Changes for IMOD 4.11

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

Changes in Tomogram Processing

** 10/8/19: Beadtrack modifications:
- Scaling of size-dependent parameters to work with a wide range of bead sizes/pixel sizes
- Ability to track closer to edge of data
- Relaxed criteria for accepting a point that increases the mean residual too based on tilt increment and lack of bead elongation
- Trying both predicted position from tilt alignment and extrapolation from position on nearby views when they differ enough
- Initial tracking of a few views on both sides of bidirectional starting point to reduce failures at the boundary
- Use of statistics on background densities to validate or reject the result of "rescue" attempts
- Option for overall low pass filtering of data, especially useful with small pixel sizes
- Improved layout of local tracking areas when area size is too small.
- One can now change pre-aligned stack binning and rerun Tiltalign (with or without retracking the seed) without opening fiducial model in 3dmod.

** 8/10/18: Ctfplotter upgraded with fitting to find astigmatism and/or phase shift, better baseline flattening, ability to work without noise files in some cases, ability to graph the values in the table as a function of tilt angles, and ability to skip some views or avoid combining views across the two halves of a bidirectional tilt series.

* 6/25/20: Added antialias filtering in prenewst and newst to cryo tyemplate.

* 5/6/20: Added script Tomocleanup and batch directives for doing final cleanup of intermediate files in a data set, equivalent to Cleanup in Etomo.

* 1/21/20: Added option to Tilt to do the super-sampling with pre-expanded input data to avoid signal loss from linear interpolation.

* 1/16/20: Implemented super-sampling option in Tilt to reduce stray lines in FFT.

* 1/4/20: Converted Tilt to C++.

* 12/22/19: Batchruntomo changes:
- Weighting of whole contours when patch tracking is now on by default;
- Improved errors when some conflicting directives are entered with Advanced mode;
- Prevented iteration of patch tracking with adjusted angle if adjustment is too large;
- Started using adjusted if one was produced by Autofidseed;
- Added a way to make both SIRT-like and regular back-projection.

* 11/6/19: Made Beadtrack able to use net shift of beads near zero tilt to get the tracking started when beads are distant in Z and moving a lot; made Autofidseed use Tiltxcorr to get estimate of one or two dominant shifts and provide these parameters to Beadtrack.

* 10/8/19: Made Tiltalign put out residuals in nanometers.

* 4/18/19: Added Serieswatcher for watching for tilt series stack and starting reconstructions with Batchruntomo.

* 11/1/18: Added Ctf3dsetup to create command files for making a reconstruction with CTF correction in 3D.

* 10/22/18: Ctfphaseflip is now able to adjust for X-axis tilt and correct unaligned images with tilt axis not vertical.

* 10/10/18: Ctfphaseflip improved to increase strip width to give enough resolution between zeros in frequency space, allow correction from full images instead of strips, extend correction closer to image edges, and run on a GPU.

* 7/4/18: Added script for making com files to generate tomograms of a selected area with different values for one of four kinds of filters in Tilt.

* 11/18/17: Added dose weight filtering to Mtffilter; it can currently be run during interactive or batch processing with template entries.

* 11/17/17: Added script to swap in an alternate tilt series stack for processing while saving existing files to a new name.

* 9/26/17: Enabled Tilt to use different kinds of GPU memory organization to avoid limitations in the number of planes that can be loaded and accessed; it will use 3D texture memory if possible for local alignments or reprojections, which is sometime significantly faster. Older cards (compute level 1, generally before GeForce 400 series) need to use a version built with CUDA 3.

11/5/20: Fixed Sorttiltframes to work on SerialEM files and added options to get an output list of tilt angles, make it unsorted, and output a dose information file if there is a fixed dose per image.

11/1/20: Fixed Tilt crash from coordinate slightly below left edge of image.

10/31/20: Fixed Beadtrack crash in Windows.

10/28/20: Fixed Batchruntomo when trimming after using SIRT-like filter.

10/16/20: Fixed Cryoposition for new naming style.

9/16/20: Added ability to input fixed X-Y-Z coordinates to Tiltalign to use in local alignments.

9/7/20: Fixed array allocation problems in Beadtrack with bidirectional series and with the starting angle outside the range being tracked for autoseeding.

8/26/20: Fixed option that RAPTOR uses to run Tilt.

