IMOD 3.7 contained some major functional enhancements plus the usual assortment of bug fixes. The highlights of this version include:
** 4/6/05: New version of Beadtrack takes PIP input, can track in local areas and/or in a local subset of views, uses improved variable mapping, and has several other changes that improve tracking somewhat. If a model file has more than one object, the program will automatically track them separately with existing non-PIP command files.
* 1/19/06: Increased default radius in eraser.com from 2.1 to 3.6 pixels.
* 10/11/05: Made Finishjoin base the average alignment on tomograms with similar rotation angles, so tomograms with 90 or 180 degree rotations do not need special handling (i.e., initial rotation, or making one section be the reference). It also uses the new Newstack option to avoid long lines of transform numbers.
* 10/8/05: Made Makejoincom adjust sample slice numbers properly when volume is turned upside down by a rotation.
* 7/1/05: Tiltalign's report of the ratio of measurements to unknowns was actually the ratio to the number of variables in the search, which omits the lateral shifts. Both the true ratio and the old one are now reported.
* 5/13/05: Switched master align.com to have tilt angles grouped by default, to avoid bad behavior without grouping near zero tilt.
* 4/19/05: Removed WARNING string from minimization errors in Tiltalign since there is nothing to worry about if search succeeds with a metro factor change.
* 4/12/05: Added button to Bead fixer to move all points in local area by residual.
* 2/28/05: Added image distortion correction and magnification gradient correction to Blendmont; added linear and cubic interpolation with cubic as the new default.
1/23/06: Fixed progress output of matchvol/warpvol for > 999 cubes.
12/13/05: Fixed problem with xfalign trying to filter odd-sized images, which broke automatic alignment of sample averages after volumes are rotated.
12/7/05: Changed Ccderaser to allow model output up to the maximum size for models in Fortran programs, and added an option for merging patches in an input model, to facilite editing and use of an output model as an input model.
11/30/05: Added an option to Makejoincom so that rotated volumes could automatically be made the right size in X and Y to hold the rotated image.
11/11/05: Changed Splittilt to make more chunks when the X axis tilt requires only a minimal number of extra slices in each chunk.
10/19/05: Increased limits on number of patches to 40000 in Corrsearch3d, Refinematch, and Findwarp.
10/8/05: Fixed Splittilt and Tilt so parallel reconstruction from binned image would work.
10/7/05: Fixed Transferfid, which was failing on old-style tracka.com that had never been run through etomo.
10/5/05: Fixed Copytomocoms to get actual size of B axis instead of assuming it is a transpose of size of X axis.
10/4/05: Made tomosnapshot collect all *.com, *.log, *.com~, *.log~.
8/22/05: Fixed Blendmont's computation of excluded border regions so that cross-correlations are not thrown off by edges in distortion corrected images.
8/15/05: Increased array limits in Mtffilter to allow 8K x 8K image.
8/14/05: Increased array limits in Beadtrack to allow 48x48 boxes for 500 beads.
8/14/05: Increased array limits in Tilt to allow up to 40x40 local areas for 120 tilts.
7/24/05: Fixed Splitcombine to insert standard commands for finding an appropriate temp directory on the machine running the command file, so it will run on a Mac with no /usr/tmp.
6/30/05: Fixed tomosnapshot for SGI and for spaces in the path.
6/13/05: The option to fix 3D fiducial coordinates with local alignments has been getting lost since IMOD 3.4.17. The command file now specifies it with a number, and Copytomocoms now fixes the coordinates only for dual axis sets.
6/9/05: Added an option to Tiltalign to specify binning factor to use in scaling entered axis shifts.
6/7/05: Added an option to Tilt to specify binning factor to use in scaling thickness, offsets, etc.
5/27/05: Changed Newstack so that transform line numbers can be entered on multiple lines and Finishjoin to use multiple lines, to avoid line length limitations with very big data sets.
5/18/05: Fixed alignlog output of surface analysis when program is run with PIP input.
5/12/05: Increased limits to allow beads up to 100 pixels in Beadtrack.
4/26/06: Made Tiltxcorr work with 5Kx5K image and work as long as the trimmed area is smaller than this.
