Feature #1277
openIntegrating Phoelix into Appion
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Description
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.
Updated by Lauren Fisher about 13 years ago
- Subject changed from Implementing Phoelix into Appion to Integrating Phoelix into Appion
Updated by Neil Voss about 13 years ago
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.
Updated by Lauren Fisher about 13 years ago
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.
Updated by Lauren Fisher over 12 years ago
Helical ToDo List:
[√] Modify Phoelix to process short helical segments with new alignment procedures (s_hip)
[√] 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 phoelix_params
[√] 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