Changes marked with ** are particularly noteworthy, ones marked with * may also be of interest to typical users.
* 12/12/08: Fixed Tilt for reconstructions from data with angles to and above 90 degrees; made Tiltxcorr give error if cosine stretching is enabled and angles are too high for it to be valid.
* 12/10/08: Added findbeads3d for automatically finding gold beads in a tomogram.
* 12/2/08: Changed Beadtrack to take true unbinned bead diameter and a binning and compute the radius for centroid as well as modify box size appropriately. Also changed Copytomocoms to feed into this properly and to give box sizes up to 100 instead of stopping at 48.
* 11/13/08: Made Tilt able to project a model built on a tomogram onto all the images used to build the tomogram.
* 10/12/08: Added ability to display images with cosine stretch in Midas if tilt angles are supplied.
2/16/09: Improved messages from Solvematch and guide instructions when the center shift is above the limit.
2/7/09: Fixed bug in Splitcorrection for Windows and made chunk sizes as near equal as possible.
1/21/09: Made Findbeads3d set mean of correlation reference to zero, needed for valid correlations.
1/12/09: Fixed problem of Midas starting up with cosine stretch on.
12/29/08: Fixed Stitchalign to avoid multiple vectors at same Z level and put out only one layer of vectors if input edges have only one layer.
12/29/08: Made Findwarp give an appropriate error when discounting zero vectors leaves no fits; adjusted ratio of measured/unknowns if one layer in Z.
12/22/08: Fixed imod2patch and patch2imod command wrappers so edgepatches will run in Windows.
12/11/08: Added output from the Tiltalign surface analysis of the unbinned thickness needed to contain gold centers and shift needed to center the range of gold in Z.
12/11/08: Fixed copytomocoms output for blending coordinates when there is a 90-degree rotation.
12/10/08: Made Transferfid work if the fiducial model was last loaded on a stack with different binning from the current stacks.
12/10/08: Changed Repackseed and Solvematch so that matching coordinates from Transferfid would still work if either fiducial model was last loaded at a different binning from when Transferfid was run.
12/9/08: Modified transferfid to use bead diameter instead of centroid radius.
12/3/08: Fixed Copytomocom's handling of output sizes for sampling and final aligned stack when images are being rotated by ~90 degrees, adjusted sample positions to account for data loss from rotation, and fixed sample parameters for very small input data.
12/3/08: Fixed field width of output in Maxjoinsize so that a shift of -1000 in Y does not screw everything up.
11/19/08: Fixed Ctfphaseflip to work with parallel processing again.
11/2/08: Added options to Tilt to allow incremental reconstructions to be computed, adding or subtracting selected views.
10/20/08: The CTFfiles option to copytomocoms was changed to specify whether to copy one file or both.
10/16/08: Changed Copytomocoms to produce com files for CTF correction, with options to set common parameters.
10/16/08: Sped up mrctaper by 7x for 4K, 32x for 7K images.
8/21/08: Fixed problem running Refinematch with > 10000 patches.
8/21/08: Increased filename length limit for montagesize to 320.
7/15/08: Copytomocoms issues a warning if tilt angles are supposed to be in existing .rawtlt and it doesn't exist yet.
7/14/08: Prevented Xfjointomo from fitting to coplanar contour segments.
7/6/08: Eliminated ratio of measurements to variables in search (old incorrect ratio) from Tiltalign output; modified Alignlog to work with this.
7/1/08: Changed Transferfid to limit the search range for all variables, to avoid collapsing transformations.
6/30/08: Changed combine.com to save volcombine script to file instead of piping to csh, to fix problem with big scripts on Windows.
6/25/08: Fixed Refinematch crash on residual output when data fit right away.
5/29/08: Added instructions to Tilt output for scaling to -15000 to 15000.
5/29/08: When the input data are bytes, Copytomocoms will set the mode for the aligned stack to integers so it can be filtered without saturating.
5/29/08: Changed Tomostitch to run Blendmont with ExcludeFillFromEdges only if that option is specified to Tomostitch.
5/20/08: Added option to Finishjoin to do local fits instead of global alignment when running Xftoxg.
