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, we still don't suggest using
them.
- Cluster parallelism doesn't handle unavailable nodes very
gracefully.
v1.5 - released 11/2003
- New refinement options, phasecls, fscls, dfilt and refine for
much more accurate image classification
- Prototype animation module for Chimera (undocumented)
- Bugfixes/improvements to PNG & PGM writing
- MRC output now more comapatible with Chimera scaling
- Fixed major alignment bug when box-size was not divisible by 4
- Realfilters 110 and 111 for iterative expansion of masks
- More binary releases
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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