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IMOD History
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3/29/14: In eTomo - PEET, fixed the loading of a non-array selectClassID
value, and fixed more problems with unnecessary errors generated because of
missing parameters (In 4.7).(Bug# 1789)
3/27/14: Fixed a communication problem between eTomo and 3dmod and rolled back
previous incorrect fixes from 2/14/14 and 3/14/14 (In 4.7).(Bug# 1792)
3/27/14: Fixed HDF writing, optimized chunk cache size for volume writing,
fixed pyramid creation, made 3dmod recognize tiling in HDF file.
3/24/14: IMOD_4-8-2
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.
3/22/14: Programs can now read and write HDF files interchangeably with MRC
files. Write performance is currently atrocious. 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.
3/22/14: Fixed newstack when -fromone used with default section list (In 4.7).
3/14/14: Fixed a Windows problem with opening 3dmod from eTomo where
imodsendevent was called incorrectly (In 4.7).(Bug# 1786)
3/14/14: Made the close button on the detached toolbar of linked slicers close
all the linked slicers (In 4.7).
3/13/14: Fixed a problem in eTomo - PEET where tilt angles where not being
loaded from a renamed tilt log file (In 4.7).(Bug# 1782)
3/8/14: Fixed deferring of initial messages to 3dmod on Mac (In 4.7).
3/8/14: Fixed lack of title bar and initial placement of toolbar for linked
slicers (In 4.7).
3/7/14: Updated the Join tutorial (In 4.7).(Bug# 1785)
3/5/14: IMOD_4-7-1
3/5/14: In eTomo - PEET, made sure that empty attributes will not generate
Matlab syntax errors.(Bug# 1784)
2/28/14: IMOD_4-8-0 and branch to IMOD_4-7-0
2/28/14: Reading the bidirectional tilt value from the header file.(Bug# 1781)
2/26/14: Add options to 3dmod for setting initial center, angles, and zoom.
2/22/14: Fix exit status, button width, splash screen for Ctfplotter on Mac.
2/21/14: Added three more colors for arrows drawn with Grab with Note.
2/21/14: Fixed changing transparency during model view movies.
2/15/14: IMOD_4-6-41
2/14/14: In eTomo, fixed a problem with slowness when opening 3dmod dialogs.
(Bug# 1778)
2/14/14: In eTomo - PEET fixed problems with defaults and the handling of
missing properties.(Bug# 1738)
2/13/14: Switched default antialiasing filter for Newstack to Lanczos 3.
2/9/14: Updated the images in the eTomo tutorial. Also exposed the
autofidseed append parameter and initialized the seed model contours in 3dmod.
(Bug# 1777)
2/9/14: In eTomo - Setup Reconstruction, allowing .mrc image files to be
selected, and renaming them to .st.(Bug# 1696)
2/7/14: Fixed problems with installer on Python 2.5 and Python 3.
2/6/14: In eTomo - PEET, accepting integer vectors in selectClassID.
(Bug# 1775)
2/5/14: Makecomfile adds option to append to seed model for autofidseedb.com.
2/3/14: Changed Bead Fixer so value-based controls show or hide appropriately
when model is changed.
2/1/14: Made installer able to take a .csh file, so it can be used to upgrade
on Windows without Cygwin.
1/31/14: Fixed installer test for 32/64 bit mismatch and added test and
message about libjpeg 6.2 on Ubuntu.
1/30/14: IMOD_4-6-40
1/30/14: Switched to outputting signed bytes by default. BYTE FILES WILL NO
LONGER BE READABLE BY VERSIONS BEFORE IMOD 4.3.
1/30/14: Fixed execute permission on Autofidseed and added option for passing
options to Imodfindbeads.
1/30/14: In eTomo fixed bugs in the Directive Editor.(Bug# 1721)
1/30/14: In eTomo - Directive Editor, fixed bugs which where causing unchanged
directives to be display in the default mode.(Bug# 1772)
1/30/14: In eTomo - Directive Editor, getting CTF defaults from origcoms.
(Bug# 1715)
1/29/14: IMOD_4-6-39
1/29/14: Changed Newstack floating to truncate images with extreme ranges
instead of scaling them to a different mean/SD.
1/29/14: In eTomo - Coarse Alignment, fixed a problem with graphing edge
errors.(Bug# 1774)
1/29/14: In eTomo improving error handling for an empty fiducial diameter
field.(Bug# 1671)
1/29/14: Fixed problems with autofidseed in eTomo - Fiducial Model Dialog.
(Bug# 1743)
1/29/14: Exposed flgNoReferenceRefinement in eTomo - PEET.(Bug# 1738)
1/28/14: Restored fortran graphics program wrappers to Mac build, lost 1/13.
1/20/14: IMOD_4-6-38
1/20/14: Fixed keypad hot keys in Model View on Mac.
1/18/14: IMOD_4-6-37
1/18/14: Further polishing of Grab with Note, which can now be used to draw
multiple arrows in Zap or Slicer windows.
1/16/14: IMOD_4-6-36
1/16/14: Jane Ding contributed Grab with Note plugin, which takes Slicer or Zap
snapshots with notes added below the image.
