Changes for IMOD 4.1.3

Changes marked with ** are particularly noteworthy, ones marked with * may also be of interest to typical users.

Changes in Tomogram Processing

** 2/21/10: Tilt modified to do multiple iterations of SIRT internally when possible (fixed X-axis tilt, no Z-factors or local alignments), using GPU if possible, and to do reprojections with local alignments on the GPU.

** 1/1/10: Tilt can now use use the GPU in a CUDA-capable NVIDIA card for all forms of backprojection and for reprojection from a reconstruction file not involving local alignments. It also allocates memory as needed for the particular reconstruction. To simplify the code, options for fast backprojection, replications, and negative slice increments were eliminated.

** 10/2/09: In Tiltxcorr, added the ability to track the centers of multiple patches specified as a regular array or by a model, and output a model that can be used for fiducial alignment; added anility to use boundary contours to constain the region correlated for alignment or the selection of patches tracked; added an option to iterate the correlation to increase the subpixel accuracy of the result; fixed the transform output when leaving the tilt axis at the center of a subarea; added an option to limit the range of shifts in the peak search.

** 8/10/09: Many changes to Ctfplotter: Eliminated two sources of inconsistency between Ctfplotter and Ctfphaseflip in the relation between defocus and frequency; implemented nearly exact shifting of spectra from off-center tiles instead of shifting by integer amounts; made the shifting variable so as to align both first and second zeros between off-center and central tiles; started caching power spectra for individual tiles so that after they are computed once it is quick to recompute a summed spectrum; added fitting to a CTF-like curve and to a polynomial and made the CTF-like fitting the default; reorganized the angle range dialog to put the important options at the top; revised the guide and added snapshots from various stages of working on an example set. Also added an option to both programs to invert the sign of the tilt angles, in case the set of angles gives reconstructions with inverted handedness.

* 3/14/10: Changes to Ctfplotter: it now shows a table of results that will be saved to file and that can be read in from a previous session. Tool buttons were rearranged to make them easier to understand, tooltips added to dialogs, angular range limited to actual range of tilt series.

* 2/28/10: Fixed an initialization problem in beadtrack (present since 3.12.5) that throws off tracking in some cases.

* 2/26/10: Made Tilt do subtractions for both reconstruction and reprojection in SIRT that cannot be done internally, and to put out statistics that are gathered in the finish log of a SIRT run.

* 2/21/10: Rewrote Sirtsetup in Python to use internal SIRT in Tilt where possible, to leave and convert reconstructions at specified iteration numbers, and to not split the command file up when going to only one processor.

* 2/5/10: Fixed problem with Ccderaser removing way too many points in data with low counts starting at -32768 (i.e., from FEI software).

* 12/10/09: Tomostitch has new options to allow stitching to be done with binned volumes then repeated with unbinned volumes; it adjusts parameters as appropriate. It also automatically updates a warping patch file from a model that has been edited.

* 11/21/09: Tiltalign now reports the mean residual for each contour (fiducial) in the table of 3D positions.

* 9/8/09: Added Fitpatches to do linear and local fitting on patch vectors in supermontage overlap zones and manage patch files and vector models when edited.

* 9/7/09: Made Stitchalign able to eliminate vectors if they are not present in all the versions of a patch file managed by Fitpatches, and if they are outliers or had high residuals in fits in Findwarp.

* 9/2/09: Fixed residual outputs into patch files from Refinematch and Findwarp; residuals were being assigned to the wrong vectors.

* 3/17/09: Added option to Tiltxcorr to enter an angle offset, which can sharpen correlations at high tilt when the specimen is tilted at 0 degrees.

5/26/10: Fixed alignlog -a output to exclude local area results.

5/24/10: Made cleanup before and after parallel Tilt much more restrictive to avoid deleting data sets named tilt-n.

5/24/10: In Tilt, fixed centering of vertical slices with large Y offset/ X axis tilt, fixed handling of fill value for output in internal SIRT.

4/27/10: Stopped Ctfplotter message about inconsistencies when there is no existing defocus file.

4/7/10: Fixed problem with edgepatches calling corrsearch3d with mins/maxes numbered from 0.

4/2/10: Fixed initialization problem in Ctfphaseflip's detection of bad view numbers and fixed the warning when a simple one-line file is used.

