Changes for IMOD 4.9

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

Changes in Tomogram Processing

** 10/2/14: Corrsearch3d can now compute a measure of local structure and use it to eliminate patches from consideration, which allows it to work without a boundary model or tight Z limits. It also takes options that allow it to eliminate patches outside the area that can be reconstructed well. Refinematch and Findwarp can try to fit after eliminating patches with a series of criteria for these local structure values. A new script, Autopatchfit, runs patchcorr and matchorwarp repeatedly with increasing patch size or density to achieve a criterion mean residual. Setupcombine was adapted to these new capabilities.

** 3/2/15: Added a script, Dualvolmatch, to get initial alignment between dual-axis volumes when there are no corresponding fiducials.

** 10/2/14: Added new version of Findsection that analyzes surfaces of a plastic section and can output a model for tomopitch, a model for flattening, and estimates of Z limits for trimming and combine.

* 10/13/16: Changed tilt and sirtsetup command files to show a true sigma value for falloff and changed default falloffs to 0.035. RADIAL FILTER FALLOFFS IN TEMPLATE FILES SHOULD BE DIVIDED BY 1.414 TO HAVE THE SAME EFFECT AS BEFORE.

* 9/20/16: In Tilt, added an option to multiply radial filter by Gaussian instead of replacing it, an option for a Hamming-window-like filter that matches the filter in tomo3d, and an option to handle transitioning away from the sigma for the Gaussian being the entered falloff times 0.7.

* 7/30/16: Added option to apply a constant phase shift from a phase plate in Ctfplotter; made Ctfphaseflip able to take into account constant or variable phase shifts and variable astigmatism, and added an option for attenuating frequencies near the zeros. Defined a new defocus file format that can hold phase shifts and astigmatism parameters.

* 5/21/16: Added option to Tilt to apply a radial filter in back-projection that should be equivalent to a given number of SIRT iterations.

* 4/12/16: Made Transferfid work when stacks have different pixel sizes.

* 4/11/16: Prevented Sobel filter centering in Beadtrack from giving a worse residual by falling back to positions from centroid centering when they do better.

* 12/1/15: Made Ccderaser iterate the peak search up to 3 times.

* 11/5/15: Added a script Cryoposition that finds angles and Z position for cryo-tomograms, but not very well. Batchruntomo can now run this.

* 9/30/15: Made Solvematch analyze whether tomograms are inverted, which fixes the ability to combine tomograms with inversion after removal of this option from the interface.

* 9/27/15: Made Tiltalign put out a model with gaps filled in for gold erasing.

* 7/15/15: Added stronger high frequency filtering for patch tracking to the cryoSample template.

* 7/4/15: Changed default padding in coarse alignment to 10% to allow bigger shifts to be detected.

* 6/3/15: Changed patch tracking size from 700x700 to 680x680 in system template cryoSample.adoc to give 4x4 patches in 2Kx2K data, also added directive to analyze 1 surface in tiltalign.

* 5/30/16: Made Autofidseed track at least a 7.5 degree range and skip views in the range when tilt increment is very small.

* 5/6/15: Added preliminary version of preNID program from Mauro Maiorca.

* 4/13/15: Added option to Tiltalign to allow grouping of tilt angles across separate view groups and put option in master com file to do this for a patch tracking model.

* 3/4/15: Added ability to run NAD from Batchruntomo, and an option to specify an SMTP server for email.

* 3/1/15: Made Transferfid and Matchrotpairs evaluate mirrored as well as unmirrored images by default.

* 2/25/15: Transferfid can now find alignments when error in 90-degree rotation is up to 20 degrees, using new rotation search in Tiltxcorr. Speed improvements in Xfsimplex and greater efficiency in Transferfid have reduced execution time by about half.

* 2/12/15: Added option to Newstack to insert or change tilt angles in the output file.

* 1/8/15: Added a script Rawtomocoords to compute positions in the raw tilt series, projection angles, and defocus for points marked in a tomogram.

* 1/3/15: Implemented a dynamic adjustment of maximum strip width in Ctfphaseflip to minimize artifactual rings of low values around the zeros in the power spectrum. Spacing between strips is increased between wider strips at low tilt, and the default spacing value in the .com file was reduced to compensate for this change.

* 1/3/15: Ctfplotter changes: Added option to fit a polynomial to make the power spectrum become flat at high frequencies. Made the CTF-like curve be fit with two exponentials when the fitting range extends past halfway between second and third zero. Smoothed noise power spectra to reduce noise added by subtracting them. Made the default power for the CTF-like curve be 1.5 Applied more constraints in the CTF-like fitting to prevent bad fits. Improved initial scaling of display. Added command-line options for setting the baseline fitting order and to extend the initial fitting range beyond the second zero.

* 10/14/14: Batchruntomo can now exclude images at the end of the series with large dark regions, do tomogram positioning for plastic sections, combine dual-axis tomograms, and trim to section limits for plastic sections.

* 9/8/14: Added script Subtomosetup to make command files for generating multiple numbered subtomograms.

* 7/5/14: Batchruntomo has changes for controlling thickness and calls Restrictalign to reduce variable being solved for when necessary.

* 7/2/14: Added script Restrictalign for setting parameters appropriately in a Tiltalign command file when there are low numbers of fiducials.

* 6/24/14: Changed surface analysis in Tiltalign to fit a pair of parallel planes instead of using two independent fits, which can give screwy angles and distances; also output line saying when X-tilt or slope can't be measured.

* 6/17/14: Added script Excludeviews for reversibly removing views from a tilt series and saving them in another file.