1/16/14: Fixed creation of patch tracking com file if mag change searched in
coarse align.
1/16/14: Change eTomo to make it independent of Cygwin. Fixed a problem with
killing processes on Windows.(Bug# 1716)
1/14/14: Fixed bug in clip multiplying while unpacking 4-bit data, added
rounding in clip multiply or divide when outout is to an integer.
1/12/14: Made Imodchopconts able to chop up or sort out contours based on
fine-grained color.
1/11/14: Fixed 3dmod crash when the I button is pressed in Zap and no image
loaded, present since 4.6.29.
1/10/14: Made 3dmod able to read single pixels from non-MRC-like files so
Pixel View and Graph windows can show file values.
1/8/14: Made all C/C++ programs except Raptor able to read TIFF and MRC-like
file formats, made it possible to direct output to a format specified by
environment variable. TIFF stacks are now written with min and max of the file
in the last image directory and these values are used when reading a stack.
1/8/14: Added control of imodchopconts to eTomo - Fiducial Model Dialog.
(Bug# 1767)
1/2/14: Replaced Fortran image I/O system with system used by C programs.
Fortran programs can now read TIFF, DigitalMicrograph, and other MRC-like
files.
1/2/14: IMOD_4-6-35
1/2/14: Fixes in 3dmod for problems with toolbar and popup menu and new model
view tool windows.
12/31/13: IMOD_4-6-34
12/25/13: Changed description of hot keys in help files and tooltips to show
plain letter as upper instead of lower case (S not s) and shifted letter with
Shift+ instead or just upper case (Shift+S not S).
12/23/13: Added ability to change object transparency during Model View
movies.
12/23/13: Made hot key popup menus for Zap, Slicer, and XYZ windows that show
up when right-clicking over a toolbar, and added a HotKey menu to Model View.
These menus allow most hot keys to be seen and selected.
12/23/13: Added hot key for resizing image inside Zap or Slicer rubber band to
fill window.
12/22/13: Added a dialog to set the size of the Model View window without
changing model zoom.
12/22/13: Added menu entry Image - Linked Slicers to open an array of slicers,
one per image file, controlled by a single slice toolbar,
12/21/13: Added a small rotation tool window to Model View with arrows for
rotating model.
12/19/13: Rubberband, arrows for view-axis based rotation, and slider for
moving along view axis added to slicer; with band on, limits can be set and
File-Extract File can be used extract selected region with Rotatevol.
12/19/13: Fixed File-Extract File when subarea of volume or volumes of
different size are loaded or when the time lock is on.
12/19/13: Allowed X, Y, and Z limits out of range for Trimvol.
12/19/13: Fixed autofidseed and findsirtdiffs for Python 3.
12/13/13: Fixed 3dmod button resizing in Windows when change font size.
12/13/13: In eTomo - Fine Alignment, exposed tiltalign - weightWholeTracks.
(Bug# 1766)
12/13/13: Updated the eTomo manpage. Improved the eTomo help statement.
(Bug# 1764)
12/12/13: Enabled modeling in XZ and YZ planes of XYZ window. New
closed/planar contours are started automatically on a new slice in all three
planes. Surface numbers are assigned automatically so that such contours
drawn in XZ or YZ planes can be meshed. Made arrows and PageUp/PageDown work
relative the plane where the mouse is located and added keypad keys to
move the current model point.
12/12/13: Made scroll wheel change point size in XYZ and Slicer windows.
12/12/13: Made XYZ window report distance from current point to mouse with q
hot key, fixed use of current model point for q report from Zap window.
12/12/13: Fixed position tracking in pixel view window from XYZ window.
12/6/13: Added option to Imodinfo to get contour lengths broken out by
fine-grained color, and made -o option provide object list for all outputs.
12/3/13: In eTomo - PEET, excluding the quoted values functionality.
(Bug# 1631)
11/30/13: Changes to Tiltalign to deal with patch tracking data: it can select
a subset of patches for the global alignment to avoid solving for too many
variables; it can do robust fitting with weights assigned either to individual
points or to whole contours.
11/28/13: Made changes in the search routine used by Tiltalign/Beadtrack to
reduce the high risk of "minimization errors" when starting close to the final
solution; also ignore particular errors after first round of robust fitting.
11/28/13: In eTomo allowing quoted values in autodocs.(Bug# 1631)
11/21/13: IMOD_4-6-33
11/21/13: Changed Corrsearch3d to use dynamic allocation, load from file more
efficiently, and use multiple threads for some steps.
11/20/13: In eTomo - Final Aligned Stack, prevented the creation of a bad
rotation.xf file when the final aligned image stack is not present.(Bug# 1762)
11/20/13: In eTomo - Serial Sections, fixed the Newstack progress bar.
(Bug# 1749)
11/20/13: Fixed 3dmod crash from loading many files through startup window.