4/1/10: Fixed bug in Ctfplotter that was putting out views numbered from 0 and made Ctfplotter and Ctfphaseflip detect erroreous view numbers in a defocus file and adjust them up by 1.

3/30/10: Fixed backup directory entry to Copytomocoms to preserve spaces.

3/18/10: Fixed Sirtsetup conversion of first srec file being left.

3/8/10: Changed Ctfplotter so that noise config file can have relative paths.

3/8/10: Added option to inform Findbeads3d of binning.

3/8/10: Fixed Ctfphaseflip to accept any size of input in Y.

2/1/10: Fixed allocation of local alignment arrays in Tilt when reprojecting. Made it print angles on setup run for parallel processing. Set link parameters to get GPU working on Mac.

1/21/10: Fixed two bugs in Tiltxcorr patch correlations and allowed the patch number to be set by a fractional overlap.

12/29/09: Fixed Makejoincom to avoid problem with entry output from rotatevol.

11/25/09: Transferfid now allows pixel sizes of two axes to differ by 2.5%.

11/2/09: Fixed bug in Edgepatches when it had to reduce patch thickness.

10/27/09: Fixed setupcombine to clean up files with find due to a change in tcsh in RHEL5.

10/15/09: In Tilt, fixed reprojection from model when there is a single X axis tilt and untilted slices are computed. Points at high tilt were miscentered. also fixed incremental mode when untilted slices are being computed.

10/9/09: Fixed some problems with solving for thinning in Tiltalign.

10/7/09: Fixed mean value used for masking in Tiltxcorr and added output of raw peak strength.

9/14/09: Made Stitchalign vary metro factor when search fails.

9/2/09: Added ability for Refinematch to put out the residual vectors as reduced patches, and for Findwarp to put out the fraction of fits in which each patch is an outlier. Patch2imod will store the outlier fraction in the model and Imod2patch will output it to a new patch file.

8/14/09: Fixed power option in densnorm.

8/4/09: Fixes for SIRT: fixed Splittilt to use a different boundary info file for reprojection; fixed Sirtsetup to pass the boundary parameter properly and to detect last reconstruction correctly; fixed parallel writing in the reprojection.

6/25/09: Changed Tilt to allocate its memory and added a temporary option to specify the memory size.

2/24/09: Colors changed so grid appears when printing from Ctfplotter.

Changes in eTomo

** 3/8/10: In Etomo added an interface for creating fiducials using tiltxcorr to track patches.

** 8/31/09: New interface added to eTomo for erasing all gold by finding it in a tomogram and reprojecting.

** 6/8/09: In Etomo added an interface for flattening to Post Processing. It runs flattenwarp and warpvol.

** 5/4/09: In Etomo added a simple interface to RAPTOR.

** 2/7/09: Etomo has a new Project Log Window that records some output from program logs, can be typed into, and is saved automatically.

* 3/4/10: In Etomo - Generation Tomogram added the ability to remove the LOG parameter in Added separate fields for a linear SCALE parameter.

* 2/16/10: Added a separate frame for flattening volumes.

* 1/11/10: Added a way to set up GPU processing using the cpu.adoc or the Settings dialog. Added a checkbox for running tilt with the GPU to the Tomogram Generation dialog.

* 12/18/09: In Etomo added smoothing to Post Processing - Flatten.

* 12/11/09: In Etomo added buttons to run clip stats in Preprocessing.

* 10/23/09: In Etomo displaying a button panel instead of automatically starting a reconstruction.

* 3/24/09: In Etomo, added Angle Offset to Tiltxcorr.

* 3/16/09: Added transferfid messages to the Project log window. Added the contents of pop dialogs to the Project log window.

5/27/10: In Etomo added the parameter CriterionForOutliers to Flattenwarp.

5/27/10: In Etomo fixed a problem where the Use GPU check box and the Parallel Processing check box were on at the same time.

5/27/10: In Etomo - Flatten Volume added default values to the smoothing factors field in the Smoothing Assessment panel.

5/21/10: In eTomo adding ActionIfGPUFails to

5/21/10:In eTomo hiding Transfer Fiducials when RAPTOR is in use.

5/10/10: In eTomo removed call to imod2vatch.

