Change for IMOD 4.9.13 on Mac

7/30/19: On Mac, made Etomo startup script look for Java in current installation location if it is not on path.

Bug Fixes for IMOD 4.9.12

3/23/19: Stopped putting wrong dependency in manifests for newer Windows versions and added supported OS information to manifests.

3/1/19: Fixed Imodtrans reading image headers of non-MRC files.

2/1/19: Fixed use of backup directory on Etomo setup page when specified as C:\Users... in Windows.

Bug Fixes for IMOD 4.9.11

1/1/19: Fixed defect correction to replace isolated bad pixels.

1/1/9: Fixed Alignframes initial alignment when using groups with refinement at end.

11/17/18: Fixed installIMOD for running at command line in Windows without Cygwin.

10/5/18: Fixed etomo startup script's test for whether to run an installed JRE on Mac OS.

Bug Fixes for IMOD 4.9.10

9/24/18: Fixed Ctfphaseflip to rotate the astigmatism angle from what was found on the raw stack to the angle in the aligned stack, provided that the transform file is provided.

9/4/18: Fixed Excise to use memory allocation.

8/20/18: Fixed Boxstartend for extracting volumes > 2 GB.

8/9/18: Fixed sphere radius output from imod2vrml2.

Bug Fixes for IMOD 4.9.9

6/29/18: Add K3 camera sizes to function that recognizes byte mode files as having 4-bit data.

6/29/18 Made installer handle lack of Python 2 in default Ubuntu install (In 4.9).

5/23/18: Fixed patch tracking in Tiltxcorr when skipping a view adjacent to the minimum tilt view.

5/17/18: Fixed setting of last object transparency value in model view making. (In 4.9).

5/14/18: Fixed bugs in Imodsortsurf and 3dmod isosurface Sort&Save.

Bug Fixes for IMOD 4.9.8

4/13/18: In Etomo - Batchruntomo fixed a null pointer exception that may prevent all or part of the interface from loading.

4/12/18: Raised Etomo memory limit from 128 to 512 MB.

4/12/18: In Etomo - Batchruntomo fixed problems with the row-level popup dataset dialog. It was not represented in the task bar and did not resize.

3/29/18: Fixed Newstack, Tiltxcorr, and Xfsimplex to allocate enough memory when doing large antialiased reductions with very large images.

3/20/18: Fix -mode command in Trimvol.

Bug Fixes for IMOD 4.9.7

3/7/18: In Etomo - Tomogram Positioning corrected the setting and saving of the gold bead size.

3/6/18: Fixed crash when image loaded through Qt does not have a colormap.

3/5/18: Fixed 3dmod loading when option to scale by mean/SD when available is selected.

2/23/18: Made Ctfplotter fix angular range so it always contains at least one angle.

2/19/18: In Etomo - Serial Sections - Preblend saved disabled values.

2/19/18: In Etomo - Serial Sections allowed any file extension when opening the raw stack.

2/9/18: Changed the copy of cygwin.exe in Cygwin to a hard link to solve "resource unavailable" errors running Tomosnapshot from Etomo.

Bug Fixes for IMOD 4.9.6

2/9/17: Changed the copy of cygwin.exe in Cygwin to a hard link to solve "resource unavailable" errors running Tomosnapshot from Etomo.

1/22/18: Prevented out-of-range min and max values from being put in TIFF files.

1/16/18: Fixed two problems with warping and boundary models in Tiltxcorr (In 4.9).

1/16/18: Fixed bug interpreting pixel sizes when reading warp files into Midas.

12/22/17: Made IMOD installer set CYGWIN to nodosfilewarning to prevent stupid messages about Windows paths.

12/17/17: Added directive to cryo template to taper final aligned stack inside instead of outside.

12/16/17: In Etomo - Post Processing corrected how trimvol values are initialized and reinitialized.

12/13/17: Qt programs set an environment variable in Linux to prevents hangs when running a process.

