Feature #1277
open
Integrating Phoelix into Appion
Added by Lauren Fisher over 13 years ago.
Updated about 13 years ago.
Category:
Image Processing
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.
- Subject changed from Implementing Phoelix into Appion to Integrating Phoelix into Appion
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.
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.
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
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