Appion

Neil,

I worked with Kai today. It looks straight forward enough. My solution is to create a subclass of templatecorrelator.py and a separate appionlib/apFindEMG.py to handle the creation of feed string, running, and peak reading from his output (see below).

His input is a one line command with same parameters as findem,exe. However, his output is a EMAN-style box file plus a correlation map. Since he uses a separate template mask diameter from correlation peak search distance, I think it is best not to do the normal apPeaks.findPeaks in the ccmap but read in his box file coordinate.

Three questions for you:
1. Does apPeaks use separate template mask diameter from correlation peak search distance already?

2. Do you see any problem in moving templatecorrelator.TemplateCorrelationLoop() into appionlib? It is the best way for me to create subclass from that.

3. I am considering not to make separate apSelectionParamsData. It is based on the same principle. However, I will need to allow some of the fields default to 1 since peak_area, for example, is not available by reading text box file (only has coordinates and correlation peak value). Do you see any problem in that or have objection?

Any other comment would be helpful.

Let me process your question and I will get back to you before the weekend.

I've added a new value to the processing host configuration in config.php. The config should now look like this:

$PROCESSING_HOSTS[] = array('host' => 'guppy.scripps.edu',
'nodesdef' => '2',
'nodesmax' => '16',
'ppndef' => '4',
'ppnmax' => '8',
'reconpn' => '8',
'walltimedef' => '20',
'walltimemax' => '',
'cputimedef' => '200',
'cputimemax' => '',
'memorymax' => '',
'appionbin' => '/opt/myamisnap/bin/',
'appionlibdir' => '/ami/sw/leginon/betaleginon/appion/appionlib/',
'baseoutdir' => '/ami/data00/appion/',
'localhelperhost' => 'guppy.scripps.edu',
'dirsep' => '/',
'wrapperpath' => '/opt/myamisnap/bin/appion',
'loginmethod' => 'USERPASSWORD',
'loginusername' => '',
'passphrase' => '',
'publickey' => '',
'privatekey' => '', 
'gpus' => array( '0.0' => 'device 0: Tesla', '1' => 'device 1', '2' => 'device 2') // use 0.0 instead of 0 to workaround issue.
);

Notice the 'gpus' array at the end. This array should have the device number as the keys and a name/desc as the values.
Also note that device 0 is entered as 0.0. this is a workaround for an issue in the PHP where zero is changed to an empty string somewhere along the way. I'm taking the floor of this value prior to creating the command in the GUI, so that it is passed to the python as an integer.

Also, I am holding off on updating the configuration wizard. It will require a bit more effort than I have time for today and it will be error prone changes.

I'm checking in the GUI now, there are a couple of things left to do:
1. the setup wizard
2. the user guide: http://emg.nysbc.org/projects/appion/wiki/Template_Picking

Hi Anchi, for your question 1, I would have to review the code, I think I only use one diameter value.

So, this new version does not output the map, only the coordinates? You'll have to remove a lot of features from the pipeline.

Sounds like everything you are doing is probably the best way.

Neil,

It does output ccmap, but since we can not run here, and he said that the separate ccsearch distance helps getting good result, I am keeping its output so that it does not degrade the performance. We can change back easily by not overwriting the findPeaks in the subclass.

Missed one file
r17308 adds apFindEMG.py.

Kai, you should feel free to change appionlib/apFindEMG.py and bin/templateCorrelatorG.py. Be more careful if you need to change others since other programs would need to use them.