Changes marked with ** are particularly noteworthy, ones marked with * may also be of interest to typical users.
Changes in Tomogram Processing and Related eTomo Changes
** 5/5/06: Set up a system for getting information about corresponding
fiducials directly from Transferfid to Solvematch: Transferfid (via
Repackseed) outputs a file with coordinates of corresponding points, and
Solvematch has options to use this information to match up the final fiducial
points even if some points have been deleted.
5/16/06: eTomo now instructs Transferfid to output a transfer coordinate
file, detects the presence of it on the combine panels, and modifies the
interface appropriately so that transfer coordinates can be used.
5/5/06: Setupcombine converted to take command line arguments and to set up
solvematch.com correctly with a transfer coordinate file.
* 8/23/06: In Solvematch, added local fitting and an assessment of the shift
of the center so Corrsearch3d can be started off with a correct shift if
necessary. Added options to specify the Z shift and tilt angle offset used
when running Tilt, so using these options in tomogram generation will no
longer screw up Solvematch. Fixed output of list of points used in B.
9/13/06: Handling bowl shaped tomograms in Combine. Added center shift limit
to Solvematch. Allowing the initial match size to be adjusted in matchvol1.
Added initial shift to Patchcorr.
* 8/16/06: Revamped Corrsearch3d so it uses displacements of neighboring
patches to adjust the center of the patch from B being correlated. Also
converted to PIP input, made it do FFT correlations internally, added kernel
smoothing, made it handle volumes well in either orientation, allowed for a
model on B and for an initial displacement between the volumes.
* 8/21/06: Converted Findwarp and Refinematch to PIP input, made them handle
either orientation of volume, changed outlier output to a summary, added
option for patch and residual output. Made automatic fitting in Findwarp more
flexible in the thin dimension and made it try to meet a series of criteria
without being run repeatedly. Modified Matchorwarp appropriately; all of this
makes the matchorwarp log file much more readable.
9/20/06: In eTomo - Tomogram Combination, giving access to cross correlation
coefficients (patch_vector_ccc.mod) created by Patchcorr. Opening the 3dmod's
Imodv Objects window, so that false colors can be viewed. Patch_vector.mod is
now being created by Matchorwarp. Matchorwarp is also creating a residual
file called patch.resid.
9/1/06: Added options to Matchorwarp to make a patch vector model with stored
residual values and clipping planes.
9/1/06: Patch2imod will store correlation coefficients or residuals as values
in the model so that they can be viewed in false color in the patch vector
model. It also sets up clipping planes to allow a subset of vectors to be
viewed easily. Imod2patch will write stored values to a new patch file.
8/29/06: Added a field for KernalSigma to Etomo - Combine - Patchcorr.
* 6/28/06: Post-Processing: Added an option in the trimvol panel which allows
the scaling to be based on a subarea in X/Y as well as a subset of slices.
3/7/06: Changed Findcontrast to take PIP input and take unflipped or flipped
coordinates, and added options to Trimvol for setting X and Y limits in
running Findcontrast.
* 6/27/06: Post-Processing: Added an option in the trimvol panel which allows
the trimmed tomogram to be rotated in X.
6/23/06: Added options to Clip and Trimvol to rotate volumes by 90 degrees
instead of flipping Y and Z.
* 6/14/06: Added a checkbox to the transfer fiducials panel which causes one
of the images to be mirrored around X.
6/2/06: Added option to Transferfid to deal with mirror-image data sets.
5/20/06: Added menu entry to Midas to mirror image around X axis, modified
amat_to_rotmagstr to handle inverted axes as negative stretch.
* 5/11/06: eTomo now sends existing positioning information to Tomopitch,
parses Tomopitch's output, and shows original, added, and total values for
position parameters.
5/2/06: Added options to Tomopitch so that it can output original and new
total values for shift, angle offset, and X-axis tilt.
10/19/06: Improved parallel processing failure reasons shown in eTomo.
9/18/06: Made processchunks able to detect and report a failure to cd to the
data directory or a failure to run IMOD commands.
10/13/06: In eTomo - Tomogram Combination - Final Match - Volcombine
Parameters, added a field to set parameter for taking low frequency data from
both tomograms.
9/13/06: Added an option to Combinefft to average very low frequencies from
both tomograms, to eliminate lines between pieces containing boundaries
between dense and light material.
4/6/06: In Join, when creating a sample, no longer recreating the .rot files,
unless the rotation angles have changed.
