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Bug #1560 » testctf.py

Anchi Cheng, 03/21/2012 04:10 PM

 
#!/usr/bin/python
import sys
import math
from pyami import mrc,imagefun,fftfun

if len(sys.argv) != 4:
print 'Usage: python testctf.py ht pixelsize mrcfile'
print ' ht: High Tension of the microscope in kilovolts'
print ' pixelsize: image pixelsie in Angstroms'
print ' mrcfile: path to a square mrc file to be analyzed'
sys.exit(1)
ht = float(sys.argv[1])*1000
pixelsize = float(sys.argv[2])*1e-10
filepath = sys.argv[3]
# Cs value is not passed in the function right not. WIll need to improve it.
cs = 2e-3

try:
a = mrc.read(filepath)
except:
print 'ERROR reading %s' % (filepath)
sys.exit(1)
pow = imagefun.power(a)
rpixelsize = 1/pixelsize/a.shape[0]
ctfdata = fftfun.fitFirstCTFNode(pow,rpixelsize,None,ht)
if ctfdata is None:
print 'FAILED'
else:
print 'average defocus: %8.3f um' % (ctfdata[0]*1e6)
print 'astigmation: %8.3f um' % (ctfdata[1]*1e6)
print 'alpha: %8.3f degrees' % (math.degrees(ctfdata[3]))
(2-2/2)