1/21/17: Fixed bug that crashed Batchruntomo only in Python 3.

1/19/17: For combine patch correlations, added extra residual targets of 0.4,0.45 to the plasticSection template and kernel sigma of 1.45 to since these are successful in batch processing.

1/18/17: Changed zero-frequency scaling of exact filters in Tilt to keep the data output range similar to other filter options.

1/17/17: Fixed Cryoposition option for leaving specific files behind.

12/1/16: Fixed patch tracking on a montage to use full area when run by Batchruntomo.

10/3/16: Added option to Sirtsetup to control whether falloff value is true sigma.

8/9/16: Added batch directive to center tomogram in Z on the gold when not positioning and there is gold on two surfaces.

8/5/16: Made Batchruntomo produce difference files for different operations and try combining even if Findsection fails to find the Z limits.

7/18/16: Stopped Batchruntomo from redoing fine alignment when starting after fine alignment.

5/31/16: Made Ctfphaseflip maintain header properly when the stack Z size is not the same as the "grid" Z size in header.

5/21/16: Added ability for Batchruntomo to run an arbitrary command in place of or after specific steps (currently CTF plotting or mtffilter).

5/18/16: Fixed reading in of XTILTINTERP option to Tilt - it was most likely just disabling reconstruction with vertical slices.

5/14/16: Fixed density computation in Pickbestseed so later phases actually add points for larger area/higher density situations.

5/12/16: Fixed possible array overrun in Beadtrack with more than 2500 points.

4/12/16: Fixed Batchruntomo for single axis, broken on 4/2.

3/28/16: Fixed loss of GPU availability when product of number of cores and clock rates exceeds 2.e9.

2/2/16: Fixed running Batchruntomo on Windows with a space in the path.

12/10/15: Made Tiltalign not make a filled-in model from a patch tracking model.

12/6/15: Made tomogram samples with twice as many slices to allow autopositioning.

12/3/15: Added "exact filter" option to Tilt.

11/10/15: Fixed problem from 9/27 change that crashes or hangs Tiltalign when there are more fiducials than views.

10/30/15: Made Batchruntomo use existing fine alignment on restart by default.

10/28/15: Fixed RAPTOR when there is a space in IMOD path (e.g., Windows).

10/5/15: Fixed batchruntomo to handle non-square sets with near-horizontal tilt axis properly.

10/5/15: Fixed transferfid putting temp files in current directory with incomplete names.

10/1/15: Fixed setting of preblend binning through directives.

9/29/15: Made Batchruntomo rebuild aligned stack if necessary to avoid applying CTF correction twice, and use fiducial model with gaps filled in for gold erasing.

9/9/15: Add options to Trimvol for scaling to a given mean and SD and for setting mode of output file; added directive to support this kind of scaling in Batchruntomo.

9/3/15: Made it possible to enter -deliver option to Batchruntomo once for each data set; eTomo will use this instead of the other new option.

8/29/15: Added option to Batchruntomo to put all data sets into subdirectories of their current locations.

8/28/15: Fixed Batchruntomo for fiducialless reconstruction.

8/27/15: Fixed three bugs that crashed Batchruntomo with Python 3.

7/16/15: Made Batchruntomo pick a good binning for 3d bead finding if no binning directive is supplied.

7/4/15: Fixed problem with autopatchfit when no extra limits are supplied.

6/28/15: Fixed Transferfid and Matchrotpairs starting Midas twice, without and with mirroring.

6/15/15: Fixed division by 0 problem in reprojections by Tilt.

6/8/15: Added preNID to program list so it will be built and distributed.

5/20/15: Fixed Findbeads3d threshold setting in model when no points stored below threshold.

5/20/15: Added ability to signal Batchruntomo to finish current set and quit.

5/20/15: Added option to Subtomosetup to make it skip subvolume numbers when it skips points.

5/12/15: Made Batchruntomo use directive value for number of surfaces in preference to the value in

5/6/15: Fixed Batchruntomo's use of boundary models and specific X-ray models when running with an FEI file where the pixel size gets transferred to the standard header; also fixed use of a generic X-ray model modeled on images at a different magnification.

4/30/15: Added an option to Tilt to get a thresholded reprojection of fixed values for pixels beyond a threshold.

4/13/15: Added option to set fallback thresholds for Findbeads3d.

4/9/15: Added options to Findbeads3d to allow a subvolume to be analyzed and started taking the square root of peak strength for analysis and display.

4/3/15: Made Ccderaser use the median instead of mean of surrounding points as the value to taper to inside a contour.

4/3/15: Improved GPU-related debug output and error reporting from Tilt.

3/4/15: Modified Setupcombine to set up for using initial volume matching, and made Batchruntomo use it when appropriate, so it can now combine data without fiducials. Changed ratio so that fallback thickness is used when calculated thickness is less by a factor of 0.4 instead of 0.5.

2/28/15: Converted Matchrotpairs to Python by extracting a big module from Transferfid for the matching operation.

1/14/15: Made Ctfplotter delete all existing values in table when autofitting to whole range, not just ones with midpoints bracketed by the new midpoints.

12/16/14: Add option to Sirtsetup to set number of chunks per processor.

10/23/14: Changed Subtomosetup to put multiple runs in each command file.

10/16/14: Added more detail to error message when Beadtrack or Tiltalign cannot read model.

9/23/14: Patch2imod can read up to 6 extra value columns and save them as general values in the model, making a selected one the primary one; and Imod2patch can restore all these data to a new patch file.