12/11/17: In Etomo - Serial Sections corrected how the values of the preblend settings ReadInXcorrs and OldEdgeFunctions are set.

12/6/17: Fixed ability to run 3dmod on Mac by clicking on it.

12/1/17: In Etomo - Template Editor removed the value of the starting angle of a bidirectional series (twodir) when it is not checked in Reconstruction Setup.

11/30/17: Limited the binning that Transferfid and Matchrotpairs send to Tiltxcorr to the maximum allowed there.

11/19/17: Fixed extraction of tilt angles from new-style FEI header where they were not stored with the wrong scaling.

11/15/17: Fixed saving of 3dmod option to not use vertex buffer objects for line drawing.

10/12/17: Fixed Midas and Tiltxcorr for > 2 gigapixel images.

10/10/17: Fixed scaling applied by -float 4 in Newstack.

Bug Fixes for IMOD 4.9.5

10/4/17: Fixed some newstack problems when using > 8 GB of memory.

9/30/17: Fixed Framewatcher failing to move directory with tilt series frame stacks.

9/11/17: Fixed -float 4 option to Newstack.

9/11/17: Fixed Copytomocoms editing of for some simple one-letter dataset names.

8/28/17: Fixed Findbeads3d computation of array size to allocate for volumes of > 2 gigapixels.

7/21/17: Fixed color box in Model View Edit Objects window on Windows Qt 5.

7/17/17: Fixed writing of image planes bigger than 2 GB to MRC files on Mac and Windows.

7/13/17: Disabled parallel reading from uncompressed TIFFs and turned off memory mapping when reading TIFF files into 3dmod.

7/5/17: In Etomo - Batchruntomo fixed a problem where the delivery choices disabled before validation succeeded.

6/29/17: Changed clip rotx/flipyz to use up to 40% of computer memory and to run faster on very large files.

6/23/17: In Etomo - Batchruntomo removed an incorrect file validation.

Bug Fixes for IMOD 4.9.4

6/20/17: In Etomo adding an empty line onto the end of multi-line messages. Also adding a new copytomocoms message to the project log.

6/19/17: In Etomo - Batchruntomo improved the handling of empty bead size fields.

6/17/17: In Etomo - Batchruntomo filling in row values from the templates on reload.

6/14/17: Added setting to 3dmod to turn off vertex buffers when drawing meshed spheres, which can screw up im Ubuntu.

6/8/17: Made build system able to produce an IMOD package without 3rd party library and a separate package with libraries to reduce download size on upgrades.

6/2/17: Fixed 17 programs that did not give usage statements with -h.

6/2/17: In Etomo changed 3D gold erasing in Final Aligned Stack to always get Z shift from the align log.

6/1/17: In Etomo - Final Aligned Stack, made the 3D gold erasing thickness an integer in the .edf file.

6/1/17: In Etomo - BatchRunTomo Interface, corrected the saving and loading of the autoFitRangeAndStep directive.

6/1/17: In Etomo - BatchRunTomo Interface, saving the correct boundary model directive.

6/1/17: In Etomo - Directive Editor, creating the location of the user template when necessary.

6/1/17: Fixed some format issues with BatchRunTomo Interface.

5/23/17: Prevented bad scaling in model view if it is opened with a model having just empty contours.

5/22/17: Made Tiltxcorr able to reject fixed pattern peak better by increasing maximum allowed shift for such a peak.

5/22/17: Made Newstack adjust for increased range of data after interpolation when floating to common mean and SD, so it doesn't truncate large numbers of pixels when making the prealigned stack. Also fixed truncation at -32767 when making aligned stack in mode 1.

5/22/17: Fixed computation of standard deviation in Clip, Newstack, and Ccderaser when it is much smaller than the mean, which makes X-ray removal and creation of a floated byte stack work correctly for K2 counting mode data acquired with FEI software.

5/18/17: Increased field widths for piece list outputs from Blendmont, Extractpieces, Edmont, and Reducemont.

5/18/17: Fixed problem with Newstack inserting tilt angles in a new extended header.

