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Make DDD movie stack » simple_correctstack.py

Anchi Cheng, 05/01/2015 12:37 AM

 
#!/usr/bin/env python
import sys
from pyami import mrc

if __name__ == '__main__':
if len(sys.argv) < 4:
print 'Usage: simple_correctstack.py inputstack outputstack normimage (darkimage)'
print ' all options are file paths'
sys.exit()
inpath = sys.argv[1]
outpath = sys.argv[2]
normpath = sys.argv[3]
# dark is optional
if len(sys.argv) == 5:
has_dark = True
darkpath = sys.argv[4]
dark = mrc.read(darkpath)
else:
has_dark = False

# stack height
header = mrc.readHeaderFromFile(inpath)
nx = header['nx']
ny = header['ny']
nz = header['nz']

#shape check
norm = mrc.read(normpath,0)
normshape = norm.shape
if normshape[1] != nx or normshape[0] != ny:
print 'Shape mismatch. raw stack (x,y) at (%d,%d) norm at (%d,%d)' % (nx,ny,normshape[2],normshape[1])
sys.exit(1)

half_way = int(nz // 2)
for i in range(nz):
print 'processing frame %d' % i
a = mrc.read(inpath,i)
if has_dark:
a -= dark
a *= norm
if i == 0:
mrc.write(a,outpath)
elif i == half_way:
# make header stats according to mid point frame
mrc.append(a,outpath,True)
else:
mrc.append(a,outpath,False)
print "------------"
print "output saved as %s" % (outpath)
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