11/20/13: Made multi-line INFO and WARNING messages more parsable in
etomo_err.log.(Bug# 1694)
11/19/13: In eTomo - Combine, prevented the dataset from being damaged when
the Combine dialog is opened too early.(Bug# 1652)
11/19/13: In uitest, fixed a problem with finding the main panel.(Bug# 1761)
11/18/13: In eTomo made multi-line error messages parsable by adding an empty
line after each one.(Bug# 1694)
11/18/13: In eTomo - Coarse Alignment, added support for tiltxcorr parameters
SearchMagChanges and ViewsWithMagChanges.(Bug# 1760)
11/15/13: In eTomo added support for parallel processing using multiple GPUs
per computer.(Bug# 1436)
11/15/13: In eTomo reduced the excessive debug output.(Bug# 1763)
11/13/13: In eTomo - Serial Sections, added a Sobel filter checkbox and
improved the behavior of the alignment panel.(Bug# 1755)
11/11/13: IMOD_4-6-32
11/5/13: Fixed bug that crashed Imodfindbeads when adjusting size downward.
11/4/13: In eTomo - Fiduacial Model dialog, fixed a problem with deleting
autofidseed temporary files in Windows.(Bug# 1759)
11/4/13: Make xfalign apply shift limits in initial cross-correlation.
11/4/13: Fixed scale bar drawing from montage snapshot of model view window.
11/4/13: Made mrc2tif use 4 or 5 digits for all output file numbers if needed.
11/2/13: Switched display of residual model to show arrows.
11/1/13: In eTomo - Serial Sections, improved the context sensitive pop-up
menus.(Bug# 1748)
11/1/13: In eTomo - Fiducial Model, added fields for AdjustSizes and
ClusteredPointsAllowed to the Autofidseed panel.(Bug# 1743)
11/1/13: Made Tiltxcorr able to find mag changes at selected views; for a
bidirectional series, Copytomocoms puts the option with the view number in
xcorr.com.
11/1/13: Fixed bug in imodtrans -3 option introduced 12/8/12.
10/30/13: IMOD_4-6-31
10/29/13: Fixed a problem in eTomo where the parallel panel did not appear
when eTomo reconnected to a parallel process. This problem appeared when
Pause and Resume had been previously used.(Bug# 1757)
10/29/13: Fixed the eTomo version string.(Bug# 1744)
10/28/13: In eTomo fixed a bug where stack header data was not getting into
the dataset file when eTomo was run from batchruntomo.(Bug# 1758)
10/27/13: Added option to Tilt to get output in parallel (X/Y) slices without
inverting handedness.
10/25/13: In eTomo removed dependencies on Cygwin.(Bug# 1713)
10/25/13: Changes in Tiltxcorr: shift limits are now applied in an elliptical
rather than rectangular region; implemented a new, more selective method for
excluding the central peak due to fixed pattern noise; added an option to
compute normalized correlation coefficients at multiple peak positions and
pick the highest (not useful so far).
10/25/13: Changed Beadtrack's elongation file output so that automatic seed
picking would not fail with only 3 beads.
10/24/13: In eTomo - Combine, removed the message complaining about tomograms
A and B not being the same size in X and Y, as this is not an error.
(Bug# 1651)
10/24/13: In eTomo, preventing embedded spaces in dataset names.(Bug# 1667)
10/24/13: Added a antialiasFilter field for the newstack panels in eTomo -
Coarse Alignment and Final Aligned Stack.(Bug# 1737)
10/23/13: In eTomo resizing when the Cleanup dialog is finished.(Bug# 1636)
10/22/13: Fixed another warping-related crash in Midas.
10/22/13: Made it possible to start Zap rubber band from ANY corner.
10/21/13: Fixed a problem that crashed 3dmod when a slicer angle is very
small, such as when doing mouse-rotating.
10/18/13: Added toolbar buttons to Zap and Slicer for drawing a single thick
arrow for snapshots; also added an object property to draw arrowheads at the
ends of contours.
10/17/13: In eTomo - Clean up, added unused, optional image files (such as the
output from mtffilter) to the file chooser.(Bug# 1509)
10/17/13: In eTomo - Clean up, added SIRT .vsr## output files.(Bug# 1533)
10/15/13: Fixed numerical problems in drawing code that crashed Midas on big
images in 64-bit Windows.
10/14/13: Added GiantCriterion, BigDiffCriterion, and ExtraLargeRadius to
eTomo - Preprocessing.(Bug# 1736)
10/9/13: Fixed a problem with running tomodataplots from eTomo under Java 1.7
that prevented the graphs from coming up.(Bug# 1754)
10/9/13: In eTomo fixed a parallel processing problem which prevented the
Resume button from working when the process was pausing. This problem
appeared in only in reconnected processes.(Bug# 1729)
10/9/13: In eTomo - Nonlinear Anisotropic Diffusion, some test.K... file names
will differ in different Java versions. This bug will not be fixed because it
does not appear to cause any harm. Only the automated tests where modified.
(Bug# 1753)
10/9/13: Fixed a problem in eTomo running under Java 1.7 where some titles
where greyed out.(Bug# 1752)
10/1/13: Prevent the "Use Raptor Result..." button in eTomo - Fiducial Model
dialog from being triggered multiple times.(Bug# 1727)
10/1/13: Saving the state of the eTomo - Fiducial Model dialog.(Bug# 1722)
10/1/13: Improved the handling of opening eTomo - Post Processing at the wrong
time.(Bug# 1712)
9/27/13: Added predefined tomodataplots graphs to various places in eTomo.