4/26/05: Fixed problem that killed Beadtrack with less than 8 points.
4/22/05: Added Archiveorig, a script to archive the original stack as a small compressed file of differences after removing X-rays.
4/21/05: Changed defaults in align.com so that local distortion solution is off; it will get turned on by eTomo when user enables global distortion.
4/12/05: Made Tiltalign set object colors in 3D model to standard colors when there are fiducials on two surfaces.
4/11/05: Made Beadtrack ignore separate objects when run from Transferfid.
4/6/05: Added option to Blendmont to create distortion-corrected copy of input stack without blending edges, to be used when fixing edges in Midas.
3/13/05: Increased array limits in Tiltalign and Beadtrack to allow 500 fiducials.
3/1/05: Added distortion and mag gradient corrections to blend com files produced by Copytomocoms.
** 9/29/05: Added parallel processing interface to eTomo for volcombine, moved the monitor table to the progress bar.
** 9/12/05: Added parallel processing interface to eTomo for tomogram generation. The interface is enabled by a file named cpu.adoc in IMOD_CALIB_DIR; a sample file is included in the IMOD autodoc directory.
** 5/12/05: Etomo changed to put the two axes in separate windows, with buttons to control single or dual window display. Autofit is now on permanently to avoid problems in the absence of autofit. Interface to new version of Beadtrack was implemented, including tracking over local areas.
** 3/10/05: Montaging interface added to eTomo.
* 12/12/05: Added a menu option to the File menu to run tomosnapshot.
* 12/6/05: In Join, when a section is rotated, the final start and end in Z entered on the Setup page now reflect the rotation on the Join page, and the new volume will be made the right size in X and Y to hold the rotated images.
* 1/21/05: Can exit Etomo and/or log off while running tilt or volcombine with processchunks.
* 11/10/05: Etomo can automatically translate from local directory paths to remote directory paths in a shared file system when running processchunks. The translation information (mount rules) should be placed in the cpu.adoc file. Etomo will pass the remote directory path to processchunks using the -w option.
* 11/2/05: Added midas limit to the Join Setup tab.
* 10/14/05: Changed Setup Join so it will create an .ejf file and save if the user exits before running Make Samples.
* 8/11/05: Added a context menu when right-clicking on the 3dmod buttons in eTomo with options Open in startup window and Bin by 2. Added the same options with checkboxes to the Options pulldown menu.
* 7/15/05: eTomo changes at various times: Implemented montage binning and building of whole tomograms with montages; fixed ability to generate whole tomograms with single-axis sets; fixed warnings when changing coarse aligned stack binning; and stopped running header over again on files that have not changed.
* 5/19/05: Added a button to run Archiveorig to Etomo Clean Up.
1/6/06: Fixed a bug which prevented starting and ending error messages from processchunks from being completely displayed to the user.
1/6/06: Fixed a bug which caused the Matchvol1 and Matchorwarp done percentage monitors to start late.
1/6/06: Fixed a bug that caused the autodoc reader to send an error to the error log when $AUTODOC_DIR wasn't set.
1/5/06: Fixed a bug where processchunks failed on a working directory path with embedded spaces.
12/16/05: Fixed a bug in Join which allowed the user to get into the align and join tabs with out of date screen values.
12/13/05: Fixed a bug in Etomo Join which caused the default X and Y sizes in the Join tab to be incorrect when a tomogram was rotated.
12/12/05: Added a parallel process checkbox to the Setup screen to specify the default parallel processing setting.
12/12/05: Fixed a bug which caused the final tomogram to appear on the clean up dialog when the dataset name had a dash in it.
12/12/05: Fixed a bug which prevented part of a process from running when the user pressed a process button while the process was running.
12/7/05: Change the exit warning, so it would only pop up when exiting would prevent the current process from completing.
12/5/05: On the Etomo Setup screen, rounded the pixel size to 6 significant digits.
11/29/05: When getting load averages for the parallel processing table, only use ssh when the computer is remote.
11/21/05: Fixed a bug in Tomogram Generation and Tomogram Combination which left the parallel processing checkbox on when cpu.adoc could not be found.
