Changes for IMOD 4.5

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

PEET Interface in eTomo

** 1/31/12: In eTomo - upgraded PEET interface overall and to match changes in PEET 1.8.

3/23/12: In eTomo - PEET, added more error checking to the startup dialog.

3/19/12: Made eTomo remember whether the project log was visible when a dataset was last opened. Fixed some PEET bugs: "Manual cylinder orientation" was not set correctly when the .prm file was copied, maskModelPts must never contain a "NaN" or a single value, pressing "Run" when a process was already running caused the .com files to be deleted.

3/16/12: In eTomo - PEET, popping up an error message when the PEET installation is not compatible with the current IMOD version.

3/15/12: In eTomo - PEET, when copying a dataset, removing any process data that came form the source dataset.

2/28/12: In eTomo - PEET fixed an initMotl bug where the incorrect radio button was selected.

1/25/12: In eTomo - PEET - Reference, converted the multi-particle reference fields to a single combo-box.

1/19/12: In eTomo - PEET, setting nWeightGroup to 0 in the .prm file when the 'Weight groups' spinner is off in the dialog.

1/18/12: In eTomo - PEET, defaulted low cutoff sigma.

1/18/12: In eTomo - PEET, added a startup popup.

1/18/12: In eTomo - PEET, avoiding the problems caused by entering a "." for the PEET dataset directory.

1/3/12: In Etomo - PEET upgraded the Run tab.

12/20/11: In eTomo - PEET, upgraded the Interations table.

12/15/11: In eTomo - PEET, upgraded Y axis and initial motive list panels.

2/15/11: Made movie making work when only the clip planes change.

12/9/11: In eTomo - PEET upgraded the masking panel.

12/6/11: Fixed eTomo - PEET copy project functionality so that it continues to point to the same files.

12/5/11: Improved the appearance of eTomo - PEET.

12/1/11: In eTomo - PEET, getting some tooltips from peetprm.adoc.

11/29/11: In eTomo - PEET improved the error messages.

11/17/11: In eTomo - PEET, upgraded the volume table with an improved format and embedded file buttons.

11/4/11: In eTomo - PEET, defaulting reference in the .prm file to 10,10 when flgFairReference is on.

11/4/11: In eTomo - PEET, defaulting to relative directory paths. Continuing to allow absolute directory paths.

10/31/11: In eTomo - PEET, removed the "Use Existing Project" panel and replaced it with one button - "Copy existing project".

10/27/11: In eTomo - PEET improved the file chooser button.

10/26/11: In eTomo - PEET moved the volume size panel to the Setup tab.

10/26/11: In eTomo - PEET upgraded the Missing Wedge Compensation panel.

Other Changes in eTomo

* 3/16/12: In eTomo added an interface for running gputilttest to the Tools menu.

* 3/22/12: In eTomo - Final Aligned Stack, displaying the expected defocus in microns.

3/23/12: In eTomo - Tomogram Generation preventing GPU parallel processing when the only GPU available in the local host.

3/22/12: In eTomo - Final Aligned Stack, fixed a bug where the erase beads "diameter to erase" value was not being binned.

3/19/12: In eTomo getting EXCLUDELIST for from align.log when possible.

2/27/12: In eTomo running comscripts and processchunks with python.

2/16/12: In eTomo added file names to the print actions functionality (the --actions parameter).

2/2/12: In eTomo changed the pixel size in to take the binning of the aligned stack into account.

1/24/12: In eTomo, finished implementing the --actions parameter (causes messages documenting eTomo actions to be printed).

Changes in 3dmod

** 2/16/11: 3dmod Model View will now use vertex buffer objects for lines and spheres if the OpenGL version is 3.1 or higher.

** 11/30/11: Used vector buffer objects to speed up model view graphics for lighted surfaces and wireframe meshes. Turned on multisampling (full-scene antialiasing) in model view to give smoother lines and polygon edges.

* 3/10/12: Fixed image drawing in model view for ATI cards, which were horribly slow (at least in Windows) from changes in 4.2.24; made drawing somewhat more efficient; added button to set black/white levels from 3dmod sliders.

* 2/18/12: Added a graphic of mouse buttons to 3dmod preferences dialog.

3/16/12: Image display in model view: fixed crash from using new black/white button with data loaded as integers; fixed problems if model view is closed and reopened; image display state is now retained if model view reopened.

* 12/15/11: Edit-Object-Move will move meshes from one saved isosurface object to another; multiple saved isosurface objects can be selected in Model view with Ctrl-right mouse; and Edit-Object-Combine will combine them.

* 11/3/11: Added ability to have global clip planes change position during movie making in Model View.