2/10/06: Added options to Makejoincom to skip rotating a volume that has
already been rotated, and to make the rotated volume as big as needed in Z.
Other Changes in Tomogram Processing and Joining
* 10/26/06: Added Xfjointomo to refine alignment of serial section tomograms
with a fiducial-type model. Added an option to Finishjoin to incorporate the
refining transformations from this program.
* 4/8/06: Changed Tiltxcorr so that it will not shift images to keep tilt axis in center when the NoCosineStretch option is given, and to avoid numeric errors when the tilt angle is 90 degrees.
* 3/24/06: Modified Tilt and Splittilt so that parallel reconstruction will write directly to a single output file, eliminating need to reassemble.
* 3/23/06: Fixed Splittilt so it takes image size from aligned stack instead of assuming that FULLIMAGE is the size to do, so it will work with an oversized or subset aligned stack.
* 3/22/06: Fixed Tilt so a negative SUBSETSTART could be used to reconstruct from an aligned stack that is bigger than the original stack.
* 2/6/06: Added Findgradient to analyze magnification gradients from montages taken at high tilt, and Makegradtable to make a mag gradient table from either a Findgradient log file or the transformations between images taken at different Z heights. Modified Blendmont to estimate the best mag gradient for correcting a montage error.
10/27/06: Converted Remapmodel to PIP and added options to allow easy remapping of a model after rejoining serial tomograms with a different spacing.
10/5/06: Made beadtrack exit with error if the seed model is empty.
10/5/06: Stopped rotating tilt axis angles from FEI/Agard headers by 180 degrees if they were beyond +/- 90; this would screw up handedness.
8/3/06: Fixed Blendmont to take mode 6 files.
7/26/05: Fixed cumulative correlation in Tiltxcorr, which failed on Windows with two equal lowest tilt angles (e.g., +1 and -1).
7/17/06: Labeled local area mean residual output from Tiltalign and provided mean and range for all local areas.
7/13/06: Fixed bug in Solvematch that made it unable to use the transferfid coordinates sometimes on a Mac.
6/28/06: Fixed bug in setting truncation limits in Findcontrast.
6/6/06: Fixed Tilt to keep min/max/mean output line from being broken in two, and converted Splittilt and Trimvol to unix line endings in Cygwin.
6/1/06: Fixed bug in Warpvol's checking of input cube sizes created 2/26/06. Increased Rotatevol, Matchvol, and Warpvol array allocation to 500 MB.
5/10/06: Added sync statements to command files for running Tilt in parallel to stop problems on Macs.
2/26/06: Changed Matchvol and Warpvol so they do not open input file and roll previous file to backup until after errors could occur.
2/26/06: Changed Findcontrast and Densmatch to process data in chunks so they will work on virtually any size data.
2/14/06: Made Blendmont put out a section with no data if there is only one piece being output; needed if a sample is empty.
1/31/06: Made Ccderaser handle adjacent lines correctly.
1/25/06: Made Beadtrack a bit more robust against tilt align failures.
Other Changes in eTomo
* 10/20/06: In eTomo - Post Processing, made Rotate around the X-axis the
default reorientation method.
* 10/17/06: In eTomo - Join, display a warning highlight in sections which will be inverted in the final join. Also added an Invert Table button, to change which sections will be inverted.
* 9/20/06: In eTomo - Tomogram Positioning, changing the interface to work with Fiducialess Tomograms.
* 8/11/06: Etomo: opening and re-reading the align log in 3dmod automatically.
11/3/06: In Etomo - Join, handling inverted samples by making sure that the final start and end slices are in the right order.
* 8/3/06: Etomo can now reconnect to a currently running tilt upon entry.
* 7/19/06: In eTomo Tomogram Combination, no longer adding default Z min and max values.
* 6/21/06: Etomo is now displaying help with Qt Assistant, and the full IMOD documentation is available and searchable.
* 3/27/06: Added advanced checkboxes "Convert to bytes", which adds "-mo 0" to prenewst.com, and "Float intensities to mean", which adds "-float 2" to prenewst.com, to coarse align page.
* 3/20/06: Etomo: Added a generic interface for parallel processing to a separate tab.
* 3/15/06: Parallel processing for a single computer with multiple CPUs is now available in Windows.
11/15/06: In eTomo join, prevented join size from being reset to default
10/17/06: In eTomo, fixed a bug in Windows where an ImodSendEvent error message pops up when fine alignment is run and the .preali is not open.
