External Package requirement of Appion scripts » History » Revision 2
Revision 1 (Anchi Cheng, 01/22/2018 11:07 PM) → Revision 2/10 (Anchi Cheng, 01/23/2018 12:13 AM)
h1. Typical Appion workflow package requirement of Appion scripts Appion python scripts are often wrappers that calls scripts or command from other packages. List here are what is needed by each typically used options. Note that users may not want to use all functions as programs go out of fashion. h2. Direct Detector Frame Alignment |appion script name|subfunction|external name|purpose|subfunction|external package|script/command within the package| ||general image manipulation||EMAN1|proc2d| |makeDDAlignMotionCor2_UCSF.py||MotionCor2| |makeDDAlignMotionCor2_UCSF.py|movie frame alignment||MotionCor2| |makeDDAlignMotionCorr_Purdue.py||motioncorr |makeDDAlignMotionCorr_Purdue.py|movie frame alignment||motioncorr v2.0 from Purdue| |makeDEAlignedSum.py||deProcessFrames.py|| |makeDEAlignedSum.py|movie frame aligment|deProcessFrames.py|| |makeDEAlignedSum.py||EMAN2|| h2. Automated CTF Estimation |appion script name|external package| |makeDEAlignedSum.py|movie frame aligment|EMAN2|| |ctffind4.py||CTFFIND4| |ctffind4.py|ctf estimation||CTFFIND4|| |gctf.py|Gctf| h2. Particle Selection |gctf.py|ctf estimation||Gctf|| |templateCorrelator.py|template-based particle selection|FindEM| selection||FindEM| |gAutomatchFast.py|template-based particle selection|Gautomatch| h2. Particle Stack Making and manipulation |makestack2.py|making selection||Gautomatch| |makestack2.py|particle stack making|making Imagic stack|appionlib|| |makestack2.py|making |makestack2.py|particle stack making|making Relion stack|Relion|relion_preprocess or relion_preprocess_mpi| |makestack2.py|CTF |makestack2.py|particle stack making|CTF correction by Wiener filtering of the full image (Imagic stack only)|ace2|ace2correct.exe| |makestack2.py|normalization |makestack2.py|particle stack making|normalization by edge|appionlib|| |makestack2.py/quickstack.py|making montage of stack mean/standard deviation map|ImageMagick|montage| |centerParticleStack.py|particle centering in a stack|EMAN1|centeralignint| |boxMaskStack.py|soft masking of helical boxed particles in the stack|Spider| stack||EMAN1|centeralignint|