(Bug# 1707)
9/24/13: IMOD_4-6-30
9/24/13: Prevented tomodataplots from putting out an empty file and Onegenplot
from going into an infinite loop on an empty or inadequate file.
9/20/13: Added option to Reducecont to replace each contour with a set of
points evenly spaced along the contour.
9/19/13: Added ability for Xfsimplex to load data with antialiased image
reduction and made Xfalign call it in this mode, so that filtering now
happens after reduction instead of before. This avoids problems with very
large images and makes the effect of filtering somewhat more predictable, but
has changed the effect of the filters for autoalignment in the Join and Serial
Section interfaces.
9/19/13: Fixed a problem in eTomo - Serial Sections where etomo could not find
the piece list file during startup. This caused it to run extrapieces despite
the existance of a piece list file in the dataset.(Bug# 1747)
9/19/13: Fixed a problem in eTomo - Serial Sections where the main frame
locked up when the log window was displayed.(Bug# 1746)
9/19/13: Fixed a problem with the xfalign panel in Serial Sections and Join in
eTomo where blanking the filter data caused the process to run with the
initial values.(Bug# 1745)
9/17/13: Fixed right-click menu in eTomo - Fiducial Model Dialog.(Bug# 1683)
9/17/13: Resolved problems with the project log window.(Bug# 1690, Bug# 1616)
9/4/13: Added SloppyMontage parameter to blend.com in eTomo - Serial Sections.
(Bug# 1742)
9/3/13: Added option to Edpiecepoint to create list ordered first by Z.
9/3/13: Added warping to the xfalign interface in eTomo - Serial Sections.
(Bug# 1731)
9/1/13: In Tiltalign, made robust fitting try not to get stuck in
oscillations, and made it restore non-robust fit upon failure.
8/30/13: IMOD_4-6-29
8/30/13: Changed options to drop and ignore models in Autofidseed to take
lists numbered from 1, not 0.
8/30/13: In Pickbestseed, implemented a new analysis of whether beads are
elongated and tuned the parameters with a variety of data sets. It will now
identify many fewer beads as elongated inappropriately when they are over a
dense background. Autofidseed and Pickbestseed now allow the elongated points
to be included without the clustered ones and generate a model of all
candidate beads color-coded by elongation and clustering.
8/30/13: Added option to Genhstplt to form linear combination of columns.
8/27/13: Improved tooltips for eTomo - PEET.(Bug# 1740)
8/27/13: Added complete version information to the etomo error log file.
(Bug# 1733)
8/27/13: Added a bidirectional tilt series option to eTomo - Setup Tomogram.
(Bug# 1732)
8/24/13: IMOD_4-6-28
8/24/13: Improved the layout, behavior, labels, and tooltips of the "Align
Serial Sections / Blend Montages" interface.(Bug# 1730)
8/23/13: There are now two system templates that can be selected in the eTomo
startup page; plasticSection just turns on Sobel filter centering in tracking;
cryoSample turns that on with the correct filter and changes a few other
settings; see Using Etomo for details.
8/23/13: Fixed Tiltxcorr to compute warping with a seed point model.
8/23/13: Fixed Newstack to set output size properly for +/-270 rotation.
8/22/13: Added ".mrc" as a default volume file extension to the file choosers.
(Bug# 1701)
8/20/13: Fixed bug in Autofidseed that made it use data only from the last
track instead of from all three (caused by 12/13/12 Clipmodel change).
8/20/13: Made contour copying work with contours selected in multiple objects.
8/20/13: Added support for dual/multi tilt missing wedge compensation during
PEET averaging.(Bug# 1688)
8/18/13: The Serial Section Alignment guide now describes how to use the
interface in eTomo.
8/15/13: Made Newstack floating scale images with extreme ranges to different
mean and SD to preserve dynamic range for other images.
8/13/13: IMOD_4-6-27
8/13/13: Added ability to draw the interior of contours in the Zap window with
transparent color (see Edit-Object-type dialog).
8/13/13: Allowed 0 to be entered for Cs in Ctfplotter and Ctfphaseflip.
8/12/13: IMOD_4-6-26
8/12/13: Added ability to scale output from clip multiply and divide.
8/12/13: Fixed problems with values not showing up in the Directive Editor,
which now shows intelligible labels for all fields and combo boxes with
descriptions for choices.(Bug# 1728)
8/8/13: Added Clip options to print histogram and unpack 4-bit data.
8/7/13: Inverted the false color ramp for value displays to match the polarity
of the ramp for image display, so that "hot" is bigger. Added color ramp bar
to the Values panel of the Model view Object Edit dialog.
8/2/13: In eTomo handling messages starting with "LOGFILE:". The message
following this tag will be treated as a local file name, the contents of which
will be placed in the project log.(Bug# 1700)
8/2/13: Added an option for the PEET Help pages to the eTomo menus.