5/20/08: Changed mrctaper to taper over 1% of the image size (mean of X and Y dimensions) when size is above 1600 pixels.
5/20/08: Changed Makejoincom to put out sequential lines for stacking sample averages to avoid having one very long line.
4/27/08: Changed Tomostitch to match densities across overlap zones instead of between centers of whole volumes and added verbose output option.
4/10/08: Fixed tomostitch when using temporary directory.
4/8/08: In Edgepatches, fixed creation of Section entry with Z values, and added options for specifying range in X and Y of pieces to add.
4/8/08: Made tomostitch produce a residual model even after failed findwarp runs.
3/4/08: Increased allowed points in Tiltalign to 1000 in 3D, 140000 in projections.
3/4/08: Changed Beadtrack to be able to track huge numbers of fiducials as long as they are done in local areas; handled image boxes better to relieve memory restrictions on them.
Changes in eTomo
** 11/20/08: Interface for transforming fiducial model and erasing gold was
added to Aligned Stack panel.
** 10/29/08: Tomogram generation panel was split into two, one for aligned stack and one for tomogram. CTF correction interface added to aligned stack panel.
* 12/5/08: Etomo error logs are now saved to $HOME/.etomologs unless the user has ETOMO_LOG_DIR set.
* 12/4/08: In Etomo - Fiducial Model dialog, sending the View Skip List to 3dmod when opening it with the Fix Fiducial Model button. The View Skip List will appear under the checkbox called "Ignore gaps at views:" in the Bead Fixer.
* 12/1/08: In Etomo added an options to Settings to default to montage.
* 11/10/08: The new aligned stack panel was split into tabs for each operation.
* 10/6/08: In Etomo, tables have been changed to have paging buttons and hot keys instead of sliders when they get too long; the user can set the maximum length of a table in the options.
* 7/24/08: In Etomo - Tomogram Positioning boundary model contours are now limited to two points. The next contour will automatically be created when the third point is added.
* 7/18/08: In Etomo Settings dialog added the ability to turn on parallel processing.
* 6/20/08: In Etomo added tilt angles to 3dmod calls which display tilt series.
* 5/13/08: In Etomo added a right click menu to most of the process buttons. This menu allows the associated 3dmod process to be run after the process started by the button is done.
* 2/28/08: In Etomo retrieve low and high Z from 3dmod with rubberband command.
* 1/14/08: In eTomo added the ability to reconnect to a parallel process.
* 12/26/07: Added Etomo arguments to allow the reconstruction Setup dialog to be completed automatically. See etomo -h.
1/26/09: Fixed right-click popup menu on Final Aligned Stack panel.
1/26/09: Fixed eTomo reporting of error messages from Ctfplotter.
12/15/08: Fixed a bug where the bead diameter came up wrong when the 3dmod instance was already running.
12/15/08: A tilt axis angle near 90 degrees is now handled properly from eTomo.
12/12/08: In Etomo - Fiducial Model exposed the beadtrack parameter BeadDiameter.
12/11/08: In Etomo - Join, popping up Warnings from xfjointomo.
12/10/08: In Etomo - Join, fixed a bug where the Alignment Reference Section was always saved under trial, even when a finish join was done. Will fix previous .ejf files only in the case where the trial join was never run.
12/10/08: In Etomo - Join, fixed the format problem affecting spinners in the Join tab.
12/10/08: Improved the Etomo log file to include time stamp and data set information.
12/9/08: In Etomo - Fiducial Model dialog, corrected the bead diameter passed to beadtrack and 3dmod. Taking Coarse Aligned binning into account. Removed centroid radius from the dialog, converting centroid radius into bead diameter in existing track.com files.
12/9/08: In Etomo - Final Aligned Stack dialog, resetting the OutputFileName in ctfcorrection.com each time it is saved.
12/2/08: In Etomo - Gold Erase, changed Better Radius to Fiducial Diameter.
11/21/08: Fixed Etomo - NAD. Opening the volume in 3dmod was failing because of a corrupt path name.
11/21/08: In Etomo - Fine Alignment saving the state of the Beam Tilt panel header.
