** 5/3/04: Enhanced image display in model view window by adding ability to display X and Y slices as well as Z slices, and ability to show multiple slices with transparency to see a projection through them. Also added the X, Y, and Z coordinates to the movie maker so that movies can be made of a changing image display.
** 1/9/04: Added ability for 3dmod to bin images. Made the cache fill completely upon startup when the user does not limit the size with a -C entry. Implemented flipping of cache data by using the existing data load if the data are completely loaded. Relieved restrictions on flipping data: RGB data from an MRC file can be flipped, and any data can be flipped without reloading if it is completely loaded into cache or otherwise, including data from TIFF files, multiple single-image files, montaged data, and data with non-isotropic binning. Also fixed problems with image reload with complex data.
** 12/29/03: When 3dmod is started with multiple single-image files, it will now display them as sections in Z instead of in time by default.
** 12/28/03: Taking a montage in the model view movie maker will now save a single large image.
* 7/11/04: Fixed failure to start new contour on a different section after autocontouring. Fixed problems with autocontouring not setting surface number or contour time correctly and line tracker not setting contour time when copying. Made all situations that start a new contour when there is no current contour use the last contour in the object if it is empty.
* 7/11/04: Made ghost mode use same line thickness as object lines and added options for ghost contours to be lighter instead of darker colors, and for ghosts to appear for all objects.
* 6/24/04: Rewrote bead fixer to store all residual data when reading the input file, changed it to go from one local area to the next area without the user pushing buttons, to go to the first residual in an area when next area is pushed, to back up more predictably, and to allow all points seen when backing up to be seen again when going forward. Changed double-quote hot key from Go to Next Area to Back Up.
* 6/22/04: Added ability for bead fixer and line tracker windows to save and restore their positions, and for line tracker settings to be saved.
* 6/14/04: Added options to vary image display thickness and transparency in model view movie maker. Also increased limit on number of image slices to 256.
* 6/8/04: In the model view window of 3dmod, restored hardware stereo for SGIs and set up the top/bottom stereo mode so that it would work with external devices that cause the monitor to do two overlapping scans of the top and bottom of the display.
* 5/16/04: Computed factors correctly for displaying multiple slices in the model view window, which improves the display. Added ability to limit size of image that is displayed; fixed problems with stereo display of images and changed drawing order so images will work as well as possible with transparent model objects; fixed problem with depth cueing an image display with no model.
* 5/4/04: Added rubberband toolbutton to Zap window and a message by which eTomo can get the coordinates of a rubberband.
* 4/30/04: Added button to keep Bead Fixer window on top, and added ability to run tiltalign from Bead Fixer window.
* 4/28/04: Model view window can now show the current contour as a thicker line, and the current contour can be deleted with D from model view if it was picked with the third mouse button. Patch2imod sets the flag to highlight the current contour, so patch vectors can now be edited conveniently from model view.
* 12/18/03: Implemented ability to movie in Slicer window, ability to take movie snapshots automatically just as with Zap window, and an option to start a movie snapshot at the current position in Slicer or Zap windows.
7/22/04: Fixed problem with contours no longer being considered coplanar after adding a point.
7/13/04: Fixed an ancient bug in pixel view when a subset is loaded flipped.
7/10/04: Fixed bug in autocontrasting subarea when zoomed image was panned enough for non-image to show in window on right or top.
7/9/04: Fixed bead fixer to run Tiltalign when current directory has spaces in the path.
6/20/04: Fixed fatal problem in beadfixer from 6/11/04 change.
6/15/04: Fixed problem with hot keys moving the current point beyond the range of the data in a locked slicer window.
6/11/04: Made beadfixer read in whole log file at once and close file to avoid problems under Windows.
6/9/04: Moved the Z clipping planes in model view far out when the sliders are at 0 and 1000, to prevent clipping of highly zoomed models.
6/4/04: Implemented ability to pass more than one action in a message to 3dmod.
6/4/04: Fixed 3dmod on SGI so line tracker did not crash it. Also fixed a bug that was crashing it on Fedora Core 1.
5/31/04: Changes to 3dmod: Added filename filters to 3dmod startup dialog. Converted plugin loading to use Qt library class, which makes plugins work on Windows. Implemented functions for writing to standard error in 3dmod so that it could flush output under Windows, needed to make rubberband report work. Restored Run Tiltalign button to bead fixer. Added a message to set the basic properties of an object, so that tomopitch.mod can be switched to open contours. Made Zap window start a new contour when the current time does not match the time of the existing contour, even for open contours, so that regular 3-sample modeling can be done with open contours.