(Bug# 1650)
7/31/13: Clip multiply/divide can have a stack as first file and a single
image as the second file.
7/31/13: Changes to Batchruntomo: option to send emails, more informative
output about what is running, a log file with a copy of program output saved
in each dataset, delivery of more files to dataset directory, running clip
stat on a fixed stack.
7/31/13: Fix a bug in Beadtrack that zeroed out the sobel sum when reversing
direction.
7/31/13: In eTomo - Template Editor, improved the labels and fields.
(Bug# 1724)
7/31/13: Made default maximum radius for X-ray erasing a little bigger for
bead diameter >= 10; turned on local tracking by default.
7/31/13: Made Makecomfile able to make xcorr_pt.com before .preali exists.
7/24/13: Added option to Archiveorig to restore multiple levels of archives.
7/24/13: Fixed 3dmod crash when etomo tells it to load an empty X-ray model.
7/22/13: Made all python scripts properly put IMOD on front of path in
Cygwin.
7/22/13: Fixed etomo script so it can run java.exe in Windows/System32
directory (In 4.5).
7/18/13: IMOD_4-6-25
7/17/13: Made Imodfindbeads able to analyze for bead diameter in averaged bead
and adjust parameters for a significantly different size (good only for cryo).
Autofidseed has an option to apply this and use the new size for tracking;
Batchruntomo will use the new size for tracking too.
7/17/13: Made processchunks set a thread limit of 1 by default unless running
a single com file or running with GPU option, with a new option to set the
limit higher.
7/16/13: FFTs: Switched to FFTW for Fourier transforms in most distributions,
which will use multiple threads depending on transform size. Changed IMOD FFT
routines to produce the same transforms. 2D transforms are now complex
conjugates of what they were. 3D transforms are now correct and no longer are
mirror images in the XZ plane. Switched to array allocation in Fftrans and
Enhance and eliminated used of disk-based routines for large images.
Eliminated broken disk-based 3D FFT from Clip. Changed the way Clip writes
transform files when Y or Z is odd to put data in proper order, made Fftrans
work properly and produce same format of output in case of odd
sizes. Eliminated ability to read old mirrored FFT files.
FFT's ARE NOW INCOMPATIBLE WITH ONES FROM PREVIOUS VERSIONS.
7/8/13: Added Copytomocoms option to specify bi-directional tilt series so
separate view group can be set up; added batch directive too.
7/4/13: Fixed Imodfindbeads when not run from Autofidseed.
7/3/13: In eTomo - PEET, suppressing warning popup dialogs.(Bug# 1634)
7/3/13: In eTomo added the thumbnail option to the tomosnapshot call.
(Bug# 1672)
7/3/13: In eTomo allowing a fiducial diameter of 0.(Bug# 1671)
7/3/13: Added Newstack option -twodir for stacking two files of bidirectional
tilt series.
7/3/13: Fixed 3dmod autocontrast for zoomed-down display of a subarea when
Subarea option is not checked.
7/1/13: IMOD_4-6-24
7/1/13: Fixed bug that prevented Autofidseed from giving Imodfindbeads the
sigma for kernel filtering, and made Autofidseed tell Imodfindbeads about
prealignment transforms so it can avoid picking peaks at edge of image.
7/1/13: Fixed bug that hung beadtrack.
6/29/13: Made Batchruntomo able to run Archiveorig and Trimvol, accept CPU and
GPU lists with the new syntax that Processchunks takes, use a binned
thickness, and time out Processchunks if no PID appears in its output.
6/29/13: Made Ccderaser able to remove "extra-large" X-rays and artifacts
automatically, and made some other minor improvements to X-ray removal.
6/28/13: In eTomo - PEET, removed an incorrect validation that prevented a
dataset from being created in a directory containing a .prm file with a
different name.(Bug# 1553)
6/28/13: In the eTomo - PEET tables, keeping the following row highlighted
after a row is deleted.(Bug# 1689)
6/28/13: In eTomo fixed some issues with the template choosers and how they
work with the Reconstruction Setup dialog.(Bug# 1720)
6/24/13: Added option to Boxstartend to taper incomplete boxes near edge of
volume inside or outside of the image data boundary.
6/24/13: Based fill value when displaying incomplete or spread-out montage on
the image mean.
6/24/13: In eTomo - PEET, added a warning popup when a value in the .prm file
will be overridden.(Bug# 1486)
6/24/13: Made Sirtsetup turn GPU failure from warning to error.
6/24/13: Added 6-7-y-u-i-h-j hot keys as an alternative to the keypad in 3dmod
model view for rotating the model or clipping planes.
6/23/13: Added an option in 3dmod preferences to use up and down arrows just
like PageUp/PageDown.
6/23/13: Rotatevol has an option to rotate by the inverse of the specified
angles.
6/23/13: Made beadtrack exit with error if a contour has two points on a view,
just like Tiltalign does.
6/22/13: IMOD_4-5-8 and IMOD_4-6-23
6/22/13: Placed all of eTomo's initialization into the Swing event loop in
order make eTomo work with Java for Mac 1.6.0_51 (update 16) (In 4.5).