4/9/10: In Etomo - fixed a null pointer exception in Setup Reconstruction.

4/8/10: In Etomo - fixed a MRC header reading problem.

4/8/10: In Etomo - Final Aligned Stack fixed the Align and Build Tomogram, which didn't always reflect the process result.

4/7/10: In Etomo fixed problem where a montaged final aligned stack generated for findbead3d did not take the Size to output field into account.

3/30/10: Fixed etomo startup script for spaces in ETOMO_LOG_DIR.

3/29/10: In Etomo, added a checkbox for running tilt on the graphics card to Tomogram Positioning.

3/26/10: In Etomo, added a front panel button and some error checking for Volume Flattening.

3/26/10: In Etomo, put a checkbox for the default GPU setting into Setup Tomogram.

3/26/10: In Etomo - find beads 3D, made binning as large as possible without making the bead size too small.

3/26/10: In Etomo - Setup Tomogram fixed the montagesize call to prevent an incorrect warning.

3/26/10: In Etomo fixed the field that goes with some of the file choosers, which didn't work when it was updated directly.

3/18/10: In Etomo - bead erasing, added a Z shift for when fiducials where not sorted into two surfaces in fine alignment.

3/18/10: Fixed Etomo not enabling parallel processing from internal setting.

3/18/10: Finished fixing the preferences file (.etomo).

3/10/10: In Etomo - Fine Alignment opening the 3dmod Bead Fixer in Look at contours mode when Patch Tracking was used.

3/8/10: In Etomo fixed a backward compatibility problem with saving to/loading from the .etomo file.

3/5/10: In Etomo - Tomogram Positioning fix continuing a problem with being updated when a sample tomogram is created with Fiducialess turned on.

2/18/10: In Etomo - Preprocessing, fixed the min/max buttons.

2/18/10: In Etomo - Tomogram Positioning, stop saving to when positioning was done with Fiducialess checked.

2/17/10: In Etomo, when running processchunks, attempting to avoid popping up the processchunk crash warning on a tcsh error which did not cause a crash.

2/4/10: Allowed Etomo to reconnect to process where the computer system time had changed by up to one minute.

1/21/10: In Etomo added overlap while running nonlinear anisotropic diffusion.

1/14/10: Fixed a bug in Etomo which happened when the ImodCalib directory did not exist.

1/13/10: Fixed bug in Etomo where it was loading a non-dataset file. Made some minor changes to the PEET interface.

1/12/10: Fixed bug in Post Processing dialog where the button responded multiple times to being pressed.

12/29/09: Standardized new dataset buttons and menu items.

10/28/09: In Etomo closing default button panel with an interface is opened in all cases.

10/27/09: In Etomo created a more stable version of the default button panel.

10/23/09: In Etomo fixed a bug where trimvol min and max parameters where null.

10/19/09: In Etomo, only displaying the parallel process panel when the current tab uses it.

10/19/09: In Etomo - CTF Correction, added the InvertTiltAngles parameters, which is used in ctfplotter and ctfphaseflip.

10/19/09: In Etomo - fine alignment, added the global ratio between knowns and unknowns to the project log.

10/16/09: In Etomo, saving the currently open tab in Post Processing.

10/12/09: In Etomo, removed embedded spaces from the Exclude Views parameters to prevent copytomocoms from failing.

10/12/09: In Etomo, fixed a bug which prevented the ctf com files from being created when the Final Stack dialog was opened.

10/7/09: In Etomo fixed bug that caused 3dmod to always close when Etomo closed.

10/6/09: In Etomo, sending selected output from flattenwarp to the project log.

10/5/09: In Etomo, fixed a bug in Post Processing where the X and Y trim values were unecessarily refreshed.

9/28/09: In Etomo, keeping the Project Log behind the main windows when the Project Log is refreshed from the one of the main windows.

9/28/09: In Etomo, no long turning off Automatic new contour in 3dmod. The checkbox is ignored in Fill gaps mode.

9/25/09: In Etomo making the scroll bars work properly.

9/24/09: In Etomo fixed the tiltxcorr progress monitor.

9/23/09: In Etomo fixed the Advanced/Basic button in the Setup dialog.

