Bug Fixes for IMOD 4.11.25

10/8/23: Fixed crash in Ctfphaseflip with X size of 4092 (i.e., K3 camera) and tilt angle of exactly 0; fixed strip width at exactly 0 tilt with a maximum width entered.

9/22/23: In Etomo - Fiducial Model, fixed the "Use Adjusted Track Com File" button, which was not functioning.

3/14/23: Fixed Batchruntomo problem running Splitcorrection with Python 3.

Bug Fixes for IMOD 4.11.24

2/3/23: Fixed Autofidseed problem with Python 3.

1/10/22: Fixed Sampletilt when the dataset name contains "slice".

12/22/22: Fixed a problem where most of the interfaces are unable to handle a missing file name style.

12/21/22: Fixed initialization of the back projection checkbox in batch interface.

12/7/22: Fixed Tiltalign crash from array that was too small when there are many views and few points.

Bug Fixes for IMOD 4.11.21

11/1/22: Fixed failure in Copytomocoms from not converting some directive values to float.

9/27/22: Add entry for autofidseed LowerTargetForClustered option.

9/27/22: In Etomo - Batchruntomo Interface, fixed a problem with the backprojection checkbox.

9/7/22: Changes to framewatcher to watch for EER files.

Bug Fixes for IMOD 4.11.20

9/1/22: In Etomo - Batchruntomo Interface, fixed some problems with the back- projection checkbox.

8/25/22: Switched to Qt 5.15.12 for Linux builds to solve a problem with being unable to resize or move windows after mouse-rotating in slicer.

8/3/22: Fixed 3dmod crash if model loaded during initial image load.

Bug Fixes for IMOD 4.11.19

7/29/22: Fixed no new line before MESSAGE: from Tilt if GPU not available.

7/28/22: In Etomo - PEET, fixed a problem where the processchunks monitor did not recognize any single-line messages from processchunks.out.

7/18/22: Changed defocus tolerance in ctfcorrection command file to 50 and made Ctf3dsetup and Subtomosetup use the slab thickness for this tolerance, since it determines the width of regions near the edges corrected at just one defocus.

7/12/22 In Etomo - Final Aligned Stack handling a config file with an incorrect path.

7/8/22 In Etomo - Tomogram Generation fixed the choosing of SIRT output tomograms to load into 3dmod.

7/7/22 In Etomo - Reconstruction Interface added missing image file name style recovery.

7/1/22: Re-enabled use of RGB data in Drawing Tools.

6/30/22: In Etomo - Batchruntomo Interface fixed a problem where a delivery was done on every run.

6/22/22: The minimum zero spacing in CTF correction is now defined as a float and setting it will no longer generate an error in Etomo.

Bug Fixes for IMOD 4.11.18

6/17/22: Fixed summing into power spectrum in Ctfplotter, which was off by a pixel in the upper half of the FFT and biased defocus by 10-20 nm.

6/14/22: Fixed wrong scaling of spherical aberration in Ctfphaseflip, which made it correct effectively 20-50 nm higher defocus and get off above ~5 A resolution.

6/11/22: Fixed Ctfplotter with pixel cropping to take tiles from correct locations; it was sampling more from one side than the other, not adjusting each spectrum properly for tile location, blurring the power spectrum, and giving increasingly biased defocus estimates with increasing tilt.

6/10/22: In Etomo - Reconstruction interface, fixing a problem that prevented a dataset created by batchruntomo from being loaded.

6/8/22: Ctfplotter: fixed the crop pixel option when running non-interactively; it was either not cropping or going into an infinite loop. Fixed the starting point for autofitting to be near zero tilt when running non-interactively. Fixed a memory leak.

6/6/22: Fixed Zap and Slicer snapshots having rubberband on edge with high-DPI monitors.

6/2/22: Fixed crash in Ctfphaseflip with GPU from accessing strip coordinates out of range.

Bug Fixes for IMOD 4.11.16

5/30/22: Made sure autocontrasting does not happen until the Zap window has been drawn.

5/26/22: Made Batchruntomo detect and recover from an Etomo error in dataset location when restarting from a step.

5/26/22: Fixed tile cache display in Zap window sometimes not being refreshed after all the tiles are loaded.

5/25/22: Made Makepyramid work with a single-image file.

5/22/22: Changed installer for Linux/Mac to put link to python, if needed, in a separate directory that is put on the back of the path.

5/20/22: Fixed skipping of global clip planes in model view.

5/20/22: Fixed sychronization of ghost and model view image display checkboxes when toggling with hot keys.

5/20/22: Stopping limiting EER Z-summing to 99 in 3dmod.

5/6/22: Fixed a test for extension types in Splitblend, Splittilt, and Splitcorrection.

4/26/22: Fixed direction of Step Up/Down buttons in Ctfplotter, broken 1/22/20, and improved treatment of autofitting range.

