- 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