8/3/14: Subdivided steps in Batchruntomo so CTF plotting and 3D gold finding could be checked at one stopping point; eliminated option to switch order of steps; CHANGED NUMBERS FOR -start AND -end AGAIN.

7/16/14: Changes for Batchruntomo: make it rerun align without local alignments if it fails with it; add ability to detect blank views at ends of series; allow pre-existing defocus file to be used; make -start option apply to all sets being run, not just the first; add start point for CTF correction separate from plotting; add option to do gold erasing before CTF correction; add option to use existing alignment. NUMBERS FOR -start OPTION HAVE CHANGED.

7/1/14: Made Ccderaser able to erase points with large differences from their neighbors in the border region where regular analysis is not done.

Changes in Etomo

** 1/23/16: In eTomo - Tomogram Positioning, added automatic positioning for cryo and plastic sections.

** 4/7/15: In eTomo - Tomogram Combination, changes to handle a combine done by batchruntomo and to allow automatic patch fitting to be done through the interface.

** 1/19/15: Preliminary version of batch processing interface added to eTomo.

* 7/17/16: In Etomo built out plugin functionality and added a demo.

* 2/19/16: In eTomo added option to remove excluded views from stack with excludeviews during Reconstruction Setup.

* 12/16/15: Added buttons to open the tomogram, and the dataset-level batchruntomo log. Also disabled the dual checkbox upon delivery.

* 11/24/15: In eTomo - Batchruntomo, added cryo positioning fields.

* 11/18/15: In eTomo - Batchruntomo, added gold erasing fields.

* 11/12/15: In eTomo - Batchruntomo Interface, added Postprocessing fields. Also fixed problems with empty metadata values overriding template values.

* 10/29/15: In eTomo -- Batchruntomo Interface, added coarse alignment binning and positioning fields.

* 7/25/15: In eTomo - Batchruntomo Interface added run batchruntomo functionality.

* 6/2/15: In eTomo - Fine Alignment, added an interface for restrictalign.

* 5/1/15: In eTomo - Fine Alignment, Added a global XTilt option.

* 5/1/15: In eTomo - Tomogram Combination, added controls for dualvolmatch.

1/23/17: In Etomo - Fiducial Model, testing for a busy axis before cleaning up autofidseed temporary files.

1/23/17: In Etomo - Fiducial Model: during transfer, moved autofidseed values from the "from" axis to the "to" axis.

1/14/17: In Etomo - Batchruntomo, changed the reset button to match the starting batch directive file field.

1/11/17: In Etomo - Batchruntomo, disabling the starting directive file Clear button when the file chooser button is disabled.

1/9/17: In Etomo improved browsing directory settings for Peet and Batchruntomo Interface.

1/2/17: In Etomo - Serial Sections, fixed a problem with reloading a dataset that was preventing the raw stack from being opened.

12/28/16: In Etomo - Setup Reconstruction made pixel size a required field.

12/26/16: In Etomo fixed problems with PEET processchunks error messages. Fixed a problem where the message log file was not getting into the project log. Prevented duplicate error and warning messages from chunks.

12/26/16: In Etomo - Batchruntomo allowing multi-line log messages.

11/18/16: Etomo - Setup Reconstruction fixed problems with error messages and handling an incorrect dual setting.

11/17/16: In Etomo - Setup Reconstruction resetting the progress bar string from the previous run.

11/16/16: In Etomo - Batchruntomo adding the gold directive when both gold fields are disabled.

11/15/16: In Etomo - Batchruntomo fixed a bug when an unchecked SurfacesToAnalyze checkbox was being treated as disabled.

11/15/16: In Etomo - Batchruntomo moved the Resources table to the dialog.

11/12/16: In Etomo - Fiducial Model Dialog improved how the seeding method directive affects the default settings.

11/12/16: In Etomo - Settings added a setting for the Batchruntomo table size.

10/10/16: In Etomo - Tomogram Generation, added more filtering options.

11/8/16: In Etomo - Batchruntomo, fixed a problem where some required fields were not popping up an error message.

11/8/16: In Etomo - Batchruntomo, improved the reliability of directive handling and field behavior.

11/8/16: In Etomo - Batchruntomo - Erase Gold, prevented "Use fiducial model" from being selected when there is no fiducial model.

11/4/16: In Etomo - Batchruntomo, added a reset button for the starting batch directive file field.

11/4/16: In Etomo - Batchruntomo, fixed validation problem when using the make subdirectory delivery option.

11/2/16: Removed a validation in Etomo - Tomogram Generation that was being done on exit.

10/13/16: In Etomo - Batchruntomo: on Run, closing open datasets that are being modified by batchruntomo. Also preventing a Batchruntomo interface from opening a dataset more then once.

10/13/16: In Etomo - Tomogram Generation, corrected the radial filter falloff label.

e 9/27/16: In Etomo, fixed a problem with getting the bidir value from the header, broken in 4.8.57.

9/27/16: In Etomo - Tomogram Generation, suppressed some validation that was being done when no batch process was being run.

9/25/16: In Etomo - Tomogram Reconstruction, fixed a problem where advanced fields where being shown in basic mode.

9/18/16: In Etomo - Setup Reconstruction, allowed stacks with binning down to 0.5.

9/18/16: In the etomo script, updated the location of the plugin directory. Also updated the plugin documentation in the Etomo source code.

9/17/16: In Etomo fixed the checkbox in the message popup.

9/6/16: In Etomo - Batchruntomo, improved the enabling/disabling of the "Start from" checkbox.

9/6/16: In Etomo - Batchruntomo, fixed batchruntomo message recognization.