11/3/05: Fixed display of the parallel processing panel when it is first opened in contracted state with no rows checked.
11/3/05: Stopped opening Tomogram Combination automatically after Done is pressed in Tomogram Generation to prevent bad display of parallel processing panel.
11/2/05: Fixed MTF filter monitor: it now works with montages and takes starting and ending views into account.
11/2/05: Added error messages for Setup Combine.
10/31/05: Fixed the Save menu option in Join so that it works whether or not Make Samples has been run. Fixed the Save menu option in tomogram reconstruction so that it saves the state of the current dialog. Prevented the use of Save As during Setup Tomogram. An error message is given when Save fails.
10/28/05: Fixed a problem in Tomogram Combination when processchunks is being run for volcombine. Splitcombine was being told to use the user's temporary directory, instead of a local temp directory. Splitcombine and processchunks are no longer affected by the temporary directory.
10/28/05: Fixed a problem in the B axis when the B stack was added after Setup Tomogram was completed. Processchunks might fail on the last chunk in this situation. Etomo is automatically fixing IMAGESIZE in tiltb.com when either Create Fixed Stack or Calculate Cross-Correlation is pressed in the B axis. At this time Etomo will also extract tilt angles, the piece list (montage only), and magnification gradients as necessary.
10/21/05: Fixed tilt progress monitor so that it works with binning, slices in Y, and thickness in X.
10/18/05: Disabling the Archive Original Stacks button when it is are not needed.
10/18/05: Fixed a problem which caused whole tomogram in Tomogram Positioning to run more then once when the Create Sample Tomograms button was pressed while a process was running.
8/9/05: Fixed View Match Check Volume button in Combine Tomograms, which was failing.
7/26/05: Made squeezevol and archiveorig killable from Etomo.
7/26/05: Removed the error message in Etomo that comes up after a process is killed. Changed message on the progress bar to reflect the ending state of the process (done, killed, or failed).
7/26/05: Fixed a bug which caused Etomo to hang when out of range Z values were used in Tomogram Combination setup.
7/20/05: Fixed a problem in Tomogram Combination setup where a X, Y, or Z value that is too big for the current tomogram caused Etomo to hang.
7/19/05: Fixed a montage bug which caused Calculate Cross-Correlation to build a .dcst file instead of a .bl file after running Make Distortion Corrected Stack.
7/18/05: Fixed a bug which caused Etomo to hang when a filename without an extension was passed to it.
6/10/05: Etomo switched from scaling Tilt and Tiltalign parameters for binning to specifying binning and using unbinned parameters, which eliminates several bugs and vulnerabilities. Also made a separate binning for whole tomogram positioning and tomogram generation.
5/26/05: Fixed bug that kept eTomo from recognizing that _fixed.st existed.
5/20/05: Fixed a bug where Etomo deletes the .edf file on exit after it tries to bring up tiltalign log(s) which are too large. Allowed Etomo to bring up tiltalign log files more rapidly and avoiding using as much memory by leaving out the rarely used sections when a log file gets very large.
5/13/05: Transitioned track.com to PIP input. Added new fields to Etomo: Local Tracking, Local area size, Minimum beads in area, Minimum beads overlapping, and Max. # views to include in align.
4/13/05: Fixed ability to get binned prealigned stack in eTomo.
4/7/05: Etomo modified to produce a distortion-corrected stack for fixing montage overlaps.
** 9/12/05: Modified Imodmesh to incorporate fine-grained display properties into the mesh, including color and transparency changes and gaps. It now puts out a more efficient mesh that is not backward-compatible; an option is provided for generating a backward-compatible mesh. 3dmod can now display all of this information and handles transparency by drawing all solid elements of all objects first, then all transparent elements. Added ability to use the rubberband to specify starting and ending points for a property change.
** 6/29/05: Implemented ability to set fine-grained display properties for points within contours and contours or surfaces within objects. 3dmod manages the information consistently but imodmesh still needs to be reworked to incorporate property changes into the mesh. Other programs will ignore or mangle the information (e.g., reducecont, clipmodel).