8/8/20: Stopped Pickbestseed from putting a seed point on a view from which tracking failed.

8/6/20: Fixed new entry in system template.

8/4/20: Fixed transferfid when autoseeding puts the shifts near zero tilt into the track com file.

7/28/20: Fixed b axis matching model name put out by Setupcombine with new naming style.

7/22/20: Tomography guide updated for new features.

7/7/20: Fixed behavior of ShiftZFromOriginal in Tiltalign so the shift doesn't depend on how offset the points are from center with an asymmetric tilt range.

5/1/20: Fixed Bead Fixer reading contour mean residuals, broken 10/8/19.

4/16/20: Fixed Batchruntomo when using SIRT-like filter, broken 12/22/19.

4/15/20: Added options to Tilt and Ccderaser so that reprojecting a model or erasing points would skip points below threshold and not visible in 3dmod.

4/11/20: Made it possible for dual-axis volcombine to write directly to a chunked HDF file.

4/9/20: Fixed Tilt supersampling with input expansion on GPU when output width differs from input width.

3/26/20: Fixed computation of defocus output from Tilt when reprojecting model.

3/17/20: Fixed reprojection of model from Tilt when there is more than one point per contour.

3/4/20: Added options to Copytomocoms and Mtffilter and a template directive to indicate that a bidirectional series has its first acquired part at the end of the tilt series stack.

2/13/20: Fixed Tilt's model reprojection, which was failing to account for the model being viewed on a flipped/rotated volume. Also fixed bad X/Y sizes being put in header at the end.

1/31/20: Fixed bug that made Tilt put out blank tomogram if it started with blank slices.

1/28/20: Fixed bug that crashed Tilt at end of run.

1/22/20: Fixed direction of Step Up/Down buttons in Ctfplotter to go by views.

12/19/19: Fixed problem with CTF correction on GPU.

12/11/19: Made Copytomocoms set Ctfplotter option for breaking at starting view of a bidirectional tilt series.

12/10/19: Fixed Tilt fallback from vertical-slice to direct output slice computation with X axis tilt.

11/18/19: Increased size of pieces used for combine and ones set up by Chunksetup to 80 megavoxels.

11/18/19: Made Makecomfile add option for Findbeads3d to take account of elongation of beads.

11/6/19: Changed Pickbestseed used by Autofidseed to avoid beads with scores that are extreme outliers.

10/28/19: Fixed definition of Beadtrack LowPassCutoffInverseNm as taking only one float so it can be used in templates.

10/14/19: Fixed extrapolation of astigmatism values in Ctfphaseflip at high view numbers past last measurement; images were highly distorted.

10/8/19: Changed Autofidseed and Copytomocoms to handle scaling of Beadtrack parameters for large bead sizes.

10/1/19: Fixed Finishjoin reading info file, broken by file naming changes.

8/28/19: Made Ccderaser able to fill patches with noise and added option to Etomo for this.

8/18/19: Fixed Ctfplotter fitting to 2 images instead of single images when run with AutoFitRangeAndStep 1,0, which is what Etomo puts out for batch files. Also made it fit to expected # of views instead of one more when actual angle ranges are set for autofitting.

8/18/19: Made Batchruntomo use GPU for CTF correction and added directive to correct for X axis tilt.

8/12/19: Fixed Splitcombine for new style filenames and made Batchruntomo do combine in parallel.

7/30/19: Added directives to replace or run after Trimvol step in batchruntomo.

5/24/19: Fixed Copytomocoms to apply directives to

4/25/19: Fixed setting of number of views to sum when loading from table in Ctfplotter.

4/25/19: Made Tomodataplots keep astigmatism angles from jumping between +90 and -90.

4/25/19: Fixed running Ctfplotter in batch with no noise config files.

4/25/19: Fixed Cryoposition, broken by file naming changes 2/28/19.

2/8/19: In Ctfplotter, fixed one-pixel error in wedge spectra that was giving errors in astigmatism of ~150 nm, depending on the astigmatism axis. Also made it possible to run program with no angle file and have it assume zero tilt for all images, and added ability to set end of fitting range with a right-double-click. Constrained astigmatism to positive values and angles with +/-90. Changed default minimum views for astigmatism to 5.

2/3/19: Added buttons to Ctfplotter to reset the start and end of fitting range based on current defocus estimate and selected number of zeros.

