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SEMCCD Socket plugin notes #3573

Open leginonbot opened 6 months ago

leginonbot commented 6 months ago

Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 3573, https://emg.nysbc.org/redmine/issues/3573 Original Date: 2015-09-21 Original Assignee: Anchi Cheng

Keep all e-mail exchange regarding the module usage here

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-21T16:04:29Z

Debug tool

Setting environment variable SERIALEMCCD_DEBUG to 1 on the K2 computer will give lots of debug output in the Results window

Setting it 2 will give even more output, most of it socket-related.

Get Source Code

new

hg clone  http://bio3d.colorado.edu/SerialEM/SEMCCDforJim

To update existing clone

go into the cloned folder

hg pull -u

Building from code

Nov 2, 2013 from David

I don't know how much Jim counted on building the plugin - but the 64-bit build has changed to use IMOD and TIFF libraries assumed to be in a SerialEM directory adjacent to the SerialEMCCD one. I know that is not a great way to organize things, but I'm trying to reduce the number of copies of libraries I have to keep track of and updated. Let me know if you need to build the plugin.

At that time the library was at ftp://bio3d.colorado.edu/SerialEM/Beta-64bit/libsForSEMCCD.zip

leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-21T16:28:13Z

Early Return

June 5, 2014 from David

The new feature is the ability to return early with a partial or no summed 
image while processing and saving is going on. This is available for all 
GMS.  When this is done in GMS 2.3.1, it only works usefully if the plugin is 
able to "grab" all the images and stack them.  This is all documented in 
DMCamera.cpp for the function SetupFileSaving2
leginonbot commented 6 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-21T18:14:23Z

Rotation and Flip

June 11, 2014 from David

One of the things I discovered is that if one takes a dose-fractionation image 
WITHOUT frame-saving, it needs to know the value of rotationFlip in order to 
cancel the operation being done by DM in GMS 2.3.1.  This is only a problem if 
such a shot is taken before any frame-saving shots are taken. I thus made an 
enhanced SetK2Parameters2 that takes the rotationFlip variable and has more 
arguments for future flags and values.  This works for me because everything 
goes in a self-consistent package, but it may be trickier for you to 
accommodate.