5/19/04: Changed to new Qt calls on the Mac to get the 3dmod preferences file back to being user-specific instead of global.
5/11/04: Fixed problem caused by removing the Run Tiltalign button.
5/7/04: Fixed a bug from adding the rubberband toolbutton that made it crash on multiple files. Removed Run Tiltalign button from bead fixer until eTomo properly updates the parsing of the log file.
4/27/04: Made 3dmod not consider a model modified if view 1 is rotated.
3/30/04: Made initial size-setting of model view windows work the same as for Zap window, so now it works in Windows.
3/25/04: Fixed problem causing crashes when opening 3dmod with no image, possibly caused by reorganizations on 1/9/04.
3/21/04: Fixed button connections in color selector (broke 1/22/04).
3/12/04: Fixed problem in tumbler window with Z size changes coming from Y value instead.
3/9/04: Fixed problem in Zap window with a panned image not holding its offset position when redisplayed at some zooms.
1/22/04: Added button to image process window so that one could toggle between original and processed image, and made intensity floating work with processing.
1/20/04: Stopped trying to free a static array when loading data.
1/9/04: Simplified startup and image loading code in 3dmod, consolidated mrc section loading routines into one routine, reorganized the multi-section byte-loading routines to reduce duplicate code, and rationalized the scaling of complex data. Made a test suite for 3dmod data loading.
12/30/03: Fixed a problem with pixelview with multiple single-image files.
** 6/17/04: eTomo now accommodates the new solvematch.com, converts from old version of the solvematch files, and presents a new option to do the initial match with matching models only.
** 6/4/04: eTomo has a new processing pathway for building a tomogram from the cross-correlation alignment, an interface for 2D filtering (including inverse MTF filtering) of the aligned stack, and an option to build a whole binned-down tomogram for positioning.
* 3/15/04: Many eTomo changes including change to using command line input to Copytomocoms, ability to specify a distortion field and apply it when generating prealigned and aligned stack, an option for binning the prealigned stack, entries for new options to Tiltxcorr for using subareas and doing cumulative correlations, a button for rerunning Beadtrack with the fiducial model as a seed. Also fixed problem with two matchorwarp command lines being issued to matchorwarp.com when using a temporary directory.
8/3/04: eTomo now makes a .rawtlt file from starting and increment tilt angles when making a tomogram with fiducialless alignment.
8/2/04: Fixed problem with eTomo not swapping corresponding point lists when matching A to B.
7/20/04: More changes in eTomo process-killing, including using the right ps command to work on Mac, Windows, and Linux regardless of how eTomo is started.
7/14/04: eTomo process killing improved to handle the multi-layered processes in combining and fixed to work on Windows again.
7/7/04: eTomo no longer removes ...log~ or patch.out~ unless there is an existing ...log or patch.out that needs to be renamed to the ~ file.
7/2/04: eTomo changes: Fixed patchcorr process monitor from locking old patch.out in Windows. Moved basic 2D filtering to basic mode in tomogram generation page. Fixed two bugs in dealing with .xf files from old data sets. Fixed problems with handling of tilt axis Z shift parameter with binned prealigned stacks and issued appropriate directions when user switches the binning of the prealigned stack after making a fiducial model.
6/25/04: Solvematch problems and other combine parameter synchronization problems solved in eTomo.
6/4/04: When align.com is run outside of eTomo, eTomo will now show the updated log file.
** 6/9/04: Changed Solvematch to work with the absolute fiducial coordinates now being produced by Tiltalign; this plus associated changes in Tiltalign, Matchshifts, and Setupcombine eliminate the need for correlation or matching models to be used with fiducial coordinates, and allow the initial match operation to be done with a single command file, solvematch.com.
** 12/24/03: Implemented a better way to solve for 3D transformations when there are insufficient data in one dimension, and used this for Solvematch's solution when there are fiducials on only one surface, and for Refinematch and Findwarp when there is only one layer of patches.
* 7/3/04: Fixed Tiltxcorr to keep tilt axis in global center of aligned images rather than letting it start at center of zero-degree image and shift to the center of shifted images. This should improve tomograms generated using only the correlation alignment.
* 5/4/05: Made Tiltalign put out 3D coordinates adjusted back to image coordinates in the fid.xyz file and the .3dmod model. This will allow elimination of the matchshifts procedure and/or the use of matching models with fiducials.
* 12/23/03: Changed Copytomocoms and eTomo to allow a dual axis data set to be started with only the first axis present.
8/9/04: Fixed fatal error in setupcombine; 7/22/04 change was done by copying incompatible version from 3.4.
