History of Changes and Known Bugs
If you find a bug or have a suggestion not on the list, please
let me know
.
Known bugs in the current version
- The 3dit/3dit2 options in refine (implemented through clean3d) have been causing occasional problems. If
your volume data exhibits horizontal 'striping', try disabling these options. In most cases they aren't
really necessary anyway
- Cluster parallelism doesn't handle unavailable nodes very gracefully.
v1.4 - released 06/2003
- Substantial improvements were made to EMAN's parallelism. When
used on small particles on a large number of processors, the previous versions
of EMAN would run at less than 100% capacity on each processor. The new
version should run at 100% on fairly large numbers of CPUs.
- Python support - EMAN now officially supports Python scripting.
Some very powerful operations can be performed with some very simple (and
easy) scripts. Just to give you the flavor, here's a quick example which
will compare class-averages to projections:
- qindex - a program for very basic indexing of 2D crystal images
was added. This program may be enhanced in future, depending on community
response.
- fitctf - improvements in fitting quality and accuracy. May still
have problems with some CCD data.
- procpdb.py - a script for basic manipulation of PDB files, designed
largely for use with foldhunter
- foldhunter - new option added to generate rotated/translated PDB
files corresponding to the best fits
- multirefine - now permits a different symmetry to be specified
for each model. This is still an experimental option.
- GNU configure -> CMake
v1.21 (43) - released 07/19/02
- Major documentation updates
- Support for reading 8 and 16 bit tiffs (not tiled)
- Support for image files/stacks larger than 2GB
- Fixed some automatic boxing problems from (42)
- Gnu 'configure' support for building EMAN
- Better support for boxing helical 'filaments'
- Many minor bugfixes
v1.2 (42) - released 5/13/2002
This page wasn't updated for over 2 years. All major changes since compile
(3) will be listed here now. Most of these happened long ago. Hopefully I'll
keep this up to date now
Changes
- Gatan DM3 file format supported (read only)
- Preliminary support for calling the EMAN library from Python using
BOOST python.
- Wider variety of 'standard' image formats (GIF, BMP, etc.) are supported
now through the use of ImageMagick. NETPBM is no longer used.
- 'seteulers' command for reading and writing Euler angles to/from the
image headers in various conventions.
- New program 'qsegment' allows for interactive segmentation of 3D volumes.
Very fast, but currently lacks isosurface display.
- New SVD/MSA based refinement techniques embodied in svdrefine, svdmultirefine.
Still quite experimental. Look for an upcoming publication.
- proc2d no longer normalizes by default. Must be explicitly requested
with 'norm', 'edgenorm', etc.
- New MSA program 'svdcmp'
- Bugfix in classalign2, now B-factors are only applied once
- 'meanshrink' option applies average filter rather than median in proc2d
- 'euler2=' was broken. Now it works again
- Program 'raw2mrc' for conversion of raw binary data into an EM format.
- New GUI for memories in CTFIT. Preparing for database interface.
- Boxing of helices as a sequence of particles now supported in boxer.
Will be improved in future.
- Major bugfix in align3dsym
- Focal pair merging program 'focalpair' and experimental mods so merged
particles can be used in a reconstruction.
- Resolution definition changed in pdb2mrc. Now uses standard EM definition
(1/2 width of Gaussian in Fourier space)
- 'slow' option added in refine. Uses exhaustive search in alignment.
Very slow, experimental.
- 'Detach' button in EMAN browser allows large images to be viewed.
- Probe option in image control panel allows pixel values in an image
to be probed, with a histogram display.
- QHelp command provides simple documentation browser.
- Multirefine works with fileserver for cluster parallelism
- New normalization used in image comparison, now calculates proper
normalized variance.
- 'selfcl' option in proc2d
- 'usefilt' option in refine allows arbitrarily filtered particles to
be used for orientation/comparison, while the real data is still used for
reconstruction.
- 'start.exclude' file allows specific particles to be excluded from
reconstruction.
- 'ptcltrace' command allows analysis of self-consistency of particle
Euler assignments over several refinement iterations
- 'alignhelix' command does primitive 2D alignments of helical 'particles'
- Fileserver added to 'runpar'. This allows EMAN to be used on Linux
clusters. Bypasses NFS for file writes as a workaround for several bugs in
NFS. Support must be COMPILED in.