* 12/11/05: Fixed perspective in model view so that the slider in the control dialog really does set the angular field of view regardless of the near clipping plane setting. Changed the placement of the default clipping planes so that they are not as far out by default but can be increased by selecting a new option, because very far out clipping planes gave bad displays on some systems.
* 11/14/05: Added ability to put wildcards (* and ?) on image filenames in 3dmod startup window.
* 10/14/05: Added Reload Model menu entry to 3dmod.
* 10/13/05: Fixed 3dmod's scaling of clip plane information when model is read in on subset, flipped, squeezed or binned data. Fixed Z-scale problems in model display when data are read in with anisotropic binning.
* 9/15/05: Added ability to generate a high-resolution internally montaged snaphot of the Zap window, available in the Movie control dialog.
* 6/16/05: Expanded Ctrl-A selection in Zap window to include open contours that travel in Z and pass through the selection area.
* 5/27/05: Enabled moving a contour to a new surface that does not exist yet.
* 4/12/05: Restructured the way the Zap window records subarea location for contrast floating and enabled floating for movements within a section, so that now the subset float option works when fixing fiducials, when panning the Zap window, or when moving the rubberband around in the Zap window.
* 3/8/05: Added an FFT mode to slicer window.
1/25/06: Fixed gaps in zap montage snapshot and set read buffer so it works on Quadro cards.
11/26/05: Fixed saving of memory to TIFF in 3dmod.
10/31/05: Implemented some workarounds to problems with loading many files through the 3dmod startup dialog when the paths total > 32767 characters: removed current directory from names, warned user not to edit a truncated list.
10/14/05: Preserved both openings when two open-type contours in a closed-contour object are joined together.
10/13/05: Added fine-grained display info to the model checksum so model changes are detected.
10/6/05: Fixed problems with undo/redo when moving all contours in a surface to another object.
9/22/05: Fixed joining of contours by concatenation when their ends are at different Z levels.
9/22/05: Fixed model view display of multicolored mesh for Linux. Made Imodmesh produce caps of the right colors when there are surface colors and take contour/surface properties into account when joining contours laterally.
9/9/05: Fixed bug in writing meshes from a model loaded onto binned data.
8/19/05: Made image loading routine allow 3dmod to respond to messages periodically while reading a large section.
8/14/05: Fixed model scaling in 3dmod when opening an externally created model (e.g. .resmod) on binned data.
8/14/05: Fixed opening 3dmod with startup dialog when an image file argument has spaces in the path.
6/24/05: Increased limit on number of buttons for object list window to 5000.
6/15/05: In Zap window, made hot keys change locked time, fixed buffer flushing problem with locked time, and allowed Ctrl A to select contours that are outside the range of the image.
* 6/6/05: Added ability to edit 2D line width for many objects in model view object edit window, and ability to display just spheres with the fill color.
5/25/05: Fixed linetrack's test for whether copy contour is on adjacent slice.
5/19/05: Fixed problem with 3dmod crashing on a tiff file that it can't open.
4/6/05: Fixed problem with model view montage snapshot that showed up on one of our Linux machines.
3/28/05: In Zap window, made cursor change when mouse is moved over edges of rubberband; moved time buttons to a second toolbar.
** 11/11/05: Implemented support for an unsigned 16-bit integer mode (6) for MRC files, including in raw2mrc and tif2mrc.
* 11/11/05: Changed test for byte-swapped files so that image files can now be bigger than 60000 in 2 dimensions.
* 11/8/05: Added options to Blendmont to control cross-correlation parameters, including a VerySloppyMontage option that sets most of them appropriately, so the program will work better with montages done by moving the stage.
* 10/19/05: Added options to Imodtrans for transforming a whole volume with one 2D transform, manipulating the flipped state of a model, and transforming it to match an image file. Made transformation of mesh normals and clip planes work for all cases except section-by-section 2D transformations.
* 10/16/05: Added model transformations to imodjoin to bring all models to a common coordinate system before joining.
* 10/11/05: Added option to Xftoxg to exclude sections with very different rotation angles from the computation of the average rotation.