9/6/16: In Etomo, reduced the chance that Etomo will lock up when exiting.

8/25/16: In Etomo - Tomogram Generation, allowed the parsing of comma-separated values in

8/22/16: In Etomo, improved the parsing of comments in the MRC header.

8/17/16: In Etomo - Batchruntomo, enabled positioning thickness made it required for Cryo.

8/16/16: In Etomo - Batchruntomo, fixed a bug where a disabled control was causing its directive to be overridden. Also fixed incorrect highlighting of radio buttons under CTF correction.

8/13/16: In Etomo handling "[:LOG]" tags.

8/13/16: In Etomo - Batchruntomo, handling message IDs from batchruntomo.

8/9/16: Fixed problem if custom final size is entered for auto patch fitting in Etomo combine.

8/8/16: In Etomo - Tomogram Reconstruction, processing tomogram size data from batchruntomo.

8/7/16: In Etomo - Batchruntomo, fixed a bug which prevented the "Reached" column from being loaded from the dataset file.

8/5/16: In Etomo - Batchruntomo, fixed a bug that made restarting fail after delivery, broken in 4.8.54.

8/5/16: In Etomo - Batchruntomo, did preliminary work to make reading messages from IMOD more robust.

7/31/16: In Etomo - Batchruntomo, fixed a problem where dual axis datasets where rerun as single axis. Also fixed a problem where the last dataset always had a "failed" status if previous dataset had failed.

7/19/16: In Etomo - Batchruntomo fixed the project log, which wasn't showing the dataset start message.

7/17/16: In Etomo - Tomogram Generation, removed unnecessary document listener processing.

7/17/16: In Etomo fixed how instances of plugins are provided.

7/17/16: In Etomo fixed tooltips, which where defaulting to usage strings.

7/16/16: In Etomo - Settings, Fixed box title.

7/11/16: Added batchruntomo MakeSubDirectory to the Batchruntomo interface, so stacks can be delivered to subdirectories of their current locations.

5/30/16: Fixed problems created if is rewritten when sample is running.

5/4/16: In eTomo -- cpu.adoc processing, removed unnecessary qos variable processing.

5/4/16: In eTomo fixed a tooltip formatting problem which affected text fields associated with checkboxes.

5/4/16: In eTomo added handling of the %{default} variable for tooltips.

4/29/16: Fixed RemoteDirectory output to batch command file.

4/19/16: In eTomo prevented the use of arrow keys to select radio buttons, as this does not cause the associated action to be performed.

4/19/16: In eTomo improved the functioning of the table hotkeys.

4/19/16: In eTomo - Reconstruction Setup, fixed the inconsistent handling of the twodir template directive.

4/11/16: In eTomo - Reconstruction Setup, fixed the "--directive" parameter functionality, which was failing on a file name without a path.

4/4/16: In eTomo - Settings fixed a bug which had caused the GPU checkbox to disappear.

4/3/16: In eTomo fixed a bug involving the "-directive" parameter: a value without a directory path was being treated as an empty file.

4/3/16: In eTomo - Subvolume Averaging (PEET), fixed the saving/loading of the reference volume when templates are used.

4/3/16: In eTomo added support for the %{qos} variable in cpu.adoc.

3/29/16: In eTomo - Fiducial Model Generation upgraded the transferfid mirroring options to match the parameter values.

3/23/16: Fixed a problem in eTomo - Align Serial Sections where the boundary model was not being opened in 3dmod for non-montaged sections.

3/23/16: In eTomo - Nonlinear Anisotropic Diffusion, added more field validation.

3/23/16: In eTomo, no longer saving the more/less state of the parallel process table in order avoid a strange dialog state when nothing is selected.

3/23/16: In eTomo - Clean Up, added _3dfind3d.rec to the list of files to remove.

3/23/16: In eTomo fixed a problem that caused invisible button text in disabled and selected buttons.

3/17/16: In eTomo - Final Aligned Stack - Erase Beads 3D, reducing binning for small bead sizes so as to avoid a validation error.

3/16/16: In eTomo added hotkeys for moving the row selection in tables ([Alt]+[Up-Arrow] and [Alt]+[Down-Arrow]). Also added [Home] and [End] table hotkeys.

3/12/16: In eTomo - Final Aligned Stack using the no-gaps fiducial model for 2D gold erasing when possible.

3/9/16: In eTomo, fixed a null pointer exception.

3/7/16: In eTomo added support for initializing and deinitializing a queue from processchunks.

3/4/16: In eTomo - Batchruntomo Interface, expanded the start and end steps table.

3/4/16: In eTomo fixed the sizing of multi-line buttons on Mac OSx.

2/26/16: In eTomo - Template Editor, changed the directive checkboxes so that they enable and disable like standard checkboxes.

2/25/16: In eTomo, allowing a greater variety of version strings.

2/19/16: In eTomo fixed a compile bug by removing a dependency on JUnit.

2/19/16: In eTomo fixed a problem where is was impossible to change the file associated with a specific 3dmod instance. This has been changed only where multiple 3dmod instances of the same type are used - generally this would be in a table.

12/21/15: In eTomo fixed a bug which prevented radio buttons from being disabled.

12/20/15: In eTomo - Batchruntomo Interface, handling the ImodCalib/Distortion file choosers in the same way as they are handled in the Setup Reconstruction dialog.

12/16/15: Fixed batch bug where the trimvol checkbox was loading incorrectly.

11/13/15: In eTomo - Fine Alignment Dialog, default "Find weights for contours..." to checked when appropriate.