10/17/06: In eTomo - Join - Setup & Join, fixed a bug where the Final Start and End values are set to zero when a value is entered only in the X (or Y) rotation angle.
10/12/06: eTomo now manages log files and files used for process monitors better to solve problem in Windows with trying to rename or delete open files.
9/21/06: In eTomo, warning the user when the pixel spacing in an mrc header is invalid.
9/20/06: In Tomogram Positioning, changing the display for fiducialess sample creation.
9/13/06: Tilt.com: removing Local File and Z Factor File when creating a fiducialess sample.
8/30/06: Etomo - Tomogram Positioning: fixed a problem with whole tomogram generation where the _full.rec file wasn't created.
8/17/06: Fixed a bug in eTomo Post Processing (trimvol) where the scaling from sub-area values decreased by 1 each time eTomo was ended and restarted.
8/10/06: Etomo: sped up the process monitors for mtffilter, prenewst, tilt, and newst.
8/9/06: Adding more status information to the newst monitor and the regular volcombine monitor.
7/31/06: Created a compact version of Etomo.
7/21/06: In eTomo Setup Tomogram, placed distortion correction and mag gradient correction into advanced when a distortion directory is not in place.
7/21/06: In eTomo fixed the font size functionality. Font sizes 10 and up work correctly after exiting and rerunning eTomo.
7/20/06: Fixed a bug in eTomo where processchunks never completed or gave an error message when the local computer was missing from the cpu.adoc and %mountname was used in the remote mount rule.
7/19/06: In eTomo Fiducial Model, changing the "Seed Fiducial Model" button label to "View Seed Model" when transferfid is used.
7/19/06: In eTomo Fiducial Model, moved the "Use Fiducial Model as Seed" button to the Basic screen.
7/18/06: Fixed bug where eTomo did not use the user specified display settings in the Setup Tomogram screen or in the first data file opened.
7/18/06: Fixed bug in Tomogram Positioning where eTomo complained about align not being run when the "Fiducialless alignment" checkbox was checked.
7/18/06: Fixed initial display of fonts and styles on setup screen in eTomo and when it is opened with an edf file from the command line.
7/18/06: Made eTomo go back to clipboard communication with 3dmod on Windows due to problems with core duo processors.
7/10/06: Fixed problem in post-processing panel with blank entries in X/Y region to use for scaling.
7/5/06: Fixed problem with buttons not working on tomogram position panel after pressing done without doing final alignment.
6/30/06: Fixed a bug where exiting eTomo caused errors in the Combine dialog.
6/30/06: eTomo: improved performance by storing environment variables rather then retrieving them each time.
6/28/06: Fixed a bug in eTomo where action listeners where not being removed from the tracking button, making it try to perform its action multiple time when pressed.
6/27/06: Fixed eTomo bug in running alignlog for single axis tomogram.
6/26/06: Etomo no longer uses imodsendevent to communicate with 3dmod.
6/16/06: Added open/close and advanced/basic mini-buttons to the fiducial model dialog.
6/15/06: If a script is being run by eTomo, a warning message that it will probably not finish will pop up when the user exits
6/9/06: In Tomogram Positioning, eTomo now warns the user if they press the "Done" button when the final Alignment has not been done or is out of date.
6/9/06: In Tomogram Combination, eTomo now turns off the Combine button when the scripts don't exist or are not up to date.
6/8/06: Added an attribute to cpu.adoc: "separate-chunks". When "separate-chunks" is present in cpu.adoc and not set to "0", splittilt will be run with a "-c" option. The "separate-chunks" attribute is a global attribute - it is only valid when it is placed before the sections.
6/7/06: eTomo now keeps data from processes in its data file when it exits. eTomo will not allow a new process to be run when a process started by eTomo is still running on the same axis.
5/23/06: eTomo now warns the user if they try to overwrite a modified seed file or fiducial file with the "Track Fiducial Seed Model" or "Use Fiducial Model As Seed" buttons.
5/19/06: Fixed bugs in new handling of tomogram positioning information and restructured code controlling the positioning dialog.
5/1/06: Big additions to testing functionality in eTomo; a full test can now be scripted.
3/30/06: Automatically checking Seed mode and Autocenter in 3dmod Bead Fixer as needed when opening the .preali file.
3/30/06: Added individual advanced/basic buttons to Coarse Alignment.
3/24/06: Fixed progress monitor for mtffilter with files > 2 GB.