* 7/15/05: In Processchunks, added ability to let running jobs finish before stopping. Started counting failures so that it will quit if nothing ever starts working after trying all machines, and so that it can drop out a machine if it fails too many times in a row. Switched to having ssh run a bash login shell, which obviates the fix on 6/30/05 and solves problems on the Mac.
* 6/3/05: Added binning to blendmont.
* 5/26/05: Added ability to sort surfaces into different objects in Imodsortsurf.
* 5/21/05: Implemented multiple passes (-P) in imodmesh for open contour objects.
* 5/12/05: Modified Processchunks to allow command files that can be used to synchronize results after running a group of files in parallel. Fixed it to work on Windows (multiple processors should work; multiple machines still untested.) Made Chunksetup insert a newline if the master command file is missing one at the end.
* 4/12/05: Modified Binvol to bin by separate amounts in X, Y, and Z and made it read data in chunks to handle larger volumes.
1/12/06: Added option to Tif2mrc to read only first image of multi-page file.
1/10/06: Fixed Imodmesh to treat a gap at the end of a contour properly.
1/10/06: Redimensioned Newstack to allow full rotation of 8K images.
1/6/06: Fixed processchunks to send standardized error messages upon failure of the start, finish, or sync files and to send the error from the log file.
12/9/05: Various changes to make programs palatable to gfortran, which seems to be usable on the Mac but not yet on FC4.
12/4/05: Changed 3dmod startup scripts used in Windows to solve a permission problem running a W2K build under XP and to preserve spaces in up to 9 arguments.
11/7/05: Fixed bug that crashed Midas when trying to fix edges in a large montage with missing pieces.
10/31/05: Fixed Imodtrans, which was transforming the model twice.
10/24/05: Added option to Xfmodel to transform a model by applying one transform per chunk of Z values for a set of chunks.
10/14/05: Fixed Rotatevol's setting of header origin to account for pixel size.
10/11/05: Made Matchvol preserve origin values so if Squeezevol is used on a volume with non-zero origin, a model will display in the correct place.
10/11/05: Added option to Newstack to have it apply the same transform for all sections in a file and just have one transform per file.
10/6/05: Added option to Processchunks to give path to directory that is needed on remote machines; after a chunk processing failure it will now try it on other machines and quit if the same chunk fails many times.
9/19/05: Fixed bug in Sumdensity when there are empty contours.
8/24/05: Fixed processchunk's ability to kill jobs by adding a new script to kill the process group, using system-dependent ps commands, and got it working to run processes on an SGI also.
7/26/05: Increased extra header array limits in Newstack and Edmont.
7/24/05: Increased array sizes in Blendmont to allow overlaps up to 600 pixels.
6/30/05: Fixed processchunks for spaces in the directory path, enhanced the messages, and figured out how to get it working for bash users in Red Hat or Fedora Core < 4; the latter fix is in the man page.
6/3/05: Made imodsortsurf copy many object properties when making new objects.
5/31/05: Fixed bad bug in Newstack created 5/27/05.
5/30/05: Fixed scaling in Reducecont for images with pixel size.
5/30/05: Made Smoothsurf load only one object at a time.
5/26/05: Switched Sumdensity to loading one object at a time and added output of count of pixels output to model.
5/25/05: Changed computations of mean/SD to use double precision in Newstack (where it was screwing up the floating of data around -32000), and in Alterheader and Subimage.
5/24/05: Converted Reducecont to PIP input, made it skip scattered point objects and load only one object at a time.
5/24/05: Implemented functions for returning only selected objects instead of whole model to Fortran programs, to allow some programs to be modified to run with much larger models.
5/23/05: Made clip stat use doubles for computing mean and SD.
5/13/05: Added options to Sumdensity to trim points out of the pixel model by requiring them to have a minimum number of adjacent points.
4/13/05: Modified Avgstack to read data in chunks so it can handle large images.
4/4/05: Fixed Imodmesh and other problems caused by duplicate function cleanup on 3/21/04.
4/4/05: Fixed Imodmesh problem with contours on last section being forced down to previous section.