11/13/15: In eTomo - Setup Reconstruction, added a default for the bidirectional starting angles.

11/11/15: In eTomo, fixed a null pointer error when processing the directives csv file, and added tests to prevent incorrect directive definitions.

11/2/15: In eTomo - Batchruntomo Interface, fixed problems with saving.

10/22/15: In eTomo - Batchruntomo Interface, fixed template handling, field value loading, field highlight values, and saving.

10/22/15: In eTomo - Batchruntomo Interface, removed the Don't use existing alignment checkbox, and added a checkbox to enable all the starting steps.

10/22/15: In eTomo - Reconstruction Setup, saving the value of comparam.golderaser.ccderaser.ExpandCircleIterations in the .edf file.

10/22/15: In eTomo, storing the results of running "setupcombine -info".

10/8/15: In eTomo, pulled in image rotation from the last newst run from batchruntomo.

9/19/15: In eTomo - PEET, fixed a crash caused by a very large number of volumes or iterations. Also wrapped .prm file values that are not wrapped.

9/18/15: In eTomo - Batchruntomo Interface fixed a problem where Start From step where not available when a dataset was complete.

9/18/15: In uitest switched a test to using automatic patch fitting exclusively.

9/18/15: In eTomo - Tomogram Reconstruction fixed problems with backward compatibility when running newstack.

9/4/15: In eTomo fixed a problem with the parallel processing table CPU total field not updating.

9/3/15: In eTomo - Batchruntomo Interface, keeping the Run Actions enabled.

9/3/15: In eTomo - Batchruntomo Interface, fixed a problem in the table where Reached values where being set incorrectly.

9/3/15: In eTomo - Batchruntomo Interface, fixed the default for the Start From radio buttons.

9/3/15: In eTomo - Batchruntomo Interface, fixed Reset button functionality problems in the table.

9/3/15: In eTomo - Batchruntomo Interface, fixed problems interpretating the batchruntomo log file.

9/1/15: In eTomo - Tomogram Combination running "setupcombine -info" with Python so that it works on Windows.

7/25/15: In eTomo - Batchruntomo Interface fixed problems found in previous version of the interface.

7/7/15: In eTomo - Fiducial Tracking - fixed a bug where was not being updated for automatic seeding, which made it work poorly for binned data.

7/7/15: In uitest created a test against BB that uses automatic patch fitting exclusively.

6/2/15: In eTomo - Fiducial Model, made generating the seed model automatically the default.

6/1/15: In uitest, added a system template to the reconstruction tests.

6/1/15: In eTomo - Setup Reconstruction, fixed a problem reading templates where the dialog was not completely updated to reflect the single/dual axis setting.

5/29/15: In eTomo, creating ta* align logs when it is necessary to read them.

5/29/15: In eTomo - Batchruntomo Interface, fixed a bug in autodoc writing - where a new line was not issued for a directive without a value.

5/20/15: Fixed problem with eTomo trying to make a patch track com file while the .preali is still being built.

5/18/15: In eTomo added a basic plugin framework and plugin niche in Tomogram Generation.

5/13/15: In eTomo - Batchruntomo Interface, connected the Two Surfaces checkbox to the right directive so that it has an effect.

5/5/15: In eTomo - Batchruntomo Interface, corrected the instructions in the project log for Windows.

5/4/15: Fixed running Batchruntomo from etomo's command file under Cygwin.

5/1/15: In eTomo - Tomogram Combination, automatically filling in Z min/max when "Use automatic patch fitting" is selected.

5/1/15: In eTomo - Tomogram Combination, converted matchorwarp parameters to PIP.

4/24/15: In eTomo - Join fixed the trial join and rejoin "use every" spinners.

3/19/15: In eTomo - PEET fixed a problem where blurMaskStdDev was not being saved when "User supplied binary file" was selected.

3/8/15: In eTomo - Fiducial Model Dialog changed the transferfid -x parameter to an integer with two values (0 and 1). A third value will be added later.

3/8/15: In eTomo, Changed the processchunks GPU list divider to ":". In the Batchruntomo Interface, temporarily added instructions for running batchruntomo to the project log, fixed a problem with GPUMachineList and multiple GPUs, fixed problems with opening 3dmod, and fixed the way defocus is being displayed. Fixed a variety of formatting problems in the processor table.

2/25/15: Fixes to batch interface: model is put in right place if 3dmod is open already when Boundary Model checked; right-click operations on opening 3dmod work with boundary model checked; tilt series is loaded as integers; defocus is now in microns in the interface; non-interface entries in a starting directive file are not lost.

2/23/15: Fixed hang of eTomo when template editor is opened; made batch interface put out : as separator in CPU list.

2/7/15: Fix batch interface to put out gold=0 when there are no fiducials, needed to get through tomogram setup for patch tracking.

1/10/15: Various PEET interface changes for working with single-particle volumes and with masks.

10/1/14: In eTomo - Tomogram Combination, added variables to hold matchorwarp parameters structurecrit and extentfit.

9/4/14: In eTomo - PEET, handling a reference without brackets in the .prm file. Also added line numbers to the parsing error messages.

9/4/14: In eTomo - uitest, fixed values that where not working with changes in IMOD. Added a test for a fiducial size of 0.

8/15/14: In eTomo - PEET, added a radio button for setting yaxisType to 3.

7/21/14: Modified uitest to work with the new way IMOD is solving for angles.

4/1/14: Improved unit tests for the PEET interface in eTomo.