3/23/06: In Setup Tomogram, improved the popup message when the dual axis image stack does not end in a.st.
3/22/06: In Tomogram Generation, backing up the fully aligned stack when "Use Filtered Stack" is pressed. Also backing up the tomogram when "Use Current Trial Tomogram" is pressed.
3/21/06: In the Join Align tab, moved the chunk display so the chunk number matched the row number.
3/15/06: Fixed a problem in Etomo - Combine Tomogram where the wrong .rec file was opened when opening patch region model.
3/15/06: Fixed a problem in Etomo - Combine Tomogram where the wrong .rec file was used for error checking.
3/15/06: Fixed a problem in Etomo - Combine Tomogram where the X and Y values could become out of synchronization with the match direction.
3/15/06: Fixed a problem in Etomo - Setup Tomogram where a failure of copytomocoms did not cause a useful error message to pop up.
2/6/06: In Etomo, running a process will cause two-state buttons associated with later processes to show their "not yet run" state.
1/27/06: Improved the error checking in the Etomo Join panel.
1/26/06: Keeping two-state buttons on when they are pressed to show that a process has been run. Saving the state of two-state buttons in the .edf file.
12/22/05: Added help message to Etomo.
Changes in Bead Fixer
* 7/2/06: Bead fixer enhanced by setting up 3 operating modes that each
display just the relevant controls; by adding a color overlay display to
seed-making mode to provide a visual cue to whether a point is on the top or
bottom surface; by making gap finding start from the last point examined even
if the current point changes, and providing the ability to go back to a
previous gap.
* 2/12/06: In Beadfixer, added autocentering and a seed mode in which a new contour is started automatically for each point.
10/18/06: Fixed beadfixer to remember "Automatic new contour" between sessions.
8/24/06: Stopped bead fixer from generating error when told to reopen a log file before one is opened.
7/17/06: Stopped Bead fixer from recentering added or moved points in Zap window, made up and down arrows in gap mode non-optional, made sure hot keys only worked in the appropriate mode.
7/3/06: Fixed running of Tiltalign from Bead Fixer on Windows (also broken by new communication scheme) and switched to using Qt process instead of thread to run it (no more flashing DOS window).
6/7/06: eTomo is now turning off auto-centering when fix fiducials is first run, and not managing it after that.
3/1/06: In Bead Fixer, made "Move All in Local Area" stop displaying images and listing residuals, and fixed limits on performance with huge numbers of residuals here and in the undo module.
Changes in 3dmod and Meshing
** 9/12/06: 3dmod can now mesh objects through a new panel in the Model View
Object Edit window. Meshing parameters are stored in the object both by 3dmod
and by Imodmesh. Imodmesh has new options to use or override the stored
parameters.
** 9/12/06: Contours at any orientation can now be meshed, provided that all the contours in a surface are at the same orientation and are properly spaced apart. Modeling in the Slicer has been enhanced to provide contours that satisfy these requirement: modeled points will now come out exactly in a plane; there is a new hot key to return to the orientation of an existing contour; when the lock button is on, continuous drawing with the mouse is possible and PageUp and PageDown step by one pixel perpendicular to the slice.
* 10/6/06: Made slicer multi-threaded to take advantage of multiple processors. The default is to use 4 threads but this can be overriden by setting the environment variable IMOD_PROCESSORS to the number of processors.
* 10/5/06: Set up a second non-TIFF snapshot format, so that both PNG and JPEG snapshots can be made without switching the primary format. Three formats are now available in image and model movie control dialogs, and Ctrl-Shift-S can be used ot snapshot with the second non-TIFF format from any window.
* 9/18/06: Added continuous display of mouse position and value in pixel view window from Zap, XYZ, and Slicer windows, as well as option to close the grid of values.
* 9/3/06: 3dmod can now read files in EM format, DigitalMicrograph 3 format, and Hanspeter Winkler's FFF format.
* 9/1/06: The model view window now allows visualization of multiple selected contours, the selection of multiple contours with Ctrl-third button, the selection of all visible contours with Ctrl-A, and deletion of multiple selected contours with D.
* 9/1/06: Added ability to control multiple clipping planes together.
* 9/1/06: Models can now contain general stored values that 3dmod can display as a modulation of intensity or in false color. The mesh view panel in the model view object edit window was changed to control of this display and to allow items above or below the contrast threshold to be turned off.
* 8/27/06: 3dmod can now display 8-bit color tiff files with embedded color maps. Multiple files and multipage files can be read. Tif2mrc can also convert these to 24-bit color MRC files.