5/17/17: Fixed Interpolator so undo only undoes the last interpolation action, not all interpolations since any other modeling was done.

5/11/17: Fixed crash from using a saved movie sequence with image display in 3dmodv.

5/11/17: Fixed two problems that made clip crash in cryopositioning on Windows (In 4.9).

5/6/17: Made Bead Fixer prevent a second point in contour on same view and duplicate seed points.

5/6/17: Fixed problem running Blendmont with -nofft option.

4/26/17: In Etomo - Batchruntomo fixing maximum table size configurability (In 4.9).

4/25/17: Prevent writing of TIFF file in parallel if no compression or if color data.

4/21/17: In Etomo - Nonlinear Anisotropic Diffusion corrected the enabling of the "Save" menu item.

Bug Fixes for IMOD 4.9.3

4/17/17: Starting using system seek call directly on 64-bit systems, solving very slow seeking for files bigger than 256 GB in Linux.

4/17/17: In Corrsearch3d, trimmed tail off bottom end of histograms to improve ability to detect dips.

4/15/17: In Etomo - Join Serial Tomograms made local fitting and reference section checkboxes mutually exclusive.

4/14/17: When Copytomocoms and Autofidseed make subdirectories, they try to make sure they are writable on Windows.

4/12/17: Made Corrsearch3d use fallback criteria initially if too many patches are eliminated after structure histogram analysis and increased fraction trimmed off of top of histogram analysis to exclude gold better.

4/12/17: Made -d option to imodhelp work for people without source.

4/12/17:In Etomo - Post Processing fixed a problem where a modified tomogram size was not reflected in Trimvol dialog values.

4/7/17: In Etomo, fixed a problem where the Batchruntomo Interface would not come up when no calibration directory was available.

4/6/17: In Etomo, reduced repetition in the error log when debug is on. The stdout from processes run by etomo will be sent to the error log starting at debug level 2.

4/6/17: In Etomo, added handling for new batchruntomo .edf file entries.

4/5/17: Made Batchruntomo use directive rather than existing value in com file to decide whether to use local alignments.

4/5/17: Fixed Subtomosetup for use with binned aligned stack.

4/2/17: Added option to Framewatcher to set time to wait after a stack stops being modified.

3/31/17: In beadhelper plugin, fixed file filter for loading tilt angle file, fixed incorrect test for problematic tilt increments, switched from hard-coded English character for degree sign to "deg".

3/31/17: Fixed genhstplt and other Fortran graphics programs to run under Qt5.

3/31/17: Increased patch size limit to 40000 in Ccderaser.

3/27/17: In Etomo fixed the tests run by uitest.

3/17/17: In Etomo reduced log messages coming from file operations.

Bug Fixes for IMOD 4.9.2

3/17/17: Made installer copy startup scripts to /etc/profile.d for Ubuntu versions > 9 since this mechanism now works.

3/16/17: Made tapering outside for tilt series aligned stack use smoothing to reduce artifacts generally and especially for K2 data.

3/15/17: Made Corrsearch3d reject implausible dip from histogram analysis and not eliminate patches for having low structure measure iff too many are eliminated.

3/15/17: In Etomo - Template Editor loading values directly from the template and batch directive files.

3/14/17: In Etomo added the templates to the setupcombine call.

3/12/17: Fixed Drawing Tools sculpt mode so that removing intersections does not take unreasonable time for huge contours, and so that sculpting in a reduced contour does not add points back everywhere, only near the mouse.

3/11/17: In Etomo - Batchruntomo fixed the handling of com/batchDefaults.adoc when saving the batch autodocs.

3/10/17: Fixed Batchruntomo to ignore errors inside the lines of CHUNK ERROR output from Processchunks.

3/10/17: Virtually all command line programs will print usage with just a -help option, in most cases with just -h.

3/4/17: In Etomo fixed the handing of empty comments in autodoc files.

3/3/17: Modified Alignframes pairwise option to specify 1/2, 1/3 or 1/4 of frames.

