Recent IVE Changes at UCSF

IVE 4

• July 18, 2008. Released Priism 4.2.4. A summary of the changes is available at http://msg.ucsf.edu/IVE/IVE4_HTML/RecentChanges.html.
• May 8, 2008. Patched gpurecon in Priism 4.2.4 to print out R-factor results and to avoid hang if one or more servers had zero lines to reconstruct.
• May 6, 2008. Released 4.2.4.
• November 12, 2007. Released 4.2.3.
• May 30, 2007. Patched Priism_setup to work around issue on lbox5 through lbox8.
• August 21, 2006. Released 4.2.2.
• December 20, 2005. Released 4.2.1.
• May 5, 2005. Now load the 0.94.4 versions of the LessTif libraries rather than the 0.93.18 versions.
• March 7, 2005. Put the insert_tilts executable into the IVE4.2.0 directories in /home2/lehua.
• February 15, 2005. Another patch to fix .bprmMn files output by the iterative alignment+recon.
• February 11, 2005. Patched the iterative alignment+recon on the MSG machines and John Sedat's Linux machines. The new version allows the user control over the tapir positivity options, turns on the positivity constraint by default when run from the graphical interface, and allows the use of .bprmMn files as the initial guess for the alignment.
• February 3, 2005. Patched libimcompat.a (except the versions for OS X and the version for Linux and the Intel Fortran compiler) in /home2/lehua/IVE4. The change relaxes a limit on the length of an argument value extracted with get_realswitch.
• December 20, 2004. Patched massnorm in the version installed in /home2/lehua/IVE4 on the MSG machines and in /opt/Priism on John Sedat's Linux machines to fix use of an uninitialized array index.
• December 9, 2004. Patched tapir in the version installed in /home2/lehua/IVE4 on the MSG machines and in /opt/Priism on John Sedat's Linux machines. The new tapir version fixes a problem that caused smoothing to not work on the Linux machines.
• September 20, 2004. Released 4.2.0. Made IVE 4 the default version on the SGIs.
• March 15, 2004. Released 4.1.8.
• November 17, 2003. Released 4.1.7.
• November 17, 2003. Removed jimi from the list of queues since it is not reachable.
• November 10, 2003. Made 4.1.5 the default version of IVE 4 on the MSG SGIs and Linux machines.
• August 21, 2003. Put a version of 4.1.2 (4.1.2.1) without the deconvolution application on the web site and removed older versions.
• May 23, 2003. Released 4.1.5 for internal testing.
• March 17, 2003. Made the 4.1.4 release (better compatibility with Apple's X11; QuickTime support on OS X) available for internal testing.
• December 11, 2002. Put 4.1.3 on local machines (patch for massnorm and Fourier tools).
• December 5, 2002. Released 4.1.2.
• September 12, 2002. Made the 4.1.0 release available for internal testing.
• August 12, 2002. Updated IVE 4 links to point to the 4.0.11 internal release.
• July 24, 2002. Updated IVE 4 links to point to the 4.0.10 internal release.
• June 21, 2002. Released a 4.0.7 to 4.0.8 patch which includes the deconvolution application and other FFT-based applications for Linux and Mac OS X.
• June 4, 2002. Patched release with a version of ccdcor that does not require an extended header to be present on the input data set.
• May 20, 2002. Released 4.0.7.
• March 14, 2002. Released 4.0.6.
• March 5, 2002. Released 4.0.5.
• February 6, 2002. Released 4.0.4.