Changes in 3dmod

** 8/7/14: Changes for 3dmod image processing: Kept track of sequence of operations so that they can be reapplied easily; added buttons to remove last one from list, redo all operations, and list the command-line operations in the Info windows; added option to save modified data to memory automatically; made thresholding able to update continuously; added File-Process File menu item to apply operations to image file or subset inside rubber band.

* 12/17/15: Improvements in Livewire to make it work better with large areas.

* 11/13/15: Made Xyz window able to average multiple slices.

* 11/13/15: Made Slicer do zooms less than 0.8 with antialiased image reduction instead of sampling.

* 8/28/15: Added preference to turn off vertex buffer drawing for line drawing; to be used on systems that give persistent artifacts.

* 7/29/15: Created an open channel between contours instead of overlapping connectors when joining closed contours in 3dmod, and made it avoid a self-crossing joined contour when one contour is inside another. Also made the join tool in Drawing Tools work with one contour inside another.

* 10/2/14: In 3dmod, added Ctrl-X hot key to open XYZ, added K to toggle centering in Zap, switched contour copy key from K to Shift+K.

* 8/30/14: Added button to export graph values to file from 3dmod Graph window.

* 7/12/14: Added Object menu item to fill in Z in all contours.

* 4/8/14: Add ability to copy a contour as its equivalent ellipse in 3dmod, and get report of equivalent ellipse parameters in imodinfo.

* 9/25/16: Made ghost display in Zap window show lighter and darker colors when displaying from two directions, and added ghost display of scattered points.

* 7/30/16: Made Imodsortsurf able to split the mesh in an isosurface object into multiple surfaces or objects, and added button to the isosurface dialog to save an object with mesh sorted into surfaces. Added ability to select a surface in such meshes by right clicking in Model View or with Surf/Cont/Point dialog, and to apply fine grain changes to them. Imodinfo can now report surface areas and volumes of surfaces in these meshes.

* 6/27/16: Made 3dmod able to read TIFF files in parallel, with big speed-ups for compressed TIFFs.

* 6/8/16: Added new ways to estimate scaling limits in 3dmod for files without scaling information, and options and preferences to control what method is used for this and for scaling data generally.

1/10/17: Added hot key for changing isosurface threshold to other side of the distribution, and made a newly displayed volume be given a threshold equivalent to that of the previously dsiaplyed volume.

9/25/16: Speeded up tapering of image at edge of fill area and fixed very long tapering times when taking an FFT in Slicer of a large, zoomed-down image.

8/24/16: Fixed some problems with the Eraser in Drawing Tools.

6/27/16: Fixed -s scaling option to 3dmod, broken 6/18/16, and made scaling work properly when reading RGB's in as gray-scale.

4/26/16: Enabled editing of extra objects when running as 3dmodv.

4/24/16: Fixed uninitialized variable that could make scale bar not work when opening as 3dmodv.

11/13/15: Added option to the 3dmod scalebar dialog to set an exact length.

10/27/15: Fixed 3dmod loading of > 2GB montages, which crashed on Mac.

10/24/15: Made loaded color ramp in 3dmod apply to value drawing; moved magenta from bottom to top of standard color ramp to make bottom and top more distinguishable.

10/8/15: Preference to turn off vertex buffer drawing applies for spheres too.

9/16/15: Made mouse point readout in Pixel View get updated when Z changes.

6/27/15: Added 3dmod preference to enable the S hot key to turn on hardware stereo, which is off by default on Macs, to prevent accidentally turning on non-functional hardware stereo.

6/13/15: Fixed saving of transparency for 3dmod movie sequences.

5/2/15: Added more 3dmod messages for setting object properties.

2/25/15: Made messages to 3dmod able to contain spaces in filenames.

10/14/14: Added rubber band size to Slicer toolbar when size is being changed.

10/10/14: Fixed -O option to 3dmod, broken in 4.8.7.

9/7/14: Fixed 3dmod loading of subset in Z for non-cached data.

8/22/14: Fixed problem with movie snapshots starting with the current image instead of starting one on some systems; made Slicer movies do double shots on ends the same as Zap ones do.

6/25/14: Fixed problem keeping track of opened files when reading multiple files into 3dmod.

6/16/14: Remove 6/5/14 automatic use of .pl file, since it then uses it inappropriately on blended file.

6/5/14: Made 3dmod automatically get piece coordinates from a .pl file with same root name as single image file entered.

Changes in General Processing Programs

** 12/28/15: Added program for aligning movie frames, Alignframes.

* 4/16/16: Color file changes: made 3dmod -G work with color TIFF files; made colormap TIFF files look like RGB files to all programs; made programs reading in data as floats, including Newstack and all Fortran programs, able to read in RGB data as gray-scale floats; kept 3dmod from turning on high-quality interpolation by default with colormap data.

* 3/7/16: Alignframes can now break a large frame file into sets for aligning and summing, and take tilt angles and a gain reference from an extended header, so it can process tilt series frame files from UCSFtomo easily.

* 3/4/16: Added expansion of wild cards in command line filename arguments on Windows, which now works for programs taking multiple input files (3dmod, Tif2mrc, Raw2rmc, Newstack, Clip, Imodmesh, Imodinfo, Imodjoin, Subm) as well as many others.

* 2/15/16: Added a program Framewatcher to watch for command files or frame stacks and run Alignframes as they appear.

* 1/10/16: New version of Alignframes can run on GPU.