11/23/18: Fixed two bugs in Ctf3dsetup and two bugs in the 3D CTF correction provided by Subtomosetup.

11/16/18: Batchruntomo can now transform a boundary model from A to B axis when patch tracking.

11/13/18: Subtomosetup can now do separate CTF corrections for subvolumes at different Z depths.

9/27/18: Added option to Rawtiltcoords to output model that fits aligned rather than raw stack.

9/25/18: In Ctfplotter, avoided refining phase and defocus on final spectrum if phase is being found from more views than defocus.

9/2/18: More changes to Ctfplotter to improve baseline fitting and fix other issues, including initial autofitting. Ctfphaseflip modified to handle cut-on frequency.

7/10/18: Fixed Batchruntomo not sending templates when making

5/12/18: Changed Batchruntomo to read in batch defaults file.

3/15/18: Made Tomodataplots able to plot Ctfplotter defocus files.

2/9/18: Added directive for Batchruntomo to keep X-axis tilt 0 for reconstruction.

12/1/17: When binning that Transferfid or Matchrotpairs send to Tiltxcorr exceeds 5, the high-frequency filter is reduced and antialiased reduction is used.

11/13/17: Added script to analyze tilt angles in frame filenames and produce list of filenames in the right order for a tilt series.

10/12/17: Made Tilt detect when the compute level of the GPU is not enough for the CUDA version it was build with and give better error message.

Changes in Etomo Batch Interface

** 6/25/18: In Etomo - Batchruntomo added an advanced dialog to handle directives that are not covered in the basic dialogs.

* 11/24/20: In Etomo - Batchruntomo Interface, made the SIRT-like reconstruction available in the Basic screen.

12/6/20: In the Etomo - Batchruntomo interface added more validation for trimvol scaling.

11/22/20: In Etomo - Batchruntomo Interface, fixed the process progress information in the process progress panel and the row table.

11/14/20: In Etomo - Batchruntomo Interface, fixed a problem with the Override buttons enabling incorrectly in the advanced directives panel.

11/10/20: In Etomo - Batchruntomo Interface, added validation for mutually exclusive directives.

11/1/20: In Etomo - Batchruntomo interface fixed a problem where advanced values did not reset when a template is removed.

10/16/20: In Etomo - Batchruntomo interface fixed a bug which prevented the template value from being restored when the field was empty.

10/9/20: In Etomo - Batchruntomo interface, fixed the pulldown lists on the Advanced Dataset Values dialog.

10/8/20: In Etomo - Batchruntomo interface, added the B copyarg directives to the advanced dataset values.

9/21/20: Added separate copyarg B axis directives to the Advanced Dataset Values dialog.

7/27/20: Incorporated batchruntomo metaData trimvol values into Etomo.

7/9/20: In Etomo - Batchruntomo Interface fixed a problem where modified advanced directives are not saved to the dataset-level batch file.

4/8/20: In Etomo - Batchruntomo Interface fixed two garbled tooltips.

5/24/19: In Etomo - Batchruntomo Interface added validation of the Starting Directive File.

4/29/19: In Etomo - Batchruntomo Interface, corrected a problem where multiple DeliverTo options where saved to the batchruntomo comfile.

4/16/19: In Etomo - Batchruntomo defaulted both binning fields to enabled (when the table is empty).

2/28/19: In Etomo - Batchruntomo added a timed-out file open to avoid an infinite loop on reconnect when the batchruntomo log file is missing.

1/24/19: In Etomo - Batchruntomo fixed some field behavior problems in the advanced Dataset dialog.

9/23/18: In Etomo - Batchruntomo fixed a problem where dataset-level batch .adoc files where being treated is if they had been loaded when they had not been.

9/23/18: In Etomo - Batchruntomo made the section buttons thinner in the Advanced Dataset Values panel.

8/23/18: In Etomo - Batchruntomo fixed problem where the Erase Gold checkbox (and other checkboxes derived from string-value directives) could not be reloaded with an unchecked value if a template had caused it to be checked.

7/11/18: In Etomo - Batchruntomo added some improvements to the advanced directive editor.

7/9/18: In Etomo - Batchruntomo fixed a bug which caused two responses to each button press.

3/29/18: In Etomo - BatchRunTomo fixed a null pointer error that happened when a dataset-level dialog was brought up.