9/22/09: In Etomo corrected, which wasn't working with no local alignments or zfactors.

9/22/09: In Etomo preserving unrecognized parameters edited in by hand in and

9/22/09: In Etomo fixed monitors in Final Stack - Erase Gold.

9/20/09: In Etomo, fixed incorrect binning in the B axis in Tomogram Positioning.

9/17/09: In Etomo, fixed final aligned stack progress message.

9/16/09: Fixed the PEET tab, which was not being set properly when a new dataset was created.

9/4/09: In Anisotropic Diffusion correcting the handling of spaces in the iteration list.

9/2/09: In eTomo preventing Use... buttons from causing invalid stacks to be used.

6/10/09: Fixed a bug in Etomo which preventing it from logging the residual when fine alignment was run from a 3dmod which has been opened from either the Coarse Alignment or the Fiducial Model dialogs.

6/10/09: Made Etomo compatible with the IMOD_BRIEF_HEADER environment variable.

6/8/09: In Etomo improvements added to RAPTOR.

5/7/09: In Etomo attempting to prevent duplicate processes from being started on different computers.

4/20/09: In Etomo saving the selected computers and CPUs when Etomo exits during a parallel process.

4/15/09: In Etomo fixed processchunks process messages.

4/15/09: In Etomo logging reconnect attempts and major failures. Preventing the deletion of the aligned stack while a process is running.

4/14/09: In Etomo fixed processchunks resume with a queue; it wasn't getting updated number of CPUs.

4/1/09: In Etomo - Join using clip rotx instead of clip flipyz handle a flipped tomogram (still creating a .flip file). Rotx does not change handedness.

2/24/09: Fine alignment run in 3dmod will appear in the Etomo project log.

3/23/09: Etomo gets a message from 3dmod after Tiltalign is run and puts entry in the project log.

3/11/09: In Etomo improved error reporting when retrieving rubberband and slicer rotation values from 3dmod.

3/9/09: In Etomo - Fine Alignment, removed unnecessary error that was popping up after Compute Alignment was run.

3/9/09: In Etomo, added the -fg option to run Etomo in the foreground.

3/5/09: In Etomo - NAD, prevented the use of huge test volumes.

3/5/09: Etomo remembers position and size of log windows between sessions and starts up with it offset from the main window.

3/2/09: In Etomo preventing processes from running the attempt to reconnect to an existing process is finished.

2/26/09: In Etomo - Generic Parallel Process allowing comscript names with more digits.

2/19/09: In Etomo fixed unit testing utilities so that they work with earlier versions.

2/19/09: In Etomo - Fine Alignment, no longer placing local area residual errors in the Project Log Window in order to avoid overloading it with too much information.

2/18/09: In Etomo corrected tooltips that where being formatted twice.

2/12/09: In Etomo got rid of the exception that is added to the etomo log when header is used to read a file that doesn't exist.

2/12/09: In Etomo - Tomogram Generation saved the trial tomogram names in the combo box.

2/12/09: In Etomo - Setup Tomogram popping up an error message if Frame Type is incorrect.

2/10/09: In Etomo recalculated trimvol parameters when the size of the file being trimmed has been changed since last time trimvol was run. A warning message is displayed when this is done.

PEET Interface in eTomo

* 3/12/10: Added the PEET manual to the help menu.

* 12/7/09: In Etomo - PEET added a button for remaking averages.

* 12/1/09: In Etomo - PEET added move up and move down buttons.

* 10/29/09: In Etomo - PEET added buttons to move volume row up and down. And made the volume file chooser more flexible.

* 10/29/09: In Etomo - PEET removed the Duplicate an Existing Project button. Moved the functionality to the Import... button.

1/21/10: In Etomo - PEET fixed problem with the validation of searchRadius.

12/22/09: In Etomo - PEET corrected the tooltips.

12/8/09: In Etomo - PEET added flgAlignAverages.

12/1/09: In Etomo - PEET removed the Set cylinder orientation from reference particle checkbox. Enabling Cylinder Orientation when reference file is used.

12/1/09: In Etomo - PEET added more error checking to the Iteration table.

11/30/09: In Etomo - PEET fixing a bug where the Open Averaged Volumes in 3dmod button doesn't work when processchunks finishes when Etomo isn't running.