* 9/18/15: Added support for a new 4-bit file mode for MRC files, 101. Made the file reading system convert this to bytes on input, and also recognize the 4-bit files written as byte mode by the SerialEMCCD plugin to DigitalMicrograph. TIFF files that are 4-bit can also be read and treated the same way, as well as the 4-bit packed byte files written by SerialEMCCD. Clip unpack now works with all kinds of input data and was given a new more general name, normalize.

* 9/10/15: Added option to Clipmodel to include or exclude parts of model inside of boundary contours.

* 2/13/15: Supported reading of nonstandard large TIFF files from ImageJ; got min/max and pixel size from image description of ImageJ files.

* 2/13/15: Made Newstack able to write TIFF files > 4 GB correctly and added an environment variable that can be used to get all TIFF files to be written in large file format.

* 2/12/15: Switched to writing bytes as signed by default.

* 1/3/15: Added option to Newstack to shift images with phase shifts in Fourier space instead of with interpolation.

* 10/15/14: Made alterheader take command-line arguments with PIP.

* 6/17/14: Made Extracttilts able to output the metadata in an HDF file in autodoc format.

* 6/6/14: Made Extractpieces and Extracttilts take information from an associated .mdoc file automatically as a fallback and work with metadata in an HDF file also; made Extracttilts able to extract the text strings for any metadata in .modc or HDF file; made 3dmod able to take piece coordinates from an HDF file.

* 4/30/14: Made Mrc2tif able to read all file types including JPEG/PNG/BMP.

* 3/23/14: Eliminated an input routine that reads line-by-line, which was giving terrible 3dmod performance on Mac laptops loading over a network.

1/8/17: Fix defect correction in Alignframes, which was being given the wrong image size; fix bad row correction in Alignframes and Clip for multi-pixel-wide rows to go over correct range of rows; fix use of truncation instead of rounding for bad/row column correction; implement averaging over several pixels outside of multi-pixel wide bad rows/columns.

1/6/17: Added option to clip for filling in dark edges left by drift correction with a OneView camera.

11/18/16: Fixed reading of BMP, PNG, and other odd image formats by Mrc2tif.

11/15/16: Added support for general reading and writing of JPEG files.

11/14/16: Fixed Alignframes with -pair -1 entry and grouping.

10/4/16: Added options to point2model to set line width in 2D and 3D.

9/22/16: Fixed reading of DigitalMicrograph files > 2 GB on Windows.

6/27/16: Added options to Framewatcher to watch stacks without a master command file, run an entered command before or after processing, and produce an MRC file with a reduced image or a JPEG with a side-by-side reduced image and power spectrum.

6/27/16: Parallelized a preprocessing step and reading of TIFF files in Alignframes.

6/23/16: Added option to Newstack to use one section list for all input files.

6/23/16: Made imodinfo report mesh volumes for each surface if available.

6/14/16: Added options to Nad and Mtk for setting name of Postscript graphics file.

6/8/16: Fixed problem with reading pixel size from some DM4 files.

6/8/16: Added ability to set file of commands as command-line argument to Mtk or Nda.

6/6/16: Added option to get unsigned byte output from Tif2mrc.

5/31/16: Added option to Nda to output all distances or angles measured between points to a file.

5/27/16: Added options to Vmstopy to add directories to the system path.

5/27/16: Fixed Processchunks to keep machine names in whatever case was entered to allow case-sensitive user names and so etomo can track progress.

5/25/16: Added an operation to Clip to get a square, scaled, reduced power spectrum.

5/22/16: Converted Assemblevol to PIP input, made it easy to use for pasting together nonoverlapping images/volumes, fixed bug when NZ=1.

5/21/16: In MtfFilter, added option for filtering equivalent to doing a given number of SIRT iterations, added option for noise tapering, and made padding proportional to image size above 1K.

5/12/16: Fixed onegenplot/genhstplt when it draws a dashed line at Y=0 to draw the right number of points, not 25.

5/5/16: Allowed Point2Model to take X,Y point lists with no Z coordinates.

5/4/16: Added script Expandargs to expand filename arguments on Windows and run a command or save a file with the list or an input list for Newstack.

4/29/16: Added Newstack option to set an offset for distortion correction of an image not centered in the camera field.

4/29/16: Increased line lengths for general PIP input to 102,400 characters and made several changes to Newstack to allow longer section list entries either through the -sec option or the -filein option.

4/26/16: Added logarithm and square root to Clip.

3/31/16: Fixed GPU memory leak in Alignframes.

3/29/16: In Alignframes, made -pair -1 work for > 10 frames; fixed problems with falling back from GPU to CPU in mid-alignments; enabled up to 10% zero weights in robust regression; fixed robust regression when no zero weights.

3/25/16: Added option to Newstack for image reduction by cropping of the FFT, which can be combined with shifting.

3/16/16: Made Tif2mrc work with big TIFF files from ImageJ.

2/19/16: Added option to subimage to get text file with difference output.

2/16/16: Fixed mtk memory allocation and some numeric problems.

2/15/16: Duplicate contours are detected when meshing or using Imodmop, so Imodmop will not fail to paint them, and Imodmesh will report them.

2/15/16: Added options to Alignframes to skip initial file checking and to write an adjusted mdoc file.

2/9/16: Added options to Alignframes to enter a file with a list of input files and to combine successive sets of single-frame files into groups to align and sum.

2/1/16: Made Clipmodel use boundary contours on nearest section unless a new option is given to keep points only if inside a contour on the same section.

1/28/16: Alignframes is complete.

1/26/16: Added script Subtractcurves for getting differences between curves in corresponding files.

1/15/16: Added option to point2model to set image max values in model header.

