Bug Fixes for IMOD 4.7.15

4/23/15: In eTomo - Tomogram Combination, setting InvertYLimits in corrsearch3d when the origcoms is present. This mitigates a problem caused by the change from flipping to rotation in 3dmod.

4/10/15: Made Batchruntomo apply directives for options in golderaser.com.

4/9/15: Fixed Corrsearch3d so that Z slice limits picked in etomo will specify the proper Y range in the unrotated volume.

4/9/15: Fixed Batchruntomo to scale fine alignment shifts by the prealign binning when combining with the prealign shifts.

3/16/15: Fixed Ccderaser taking mean inside instead of outside boundary contours.

3/15/15: Fixed fixCygPython.sh to put Cygwin on path before running commands.

2/11/15: Fixed Makepyramid to work with one input argument.

2/11/15: Fixed 3dmod Extract File entry being disabled after cancelling the file chooser.

Bug Fixes for IMOD 4.7.13

2/1/15: Fixed robust fitting with whole contours that aren't cut into pieces.

1/29/15: Fixed problems with running SIRT with binned K2 data by making eTomo put out an even size for binned stack and by improving Tilt's evaluation of whether the tilt axis is centered.

1/10/15: Fixed bug in Imodauto if there are empty boundary contours.

1/3/15: Fixed error in the last interpolation region between strips in Ctfphaseflip.

Bug Fixes for IMOD 4.7.12

10/25/14: Fixed Beadtrack failure if it has to reduce local area target size.

10/24/14: Stopped Imodauto contouring of exact values from always doing contours around vales equal to the file maximum.

10/24/14: Removed 100-pixel limit on 10% tapering in Tiltxcorr.

Bug Fixes for IMOD 4.7.11

10/17/14: In eTomo - Setup Tomogram, added INFO messages about pixel spacing to the project log.

10/17/14: Added a call to fixCygPython.sh to IMOD installer so it takes care of the Python link just as the self-installing file does.

10/16/14: Fixed Interpolator for Mac.

10/15/14: In eTomo - Post Processing, removed the lock from the flatten and squeeze panels that was active when the sum.rec or _full.rec file was missing. This state should only affect the trimvol panel.

10/15/14: Added information from the autodoc file to all autodoc tooltips.

10/15/14: Fixed INVERTORG in Alterheader.

10/14/14: Made dm2mrc write temporary files to output file directory and added option to set a directory for these files.

10/9/14: Fixed two-sided display of meshes in models built on flipped tomograms before IMOD 4.7.

10/8/14: Made the self-installing package script update python.exe in Cygwin bin if it exists but no longer matches the python link target, added script for executable installer to call to make or update python.exe.

Bug Fixes for IMOD 4.7.10

9/24/14: In eTomo, fixed the system template pulldown list, which was loading the wrong template.

9/22/14: Fixed CCC values in reduced vector output of Refinematch if more restrictive boundaries are applied.

9/16/14: Fixed Tiltalign crash when robust fitting doesn't converge.

9/8/14: Changed autofidseed to create a specified temporary directory, not just the default one.

9/8/14: Fixed imodinfo listing objects multiple times with multiple input files.

9/4/14: Fixed number of processors used for SIRT run from Batchruntomo.

Bug Fixes for IMOD 4.7.9

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.

Bug Fixes for IMOD 4.7.8

8/15/14: Fixed bug that caused crash in Nda.

8/5/14: Allowed File-Extract in 3dmod to be run on non-MRC files.

Bug Fixes for IMOD 4.7.7


7/24/14: Fixed transferfid for bidirectional series and other cases with a separate view group option in tracka.com.

7/21/14: In eTomo - Fine Alignment, changed the title of the MaximumCycles parameter to "Iteration limit".

7/21/14: In eTomo fixed a bug that made ineditable table fields editable. This bug can lead to problems with dataset stablility if these fields are modified.

7/15/14: Tiltalign issues warning instead of error if WeightWholeTracks is entered for non-patch track model.

7/11/14: Fixed inability to use patch tracking if cumulative correlation was checked in coarse alignment.

7/6/14: Made Batchruntomo convert a directive for chopping up patch tracking contours into option to Imodchopconts instead of Tiltxcorr; fixed problem with Imodchopconts testing for whether incompatible options were entered.

7/2/14: Fixed problem with fiducial number that Batchruntomo uses to decide if stretching can be solved.

7/1/14: Changed Newstack antialiased reduction to give same image size and centering as binning.

6/27/14: Added option to Alterheader to set space group and made Tilt set it to 1 for tomogram output, following new MRC conventions.

Bug Fixes for IMOD 4.7.6

6/22/14: Allow robust alignment in Batchruntomo with patch tracking and contours cut into pieces.

6/18/14: In eTomo - Tomogram Combination, fixed problems with validation and handling missing tomograms.

6/17/14: In eTomo using the piece list file (when available) to open montaged raw stacks in Reconstruction and Serial Sections.

6/5/14: Fixed Tomopitch so its output is parsable by eTomo for shift or thickness more than 1000.

6/3/14: Made 3dmod automatically look for piece coordinates in an associated .mdoc file and eliminated -pm option, which was not in the man page.

5/21/14: Stopped Makecomfile from giving error when run with a bead size of 0.

5/14/14: Fixed transparent background when saving model montage.

Bug Fixes for IMOD 4.7.5

5/4/14: In eTomo fixed the icon for warning message popups.

5/1/14: Fixed ability to run certain steps on single axis datasets in a Windows installation without Cygwin.

5/1/14: Fixed setting of IMOD_CALIB_DIR by installer for Windows without Cygwin.

4/30/14: Fixed Tiltxcorr when using shift limits.

4/27/14: Changed Squeezevol to allow odd output sizes in X and Z.

4/16/14: Fixed loss of bottom and top lines in interpolation routine when there is 0 or 180 degree rotation.

4/16/14: Fixed clip flipxy when writing signed bytes.

Bug Fixes for IMOD 4.7.4

4/15/14: In eTomo - Tomogram Generation fixing an initialization error in logarithm density scaling. Also handled the logarithm offset from copytomocoms.

4/14/14: Made Copytomocoms set the linear scaling properly in tilt.com when the cryo template is used and turns off logarithmic scaling.

4/9/14: Suppressed Newstack warning about truncated sections unless a lot of pixels were truncated.

4/2/14: Fixed pixel size and model scaling set from a TIFF file when there is a resolution with no units.

4/2/14: Fixed setupstitch when there is an error reading header.