11/23/09: In Etomo blocking the PEET interface when PARTICLE_DIR is not set.

11/23/09: In Etomo - PEET supporting yaxisObjectNum and yaxisContourNum instead of yaxisContour.

11/20/09: In Etomo - PEET Added a button to make a copy of a row (excluding relative orientation).

11/20/09: In Etomo - PEET added flgRemoveDuplicates, duplicateShiftTolerance, and duplicateAngularTolerance.

11/4/09: Added a PEET manual to the PEET right-click pop up menu.

10/30/09: In Etomo - PEET changed the ccMode default to one.

10/26/09: In Etomo disabled non-working Save As functionality in PEET.

10/19/09: In Etomo - PEET, made the fix file paths panel more understandable.

10/16/09: In Etomo - PEET, added error checking for the volume table.

10/15/09: In Etomo, added more error checking to PEET.

9/28/09: In Etomo - PEET, removing edgeShift when it is empty.

4/27/09: In Etomo added a panel for changing the file paths when files are moved.

4/27/09: In Etomo fixed a problem where PEET was not displaying its data file at the bottom of the dialog.

4/20/09: In Etomo - PEET added more validation.

3/23/09: In Etomo - PEET added a useful error message when PARTICLE_DIR is not set.

2/26/09: In Etomo - PEET added an error check for szVol.

2/5/09: In Etomo added more error checking to the PEET interface.

Changes in 3dmod

** 9/4/09: Andrew Noske's Interpolator plugin added to 3dmod.

* 4/21/10: Fixed scale bar truncation or loss in montage snapshots, particularly with 1:1 zoom whole image shots.

* 3/31/10: Made text panel in Info window editable so it can be copied and pasted from on Windows and Mac, added File menu entry to save it to file.

* 3/31/10: Made File->Extract extract region of single section defined by window if no rubberband is on.

* 3/31/10: Allowed Apple-W to close all 3dmod windows and Apple-Q to quit on Mac.

* 3/30/10: Added 3dmod hot keys < > ( ) to duplicate actions of [ ] { } since the latter are often not available on European keyboards without modifiers.

* 3/29/10: Improved merging time when running isosurface with multiple threads; multipled threads are now enabled by default, with the number set to the number of processors on system (or value of IMOD_PROCESSORS), limited to 4.

* 3/10/10: Added a Look at contours mode to Bead Fixer so that one can step to contours with the highest mean residuals and examine them or delete them.

* 1/21/10: Made zap and model view montage snapshots with scale bar try to adjust position and size to keep bar within one panel of the montage.

* 11/21/09: The number of threads in Slicer will now equal the number of processors on the system, unless specified otherwise with IMOD_PROCESSORS.

* 9/8/09: Added hot key for toggling the clipping plane in model view.

* 3/25/09: Implemented new ghost mode that displays contours just from nearest section with contours for the particular object and made this the default.

* 3/9/09: In fine-grained dialog, added an option to see points with mesh connections as squares in the Zap window, ability to change multiple selected contours, and output of the general value for the current point or contour.

* 3/9/09: Added ability to define mesh connection numbers that block the mesh from going to the end of one contour when meshing between two open contours, or from filling a gap on one side when meshing between a contour with a gap or open end and one without (see fine grain dialog help).

* 3/9/09: Added hot key O for toggling between open and closed contours; added ability to toggle multiple selected contours with hot key or radio buttons, and made the ends of the current contour have triangles instead of circles for an open contour.

* 2/25/09: Added keypad / and * to page up/down in big steps, step size settable in Options.

* 2/24/09: Added Shift-PageUp and PageDown to move to next or previous Z with contours in the current object.

* 11/16/09: Added button and hot key to bead fixer for moving all points in all local areas by residual, and added ability to move all points by global residuals when there are no local alignments.

* 11/10/09: Added option to break contour at current model point, and a hot key for breaking a contour.

5/28/10: Stopped short labels from going on upper line in Info window.

4/19/10: Fixed crash when messages received by 3dmod during loading in Windows by keeping load status updates off of clipboard.

4/5/10: Fixed isosurface crash on system with more than 4 processors.

3/31/10: Eliminated Edit-Object-Info output with statement to use imodinfo.