11/19/08: Bug fixes. In Etomo - Final Aligned Stack, fixed a problem where CTF Correction attempted to run more then once when the button was pressed, and a problem where binning was overridden by Tomogram Positioning. In Tomogram Generation fixed a problem that prevented trial tomograms from running.
11/11/08: In Etomo fixed a problem with Final Aligned Stack dialog's binning value, and a problem with Trial tomogram.
11/7/08: Added ctfcorrection log and mtffilter options to the Etomo Final Aligned Stack dialog's right-click menu.
11/2/08: Etomo now supplies tilt angles to Midas for fixing coarse alignment to allow cosine stretching, but the cosine stretch is initially turned off.
9/29/08: Fixed Replace Patch Vectors on Windows.
9/11/08: In Etomo fixed a null pointer exception which stopped execution in Combine.
8/26/08: In Etomo - NAD making sure that the clean up button works properly by asking the user to exit from files that will be deleted.
8/18/08: In Etomo - Join added the Finishjoin option -local, which causes Xftoxg to do local fits to 7 adjacent sections.
7/16/08: In Etomo - Fine Alignment exposed Rotation Angle so that it can be adjusted when it is a fixed value.
7/15/08: In Etomo - Postprocessing, changed the dialog to show that it can retrieve Z settings from 3dmod as well as X and Y.
7/15/08: In Etomo, preventing tilt from using XTILTFILE when align was run fiducialess.
7/2/08: Made "Examine patch vector model" open model view object edit window so residual values can be displayed more easily.
6/20/08: Fixed a bug in Etomo - NAD where the test K value list would only accept whole numbers.
5/28/08: Fixed problems with Etomo Join table handling after a row deletion and some problems with very large tables.
5/27/08: Fixed running of Tilt from Whole Tomogram Positioning (broken in 3.12.9).
5/16/08: In Etomo making kill and pause work for a reconnected processchunks process.
4/21/08: In Etomo - Join remember the location of the previously added section (while Etomo is running).
4/17/08: Fixed an error when running etomo with --help.
4/2/08: Fix problem displaying "<" in tooltips.
3/21/08: Changed to a less memory intensive method of popping up the log files in eTomo.
3/21/08: Made the opening of fine alignment logs files more flexible, so that the solutions logs is more likely to be opened in low memory conditions.
3/17/08: Added an environment variable ETOMO_MEM_LIM to set the java memory limit in etomo.
2/29/08: In Etomo fixed "Start Combine" button in the Tomogram Combination dialog so that it is enabled correctly when the "Create Combine Scripts" button is pressed.
1/14/08: In eTomo handling an Imod directory path with embedded spaces.
12/28/07: Added the directory size to the Clean Up dialog.
PEET Interface in eTomo
9/10/08: In Etomo - PEET fixed some reliability problems with Etomo writing to
.prm file. The .prm file array descriptors should no longer contain "NaN".
9/5/08: In Etomo - PEET fixed a problem where nWeightGroup appeared in the .prm file when it was disabled in the dialog.
8/21/08: Added equalization of CCCs across missing wedge weight groups to the PEET interface in Etomo.
8/20/08: Fixed a bug in Etomo - PEET which prevented the use of zero Phi, Theta, and Psi values.
5/1/08: In Etomo - PEET, automatically bringing up isosurface display for averaged volumes.
4/15/08: Fixed the reading of .prm files by Etomo - PEET.
4/2/08: In the PEET interface fixed the handling of a missing model file entry.
4/1/08: Fixed PEET prm file put out by eTomo, broken in last version.
4/1/08: In PEET interface, added controls for masking.
3/5/08: PEET interface in eTomo has new controls to select efficient full range searching.
2/27/08: In the PEET interface in Etomo added "Add Row" button to the iteration table.
Changes in 3dmod
** 4/29/08: Isosurface display of image data added to model view based on mesh
code from Chimera.
** 1/25/08: Added scale bar dialog to 3dmod (from edit menu of Info window, View menu of Model View).
** 1/13/08: Added a Multi-Z window to display successive slices in an array of panels.
* 12/9/08: Added hot key k for copying contour when contour copy dialog is open.