* 8/27/06: Allowed custom false color maps to be read into 3dmod and imodcurvature.
* 8/24/06: Enhanced 3dmod graph window to average multiple lines of pixels, show mean value, graph subsets of data selected by the Zap rubber band, and to have a help page.
* 6/24/06: Added button to 3dmod image processing window to report the frequency of a position in an FFT.
* 6/9/06: Added option in Edit-Object dialog to display spheres only on the central section in the Zap and XYZ windows.
* 5/8/06: In fine grain dialog, added ability to set contour connection numbers to force or prevent mesh connections between contours on adjacent sections. In Imodmesh, implemented use of these connection numbers and fixed the forcing option to connect nearest pairs of contours.
* 1/14/06: Made 3dmod initialize a model with pixel size and Z scale from image file. Added an ability to set an incremental Z-scale when the image header contains a difference between pixel sizes in Z and X/Y.
11/22/06: For model view movie-making, fixed behavior of file type buttons when montaging and added check for perspective.
11/2/06: Fixed problem of gaps and missing contours when contours with color changes are displayed in model view.
10/11/06: T now turns off current and endpoint symbols in slicer too.
10/11/06: Fixed crash from closing Xyz window with Esc if pixel view open.
10/4/06: Fixed problem with zap window having wrong size to fit toolbar.
9/21/06: Fixed problem with reading FFF files with one section, made 3dmod go right to checking for raw files if any of the raw specifications are entered, and fixed setting mode with a MRC-like file so pixel view displays correctly.
9/18/06: Stopped time movie when 1, 2, or time arrow in zap toolbar is pushed.
9/1/06: Added 3dmod menu option to flatten all contours in an object, i.e. make their points have a single integer Z value.
7/17/06: Made reading and writing JPEG's in 3dmod available on the Mac.
7/13/06: Made the default image format for non-TIFF snapshots be jpeg, except on SGI.
7/3/06: Fixed problem in Windows of 3dmod started from eTomo not really dying when killed by user, due to new communication scheme.
6/18/06: Added ability to use standard input instead of clipboard for messaging to 3dmod.
6/9/06: Fixed problems with missing triangles in multicolored meshes seen on some NVidia cards on Mac and Linux.
5/10/06: Fixed model view movie maker which was taking first two pictures at same X/Y/Z image location.
4/20/06: Fixed display of ghost contours when there are tiny differences in Z values of points in a contour.
4/1/06: Added continuous output of window or rubberband size to Zap toolbar.
2/27/06: Added a button to the Fine Grain dialog to go to the next point, contour, or surface with a change.
Changes in General Processing Programs or Infrastructure
* 10/14/06: Added option to Imodcurvature to rotate arbitrarily oriented
contours into a Z plane and to fit circles to them.
* 10/6/06: Startup files now source site-specific startup files IMOD.sh and IMOD.csh if they exist in $IMOD_CALIB_DIR.
* 10/5/06: Added xf2rotmagstr for converting a transform file to rotations, magnifications, and stretches.
* 10/4/06: Implemented a structure for using Python within IMOD. This consists of: a module for running programs and getting MRC header information conveniently; an extension module for the PIP parameter parsing interface; and a program, vmstopy, that converts the IMOD command file format (and some of the C-shell constructs found in them) to a Python script.
* 10/1/06: Added .cmd wrappers for scripts in Windows so that they can be run from a DOS window as long as IMOD and Cygwin are on the path.
* 10/1/06: Added a capability for brief header output from Fortran programs when they read MRC headers; it is activated by setting an environment variable IMOD_BRIEF_HEADER. This is now used in volcombine.com.
* 10/1/06: Fixed large-file seeking routine to handle files with X/Y planes bigger than 2 Gpixels, and fixed Fortran and C I/O routines to work with such images as far as possible. Newstack works with such large images, 3dmod appears to work as well. Other programs may need to be fixed when needed since the assumption that the expression nx * ny will give a valid product is ubiquitous.
* 9/1/06: Imodcurvature can store curvature values directly; Imodmesh can encode stored values in the mesh for dynamic color display of curvature.
* 7/8/06: Added ability to stretch around two fixed points in Midas, which should make it easier to correct stretches.
* 6/26/06: Added autocontrast function to Midas.
* 6/13/06: Added imodcurvature to measure radius of curvature and encode in model as color changes or point sizes.