3/31/10: Put model name on its own line in info window when it is too long.

3/31/10: Stopped model view objects window from closing while meshing.

3/30/10: Made 3dmodv raise window on Mac when started.

3/23/10: 3dmod will load plugins from locations defined by IMOD_DIR, or default install locations, if IMOD_PLUGIN_DIR is not defined.

3/19/10: Made Bead Fixer reread log when etomo sends message from View/Edit button, initialized max contour residual properly, updated disabling of action buttons when tiltalign is run.

3/17/10: Fixed slicer crash with -180 Z rotation and offset image.

3/2/10: On 64-bit Mac, prevented preferences dialog from coming up when already open, mostly stabilized the Help entry in 3dmod menu bar with model view open, and changed bead fixer's file filter when opening log file to omit the align*.log filter that doesn't work.

2/14/10: Fixed turning off of spherical points in model view based on value, and of symbols and points in image display windows.

1/5/10: Fixed pixel offset in drawn lines on some systems.

11/23/09: Fixed crash when opening 3dmod without image on model with multiple times.

10/22/09: Fixed problems with ghost mode when using Drawing Tools and other Noske plugins.

10/7/09: Made Slicer pass on Shift-PageUp/Down so it will still work to make a step to next Z with contours.

9/2/09: Fixed 3dmod crash when starting a new contour with limited points per contour and there are two empty contours.

8/19/09: Stopped 3dmod from dismissing filesystem cache under Linux unless directed with an environment variable. Files will now load faster when opened a second time.

8/19/09: Fixed problem with slicer processing mouse moves after the button release.

6/22/09: Fixed raw image dialog.

6/5/09: Fixed problem with Zap HQ mode not being turned back on after pan or rubberband change.

5/7/09: Fixed scalebar when data are loaded with binning.

4/21/09: Fixed problem with panning while drawingtools is open on 64-bit Mac.

4/6/09: Workarounds to Qt 4.5/Mac cursor problems: preserve the model cursor when clicking on a window, keep the right cursor when using rubberband.

3/30/09: Mac fixes: Raise windows at start, raise and activate window on mouse press in Qt 4.5, set current directory in file chooser.

3/26/09: Improved performance of Object List window when adding or removing group checkboxes for lots of objects.

3/22/09: 3dmod makes sure dialogs and image windows are fully on the screen and, on Mac, keeps them from overlapping their parent (Info window or model view).

3/21/09: Fixed bug in using O hot key when cont/surf/point dialog not open.

3/12/09: Fixed layout of Open buttons in startup window.

3/4/09: Changed Zap, Slicer, Xyz, and Locator windows to process mouse move events when appropriate to avoid falling behind with events from tablet.

2/27/09: Fixed trimvol command in info window (missing -x).

2/25/09: Turned off keyboard tracking for remaining spin boxes.

2/24/09: To avoid problems with tablets, process mouse move events so as to skip to the current event in model view, and skip updating dialogs when doing continuous drawing in Zap window.

2/15/09: Fixed geometry problems in model view object edit and object list windows.

* 11/21/09: Slicer will start a new closed contour automatically when you step to a new position perpendicular to the slice or when you change angles, and it will also start a new surface when you change angles.

Changes in General Processing Programs or Infrastructure

** 12/10/09: Flattenwarp can smooth surfaces by fitting thin plate splines, can output a model for visualizing the surfaces and picking the right smoothing, and can accept models of gold beads based on either Tiltalign or Findbeads3d output. A new program, Sortbeadsurfs, is provided to process such models before running into Flattenwarp.

** 6/14/09: Rotatevol, Matchvol and Warpvol were improved by: converting to Fortran 95 and using dynamic memory allocation, where the array size can be set by the user; setting up rectangular input and output volumes to use memory and read from disk more efficiently; computing data within cubes and cubes in a more efficient order; parallelizing with OpenMP.

** 1/6/09: Added Flattenwarp, a program to produce warping transformations for flattening a volume.

* 1/8/10: If the machine list to processchunks is a single number, it is interpreted as the number of processors to use on the local host.

* 12/7/09: Allowed Midas to open a montage file without an existing edge displacement file.

* 12/4/09: Programs using PIP input now print a listing of input entries when run from command files.

