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CHANGES.txt
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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