(Bug# 1717)
6/20/13: IMOD_4-6-22
6/18/13: Made a subm script to start submfg in the background in cases where
the subm alias is not available; added a man page for subm.
6/17/13: Standardized the Mac ps command to be the same as the Linux one.
(Bug# 1714)
6/17/13: Made a new Imodkillgroup that can kill a process tree as well as a
process group, and that works on Windows without Cygwin. Changed
Processchunks to use this for all non-queue kills, thus fixing killing on
Windows. Also added b3dwinps and b3dtouch for eTomo to use instead of Cygwin
calls.
6/13/13: Made processchunks watch for jobs taking way too long and kill them.
6/11/13: Made processchunks able to send jobs to specific GPUs.
6/9/13: Added options to find warping transforms to Xfalign and changed
Tiltxcorr to take pairs of raw and aligned sections so that it can find
warping when only F transforms exist.
6/9/13: In Xfalign, implemented local fitting for warping transforms to avoid
bad buildup of cumulative warps over many sections, made the reference section
option work with warping, and added an ability to do robust fitting to
transform components to keep the alignment from being thrown off by isolated
aberrant images.
6/7/13: Fixed 3dmod icon missing from dock on Mac, adopted a higher-resolution
version from Mike Strauss.
6/6/13: Switched to makecomfile for the creation of patch tracking and
sirtsetup com files in eTomo.(Bug# 1705)
6/5/13: Added value for maximum distance between contour points for the
surface output of imodinfo.
6/5/13: Handling null values during tomogram reconstruction setup that are
caused by running eTomo through batchruntomo.(Bug# 1708)
6/4/13: Added options for inverted the Z order of the output to dm2mrc,
raw2mrc, and tif2mrc.
6/2/13: In eTomo fixed the batchruntomo error message.(Bug# 1702)
6/2/13: Added an editor for directives derived from the dataset.(Bug# 1685)
5/30/13: Fixed Tomodataplots to send right color option to Onegenplot.
5/29/13: IMOD-4-6-21
5/29/13: Ctfplotter: added version number to defocus file so the old bug of
view numbers off by 1 will not be detected in error, allowed double-clicking a
row to set the angles to that row, and added checkbox for fitting to each view.
5/28/13: In eTomo - Join, using the -cs Midas parameter instead of the -c
parameter.(Bug# 1704)
5/28/13: Changed the local load average process to use the bash shell unless
the user's shell is tcsh.(Bug# 1703)
5/27/13: Tiltxcorr can now produce a file of warping transformations with a
variant of patch tracking.
5/27/13: Made Patch2imod able to produce a model from warping transforms.
5/27/13: Midas: Added input option to specify sample sizes instead of chunks
sizes so that selected sections can be constrained better; added controls for
see warping vectors and selecting warp points based on size of their shifts;
improved cross-correlation around warp point to reduce need for iterating.
5/27/13: Made Xf2rotmagstr able to read warping files.
5/22/13: Fixed 3dmod recognition of DigitalMicrograph files to work with file
from tilt series.
5/21/13: Batchruntomo will now accept .mrc stack files and rename them to .st,
will take template entries with no path and find files in default locations,
and gets the pixel size correctly from FEI files.
5/7/13: Added option to Ctfphaseflip to set maximum strip width, for reducing
artifacts at zeros in FFT at low tilts.
4/10/13: Fixed Batchruntomo's reading of processchunks log hanging on Mac.
4/9/13: Handled multi-line INFO and WARNING messages in copytomocoms.
(Bug# 1694)
4/9/13: Made shift limits to Tiltxcorr apply to shift from one view to next
when using cumulative correlation.
4/9/13: Fixed a few bugs in Batchruntomo for single axis and for running in
Windows.
4/7/13: Added options to Batchruntomo to specify the data set name and
directory so that a batch directive file is reusable without editing it, an
option to deliver data from central location to separate directories, and
ability to process only one axis.
4/5/13: Fixed a null pointer exception, which happened while running
copytomocoms from eTomo - when a directive file that did not contain any
setupset.copyarg directives was included.(Bug# 1693)
4/5/13: Made it possible to do a model view movie with no change in display.
4/4/13: Made copytomocoms put out a command file for extracting data from a B
axis added later.
3/22/13: IMOD_4-6-20
3/13/13: Tiltxcorr can do its image reduction with antialiasing instead of
simple binning and it has an option to start from the last image at minimum
tilt instead of the first, which reverses the order for untilted images.
3/12/13: Newstack has an option -fromone to allow section and line numbers to
be numbered from 1 instead of 0, and an option -exclude to specify sections to
exclude; Colornewst accepts -fromone but not -exclude.
3/12/13: Newstack can read input with antialias reduction instead of binning,
so -shrink can be combined with essentially all image transformations.
3/7/13: Xfalign can now do cross-correlation only with -params -1.
3/4/13: IMOD_4-6-19
3/3/13: Fixed a problem with recording Exclude Projections in the .edf file.