4/19/22: Stopped ctfplotter from interpreting a zero astigmatism as not being measured at all.

Bug Fixes for IMOD 4.11.14-15

3/29/22: Fixed Alignframes making unweighted sum with CPU.

3/21/22: Changed installer for Linux to make link to python3 or python2 in IMOD/bin instead of in /usr/bin when there is no "python" on the path, but for Mac OS 12 it will look for python3 from python.org, homebrew, or Apple Developer Tools and make the link directly to the first one it finds.

3/16/22: Fixed Imodtrans -I to store information needed for Point2model to give correct values.

3/15/22: Fixed excessive rounding of labels and improved axis limits in graphs from Genhstplt and Onegenplot.

3/7/22: Fixed Batchruntomo running Raptor with raw stack.

Bug Fixes for IMOD 4.11.13

1/10/22: Fixed some problems with Serieswatcher.

1/9/22: In Beadtrack, prevented the "rescue" search from taking increasing amounts of time for larger beads/smaller pixel sizes.

1/6/22: In Etomo - Batchruntomo Interface added a method to repair most batchruntomo datasets effected by the image filename style changing after the dataset has been created.

1/5/22: In Etomo - Batchruntomo Interface fixed a problem with image filename style changing after the batchruntomo dataset has been created.

12/6/21: Fixed setting linked slicers to the same zoom.

11/27/21: Fixed Xyzproj -90 deg projection using ray intersections.

11/19/21: Fixed Xyzproj accessing bad data in 90 degree projections.

Bug Fixes for IMOD 4.11.12

11/17/21: Made Sirtsetup pass through a MASK entry in the the tilt.com if it is larger than its default value.

11/17/21: When Framewatcher is used just to copy files, it will now avoid copying a tilt series file from SerialEM that is not finished, and it will copy gain reference and defect files listed in a frame stack header.

11/11/21: Allowed errors in encoding command output to Unicode in Python 3, so Copytomocoms will not fail if header titles have bad characters.

11/10/21: Switched to new Qt version for Mac package that allows closing Zap and other windows with the red close button.

11/10/21: Packed some "api-ms..." DLLs missing in some Windows 10 installs into the CUDA 10 package.

11/2/21: Fixed crash in Batchruntomo using fallback thickness when there is no measured thickness.

Bug Fixes for IMOD 4.11.11

10/27/21: Fixed crash exiting 3dmod with dialogs open on Mac.

10/25/21: Fixed zooming of Locator window on high-DPI monitor.

10/23/21: Added option to Framewatcher to avoid using Robocopy and possibly Xcopy as well.

10/19/21: In Etomo - Final Aligned Stack fixed a problem with tooltip formatting which caused Etomo to lock in rare cases.

10/13/21: Fixed Windows command-line installer to fix cygwin python properly.

10/13/21: Added workaround to EER gain reference defect string having a point defect with a / in it.

10/5/21: Fixed keyword substitution in Framewatcher.

Bug Fixes for IMOD 4.11.10

9/26/21: Fixed test for lines too short in Findsection.

9/26/21: Turned off fix for cursor problems on M1 Mac, which seem to have been solved in OS 11.5. The fix can be re-enabled with an environment variable, IMOD_M1_CURSOR_FIX.

9/16/21: Made Findsection not put out lines too short, and made Batchruntomo proceed if there is an error in Tomopitch.

9/13/21: Changed file move/copy routine used by Framewatch and Serieswatcher to use native Windows commands if possible even in cygwin.

9/12/21: Fixed command file names put out by Splitblend.

9/9/21: Added a warning to Excludeviews if an mdoc is missing PriorRecordDose entries and the new mdoc would give incorrect dose weighting.

9/9/21: The checkboxes for parallel processing and use the gpu are not mutually exclusive if there is a local host which is the only machine available with multiple GPUs.

9/6/21: For dose weighting with doses from an .mdoc file, made ordering based on DateTime entries override the order implied by the -bidir option to Alignframes or Mtffilter, since that option could be erroneous.

Bug Fixes for IMOD 4.11.8

8/20/21: Added a script, fixMacInstall, to the IMOD directory to fix system files after an OS 11 update overwrites them

8/16/21: Increased maximum diameter in bead fixer to 100 pixels.

8/16/21: Made Sorttiltframes ignore blank lines.

8/5/21: Made Findsection exit with an error when it cannot find boundaries in cryopositioning, and made Batchruntomo go on after Cryoposition fails.

8/5/21: Allowed binning spinner in 3D gold finding dialog to go up to 32 to handle very small pixel sizes.

7/14/21: Fixed Raptor for new naming style.

6/28/21: Fixed Ccderaser so it could erase inside long narrow contours containing fewer than 1000 pixels.