* 2/26/06: Fixed Blendmont to work when pieces are displaced more than one frame width from their nominal positions, and switched matrix inversion to double precision to make it work better for large numbers of pieces.
11/10/06: Added attempt to deal with SELinux in install script.
11/4/06: Fixed treatment of ends of open contours in Imodcurvature.
11/4/06: Add time values to tube meshes so multiple times don't all show up at once.
11/2/06: Fixed a problem with numeric precision of circle fits in Imodcurvature.
10/31/06: Made Imodmesh propagate properties like gaps to created connector points made when meshing complex geometry.
10/30/06: Fixed Resamplemod rotation when mean vector has a negative Z component.
10/30/06: Fixed Mtk moving surface contours to a new object for last or only meshed object.
10/24/06: Added an option to xftoxg to make one section be the reference that others are aligned to.
10/20/06: Fixed install script so its new offer to remove previous versions does not include the current version.
10/17/06: Added Findhotpixels so it will be easier to use for people setting up SerialEM.
10/17/06: Added a module for reading and writing autodoc-type files and providing data from key-value pairs to C or Fortran programs.
10/11/06: Changed routine for finding mean normal to a contour, so slicer will be more robust with open, almost straight contours.
10/9/06: Took ERROR: out of Imodkillgroup's message when it can't find process.
10/5/06: Set the model max values to the new size if -n is used in imodtrans.
10/1/06: Alterheader now reads data in chunks for mmm and rms commands so it will work with any size data.
9/18/06: Stopped imodmesh from rotating or flattening contours to be meshed as tubes.
8/17/06: Added LC_LOCALE C setting to scripts doing arithmetic with awk to prevent comma instead of period in floating point output.
8/15/06: Changed trimvol to treat -sx and -sy arguments as 3dmod coordinates.
8/4/06: Made clip stat a bit more efficient for mode 1 files and output location of minimum.
7/14/06: Fixed mtk to transfer the power of a graph to the mean and SD graphs from random shifting.
7/11/06: Changed binvol to write in chunks so it will work with any size data.
7/8/06: Increased array limits for extra header in Edmont, Newstack, Extractpieces, Extracttilts.
6/19/06: Added ability for Tilt to make reprojections at multiple nonzero angles.
6/19/06: Fixed polarity of projections from Xyzproj so that it will match input to Tilt, fixed a half-pixel shift, and converted to PIP.
6/19/06: mrc2tif will now write unsigned integer files.
6/19/06: Fixed a scaling problem in newstack when input was floating point.
6/18/06: Fixed programs using new version of amoeba search routine, broken at least in 64-bit Linux.
6/8/06: Made Xfsimplex read in data binned so there are no limitations on input data size as long as data are binned to < 2Kx4K; changed it so that the reduction parameter specifies binning rather than successive reductions by 2. Changed Xfalign, Transferfid, Matchrotpairs, Setupcoms and Setuplong to accommodate this.
5/16/06: Prevented xyzproj from amplifying data near edges of tilted block.
5/13/06: Added option to Midas to set colors used in overlay display.
5/13/06: Added option to Newstack to set fill value for areas without image data.
5/13/06: Normalized difference measure output by Xfsimplex, added an option to Xfalign to output the difference measure, and adjusted scaling of difference measure in Transferfid and Matchrotpairs.
5/12/06: Fixed Mtk's reassignment of contours with close approaches to new objects when contour to mesh measurements are being done, and allowed contours associated with the meshes to be reassigned also.
5/1/06: Increased allowed number of bins in nda, mtk, and sda to 1000.
5/1/06: Fixed function passing mesh to Mtk so it will shift coordinates correctly when model loaded on a subset of the image.
3/27/06: Fixed problem in cubic interpolation routine that showed up when running Tiltxcorr with a rotation angle of exactly 90 degrees.
3/23/06: Fixed bug in Avgstack that averaged all sections when 0,0 was entered, which was making auto alignment of first section boundary in a join fail when there was only one sample slice from the first section.
3/7/06: Changed Finddistort's model for finding stretch from rotated images.
2/27/06: Finddistort and Matchrotpairs, used to find image distortion fields, now have man pages.
2/9/06: Added hyperlinks to the html versions of the man pages.
1/23/06: Added Idfprocess for doing simple operations on image distortion fields.
1/21/06: Made new version of image distortion field file that can hold more than one field, and made Newstack able to apply a different field to each section.
12/20/05: Changed reading of piece coordinates from header to treat X and Y as unsigned instead of signed integers.