6/13/17: In Etomo - Batchruntomo Interface setting dialog buttons from batchruntomo output.

Other Changes in Etomo

** 9/21/18: In Etomo - Tomogram Generation added the Filter Trials panel, which allows the SIRT-like filter (as well as some other filters) to be tried with multiple settings on a subvolume.

* 11/2/20: Add GPU information columns like gpu type, speed, memory and n_cores for GPU parallel processing.

* 8/17/20: In tomogram generation, added supersampling options which include two checkboxes and a spinner. These are visible in advanced mode and for backprojection only.

* 7/10/18: In Etomo - Tomogram Generation clarified the filter box by splitting it into two boxes.

11/20/20: Fixed reconnect to queue not showing selected number of CPUs.

11/15/20: In Etomo - Reconstruction Setup, fixed the template validation error message popup.

11/06/20: In Auto Alignment Parameter's, Midas button is kept disabled if Refine with Auto Alignment catches Axis Busy Exception.

10/22/20: In Etomo - Clean Up add the .mat file to the intermediate file clean up filter.

10/19/20: In Etomo fixed a problem with 3dmod receiving messages such as the open Bead Fixer message.

10/09/20: For command-line options, make single dash valid for all options and add "run etomo --help" message for further assistance.

10/02/20: In the Options menu changes to the "Open 3dmod..." items should affect all instances of the menu.

9/30/20: When an error message pops up when Use Fixed Stack is pressed before the fixed stack was created, the process bar now ends up with a failed state.

9/29/20: Inside join interface, when user presses Refine Join, joinwarp2model is run.

9/9/20: In Etomo - UI Test, clarified and fixed the end command functionality, which was not useful for dual axis.

9/9/20: In Etomo - File Alignment, removed unnecessary copy created by Etomo after align is run. This is to avoid duplication because already creates them.

8/27/20: In join interface, inside the boundary table of rejoin tab, the adjusted start and end buttons are enabled.

8/21/20: In tomogram combination, validate for CPU's if parallel processing is selected and stop before running volcombine is not selected.

8/19/20: In Setting added the scroll bar and changed the CPU label to "Number of true CPU cores".

8/17/20: Made uitest faster and more reliable.

8/5/20: Made the uitest faster and more reliable.

7/24/20: Validate for CPU's if parallel combine is selected before starting any combine operation.

7/24/20: Add an option to extract montage piece list from mdoc file.

7/16/20: Changed box name from 'Beam Tilt' to 'Single Variables: Beam Tilt,..' and added 'Solve for...' checkboxes in this box.

7/9/20: Upgraded Etomo developer scripts.

7/8/20: In Etomo - Fiducial Model Generation improved the option choices for

7/8/20: In Etomo - Fiducial Model Generation saving when autofidseed is run.

6/25/20: In Etomo, got rid of unnecessary warnings in err.log file.

6/25/20: In Etomo, changed text label from fiducialless to 'coarse alignment only'.

6/8/20: In Etomo - Final Aligned Stack modified some dose weighting tooltips.

6/8/20: In Etomo fixed problems with old-style and standardized raw stack extensions.

6/8/20: In Etomo increased unit test speed.

3/17/20: Modified the way Etomo is calling Midas in an attempt to prevent a Midas crash associated with printing out messages.

3/9/20: Fixed a serious problem which occurred when the pixel size was not filled in during Reconstruction Setup.

2/6/20: Fixed an "array out of bounds" error which was associated with reconnecting to running or finished processes.

2/6/20: Added functionality to handle both standard and the original image file extensions. Input image files extensions are not controlled. The .mrc extension is fully supported. The .hdf extension is partially supported (more support is available depending on user interest).

12/11/19: Fixed Etomo setting BidirectionNumViews in as float.

10/7/19: In Etomo - Final Aligned Stack fixed the way is loaded, so that the dialog is compatible with Batchruntomo Interface.

5/13/19: In Etomo - Tomogram Generation fixed a problem with label enabling and improved tooltips.

5/5/19: In Etomo - Final Aligned Stack - CTF Correction, defaulted "Correct for X axis tilt" checkbox to off..

4/8/19: Added a pause command to uitest.

4/3/19: In Etomo - Final Aligned Stack - MTF Filter fixed a problem with saving LowPassRadiusSigma in the .com file.