1/14/16: Fixed clip norm to work on integer/floating point files, fixed scaling problems, made it truncate normalized data, and made it replace values being truncated with surrounding mean by default.

12/28/15: Transferred description string in Tiff file into titles in MRC-like header.

12/28/15: Fixed problem in Clip defect correction.

12/10/15: Fixed memory allocation bug in Clipmodel.

12/6/15: Added option to Imodtrans to rotate model like "clip rotx".

11/8/15: Made Binvol able to do antialias reduction in X and Y.

10/30/15: Fixed Mtk for Mac.

7/1/15: Added option -title to alterheader for adding one title.

7/1/15: Fixed MRC header library to replace 10th title when adding a new title, as old library used to.

6/23/15: Fixed header output for -origin for negative values.

6/15/15: Fixed bogus warnings in header output.

6/13/15: Changed fortran program model reading to open read-only.

5/9/15: Parallelized Imodauto.

5/6/15: Added option to Imodtrans to set the image reference information of model to a given image file before any operations.

5/3/15: Added RMS value to standard Fortran header output if it was apparently computed and added -rms option to Header program. Started initializing RMS as -1 to conform to new 2014 MRC standard and added support for the MRC version number.

4/30/15: Added -M option to Clip to do thresholding with a minimum size in 2D or 3D for regions beyond the threshold on one side.

4/3/15: Clip histogram has a new option to report a percentile point and options for some more specialized analysis.

3/31/15: Fixed clip average and other operations broken by 2/14/15 changes.

3/28/15: Made clip unwrap copy extra header when full file is processed.

3/26/15: Fixed slashmasksort.

3/3/15: Fixed clip filter to work with images having only one factor of 2 in X (e.g., K2 images).

2/25/15: Fixed Midas for reference section other than 0.

2/20/15: Processchunks and Batchruntomo changed to take : instead of # as separator in CPU entry; Batchruntomo now allows entries of 1 and limits the number of threads used when running a single command file.

2/13/15: Added option to Queuechunk to allow resources to be set.

2/11/15: Added option to Newstack to process some or all input files in reverse order.

2/11/15: Added options to Densmatch to scale to a given mean/SD, change the mode for a new output file, and assess the existing density using all pixels instead of a sample of pixels.

1/8/15: Make Boxstartend fill to mean of existing data when extracting only one slice per point.

12/4/14: Made Processchunks give an error with more than 100,000 chunks.

11/28/14: Various fixes related to model Z coordinates starting at -0.5 instead of 0: fixed half-pixel error when rotating model by 90 degrees; fixed Findbeads3d to put out Z coordinates starting at -0.5; fixed Tilt to reproject models other than those from Findbeads3d correctly; added options to Model2point and Point2model for working with point coordinates that have Z starting at 0; clarified in documentation.

10/12/14: Fixed uninitialized quiet option in Newstack.

10/7/14: Clip histogram with -s option will analyze for bimodal distribution of values and report fraction with low values.

9/25/14: Added option to Newstack to suppress most typical output.

9/17/14: Added a threshold command to Clip and made 3dmod image processing able to apply this in some cases.

8/18/14: Added options to Mtffilter to filter in 1-D and to apply an R-weighted filter.

8/7/14: Added option to change output mode from Mtffilter, and a warning when output is out of range for the existing mode.

7/31/14: Fixed clip corr giving non-zero exit status on Windows.

6/17/14: Added option to Edmont for entering sections numbered from 1; made it access piece list in .mdoc or HDF file; made it able to transfer metadata in .mdoc or HDF files from input to output.

6/6/14: Added script for copying header of MRC file.

5/8/14: Added an option to Clip to specify a defect correction file for K2 images.

4/16/14: Allowed new output mode for clip flip operations except yz and rotx.

Changes in Infrastructure

** 3/22/14: Programs can now read and write HDF files interchangeably with MRC files. Metadata can be stored as well; Newstack will move metadata between an HDF file and an .mdoc file associated with another file type, or even between two mdoc files. Supported HDF files can consist of stacks of 2D images of the same size, or files with multiple 3D volumes, which 3dmod will open like multiple files. Makepyramid can make a multi-volume HDF file that 3dmod will recognize as an image pyramid.

* 4/4/16: Added support for slurm-type queues with or without exclusive allocation.

* 12/7/15: Changed starting install script to bash, so it is now run with "sh" instead of "csh -f".

11/13/16: Limited routines using OpenMP to using number of physical cores.

11/12/16: Mrc2tif will now do ZIP or LZW compression in parallel.

11/9/16: Improved reading time of Clip generally, made it read in parallel from compressed TIFF files, and parallelized normalization.

9/7/16: Fixed some problems with HDF file access and enabled parallel writing to HDF files.

8/24/16: Made Etomo startup script find and use Oracle java after faulty installation of JRE on Mac that fails to set link in /usr/bin properly.

7/17/16: Changed the name of etomo (eTomo to Etomo).

6/9/16: Made analysis of header data in DigitalMicrograph files run much faster on a series of similar files.

4/4/16: Windows IMOD installer can now find Windows Python regardless of 32/64-bit types on Windows 7 and 8.

12/29/15: Fixed help viewer display of JPEG images on Windows.

11/13/15: Fixed linklibs-mac to make links in permitted directories on OS X 10.11 and above.

7/1/15: Fixed plugin help on Mac.

1/3/15: Added script imoduntar for listing or untarring a file, to use on Windows without Cygwin.

3/27/14: Fixed HDF writing, optimized chunk cache size for volume writing, fixed pyramid creation, made 3dmod recognize tiling in HDF file.