Integrating Phoelix into Appion

[leginonbot]

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Author Name: Lauren Fisher (Lauren Fisher) Original Redmine Issue: 1277, https://emg.nysbc.org/redmine/issues/1277 Original Date: 2011-04-28 Original Assignee: Lauren Fisher

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Write a python wrapper for the Helical Image Processing/Phoelix package. Create a GUI in PHP to intake and generate necessary parameter files and execute HIP. Insert and keep track of helical data in the mysql database. Create a preHIP script for generating mandatory indexing and averaging files with minimal user input and interaction. Incorporate a helical function in manual picker and stack creation to box filaments in short segments and align them vertically in a stack.

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2011-05-05T18:06:03Z

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Hi Lauren, you may have talked about this with Christopher and others, but see we have a myami/appion/appionlib/apPhoelix/ folder now. I would like to keep the appionlib folder to only contain python scripts. Since these are binaries; technically binaries should not be in subversion at all.

It would be best to have the source code in the myami/programs folder and then add to the list of programs that need to be installed.

[leginonbot]

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Original Redmine Comment Author Name: Lauren Fisher (Lauren Fisher) Original Date: 2011-05-05T18:27:04Z

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Hi Neil, Ironically, Christopher and I were just discussing this this morning. I now realize that the way I had the phoelix package set up was not the right way. We are planning on doing pretty much exactly what you said...combining all of the CShell/Phoelix/Suprim/Mrc scripts into a Helical Package that needs to be installed just like Eman and the other packages. Christopher is going to work on getting this all set up.

[leginonbot]

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Original Redmine Comment Author Name: Lauren Fisher (Lauren Fisher) Original Date: 2011-10-12T15:53:24Z

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+Helical ToDo List:+ [√] Modify Phoelix to process short helical segments with new alignment procedures (ship) [√] Clean up Phoelix param files and cshell scripts [√] Clean up log file outputs [√] Debug autoboxer so it is more robust [] Debug autoavg to find out why it adds to radius of LL and causes seg fault [√] Modify s_hip to take in vertical (not horizontal) filaments [√] Write python wrapper (HIP.py) for s_hip [√] Create PHP page for generating and submitting HIP.py [√] Write apHelicalParams.py to setup dictionary with variables required in phoelixparams [√] Write preHIP for interactive setup of required indexing files [] Make filter value default in runHIP.php after preHIP completes [√] Connect HIP with database [√] Write PHP summary and report pages for HIP [√] Integrate Helical tools into the sidebar menu with job updates [√] Integrate all pop-up help information [] Compile all Phoelix, HIP, MRC, SUPRIM, and Tcl/Tk programs on Guppy/Goby [√] Incorporate helical functions into Manual Picker for inserting helical picks and determining rotation angle [√] Integrate rotate function into Stack Creation [√] Make default boxsize in Stack Creation based on helical step not diameter for helical specimens [√] Eliminate need for EMAN's batchboxer within Stack Creation (replace with Neil's apBoxer) [] Integrate single interpolation into Stack Creation [] Integrate diffmap into the post processing page [] Replace FSC with phase residuals or point quality for better resolution estimation [√] Test HIP on microtubules [√] Test HIP on TMV [] Run HIP on a full microtubules dataset to try to get higher resolution [] Run HIP on a full TMV dataset to try to get higher resolution [] Integrate next helical package (Frealign or IHRSR?) [] Parallelize HIP [√] Write wikipages for HIP