* 11/23/09: Added object name option to point2model.

* 11/9/09: Processchunks will now run start, sync, and finish chunks asynchronously on the first machine instead of synchronously on the local host, so start and finish are now killable, and will be treated properly on resume. It can also be used to run a single command file on a remote machine.

* 9/22/09: Fixed Point2model so that there can be blank lines in the file, and added options for setting color, symbol and point sizes, and image reference coordinates.

* 8/19/09: Made Mtffilter allocate memory dynamically, so it can filter moderately large volumes in 3D without breaking them into pieces.

* 6/22/09: Changed Newstack to allocate needed memory; added option for user to limit memory usage, and made newstack and Fortran I/O code work with images bigger than 2 gigapixel.

* 6/18/09: 3dmod and tif2mrc can now read 32-bit integer TIFF files and RGBA files.

* 6/15/09: Cubic interpolation routine was parallelized with OpenMP, which will speed up Newstack somewhat.

* 6/5/09: Implemented a new method of filling in missing transforms in Warpvol to avoid discontinuities in transforms and other problems when they are extrapolated to long distances from existing transforms. Modified Findwarp to put out a warp file with missing transforms so that filling in and extending transforms is done only once, in Warpvol.

* 3/31/09: Tif2mrc and 3dmod will both read grayscale TIFF files with multiple samples per pixel by treating each sample as a separate image. When a multipage TIFF file has multiple image sizes, the smaller ones (e.g., thumbnails) are now ignored. Mrc2tif now writes data using libtiff and supports compression options.

* 2/15/09: Added structure for avoiding artifacts when writing to one file from multiple computers, implemented it for Tilt/Splittilt and Ctfphaseflip/Splitcorrection. ALL MACHINES USED FOR PARALLEL PROCESSING WITH DIRECT WRITING MUST BE UPGRADED TOGETHER.

* 2/15/09: Added options to Alterheader to set pixel spacing from pixel size in FEI/Agard style extended header, and to invert sign of origin. Wrote proper man page for Alterheader.

* 1/15/09: Port to Qt 4.4 of all Qt-based programs.

* 12/22/08: Blendmont uses a new method of padding for cross-correlation to reduce artifacts, and has an option (activated with VerySloppyMontage) to evaluate multiple correlation peaks with a real-space correlation coefficient computed from filtered images.

5/26/10: Added check to mtffilter for padded volume > 2 gigavoxels.

5/26/10: Fixed allocation bug in Flattenwarp when processing scattered points; made Findbeads3d put image size in model so Sortbeadsurfs and Flattenwarp will do the right rotations by default.

5/20/10: Fixed detection of 64-bit system in G5 installation, default install location when running Assistant, and linklibs-mac for location of frameworks on Mac.

4/26/10: Allowed spaces in log filename in vmstocsh and removed length limit.

4/13/10: Fixed imodinfo volume inside mesh for central point not inside the mesh.

4/9/10: Increased log filename length in vmstocsh to 320.

4/1/10: Added option to Sortbeadsurfs to handle the case of beads on one surface but in multiple objects.

3/31/10: Changed the way imodsendevents exits to stop Qt complaints.

3/31/10: Eliminated error when meshing object with no points.

3/30/10: Fixed contour center of mass in Imodinfo for scattered points or contours with 1 or 2 points: the centroid of the points is reported.

3/27/10: Fixed machine stamps in MRC files to follow CCP4 definition.

3/11/10: Fixed outlier detection in clip stats.

3/11/10: Made imodtrans able to use the -i option when a model file has no image reference information.

3/10/10: Fixed Xfsimplex when run with fewer than 6 variables, broken 10/12/09.

3/10/10: Replaced amoeba routine of Press et al. to satisfy requirements for being open source. Some searches such as in Xfalign, or Solvematch/Findwarp with one layer of patches, will give slightly different results.

3/2/10: Fixed install script for rename failures on Win 7.

1/14/10: Fixed problem created 1/5/10 with matchvol/warpvol/rotatevol.

1/8/10: Converted Taperoutvol to PIP input and added an option that sizes should not be increased to be suitable for FFTs; added same option to Tomopieces and Chunksetup so NAD chunks can be run with no padding at all.