4/1/19: In Etomo - Final Aligned Stack fixed the best GPU setting which was being set to 7 instead of 0.

3/29/19: In Etomo added save to the File - Close menu option.

2/28/19: In Etomo changed the processing of tilt angle spec directives so they exclude each other..

2/25/19: In Etomo - Final Aligned Stack corrected the Erase Gold fiducial-based/3D setting.

2/14/19: In Etomo - Trimvol fixed a problem where etomo was ignoring the "convert to bytes" setting from batchruntomo.

2/14/19: In Etomo - Final Aligned Stack fixed a backward compatibility problem with the dose weighting file field.

2/14/19: In Etomo - Final Aligned Stack added more parameter fields to the CTF phase flip panel, including GPU processing.

1/29/19: In Etomo - Setup Reconstruction fixed some problems with excluding views during setup.

1/28/19: In Etomo - Setup Reconstruction fixed the cancel functionality.

12/19/18: Cleaned up Etomo's popup messages.

12/11/18: In Etomo - Final Aligned Stack, added dose weighting to 2D filtering.

9/21/18: In Etomo did some internal improvements involving the displaying of fields when an error message pops up.

6/22/17: In Etomo placed all INFO messages in the project log, except for some copytomocoms message.

Changes in 3dmod

** 11/28/19: Made Drawing Tools work in Slicer and fixed several problems in existing functions.

** 4/4/19: Added support for high-DPI monitors for 3dmod, Midas, Ctfplotter when built with Qt 5, described in section 1.13 of the IMOD Guide.

** 3/19/19: Most 3dmod dialogs are now docked in a stack attached to the Info window or the Model View window, each with a button to collapse or expand it.

* 9/10/20: Added ability to display mesh lines in the Zap and Slicer windows.

* 9/10/20: Added ability to display meshed surfaces in model view with thickness by displaying a pair of offset meshes.

* 10/31/19: Added option to 3dmod image processing Fourier filter dialog to filter image in Slicer instead.

* 10/31/19: In Isosurface dialog, added option to do Gaussian smoothing of the image data before thresholding, added ability to use multiple paint objects, and made some parameters be saved in model to allow reopening in same state.

* 10/18/19: Made transparent fill in Zap window work with nested contours.

* 7/23/19: Added hot keys to Model View to toggle specific clipping planes, mesh an object, toggle X and Y image planes, and switch between different display type/styles. Made some modeling functions work properly with alternatives. Added an option to keep the current model object and the one being edited in the Edit - Objects window the same.

* 4/8/19: Added option to label scale bars with the length.

* 3/6/19: Added option to apply global clipping planes to image in model view.

* 11/17/18: In 3dmod, labels can be drawn in Model View also.

* 11/4/18: In 3dmod, labels for points will now be drawn in the Zap window.

* 3/6/18: Added ability to display color images in model view window.

* 5/25/17: Added option to 3dmod to load a montage with aligned piece coordinates from an mdoc file, and a setting in the preferences to do this by default.

10/15/20: Added 3dmod menu item Edit-Surface-Sort to sort contours by surface number and by Z within each surface.

9/15/20: Fixed distance measuring with "Q" in Slicer for high-DPI monitors.

8/3/20: Fixed modeling cursor in Wondows for high-DPI monitor.

8/1/20: Fixed drawing of isosurface with transparent background.

7/15/20: Added ability to specify a contour is not to be capped when meshing in Fine Grained dialog.

7/8/20: Fixed crash on Windows (with non-Nvidia graphics?) when picking with right mouse button in Model View.

4/28/20: Fixed 3dmod OpenGL library loading in Ubuntu (used for vertex buffer drawing).

4/28/20: Made removal of contours by clipmodel and 3dmod Object-Clean much more efficient for objects with many contours.

4/15/20: Fixed 3dmod loading signed byte file as shorts in 3dmod with -I 1 option or preference set to load as shorts.

4/15/20: Fixed scanning of file in 3dmod for min/max when it is invalid.

4/10/20: Fixed Drawing Tools starting a new contour at adjacent Z, and made smoothing preserve gaps in contours.

1/16/20: Fixed scale bar label positions for high DPI monitors.

12/19/19: Made Isosurface able to set area from Slicer or Zap rubber band.

12/19/19: Scaled the interval between added points when mouse dragging for high-DPI.

12/19/19: Prevented bogus point from being added at end of contour by Livewire.