8/2/04: Made Transferfid require that A and B prealigned stacks have the same pixel size to protect against them having different binnings.
7/16/04: Made Tiltalign put out pixel size in ...local.xf file and Tilt use this pixel size to scale local alignment information, which is needed for local alignments to work right with binning of aligned OR prealigned stacks.
7/16/04: Fixed a bug in Tilt in which an EXCLUDELIST line would turn on the LOG processing with 0 base.
7/12/04: Fixed copytomocoms problem with starting and increment tilt angles.
7/9/04: Fixed Finishjoin to not rely on /usr/tmp as temporary directory.
7/8/04: Added workaround to Cygwin tcsh 6.13 bug to transferfid, finishjoin, matchrotpairs, and matchshifts.
6/22/04: Fixed computation of output file mean density by Matchvol, Rotatevol, and Warpvol.
6/20/04: Setupcombine will reduce patch thickness to keep it within Z limits.
6/17/04: Made Tiltalign reset the Z-scale and rotation angles of the 3D fiducial model in case user rotated and stretched the actual fiducial model.
6/16/04: Put some error checks into Corrsearch3d to protect against bad entries and patch sizes too big for the limits to be analyzed.
6/14/04: Made tomopitch generate an error for contours with more than 2 points when the model is from a whole tomogram.
6/14/04: Added option to Ccderaser to specify width of annulus so that only one parameter needs to be changed when increasing maximum X-ray size.
6/14/04: Converted Tomopieces to PIP input and modified it to allow division of volume in Y dimension; also changed Assemblevol so that it could handle data from large numbers of files in X and Y.
6/11/04: Made Refinematch exit with error if insufficient data are available.
6/11/04: Added workaround to erroneous header entries produced by FEI tomography software so that tilt angles can still be extracted properly.
6/11/04: Copytomocoms now looks at the min and max density of the raw image file and if the max is negative and the min < -10000, it sets the offset for taking logarithms in Tilt to 32768.
6/3/04: Fixed problem with imodsendevent putting spaces after filenames. Improved problem with 3dmod crashing when it receives message to load seed model.
5/7/04: Fixed a problem with shifting Z introduced in Tiltalign on 5/4.
4/25/04: Fixed setupcombine to work when there is no XAXISTILT entry in tilt[ab].com and assume 0 tilt.
4/19/04: Added newlines before ERROR: outputs from Fortran MRC file I/O routines and made eTomo strip everything before ERROR: when reporting an error.
4/18/04: Modified imodsendevent to work with Qt versions 3.2 and above under Linux.
4/1/04: Fixed uninitialized variable in new version of Extracttilts that made it fail on Windows, possibly on Mac.
3/31/04: Reduced the artifacts that Tilt produces when taking logs of numbers that would be negative after adding the log offset.
3/30/04: Added Mtffilter to do filtering by the inverse of an MTF and/or general low-pass filtering to the package and made Copytomocoms generate command files for running it between Newstack and Tilt.
3/21/04: Added magnification gradient correction to Newstack and Xfmodel. Added a program, Extractmagrad, to extract intensity information from the image file header and compose the file of mag gradients needed by the other programs.
3/17/04: Changed Extracttilts and associated routines to work with headers containing intensity values. Converted Extracttilts to PIP input and added options to extract stage position, magnification, or intensity.
1/26/04: Converted Copytomocoms to accept command line argument input and added option to insert distortion correction in newstack commands.
1/13/04: Fixed problems with copytomocoms and setupcombine under csh on SGI.
12/30/03: Sampling was broken with the new Newstack, so changed it to treat center offsets the old way, after transformations, with a new option to apply offsets before transformations.
* 6/27/04: Added a script, Processchunks, to run jobs in parallel on multiple processors or machines.
* 6/19/04: Mtffilter can now filter a 3D FFT, allowing inverse filtering and general low-pass 3D filtering to be applied to tomograms.
* 6/17/04: Added a script, Chunksetup, to create command files for processing a large volume in chunks and reassembling the chunks.
* 6/17/04: Fixed Smoothsurf to work with models built on image files with pixel sizes in the header, fixed a bug in the contour smoothing part, prevented it from smoothing scattered point objects and non-planar open contours, converted to PIP input, provided default parameters, and revised man page to make it easier to see how to affect smoothing by varying parameters.
* 6/5/04: Added an option to raw2mrc to convert 32-bit integers to 16-bit integers, fixed a problem with dm2mrc and added options to dm2mrc to control the treatment of unsigned and 32-bit integer data, specifically so that data can be put into a signed 16-bit format if it fits there.