* 12/9/08: Added entry to File menu for conveniently changing JPEG quality.
* 12/8/08: Added ability to scale line thicknesses and symbol sizes when taking a montage snapshot, added an option for taking the whole image at 1:1 zoom, and saved all the montage snapshot settings between sessions.
* 12/6/08: Slicer in centering mode will now stay exactly centered on model points when stepping through a contour.
* 12/1/08: Switched bead fixer autocentering to use correlation with a sobel-filtered model bead.
* 11/29/08: Enabled selection of contours, deletion of contours, and undo/redo when running as 3dmodv (standalone mode).
* 11/29/08: When stepping through contours (c/C), a new current point is picked that is the closest in X/Y on the closest Z plane.
* 11/29/08: Bead fixer: added ability to ignore gaps on list of skipped views, output global and local mean residuals to info window, allowed the keypad Insert key to be used instead of middle mouse button for seeding and gap filling.
* 11/29/08: Added ability to link slicers together when multiple volumes are loaded.
* 11/27/08: Added sphere at the current point and a bounding box display to model view, with menu entries in the View menu, ability to edit their properties, and a hot key to toggle the current point.
* 11/15/08: In meshing panel of model view object edit, added checkbox for dome caps, added a progress report, and allowed meshing parameters of multiple objects to be changed together.
* 10/2/08: Fixed hardware stereo.
* 10/2/08: In isosurface display, added binning, ability to delete small pieces, and ability to unlink the X/Y/Z coordinates of the displayed box from the current point.
* 9/23/08: Made attach to nearest point consider only objects that are on, added a preference to select the old behavior.
* 9/23/08: Added ability to adjust point size with scroll wheel.
* 9/19/08: Fixed/finished ability to make tube meshes with different size segments. Fixed display of mesh and spheres with diameter -0.5.
* 7/15/08: Added ability to start new contour automatically when contour reaches a set number of points.
* 6/17/08: Implemented three ways to change diameter of a tube mesh within a contour, available from both Imodmesh and 3dmod.
* 5/29/08: Right mouse button can now be used to select points in the isosurface display; the current image point is set to the picked point.
* 5/27/08: The isosurface display position can now be set from the rubber band. The computation is now multithreaded but this is not used by default and requires IMOD_PROCESSORS to be set to activate it.
* 5/26/08: Added options settable in Preferences for starting at middle section (default on) and for doing autocontrast on the first section seen (default is to do this when starting without loading a model).
* 5/26/08: Added hot keys t, b, l, r, f, k for looking at all 6 faces of model in model view, fixed orientations for rotations around Z in object edit move panel, remapped low-resolution toggle to hot key R.
* 5/26/08: Added Ctrl T hot key for toggling the current object on/off.
* 5/25/08: Added option for reading in a tilt angle file; angles are displayed in the zap window toolbar instead of the window size.
* 5/24/08: Added option to apply image processing filter automatically when changing sections. Added option to smoothing filter to not rescale the data, so that thresholds are comparable between slices.
* 5/24/08: Implemented interpolation in the conversion from pixels above threshold to boundary contours in auto-contouring and in imodauto. Added an option for kernel smoothing to imodauto to match what is done in 3dmod.
* 5/23/08: Added checkable option in File menu to save TIFF snapshots of image windows as 8-bit grayscale.
* 5/23/08: Pixel view window can now show value of any loaded data from memory, including RGB triplets for color data, and can show RGB as gray scale.
* 5/22/08: Zap and model view montage snapshots can now be either TIFF or non-TIFF types.
* 5/22/08: Made it possible to edit extra objects like the isosurface object in the model view object edit dialog. Made the on-off buttons in that dialog appear and disappear as needed when the real object count changes.
* 3/5/08: Made 3dmod save and restore settings of float and subarea checkboxes.
* 2/21/08: In 3dmod added Extract File... option to the File menu. This option runs trimvol based on rubberband coordinates and low and high Z choices.
* 2/6/08: In the ZaP windows added section selection to the rubberband functionality.
* 2/3/08: In Model View, added scroll wheel zoom, option to swap left and middle buttons, and ability to rotate model or clipping plane with Shift-Right button.