12/19/19: Fixed isosurface crash when filtering very thin volumes.

12/17/19: Fixed crash when using Drawing Tools in warp mode.

12/11/19: Fixed font scaling issues for high-DPI in Linux when QT_SCALE_FACTOR is set, such as by 3dmod, Midas, and Ctfplotter wrapper scripts.

12/10/19: Fixed ability to switch to extra object in Model View Edit Objects when the synchronize option is selected.

12/10/19: Fixed binning in Isosurface, broken 10/31.

12/10/19: Fixed Save Object buttons in Isosurface window, broken 10/31.

11/28/19: Improved behavior of docked dialogs when changing Linux desktops.

11/28/19: Made label drawing work in Slicer window. Fixed label positions in model view for high-DPI display

11/19/19: Fixed Interpolator so that Smooth and Smooth Pts delete existing contours properly.

11/18/19: Changed "Replace spherical point" option in Contour Move dialog to produce a single circle if points are being drawn only on one section.

11/1/19: Provided larger cursors for model mode with high DPI.

10/31/19: Added hot keys for changing current object in Model View and for toggling FFT in Slicer.

10/28/19: Fixed xyz window when resized, broken 7/31/19.

10/22/19: Made model view window position be saved between sessions when opened from 3dmod.

10/6/19: Changed openIn3dmod for Mac to allow clicking on more than one file at a time.

7/31/19: Fixed problems initially drawing Zap, Slicer, and Xyz windows in Linux with Qt 5 (RHEL7 distribution).

7/30/19: Made the intensity scaling of slicer window with summed slices be constant when taking a montage snapshot.

7/24/19: Added Previous change button to Fine Grain dialog.

7/19/19: Possibly fixed slicer and XYZ window problems with initially drawing images the wrong size in Linux.

4/17/19: Fixed mouse coordinates sent to beadfixer and plugins when scaling for high-DPI.

4/17/19: Allowed Ctrl-Shift-G to be used to toggle ghost mode because of interpolator conflict.

6/22/18: Added 3dmod menu entry to sort all contours in object by distance.

5/12/18: Added hot keys to open Image Processing window and apply current process if it is open.

9/18/17: Made Ctrl-arrow key give subpixel steps in slicer.

5/17/17: Added a button and hot key to Interpolator to make it easier to change marking of contours as key or interpolated.

Changes in General Processing Programs

** 4/12/20: Changed default naming style to have .mrc extensions. To use the old style for a new data set, start etomo with "--namingstyle 0" or set the environment variable ETOMO_NAMING_STYLE to 0.

* 11/22/20: Added ability to use ZIP compression when writing HDF files, controlled by an environment variable for all programs or by an option to Newstack and Makepyramid.

* 7/22/20: Made Alignframes and Clip able to do normalization and defect correction of EER files.

* 7/2/20: Added initial support for EER (electron event representation) files: they can be read with selected amount of super-resolution and summing of frames, with specific options to control that in 3dmod and Alignframes, and environment variables to allow all programs to read them similiarly.

* 5/4/20: To reduce noise when zoomed down in Midas, added the ability to zoom with binning instead of sampling for the display, and added an environment variable to set a target size for the initial binning when reading images.

* 5/4/20: Changed the default sign of origins stored in the file to conform to the MRC standard.

* 3/19/20: Programs can now take .idoc files from SerialEM interchangeably with image stacks.

* 1/19/20: Added option to Newstack for expanding an image by Fourier padding.

* 12/16/19: Made Alignframes handle a FISE tilt series with a frame stack mdoc file from SerialEM, which will have dose information too.

* 12/6/19: Alignframes changes, mostly for working with single-exposure tilt series:
- Frame list can specify frames to drop and some missing frames can be tolerated;
- Thresholds can be set for eliminating partial exposures at start or end of frame set
- Tilt series with tilt angles supplied will be reordered if necessary
- Truncation limit can be specified as number of SDs above mean
- Output can be scaled to a specified mean or specified mean and SD.
- Shifts between the first 4 frames will be reported for frame series
- Summary output can be adjusted to be between 1 and 3 lines as in SerialEM

* 10/21/19: Changed Model2point to output floating point values by default.

* 11/21/17: Added dose weight filtering and option to rotate/flip summed output to Alignframes.