* 4/24/04: Made distribution files be self-installing runnable scripts, with installation to the default location and renaming of existing version (not documented yet).
* 1/17/04: Made Mac version work for files > 2 Gb by using the file I/O routines set up for solving the problem in Windows (the old way of doing it broke going from 10.2 to 10.3).
* 1/5/04: Added option for linear interpolation to squeezevol and made it adjust pixel size in the output file.
* 1/13/04: Added splitrgb and joinrgb options to Clip so that color files could be disassembled into gray-scale components that can be operated on separately and recombined.
* 12/27/03: Converted Xfmodel to PIP input and implemented ability to undistort a model built on distorted images.
* 12/24/03: Converted Newstack to PIP input and made it replicate the behavior of the Newst script. Added capabilities for binning and undistorting images, and retired Newst.
* 12/17/03: Added global rotation mode to Midas so that tilt series images can be rotated to make the tilt axis vertical.
* 12/12/03: Changed reducemont to preserve Z pixel size, added options to reduceby2 to preserve pixel size and to specify binning.
8/4/04: Fixed display bug in Midas on AMD64.
8/2/04: Made get_nxyz subroutine handle numeric filename properly.
7/22/04: Changed to better sed command for stripping Ctrl M in Cygwin; previous way broke several things with the sed version in Redhat AWS for AMD64.
7/8/04: Raw2mrc was not working in Windows, needed one more b3dFwrite.
7/7/04: Changed all exit(-1) to exit(3) because this was giving 0 exit status in Cygwin and failing to stop command file processing.
7/7/04: Fixed a bug processing arguments in subm (submfg).
7/6/04: Enhanced output from self-install script and made it work from or in directories with spaces in their path; switched from link to rename for OSX.
6/28/04: Added nohup to submfg, vmstocsh output, and all scripts to keep submitted jobs alive upon logout.
6/28/04: Added -n option to subm (submfg) to run jobs niced.
6/24/04: Added -c option to subm (submfg) to allow it to continue with multiple command files after one fails; used this in chunksetup.
6/20/04: Fixed one-pixel shift in mirror image side of FFT produced by clip.
6/14/04: Added a -t option to subm (submfg) to get the time for each command.
6/11/04: Fixed bug in Imodjoin that made it crash on models that had not been through 3dmod.
6/11/04: Improved error messages from PIP to include the option when there is a problem with the values entered for an option.
6/3/04: Made the Qt utility library be a DLL in Windows.
4/27/04: Fixed one-pixel edge effect when undistorting with Newstack.
4/27/04: Found that environment variables set in Cygwin startup scripts needed double backslashes for Windows format pathnames.
4/22/04: Made clip test for errors in MRC file I/O and exit properly; also fixed problems with header of output file showing extra bytes if the input file did.
4/21/04: Added bash startup routines for Mac and completed bash startup routines for SGI.
4/19/04: Fixed some uninitialized variables in Mtk and Nda and some misprints in Mtk that kept it from running under Windows.
4/9/04: Incorporated changes for building under Amd64 into Linux build scripts.
4/3/04: Added ability to pack QT library into Linux distribution since message passing to 3dmod won't work with Qt 3.2 or 3.3.
3/12/04: Added options to Blendmont to set the size parameters for finding the edge functions and made these parameters scale up for images above 1K.
2/27/04: Fixed problem in midas with transforms getting screwed up after moving the center point, created by changes on 12/17/03.
1/27/04: Made Midas redisplay properly when the box size changes.
1/26/04: Made distributions have only the startup files needed for the machine.
1/26/04: Converted Xftoxg to PIP input, retired Xf2xg, and fixed hybrid method in Xftoxg which never worked for eliminating trends in rotation or magnification.
1/26/04: Converted Xfproduct to PIP input and added option to scale translations when there is mismatch in scale between images at the two stages.
1/19/04: Added an option to Xfmodel to apply a single line of the transform file to the whole model, made this behavior the default when there is just one line of input, and fixed two problems with transforming and back-transforming when using PIP input.
1/13/04: Fixed problem with Xfmodel and Newstack deciding that they needed to know binning when undistorting images.
1/13/04: Fixed problem with imodpsview when printing.
1/13/04: Changed default scaling in tilt.com from 1000 to 500 to avoid saturation in extreme cases.
1/6/04: Made raw2mrc and tif2mrc preserve an existing output file by making it a backup file.
12/30/03: Made most libraries be DLLs under Windows.
12/24/03: Converted subimage to PIP input and made it default to subtracting all pairs of sections in two volumes.