(Bug# 1686)
3/1/13: Added support for templates to eTomo.(Bug# 1677)
2/27/13: Fixed array allocation problem in Pickbestseed.
2/27/13: Fixed problem of 3dmod quitting during initial load due to messages
to Bead Fixer.
2/26/13: 3dmod can take an image pyramid (multiple copies of same volume at
different resolutions) and has a new kind of cache that allows rapid access to
subareas at any zoom when a pyramid is loaded; ordinary (non-tiled) files can
also be cached as strips for somewhat faster access.
2/26/13: Fixed suppression of "unknown field" messages in Tif2mrc.
2/23/13: Added script Makepyramid for making an image pyramid.
2/21/13: Fixed bug in Vmstopy when translating cp and mv with a filename
starting with f.
2/21/13: Made Binvol able to use antialiased reduction in Z instead of
binning.
2/10/13: Redefined blank values in batch/template directives to mean unset the
parameter for other than comparams, and required all booleans to be 0 or 1.
2/7/13: Fixed ability of Fortran programs to read more than 2 GB in one call.
2/7/13: Changed Reducemont to PIP input and made it able to handle arbitrarily
large input pieces or images so that large images can be broken into tiles.
2/1/13: Added option to stop Batchruntomo processing at a chosen step.
2/1/13: Fixed blendmont array allocation.
1/31/13: Fixed graphics module so Onegenplot will exit when window is closed
on all platforms.
1/31/13: In Batchruntomo, implemented definition of scope file as just another
template file and changed the way that boolean copytomocoms arguments are
treated so that they can be used in templates.
1/31/13: Fixed the processing of the directive file parameter.(Bug# 1681)
1/28/13: XYZ window now has a toolbar button to apply the current Z scale to
the XZ and YZ views; the setting is saved between invocations.
1/22/13: Switched Addtostack to dynamic array allocation.
1/19/13: Mauro Maiorca contributed preNAD for NAD-type filtering of tilt
series prior to reconstruction.
1/17/13: Added selectClassID to eTomo - PEET.(Bug# 1673)
1/16/13: IMOD_4-6-18
1/16/13: Added the creation of an empty .xf file to the Serial Sections
interface.(Bug# 1679)
1/16/13: Removed the SetFEIPixelSize copytomocoms parameter checkbox from
Setup Dialog(Bug# 1661).
1/15/12: Defined a file chooser plugin for 3dmod.
1/15/12: Fixed behavior when startup window is used when started as 3dmod
and model view is selected, so that it actually runs 3dmodv.
1/14/12: Made Mrc2tif able to save TIFF files organized in tiles.
1/13/13: Fixed an unhandled exception when montaged stack with an extension
other then ".st" is used with Align Serial Sections.(Bug# 1676)
1/13/13: Fixed incorrect betterRadius in golderaser.com.(Bug# 1662)
1/13/13: Fixed two problems with the behavior of eTomo - Fiducial Model.
(Bug# 1675)
1/11/13: Added back to non-PIP support for colornewst.(Bug# 1665)
1/10/13: Fixed problems with list reading from fortran introduced 8/24/12.
1/9/13: Fixed problems with 3dmod messaging caused by change to rotation.
1/8/13: Creating a second backup file for dataset files, the .prm file, and
the project long.(Bug# 1488)
1/8/13: Changed the processchunks control panel to allow a Resume to be
ordered before the Pause is completed.(Bug# 1434)
1/8/13: In eTomo, handled the change from flipping to rotation in 3dmod, so
running trimvol will work both with newly selected Z values and ones set
previously with old-style flipping.(Bug# 1674)
1/2/13: Made Ctfplotter not open windows when autofitting in batch mode.
1/1/13: Turned YZ flipping in 3dmod into 90 degree rotation about X to
preserve handedness; models saved from this state still have Y and Z swapped
to keep other programs working. Modified Trimvol and Findcontrast to work
with new Z values and to have an option to treat Z values in old way.
12/31/12: Fixed reading of views from ascii model file.
12/31/12: Fixed -scaled option to Model2point, which was never read in.
12/28/12: Converted Filltomo and added options to specify the area in the B
tomogram that has valid data and made Setupcombine add these options when
appropriate. This helps fill in bad regions when using over-sized
reconstructions that have a substantial shift between them.
12/26/12: Added dialog to Model View for saving and running a sequence of
movie segments with different settings.
12/20/12: Added Tomodataplots for graphing various data from tilt series
processing (clip stats, blendmont errors, tiltalign mean residuals).
12/19/12: Fixed Tilt when running internal SIRT on CPU with 90 degree angles.
12/19/12: Modified eTomo to run from a directive file. ETomo will run without
an interface in this situation.(Bug# 1662)
12/18/12: Fixed Edgepatches to use original Z shift when using X/Y shift from
projxf.
12/18/12: A new script, Batchruntomo, can build tomograms automatically with
fiducial, patch tracking, or fiducialless alignment given a text file of
"directives" to set parameters.
12/18/12: Added the SetFEIPixelSize copytomocoms parameter to Setup Tomogram.
The standard pixel spacing will be set automatically in files from FEI
software unless the option to do this is unselected in eTomo
settings.(Bug# 1661).