* 8/23/17: Switched all builds except the RHEL5 one to use the Intel Math Kernel Library FFT routines instead of FFTW; they are about 3-4 times faster.

* 6/2/17: Made Imoduntar able to download tar files given a full URL, and IMOD tutorial files given the beginning of their names.

* 5/17/17: Added option to Newstack to reorder sections by tilt angle.

* 3/12/17: Added script Justblend for batch blending of 2-D montages.

* 3/12/17: Modified Processchunks to run multiple files with independent names, take extension pcm as well as com, and take up to 999,999 chunks.

12/9/20: Added environment variable IMOD_TIFF_RESOL_IN_CM to make pixel size be stored in TIFF files in dots per cm instead of dots per inch.

12/8/20: Added option to Xyzproj to use areas of intersection between projection rays and pixels instead of interpolation between pixels when summing along rays.

12/1/20: Updated installation instructions and fixed some install problems in Windows and Mac.

11/20/20: Fixed problems managing non-Z-section metadata in an HDF file, added ability to reorder an HDF file by changing section names, made Newstack copy other metadata between autodoc structures.

11/20/20: Allowed no radius criterion to be entered for Imodcurvature.

11/5/20: Added options to Alignframes to specify tilt axis rotation angle, have it take gain reference and defect names from titles in header of frame file, and set the target size for alignment binning.

10/28/20: Added signing of Mac installer package built on OS 10.14.

10/28/20: Added a library to distributed package to fix Qt programs on RHEL8.

10/19/20: Fixed processchunks crash with queues, broken 3/26/20.

10/16/20: Fixed -replace option in Newstack when no input section list given.

10/15/20: Made Tomodataplots able to plot residuals and shifts from Alignframes.

10/14/20: Fixed Alignframes for Windows, apparently broken since 4.10.38.

9/24/20: Made the target size for default binning in Alignframes be 1560 instead of 1250 for frames in a size range that could come from a K3, so the binning will be the same as for K2 frames.

9/22/20: Improved handling of padding around defects in EER file; made Alignframes work on GPU with 4 x 4 super-resolution EER images if there is enough memory; added clip command to get adjustment factors for normalizing super-resolution EER images and made clip norm and Alignframes able to apply such factors.

9/12/20: Added option to Clipmodel to select closed contours by area.

9/9/20: Fixed setting of image reference information in models output from Fortran programs to include current tilt angles.

8/31/20: Fixed clip hist -s for essentially blank images.

8/29/20: Fixed crash from closing TIFF files after parallel reading, broken 7/2/20.

7/27/20: Made Fortran graphics window a better size for high DPI monitors.

7/23/20: Added options to Alterheader for removing titles and specifying position of new title.

5/26/20: Fixed JPEG writing in Linux at least.

5/3/20: Default naming style switched to new style again.

5/2/20: Switched back to old naming style as default for this beta release.

5/1/20: Fixed problems with image file name standardization.

5/1/20: Fixed Alignframes crashes with dose weighting from mdoc and output of unweighted file.

4/30/20: Fixed Alignframes defect correct with GPU on edges bigger than 4 pixels.

4/26/20: Changed Fortran programs to use dynamically allocated model arrays.

4/11/20: Rotatevol, Matchvol, Warpvol: made memory limit bigger and dynamic to reduce need for scratch files, made quadratic interpolation use higher-order terms, and implemented output to chunked HDF files as another way to avoid scratch files (not as good as having more memory).

4/10/20: Fixed 2D averaging of one image file in Clip.

3/26/20: Made Processchunks skip probing and asking for confirmation when the only machine is localhost.

3/19/20: Made Clip able to produce chunked HDF output and optimized this for the flipyz/rotx operations.

2/27/20: Added option to Newstack to specify range from which to map densities with two of the other scaling options.

2/27/20: Made Vmstopy make an output script file executable only if an option is given.

2/26/20: Added imodholefinder to find regular array of circular holes in carbon films.

2/13/20: Added option to Remapmodel to map Z values to positions based on thickness measurements of individual sections.

12/27/19: Fixed new -set option to Alignframes for FISE series.

12/19/19: Added options to Alignframes to drop initial frames in a set if their drift is above a threshold, and to do a subset of frame sets. Made it transfer the title and tilt axis rotation from a frame stack mdoc. Added Framewatcher option to pass that drift option to Alignframes.