* 1/27/08: Added ability to define and name multiple object groups in object list window.
* 1/23/08: Andrew Noske's drawingtools plugin added to IMOD.
* 1/21/08: Added grouping capability to object list window to allow objects to be edited in groups.
2/2/09: Sychronize all on/off buttons when meshing turns an object on.
1/23/09: Fixed size of current point sphere in model view if data loaded with binning.
1/15/09: Stopped beadfixer from deleting current contour when deleting ones below threshold.
1/11/09: Made object list window get updated for model or view change even when object edit window not open.
1/6/09: Fixed model view display problem on some Macs caused by stereo changes by swapping buffers twice more after the draw.
12/18/08: Changed isosurface color again, changed object names and scaled down new color when saving an isosurface.
12/16/08: Changed trimvol command output to info window and used for extract from -yz to -rx when data are flipped, figuring it is better to preserve handedness in extraction.
12/15/08: Use a stereo-capable widget only when stereo is turned on to avoid problems on Macs.
12/14/08: Set a color and modified material properties for the isosurface so that detail will not be washed out when viewing a surface face-on.
12/12/08: Made it harder for autocentering in Bead Fixer to go to an adjacent stronger bead when clicking within a bead.
12/11/08: Fixed model view update when running from 3dmod and there are no image windows, as when editing patch vectors.
12/8/08: Fixed a potential crash and eliminated extra lines of background in montage snapshot.
12/6/08: Eliminated 1 pixel shift and ability to shift image with mouse when zoomed image fits exactly in window.
12/3/08: Turned models on when loading into 3dmod, so if the user turns it off by mistake and doesn't know about 't', it will reappear when they reload it.
12/2/08: Made 3dmod detect a 3D FFT and not mirror it.
11/30/08: Fixed a problem with contrast floating when starting in middle Z and contrast set from model.
11/27/08: Fixed slicer angle table display of coordinates to start from 1.
11/27/08: Made scale bars go away when dialog is closed. Made scale bar menu item be permanently present in model view View menu.
11/15/08: Model view object edit will make the isosurface be the current object when either window is opened, so the user will realize it is editable.
11/11/08: Fixed problem with bead fixer when prealigned stack loaded binned.
11/7/08: Isosurface now keeps a separate threshold for each time (volume).
11/7/08: Fixed the zap subarea coordinates after dragging a rubber band.
11/6/08: Fixed bug in 3dmod float that froze program.
9/21/08: Added *join to file filter in startup list, added filters for PNG and JPEG.
8/22/08: Fixed bug in extra object code from 7/13/08 that crashed 3dmod when using bead fixer on Mac (and should have crashed elsewhere...).
8/19/08: Made + zoom up as well as = in all image windows except slicer; made keypad + zoom like = in slicer and model view.
8/18/08: Fixed ability to delete surface and point labels.
8/1/08: Fixed bug in drawing large non-integer zooms in nonHQ display.
7/30/08: Fixed the stay-on-top function in Info window, broken 5/26/08.
7/16/08: Changed Beadfixer to start at beginning when model is reloaded in gap filling mode; finished features needed for examining seed contours with values from Imodfindbeads and deleting contours below threshold.
7/13/08: Fixed problem of model view object edit not dropping extra objects when they stop being used.
7/13/08: Prevented saving model and opening image windows during initial data load.
7/11/08: Fixed bug when resizing locator window that made it become square.
7/2/08: Fixed bug that crashed 3dmod when opening a model without an image and going to section 1 (broken in 3.12.12).
6/17/08: When inserting fine-grained changes, no longer wipe out later matching changes inserted by the users.
6/12/08: Made scale bar and light vector display come out on top of models.
6/10/08: Fixed some problems with lighting direction with multiple models, and added a vector display of light direction while moving the light.
5/29/08: Fixed crash when starting a new model with model view open.
5/28/08: Fixed sphere drawing in slicer when there is a Z scale or differential binning.
5/27/08: Synchronized contrast radio button in autocontour window with F9/F10. Made autocontour Next operation work with autoapply in image processing.