IVE 3.3

• March 22, 2004. Released new version. See the /home2/lehua/IVE3.3/README file for details.
• November 17, 2003. Released new version. See the /home2/lehua/IVE3.3/README file for details.
• August 21, 2003. Put a version of the May 2002 release without the deconvolution application on the web site and removed older versions.
• March 24, 2003. Released new version for internal use.
• August 12, 2002. Patched release with a Monitor that does not crash when displaying wavelengths with different offsets in RGB mode and a zoom less than one.
• June 4, 2002. Patched release with a version of ccdcor that does not require an extended header to be present on the input data set.
• May 24, 2002. Moved files from /lehua in /home2/lehua to avoid dependence on oahu.
• May 23, 2002. The queues on oahu have been turned off; removed them from the list of queues.
• May 20, 2002. Released new version. See the /home2/lehua/IVE3.3/README file for details.
• May 7, 2002. Removed ashbury from list of queues since it is offline and does not seem likely to come back soon.
• March 5, 2002. Changed applycal executable for Alpha Linux; previous version would improperly complain: "ERROR: could not open bad pixel list \0".
• November 26, 2001. Released new version. See the /home2/lehua/IVE3.3/README file for details.
• May 17, 2001. Added the non-clustered Linux queues to the list of queues and modified Priism_setup so it could be sourced by batch jobs on Alpha Linux systems.
• March 19, 2001. Released new version. See the /home2/lehua/IVE3.3/CHANGELOG_OLD.txt file for details.
• February 5, 2001. Patched release with updated simplex help.
• January 30, 2001. Patched release with fix to last patch. The center of mass calculations did not correctly handle values flagged as outside the current object (possible invalid values or infinite loops).
• January 18, 2001. Patched release with FindPoints that includes option to subtract patch minimum when doing the local center of mass calculation (executable and help file only).
• January 2, 2001. Patched release with fixes for IMRtMap and Monitor (stepping and synchronization with multiple waves and autorepeat bug).
• September 11, 2000. Patched release with sgimath.complib based versions of the decon, ffilter, and the new Fourier tools executables.
• September 5, 2000. Patched release with fixes to Scale.
• August 28, 2000. Released new version. See the /home2/lehua/IVE3.3/CHANGELOG_OLD.txt file for details.
• April 14, 2000. Patched release with changes to appl_prm and EMRECON.
• March 28, 2000. Patched release with more fixes for EM reconstruction (ewbp, EMRECON) and bug in Merge/Reorder interface.
• March 17, 2000. Patched release with fixes for EM reconstruction problems (massnorm, EMRECON, Monitor) and bug in Merge/Reorder.
• March 13, 2000. Released new version. See the /home2/lehua/IVE3.3/CHANGELOG.OLD file for details on this release and those prior to it.

IVE 3 Library and Image Window Changes

• January 15, 2001. Introduced image window changes from IVE 3.3 to fix problems when deleting or changing the depth of a scratch window (IMKS/MONITOR/MonClient.c, IMKS/MONITOR/MonGraphics.c, and IMKS/MONITOR/Monitor.c changed).
• April 14, 1999. Changed scripts to setup Priism's environment so oahu is the only host used by jobs submitted to the queue.
• November 30, 1998. Modified startup script to set IVE_WORKING_SET based on the physical memory of the machine (BIN/ive3 changed) to avoid thrashing when both IVE and the operating system try to swap.
• October 19, 1998. Fixed the September 30 changes to correctly clear window when it is overwritten with another data set (IMKS/MONITOR/MonClient.c changed).
• September 30, 1998. Multiple fixes made for switching graphics context to fix Indy and Indigo2 drawing problems under 6.5 (IMKS/MONITOR/Monitor.c and IMKS/MONITOR/MonClient.c changed).
• April 20, 1998. Brought data collection communication library in sync with IVE 3.3 changes for EMCAT to better handle nesting needed by IVE 3 version of Resolve3D for om0 (IMKS/IWL/IWComm.c changed).
• March 16, 1998. Added lock calls to internals of IWAlSecScl to prevent core dumps with IVE 3 version of Resolve3D on om1 (IMKS/IWL/IWImsubDisp.c changed).

IVE 3 Application Changes

• January 15, 2001. For OM1's Resolve3D, reopen image window when the image size is changed to avoid crashing Resolve3D or the image window because of problems in the IW library. Also for OM1, if a macro fails to open a file, terminate immediately (APPL/RESOLVED3D/CCDCommon.c and APPL/RESOLVE3D/CCDComfile.c changed).
• March 3 and 17, 1999. Put versions of Resolve3D for om0 and om1 in the IVE 3 source tree (New directories APPL/RESOLVE3D/OM1, APPL/RESOLVE3D/OM0, APPL/RESOLVE3D/Util).
• January 21, 1999. Made BIN/EMPROGS a link to APPL/EMCAT to handle case where EMPROGS_DIR hasn't been set.
• October 21, 1998. Fixed bead list editor in the EM alignment package to prevent out of space errors from the image window (APPL/EMCAT/PEditUtils.c changed).
• June 17, 1998. Changed bead alignment software to not print out binary characters in log files (APPL/EMCAT/bead_align.f and APPL/EMCAT/ba_int.f changed).
• June 5, 1998. Changed how Scale responds when the bounds for the scale are very close (APPL/PRIISM/MON_FUNC/Scale.C changed).
• May 13, 1998. For decon's 2D processing of a single section, changed to ignore z pixel spacing in header (APPL/QIP/decon_mem.f changed).
• March 16, 1998. Added more checks on inputs to CCDCor and fixed indexing problem in it's fitting routine (APPL/QIP/ccdcor.f changed).

modified July 18, 2008