- Tomographic in-plane alignment program.
- Spider file writing fixed.
- 'glmatrix' and associated changes to provided dimensional reduction
capabilities.
- Particle tracking (through refinement iterations) added to several
programs. Stored in 'particle.log'.
- 'reproj' option in project3d allows for quantitative comparison of
projections and class-averages
- 'make3dreal' provides simple filtered back-projection based reconstruction.
- 'lst' filetype added. Simple text files that reference images in other
files. Now used for 'cls' files, etc.
- 'align3dvec' a 3d alignment program using vectorization of volumes
- better support for 'D' and 'oct' symmetries
- Automasking in proc3d and refine (refine uses automask2= in proc3d)
- 'segment3d' k-means based automatic volume segmentation
- Improved equation editing in ctfit
- CTF correction now incorporates Wiener filter based on 1D structure
factor of protein.
v1.0 beta1 (3) - released 1/10/2000
Changes
- Documentation updated, much more complete.
- New 'tree' option produces 2-5x speedup in refinements.
- Redid parallelism, now supports workstation clusters as well as shared/distributed
memory supercomputers.
- New '3dit' and '3dit2' options for better 3D models from class averages.
- New ctfit interface with database features for tracking changes in
microscope/sample quality.
- Median filters in boxer to aid in locating particles.
- Fixed bug in t-test, previously used 1/4 data rather than 1/2.
- Added print button to image windows.
- Fixed masking/padding problems so edgemean is used rather than mean.
- Fixed bug requiring initial drag in astigmatism slider on some SGIs.
- New filefilt option in proc3d allows generic filtering.
- Fixed bug in r/w certain MRC files.
- Fixed display of angles in Euler view in eman. Selected point in asym
tri was updated incorrectly.
- Inconsistencies in step 1 and step 3 in use of CTF correction.
- Classalign2 used to require median option when CTF correction was
disabled. No longer.
- Basic write support for VTK file format.
Known deficiencies/planned improvements
- This is a BETA release. That is, it still has a few bugs, and there
are still a few holes in the documentation. If you find a bug, PLEASE report
it. If you're looking for missing documention, let me know. Requested items
receive higher priority.
- Optional Wiener filtration in CTF correction
- Structure factors from PDB for Wiener filtration and CTF parameter
determination.
- Image drag/drop not finished yet.
- More lowpass filter types neeeded.
- Spider file support doesn't handel Euler angle conversion yet.
- Support for 12 bit tiffs.
v1.0 alpha3 - released 8/30/99
Changes
- A serious bug in automatic boxing has been fixed
- New option in boxer allows automatic box alignment for focal pairs
- Fixed single image display in ctfit
- Switched from QT1.44 -> QT2.0.1
- Easier directory navigation in 'eman' file browser
- Middle mouse button on plots brings up an inspector with picture saving
v1.0 alpha2 - released 8/8/99
Changes
- Many bug fixes in boxer.
- particle view is now scalable
- clicking on a particle to center it in the image view now works
when the image view is scaled
- Autoboxing thresholds work properly
- When the particle view is more than 32768 pixels high, the display
works now
- All programs can now read Spider files, proc2d can write Spider files
- Support for 'stack' files seems ok, single images may or may not work
- Euler angles are not read properly from the Spider file headers
yet.
- When writing Spider files, all files will be 'stacks'
- New option in refine: sep= allows particles to be put in multiple
classes. This can make a BIG improvement, and only takes about 5-10% longer
to run.
- New 'Analyze' menu in eman/
- Initial version of multirefine for functional state separation.
- Multiple image view control panel (middle click) has many new options.
drag/drop, delete, save file, etc.
- cls files now have 4 digits, ie. cls012 -> cls0012
- misc bugfixes
v1.0 alpha1 - released 6/20/99
- boxer crashes if you run it without specifying an image file to box.
- Documentation is in a sorry state. Some links are missing.
- Can only read single image Spider files. Stacks are broken.
- The tutorial doesn't use the user parameters as much as it should.
- 'D' symmetry support isn't perfect yet.
- Bug with reading 3D models in ctfit. Power spect. looks wrong.
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