12/13/19: Made Alignframes able to figure out which tilt angles were lost from a FISE tilt series with new tilt angle file from SerialEM.

12/5/19: Added option to Mrc2tif to scale to mean and SD.

11/18/19: Made Smoothsurf delete meshes of smoothed objects by default and added an option to retain them.

10/31/19: Added 3D smoothing to clip and to 3dmod image processing window.

10/22/19: Added option to Clonemodel to set image reference information.

10/18/19: Added option to Alignframes to align the frames from a single-exposure tilt series with the list of retained frame numbers.

8/22/19: Added libjpeg to RHEL7 package so it will run on Mageia-7, should also work on Ubuntu without installing legacy libjpeg.

8/14/19: Added options to framewatcher to change the scaling, do dose weighting with values in an .mdoc file, use dose weight filters normalized within each set of frames, and output an unweighted aligned summed.

8/14/19: Added option to alignframes to normalize the dose-weighting filters for each set of frames.

8/13/19: Fixed two problems with Framewatcher, one Windows-specific, one introduced when Serieswatcher was added.

6/25/19: Changed java compatibility level for Etomo to 1.7.

6/6/19: Fixed meshing with gaps set in contours, broken 2/15/19.

5/28/19: Added options to Point2model for setting model pixel size and Z-scale and changed it to set pixel size from image file or entered pixel size.

4/17/19: Enabled 3D FFTs of more than 2 gigavoxels in Mtffilter.

4/8/19: Made Framewatcher copy a frame stack mdoc file.

3/4/19: Fixed using multiple binnings in Alignframes.

2/20/19: Fixed Assemblevol to work with > 2 Gpixel images.

2/15/19: Sped up contour reduction in meshing for very large contours.

2/8/19: Added option to Onegenplot to display with default colors

1/22/19: Fixed meshing error where there are inside contours.

1/18/19: Sped up the IMOD (open source) FFT library, especially for large images.

1/2/19: Moved initial processing steps in Alignframes to GPU, depending on GPU memory available. Added option to get non-dose-weighted output when dose weighting and fixed dose weighting on GPU.

9/25/18: Made Xyzproj able to project at arbitrary angles.

9/24/18: Framewatcher changed to assess whether a stack's modification time has stopped changing for long enough, instead of comparing it to the current time, which is vulnerable to clock skew between systems.

9/7/18: Made Framewatcher take multiple directories to move files to.

8/20/18: Added an option to Processchunks and an environment variable to set the time to wait for a queue initialization command to complete.

8/9/18: Added option to nad_eed_3d to use a faster eigenvector routine.

7/24/18: Changed Framewatcher to copy .pcm files even with -nocom option if they exist, and to use robocopy for Windows files moves if possible.

4/18/18: Modified dose weight filter to remove total attenuation above optimal dose.

3/30/18: Added options to Xfalign to specify a seed model for warping and to control image reduction in initial and warping cross-correlations.

3/8/18: Fixed setting of number of threads to use in Midas.

1/15/18: Added an environment variable to force IMOD routines parallelized with OpenMP to use more threads than are assumed to be optimal.

12/24/17: Parallelized main step in meshing.

11/5/17: Implemented faster method for padding with noise in Alignframes, Newstack, and Mtffilter; added noise pad option to Taperoutvol.

11/5/17: Added options to Imodmop to set a different mask value for each object or add mask values to a volume that already has mask them; also made byte output from masking be unsigned.

10/30/17: Made raw2mrc and dm2mrc able to convert doubles to floats or 16-bit integers

10/10/17: Changed Newstack to reduce memory usage when possible, avoid writing to scratch file when possible, and base its default maximum memory usage on the amount of memory in the system.

10/3/17: Made Framewatcher avoid Python file/directory copying functions if possible; they are very slow on Windows.

6/24/17: Added operation to Clip to convert a defect list from SerialEM into a pixel map for MotionCor2, and an option to specify output file type.

5/26/17: Added option to Newstack to provide shifting of range and/or scaling of data when necessary to prevent excessive truncation or loss of precision. This is applied when transforming integer data occupying few gray levels at the bottom end of the range for the data mode.

5/6/17: Added option to Blendmont to get file of aligned piece coordinates.

4/11/17: Made Framewatcher rerun the command file when watching for stacks if the stack size increased during the run.