3/2/17: Made preNAD copy extended header properly to output file.

3/2/17: Fixed preNID option specifications so that it runs, made it copy extended header to output file and set min/max/mean of output file, added some detail to the man page to make the program potentially useful.

2/28/17: In Etomo - PEET corrected that storage and display of the Missing Wedge Mask in the Volume Table.

2/28/17: Added option to 3dmod Contour Move dialog to do all points in contour when converting spherical points to a set of circular contours.

2/28/17: In Etomo - Tomogram Positioning fixed a dialog update problem that was occurring after running cryoposition. 2/27/17: Made initial Zap window be sized right when -iz option is used and there is not a previous window size available

2/27/17: Made tomosnapshot copy header of .st file and take thumbnails of .preali or .ali for montage if possible.

2/27/17: Made Copytomocoms give a warning when starting and increment angles seem to go in wrong direction, and Tiltxcorr suggests this in its error message when cosine stretching is on and the angle goes through 90.

2/27/17: Fixed 3dmod going back to previous surface when a new contour is started after pressing N or New surface.

2/27/17: Made Colornewst work if JPEG output is specifed by environment variable and indicated HDF and TIFF capabilities in man page.

2/26/17: Cleared out offsets in 3dmod model offset dialog and updated model header dialog when new model is loaded.

2/26/17: Fixed problems in Transferfid when Edmont is used to extract a subset of montaged stacks for processing.

2/26/17: Made Midas report error and not try to work with warp transforms if the pixel size was set in the volume after finding the transforms.

2/26/17: Fixed some problems in Blendmont with only one piece.

2/26/17: Added environment variable to set size of boundary region when writing in parallel to an MRC file.

2/24/17: Fixed Tiltxcorr crash when finding warping and there are fewer than 3 points on a view.

2/24/17: Fixed some problems with freezing and slow loading with the 3dmod tile-strip cache.

2/23/17: Fixed reading of image planes bigger than 2 GB from MRC files on Mac and Windows.

2/22/17: In Etomo - Fiducial Model Generation solved a problem where the autofidseed values did not transfer when transferfid was run if the "from" axis dialog had not been opened.

2/22/17: In Etomo - Tomogram Positioning when cryoposition is used, zeroing out X axis tilt and Also fixed tomopitch.scaleFactor.

2/21/17: Added option to Clip normalize to specify rotation of gain reference.

2/18/17: In Etomo - Fine Alignment setting tiltalign.XTiltDefaultGrouping to a default when it is missing.

2/18/17: In Etomo - Tomogram Combination defaulted automatic patch fitting to on.

2/14/17: In Etomo - Tomogram Positioning corrected binning removed temporary binning fix for cryoposition.

2/14/17: Fixed Beadtrack light/dark bead detection if there is one bead.

2/13/17: In Etomo - Tomogram Positioning defaulted LeaveTempFiles to -1 in

2/12/17: Enabled all builds to be done with Qt 5.

2/12/17: Added new flag to Ctfplotter/Ctfphaseflip defocus file to invert tilt angles and indicated in man pages what to do when importing data with the -invert option set.

2/8/17: Changed ERROR: tag on messages from processchunks when it goes to kill a delayed job that never started to avoid confusing Etomo.

2/8/17: Fixed detection of need for light beads option in Beadtrack.

2/4/17: Fixed reading of gray-scale PNG files by Mrc2tif.

2/4/17: Made -G option of 3dmod work to read in PNG and other image formats read with Qt as gray-scale.

2/4/17: Fixed program name completion in Imodhelp for Cygwin.

2/2/17:In Etomo - Batchruntomo fixed a problem where removing excluded views did not work for dual axis tomograms.

2/1/17: Made Batchruntomo report when excluded views are removed and prevent removing them again if the list matches what was removed.

1/31/17: Added support for new FEI extended header and ability to read in new FEI files with inversion in Y.

1/24/17: Fixed extraction of piece coordinates over 32767.