1/6/10: Made install script copy DLL's out of Microsoft folder into bin for Win2K, added warnings for 64/32-bit mismatch on Linux and Mac.

1/5/10: Fixed problem with Matchvol not making input array large enough

12/28/09: Fixed tomopieces to suppress entry output, which crashed setupcombine.

12/7/09: Made Processchunks responsible for echoing CHUNK DONE at the end of every command file; stopped it from overwriting a sync log with CHUNK DONE.

12/5/09: Added option to Warpvol to scale transforms to apply to a volume at a different binning; fixed half-pixel shift in Warpvol and Matchvol when image size is odd.

11/21/09: Clip has an option to number Z values from 1 and options for clip stat to mark slices with min and max values that are outliers.

10/14/09: In Extractpieces, Extracttilts, Extractmaggrad, and Newstack, switched to allocating arrays for extra header data.

10/14/09: Fixed a problem with Corrsearch3d (no patches fit within constraints) when no transformation or shift was specified.

10/12/09: Added option to Xfsimplex to measure difference or correlations in patches, to save having to do low frequency filtering.

10/9/09: Added option to Newstack to taper image as in Mrctaper.

10/8/09: Changed startup scripts for Linux and Mac to put IMOD man pages on the MANPATH if it exists.

10/7/09: Changed Flattenwarp to allow separate binning in X/Y and Z.

9/16/09: Xyzproj modified to make projections suitable for common line analysis and to make simple vertical projection more efficient.

9/8/09: This time thread number really will be controlled by OMP_NUM_THREADS.

9/7/09: Switched centering of transform in Xfsimplex to conform to centering in interpolation routine.

8/17/09: Added variant of PBS queue type for getting load under Maui.

8/4/09: Implemented ability to read DigitalMicrograph stack files with dm2mrc and 3dmod, allowed dm2mrc and raw2mrc to work with filenames starting with dash, fixed problem with dm2mrc accessing files not in current directory, and removed -d option and cleaned up dm2mrc man page since all files are scanned.

6/22/09: Changed cubic interpolation so thread number is controlled by OMP_NUM_THREADS.

6/22/09: Fixed mrcx for 64-bit systems.

6/10/09: Fixed problem running Xfmodel to find transforms with PIP input.

6/10/09: Fixed imodhelp for Linux, broken since Qt 4 upgrade.

5/29/09: Fixed crash when meshing some open contours.

5/26/09: Fixed processchunks to ignore error lines when getting ssh version.

5/7/09: Added option to Extracttilts to get information for all frames of a montage.

4/30/09: Fixed problems in dm2mrc for latest tcsh and in DM conversion when there is an unsupported image type in front of the one of interest.

3/30/09: Try to prevent degenerate solutions in Findwarp by detecting when most patches are on a diagonal.

3/23/09: Switched clip stat -2d maximum position from centroid over 49 pixels to parabolic fit over 9 to avoid misleading positions.

3/22/09: Changes for 64-bit version with Qt 4.5 on Mac OS X 10.5.

3/13/09: Changes to produce new 64-bit Windows version.

3/5/09: Fixed value set into global rotation spin box in Midas.

3/5/09: Removed extensions from tomosnapshot name, may make it more mailable.

3/3/09: Changed Processchunks to handle up to 99999 com files and to avoid problems from * in error strings.

2/24/09: Fixed fatal bug in parallel writing routine.

2/24/09: Imodinfo -c option now reports a centroid based on line segments rather than enclosed area for open contour objects.

2/19/09: In Imodjoin, increased maximum size in model header to hold new joined model so whole model can be viewed in Zap window. In Remapmodel, adjusted maximum Z to hold remapped Z values.

2/15/09: Added details on the contents of the extended header and commands for extracting data to Header program output.

1/25/09: Fixed a bug in Flattenwarp in handling non-planar contours.

1/23/09: Processchunks now prevents etomo from dropping machines until at least one chunk has succeeded.

1/17/09: Fixed problem getting min and max X of contours in Flattenwarp.

12/31/08: Added option to Warpvol to set default output size the same as input.

12/19/08: Trimvol fixed to avoid 1-pixel errors in X/Y when extracting odd sizes from even or vice versa.

12/19/08: Taperoutvol changed to not add padding to a single slice in Z.