5/26/08: Bug fixes: Fixed drawing of multiple X or Y image planes in model view (it was drawing the same plane at different positions). Fixed changing of current point on mouse release when starting movie. Fixed crash if model view or object edit closed while meshing. Prevented autocontour and line tracker windows from opening when color data is loaded.
5/26/08: Added options to make a scale bar be a false color ramp.
5/26/08: Added hot key and menu item for opening model view and isosurface from 3dmod.
5/25/08: Added option to rotate slicer around model view center of rotation when their rotations are linked.
5/25/08: Added ability to mesh all objects in model view object edit.
5/22/08: Added Others On button to object list dialog.
5/21/08: Fixed crash when closing model view window during montage snapshot.
4/28/08: Fixed bug in 3dmod floating that let black slider go above 255.
4/4/08: Fixed some problems with allocation and freeing of extra objects and fixed some memory leaks in 3dmod.
4/1/08: Added option to pass image data into 3dmod from standard input.
4/1/08: Fixed transparency when running model view from 3dmod, broken 3/5/08.
3/10/08: Fixed crash from key handling by scale bar dialog in 3dmodv mode.
3/5/08: Fixed artifact on right edge of image in HQ highly zoomed slicer.
3/5/08: Added option to make scale bars vertical.
3/5/08: Made rubber band moving work when bead fixer or other plugin is taking mouse events.
1/28/08: Fixed bug that made program crash if object list window not open.
Changes in General Processing Programs or Infrastructure
* 12/12/08: Added a file index.html in the html directory and an alias
"imodhelp" to the startup scripts to start Qt Assistant with all IMOD
documentation accessible.
* 12/9/08: Made imodmesh turn mesh drawing on when meshing and off when erasing.
* 11/28/08: Added option to Imodjoin to change the colors of objects being added to a model, to avoid getting a model with all green objects.
* 11/15/08: Implemented option for capping tubes with hemispheres (domes), made open contour meshing maintain consistent lighting direction in most cases, and fixed a bug in getting the next Z value that could crash meshing.
* 11/13/08: In Imodinfo, added a computation of volume inside a mesh, renamed "mesh volume" to "contour volume", and made it omit the "cylinder" values if the mesh-based values exist.
* 6/19/08: Added filterplot for plotting IMOD filter functions.
* 6/19/08: Added imodfindbeads for detecting gold particles in images.
* 6/8/08: Added ability to fit a cylinder instead of a sphere to Imodcurvature, using a stupid exhaustive angular search; also fixed bug in 3D fitting when the points are spaced apart farther than half the window length. Made value output in model be scaled from pixels into user's units, and added option to get curvature values rather than radius of curvature values.
* 5/31/08: Added general values and point sizes to ascii model output.
* 5/23/08: TIFF changes: Added an option to mrc2tif to make a single TIFF stack. Added support for floating point data in mrc2tif and tif2mrc, and 3dmod will read such data. Mrc2tif also puts out the minimum and maximum when data are 16-bit integer or floating point.
* 5/20/08: Added ability to do 3D filtering directly on an image file and not just on an FFT with mtffilter.
2/16/09: Set working directory permissions in Copytomocoms and Makejoincom and set permissions of copied files in align.com, Finishjoin, Xfalign, Tomosnapshot to get around problems in Vista.
2/16/09: Made error messages produced by PIP come out on one line.
2/15/09: Fixed problem with getting max coordinates in Point2model.
1/21/09: Matchshifts makes sure solve.xf is readable by owner to solve problem on Vista when files appear to have no permissions to cygwin.
1/16/09: Fixed runimodqtapp for spaces in IMOD_DIR.
1/7/09: Added option to imodmop to paint tubes only in planes.
1/2/09: Made a script for imodhelp to run it properly.
12/10/08: Fixed bug in Remapmodel when entering shifts with -add option.
12/9/08: Fixed bug in reading ascii models written with reference info.
12/8/08: Fixed Processchunks "hold" to hold off only a failed machine.
12/2/08: Point values will now be stored when meshing a contour as a tube.
12/1/08: Made imodfindbeads do kernel filtering with 0.85 ("smooth") as default.
