1:
Users:
- Fix: re-align aligned tilt-series after having excluded views is now possible (validation is now a warning).
3.10.0:
Users:
- Add input tilt-series excluded views management.
- Add odd/even tomograms reconstruction,
- Fix: amplitude contrast is read from the tilt-series metadata and passed to AreTomo.
- Do not support old AreTomo versions.
Developers:
- Write new tests with a better characterized test dataset.
- Tests renewed with a better adapted (real dark frames) test dataset and with cases of TS with excluded views.
- Add needsgpu attribute to the steps generation.
- Aln file writer method added to adapt the plugin to the API of AreTomo2-1.1.3 when only reconstructing the tomograms.
3.9.5: add aretomo2 1.1.3
3.9.4: set aretomo2 1.0.0 as default, because 1.1.2 has broken remove dark option
3.9.3: hotfix: _defineVariables method must be a class method to be compatible with scipion command config -p
3.9.2:
- Aretomo does nos fail when closing its output when process is killed
- Listed protocol's names are defaults ones.
- Tolerate failed tilt-series, avoiding the protocol interruption and generating a specific output for the failed
tilt-series.
- Force enable DW when saving extra IMOD output
Developers:
- Steps now use the tsId instead of the objId.
3.9.1:
Users:
- Add aretomo2 1.1.2
- Fix backwards compatibility.
- Add an option to specify AlignZ per TS.
- fix dose weighting bug related to the tilt angle file (aretomo2 only)
Developers:
- The tests now use the Test Centralization Layer update and expansion of the used test set definition
from em-tomo v3.6.0.
- Update the acquisition order in the CTFTomo objects (field added to that class in scipion-em-tomo v3.7.0).
3.9.0:
Users:
- The protocol form now present CTF-related parameters, to choose if estimate it or
not and phase plate acquisition related params (estimate the phase shift).
- Generates the output SetOfCtfTomoSeries if the CTF files are found
- Add dataimport module to parse the CTF generated so it can be called from the
centralized protocol for importing CTFs.
- Fix the origin set by Scipion to the generated tomograms.
- Outputs are not stored in case the are not correctly generated.
- If dose-weighting active, the accumulated dose of the interpolated TS is set to zero to avoid double dose
correction if using the interp TS for the PPPT.
Developers:
- Rewrite tests using the TCL from em-tomo and the reliontomo test dataset.
3.8.3: typo bugfix
3.8.2: bugfix: tomograms origin fixed and more robust
3.8.1: bugfix for reading aln file with dark views removed
3.8:
- add aretomo2 1.0.0
- fix output aln file parsing during local alignment
- add extra output option
3.7.2:
- minor changes
- Fix origin of tomograms when there is binning.
3.7.1: fix pw requirements
3.7 : initial streaming support (@albertmena)
3.6.5: allow unsorted tilt series
3.6.4: adding type hints
3.6.3: reduce number of Set[item] calls
3.6.2:
- fix applyTransform in the convert step
- add interpolated flag
3.6.1:
- add aretomo 1.3.4, remove support for versions < 1.1.0
- fix alignment matrix for excluded TS views
3.6:
- set tilt axis angle to 0 for interpolated aligned TS (fixed issue #36)
- remove updateDim calls
- use Acquisition from TS for new tomo objs
3.5.1: add aretomo 1.3.3
3.5:
- get rid of xf file conversion, use aln directly
- add aretomo 1.3.0
- update citation
3.4: always output stack with alignment info
3.3: scaling should not be applied to transforms, as xf refers to original TS
3.2:
- fixed output TS shifts scaling when using binning
- hide flip volume option when not making a tomo
- guess cuda version
3.1:
- add possible outputs class
- two default TS outputs: aligned (interpolated) TS and original (with alignment metadata)
- added DarkTol parameter to GUI
- add AreTomo 1.2.5
3.0.16 - add AreTomo 1.2.5
3.0.15 - add possible outputs class
3.0.14 - AreTomo 1.2.0 added
3.0.13 - fix default installed version
3.0.12 - AreTomo 1.1.1 added, now can use previous alignment as input
3.0.11 - AreTomo 1.1.0 added
3.0.10 - parse and save tilt angles correctly
3.0.9 - remove tilt axis angle from GUI, fix validation, fix accum.dose and dose weighting
3.0.8 - fix output TS file loc index
3.0.7 - fix bug: writing output alignment info to an already aligned TS
3.0.6 - fix dose-weighting error, update citation
3.0.5 - added refine tilt angles param for 1.0.12+
3.0.4 - added refine tilt axis param, switch off volume flip for v1.0.12+
3.0.3 - bug fixes (reported by Bram Koster)
3.0.2 - add version 1.0.12
3.0.1 - add version 1.0.10
3.0.0 - first version of the plugin