3/6/12: Fixed image display in model view when last object drawn is lines.

3/2/12: Got rid of glFlush's in model drawing, which were slowing things down a lot in the absence of vertex buffer drawing.

2/29/12: Fixed problems with using outdated or invalid vertex buffer data, particularly in sphere drawing.

2/29/12: Fixed crash after saving isosurface to object.

2/27/12: Fixed some problems with iterating move all by residual in bead fixer and made it give a message when it stops because user released Shift key.

2/13/12: Fixed 3dmod model view movieing when Ctrl key is pressed.

2/1/12: Fixed crash from failure to clear vertex buffers when model view is closed.

Changes in Tomogram Processing

* 1/3/12: In Ctfplotter, added ability to step the angular range up or down, ability to fit automatically to a whole set of ranges, and an option to start the program with automatic fitting. Also switched frequency units to be cycles/pixel going from 0 to 0.5.

3/25/12: Made Findcontrast scale data properly for float data regardless of range and made it handle incorrect file min/max as well as possible.

2/7/12: Fixed Setupcombine problem when there is only one number in SHIFT entry in

2/1/12: Increased limit on number of views for tiltalign and beadtrack to 1440.

1/9/12: Fixed tests for a view-number bug that made Ctfphaseflip fail with one image per range.

1/4/12: In Ctfplotter, added defaults so some options aren't required, added options for controlling the curve fitting, and added an option for saving autofit results and exiting.

1/3/12: Add options to Ctfphaseflip to adjust for the shift of images during alignment.

Changes in General Processing Programs or Infrastructure

** 12/19/11: Programs Clonevolume and Clonemodel were added to allow multiple copies of a rotated volume or model to be inserted into a tomogram or composed into one model.

* 3/11/12: Added -F to Tif2mrc to set fill value for images smaller than the output.

* 3/8/12: Added nearest neighbor (non)interpolation to Newstack for linear and warping transformations.

* 2/29/12: Switched imodhelp to python; note that "imodhelp program" can now be used to display a program man page directly.

* 2/24/12: Converted help system to use compressed html file in Qt 4 Assistant.

* 2/16/11: Added options to Imodauto to specify an exact value for contouring around areas with uniform values, and for using a boundary contour model to enclose the area to be contoured.

3/21/12: Fixed problems in warping due to accessing data out of range, unmasked by fixes on 3/7/12.

3/19/12: Fixed problem running new etomo script on cygwin with python 2.5.

3/15/12: Fixed what installer puts in bash.bashrc in Ubuntu.

3/12/12: Made it possible to delete all labels in Alterheader.

3/12/12: Made Processchunks exit properly when sync chunk fails on a queue.

3/7/12: In Newstack, made it load only the lines needed to compute output, and to scan only those lines to get a fill value, skipping that if possible. Fixed warping and undistorting when loading or output is broken into chunks and made a default 15 GB memory limit.

3/6/12: Converted install script to python, made it able to edit install location in system files instead of just saying it needs to be fixed.

3/6/12: Fixed help paths in 3dmod plugins.

3/3/12: Converted etomo startup script to python, set user home variable for Vista/Win 7 to fix rare problem from java bug.

2/29/12: Made imodinfo -c give mesh volume and surface area for isosurface objects.

2/28/12: Fixed bug in blendmont due to fixed size temporary array.

2/13/12: Fixed Vmstopy to convert backslash to / for Windows.

2/13/12: Fixed Vmstopy initial scanning for goto, etc, in files with DOS line endings in Cygwin.

2/8/12: Changed Vmstopy to remove spaces between $ and command when there are no Python statements in a command file, to avoid indentation errors.

1/27/12: Added a Python script startprocess to run jobs in background for eTomo.

1/25/12: Made Midas able to read files with DOS line endings on other systems.

1/19/12: Fixed problem with trying to do more than 50000 peaks in Findbeads3d.

1/17/12: Added cygcheck back in to tomosnapshot.

12/24/11: Fixed test in simplex search routine that terminated searches with only one variable very early, maybe terminated other searches a bit early.

12/19/11: Added options to Genhstplt for dividing by column and loading new column while retaining X values in previous column.

12/9/11: Fixed problem with vmstopy when command line ends in a quote.

12/9/11: Fixed problems with division by zero in routine that solves linear equations with outlier removal for solvematch, findwarp, and refinematch.

12/8/11: Made processchunks run programs with python. Added options to vmstopy for setting nice and environment variables.

12/8/11: Made bead fixer run tiltalign with vmstopy.

11/30/11: Changed Corrsearch3d to scale boundary models to image file coordinates, so a model from unbinned data can be used on binned data in Edgepatches.