Bug Fixes for IMOD 4.11.7

6/4/21: In Etomo - Post Processing fixed a bug that prevented Full Volume from being opened.

6/3/21: Made it possible to make a reconstruction even if there is a problem accessing the program autodocs.

5/21/21: Added test to installer for whether Rosetta2 is installed on M1 Mac.

5/10/21: Added limit on number of jobs Processchunks starts per one-second cycle and option to set it.

5/9/21: Made Processchunks require at least 2 failures before holding off on sending more jobs to a machine when no chunks have finished.

5/5/21: Fixed crash in Imodfindbeads with large bead sizes.

Bug Fixes for IMOD 4.11.6

4/30/21: Fixed Ctfphaseflip crash when nx = 4092 at 0 degrees.

4/15/21: Fixed final output file name from Ctf3dsetup with new naming style.

Bug Fixes for IMOD 4.11.5

3/30/31: Fixed pixel size for dose weighting to be correct for binned aligned stack.

3/29/21: In Etomo - Preprocessing, fixed tomodataplots.

3/28/21: Required Slicer windows to be closed with Esc instead of the close button in the 10.14 package on the Mac to prevent crashes.

3/23/21: Fixed tomodataplots/onegenplot for Python 3.8.

3/22/21: Fixed remaining 1-pixel offset in cursor on M1 Mac.

3/22/21: Fixed Ctf3dsetup slab sizes with a binned aligned stack.

3/16/21: Fixed undo for Drawing Tool Eraser tool.

3/16/21: Fixed axis angle put into header title by Alignframes when given the .mdoc file for a FISE tilt series; it was off by 90.

Bug Fixes for IMOD 4.11.4

3/11/21: Used a new Qt version for the Mac OS 14.14 build to prevent some 3dmod crashes on closing windows.

3/11/21: Moved the Ctfplotter option to crop spectra out of the Tile Parameters section and added a colored output line to indicate when cropping is needed. Revised the Ctfplotter guide to add a whole section on cropping, with example images.

3/9/21: Made Pickbestseed give better error message when no beads accepted, and added batch defaults to accept elongated beads when there are fewer than 5 accepted otherwise.

3/9/21: Fixed Batchruntomo crash when given a binning over 4 for plastic-section type positioning.

3/2/21: Fixed xcorr.com output from Copytomocoms with new naming style for a montaged stack not ending in .st.

2/25/21: In Etomo fixed a failure to display chunk errors.

2/24/21: Stopped Batchruntomo from splitting up tilt and ctfcorrection jobs when there is only one CPU.

2/19/21: Fixed Tilt to pay attention to IMOD_USE_GPU2 which is needed for parallel processing with multiple GPUs.

Bug Fixes for IMOD 4.11.3

2/16/21: Made Copytomocoms extract an .mdoc file from an HDF file so that the dose weighting works both in Etomo and in batch processing.

2/16/21: With the -v option, the -p option to imodinfo will produce constant point size outputs for non-scattered point objects.

2/10/21: Fixed setting of pixel size in Mrc2tif.

2/9/21: Fixed reading from .idoc file not in current directory.

2/9/21: Fixed 3dmod cursor size and center on M1 Mac (center is still off by a pixel on high-DPI display).

2/5/21: In Newstack, prevented variability in the SD of the output when floating to mean and SD except when outputting bytes.

2/3/21: Made Bead Fixer in all modes do a regular PageUp/PageDown even if the keypad key is used, instead of moving the current point.

Bug Fixes for IMOD 4.11.2

1/26/21: Stopped Subtomosetup from skipping some of the particles in each Z level.

1/25/21: Fixed batch advanced option for solving for all tilt angles except one at minimum tilt.

1/23/21: Fixed Ctf3dsetup when using a temporary directory with a space in its full path.

1/13/21: Fixed option not to fill gaps in Beadtrack.

1/7/21: In Etomo - 2D Filtering fixed file chooser being enabled only for mdoc file.

1/3/21: Fixed Rawtiltcoords (used by Subtomosetup and Ctf3dsetup) for new style filenames.

Bug Fixes for IMOD 4.11.1

12/30/20: Fixed Subtomosetup for new style filenames. Made it find or take an entry for tilt axis rotation angle in order to get entries to Tilt correct when there is a ~90 degree rotation between raw and aligned stacks

12/28/20: Fixed Serieswatcher using CPU option entry for GPU list.

12/24/20: Fixed location of Tilt reconstructed with aligned stack that is a binned subset not centered in X.

12/12/20: Added FixCygPython.sh to IMOD/bin on Windows so it is available after installing from .sh file.

12/11/20: Fixed clonemodel for Windows.

12/10/20: Changed default to dots per cm for storing pixel size in TIFF files and changed environment variable to IMOD_TIFF_RESOL_PER_INCH.