12/17/12: Added right click menu to Plax graphing window to allowing printing
the graph or saving to a PNG file; also, in Genhstplt, left-clicking pops up
the coordinates clicked. Made Genhstplt draw black on white by default.
12/17/12: Added option -t to Tomosnapshot to take thumbnails of selected files.
12/17/12: Fixed some of the log file monitors, which had the file size defined
as an integer rather then a long, causing an overflow for larger tomograms.
(Bug# 1632)
12/16/12: Made Genhstplt able to plot in color in the graphics window and in
the postscript output; added option to Onegenplot to specify color by R,G,B or
by a standard color name.
12/14/12: Converted newstack comscripts to PIP.(Bug# 1665)
12/14/12: Added a button for viewing the seed model to the Transfer Fiducials
panel.(Bug# 1669)
12/13/12: Made Clipmodel able to clip contours or points by value and retain
fine grained properties in all operations; added option to update object min/max
value; changed it to remove empty contours and added option to keep them.
12/13/12: Added button the Model View Edit-Models dialog to show all models at
the same scale.
12/12/12: Made 3dmod print length and area of lasso when it is completed.
12/10/12: Made Splittilt turn GPU failure from warning to error so that one
machine doesn't fall back to CPU while others are on GPU.
12/9/12: Fixed Xyzproj and clip 2D average to preserve pixel size.
12/9/12: If Z pixel size is 0, MRC header gets fixed so it matches X pixel
size.
12/8/12: Modified Imodtrans to adjust model max coordinates when image file is
given for reference coordinates, added option to allow scaling of transform
shifts, and allowed translations to be combined with transforms.
12/8/12: Changed Imodfindbeads and autofidseed to provide a default minimum
guess and a fallback number to store in model if histogram dip is not found.
12/8/12: Modified Imodtrans, Imodjoin, and raw2mrc to put error output to
standard output.
12/2/12: Added script Makecomfile to make optional com files for tomogram
generation.
12/2/12: Made Autofidseed able to append to an existing seed model, modified
Repackseed to retain surface numbers and values in Transferfid.
11/17/12: Added option to Tiltalign and align.com so that Z shifts will be
relative to the original centering produced by coarse alignment.
11/16/12: Fixed installer to put pylib on front, not end, of path (In 4.5)
11/14:12: Fixed imodtrans so output file can be same as input file on Windows.
11/12:12: Processchunks: fixed a problem where a "+" in the dataset name caused
processchunks to fail.(Bug# 1649)
11/12/12: Added ability to select multiple contours in slicer and made slicer
draw selected contours thicker.
11/7/12: ETomo: Fixed the estimated time of completion for process monitors
that watch a log file.(Bug# 1632)
11/7/12: ETomo - PEET: handling parsing failures in the .prm file.(Bug# 1644)
11/6/12: IMOD_4-6-17
11/6/12: ETomo: Added an interface for autofidseed to the Fiducial Model
dialog.(Bug# 1655)
11/5/12: ETomo: Added field validation and better white space handling for
numeric text fields.(Bug# 1614)
10/30/12: Removed underscore from Autofidseed info file and temporary
directory names for eTomo.
10/29/12: Made Header report of pixel size from extended header take account
of binning up to 4; made Alterheader FEIPIXEL do the same and set a flag to
prevent the operation from being done twice; added option to Copytomocoms for
converting pixel sizes of FEI files.
10/24/12: IMOD_4-6-16
10/24/12: Removed Tilt's setting of pixel size from extended header (8/28/12)
because it screws up bead erasing and combining.
10/23/12: Added ability to get Z pixel size from DigitalMicrograph files.
10/23/12: Fixed Model View shifting with mouse and montage snapshot when
Invert Z is on, and added flush statements to prevent failures in montage
snapshots with vertex buffer drawing on (In 4.5).
10/19/12: Made Tif2mrc able to read metadata in files from TVIPS acquisition
software and produce a .rawtlt file and a title in the header with tilt axis
rotation angle.
10/4/12: IMOD_4-6-15
10/4/12: Pixel sizes are now obtained from DigitalMicrograph files and stored
in output file by dm2mrc. They are read from TIFF files and stored in output
file by tif2mrc if they are less than 1 micron, with an option and environment
variable to override that limit. 3dmod will assign these pixel sizes to a new
model when reading such files.
10/4/12: Fixed Blendmont for using good edge limits with the new stitching
scheme.
10/2/12: Changed Autofidseed to keep Beadtrack from solving for tilt angles
and to save a copy of the track com file for comparison.
9/28/12: Keeping most of the 3dmod debug code in eTomo (debug level 3).
(Bug# 1646)
9/27/12: ETomo: fixed a problem involving the incorrect handling of 3dmod's
stderr, which could potentially cause eTomo to lock up until 3dmod exits.
(Bug# 1647)
9/27/12: ETomo: fixed null pointer exceptions.(Bug# 1645)
9/27/12: Enabled the GPU check box in the Setup Tomogram dialog when the local
host has a GPU available (eTomo).(Bug# 1642)