11/30/08: Reduced edge artifacts in some kernel filtering operations (e.g., clip) by extending image with replicated pixels instead of mean.
11/27/08: Made Delete do same as Insert in Midas and Shift-Home do same as Insert in 3dmod because new Mac keyboards have neither Delete nor Help there.
11/21/08: Increased filename length limits in Maxjoinsize, Xftoxg, and Xfmodel.
11/21/08: Increased array sizes in Blendmont to allow 8Kx8K frames and output line length up to 500000.
11/20/08: Added image reference information to ascii model.
11/14/08: Fixed clip flipz for odd-sized files and made clip flipyz/rotx be a little faster for large files by using up to twice the memory.
11/14/08: Added option to imodcurvature for getting mean of stored values.
11/6/08: Fixed autocontrast of reference slice in Midas in reference mode.
11/2/08: Added option to Xfproduct to multiply by just one of the transforms in a file of multiple transforms.
11/2/08: Added option to Newstack to overwrite sections in existing output file.
9/26/08: Added a -name option to the installer to change the name of the actual directory from IMOD.
8/20/08: Fixed bug in accessing connections numbers during meshing that made wrong connections if contours had other fine-grained properties set.
8/18/08: Fixed chunk size value written to model file for labels.
7/31/08: Modified install script for Ubuntu to avoid using /etc/profile.d and to take care of libtiff and libg2c problems.
7/15/08: Processchunks needs to list all log files if one does not seem to exist to avoid spurious timeouts (Redhat 5 update 2 NFS problem?).
7/15/08: In Ccderaser, order 0 can now be specified in order to replace points with the mean of the border points instead of fitting to them.
7/6/08: Made Processchunks killing more robust on our system by listing the .pid files if they do not seem to exist.
7/4/08: Fixed clip splitrgb, broken 1/11/08.
7/1/08: Upgraded Xfsimplex to PIP input, and added options for limiting the range of the search and for filtering and selecting an arbitrary area to align within the program.
6/23/08: Added option to Blendmont to prevent trimming of fill areas produced by distortion correction from overlap areas used for correlations.
6/21/08: In Imodfindbeads, fixed black level in file when dip is below minimum.
6/21/08: Added option to Beadtrack to get information about which surface each bead is on.
6/19/08: Fixed imodinfo to give extra verbose output with -vv as advertised.
6/17/08: Added centroid calculation to integrals in Nda and Mtk.
5/30/08: Rewrote mrcbyte and imodauto to read data slice by slice instead of reading the whole file into memory.
5/30/08: Added option to Boxstartend to specify a size in X, Y, and Z, so square boxes are no longer required; fixed centering in Z so that the option to set slices before and after actually works.
5/23/08: RGB changes: Added option to tif2mrc to convert RGB to gray-scale by NTSC weighting, but kept old option for equal weighting. Made 3dmod use this conversion when reading in RGB as gray-scale and when snapshotting to grayscale.
5/20/08: Fixed Densmatch to work on a single section.
5/7/08: Fixed xfalign when run with filtering, broken 1/4/08.
5/7/08: Increased line length in vmstocsh so that startjoin.com will work when combining lots of files into sample average.
5/6/08: Made object bounding box routine get bounding box from meshes if there are no contours, so that centering on a saved isosurface object works.
5/2/08: Fixed imodmop painting of tubular lines when points are spaced farther apart in Z than the diameter.
4/25/08: Added options to Densmatch to specify the region to be matched and to allow for an offset between volumes; also made it do at least 10 samples along each axis, so large area tomograms will still be sampled on 10 planes.
4/14/08: Fixed Blendmont bug when using ExcludeFillFromEdges, which tomostitch uses.
4/14/08: Made Findwarp detect and eliminate degenerate fits that would give numeric errors in the transforms.
3/6/08: Made Boxstartend scale model coordinates to the volume being extracted, so the model can be made on a binned-down volume.
2/27/08: Fixed vmstopy, broken 1/5/08.
1/4/08: Translated PIP to plain vanilla Python to avoid version problems with extension module.
1/4/08: Fixed scripts to handle space in IMOD_DIR and IMOD_TMPDIR.