def subtract_background_from_stacks(scanfile, indir, outdir, scannumber=-1):
"""Subtract background from SAXS data in MAT-file stacks.
"""
scans = read_yaml(scanfile)
if scannumber > 0:
scannos = [ scannumber ]
else:
scannos = scans.keys()
scannos.sort()
for scanno in scannos:
print("Scan #%03d" % scanno)
try:
bufscan = scans[scanno][0]
except TypeError:
print("Scan #%03d is a buffer" % scanno)
continue
try:
conc = scans[scanno][1]
except TypeError:
print("No concentration for scan #02d." % scanno)
conc = 1.0
print("Using concentration %g g/l." % conc)
stackname = "s%03d" % scanno
stack = loadmat(indir+'/'+stackname+'.mat')[stackname]
subs = np.zeros_like(stack)
(npos, nrep, _, _) = stack.shape
for pos in range(npos):
print(pos)
buf = get_bg(indir, bufscan, pos)
for rep in range(nrep):
subs[pos,rep,...] = errsubtract(stack[pos,rep,...], buf)
subs[pos,rep,1:3,:] = subs[pos,rep,1:3,:] / conc
outname = "subs%03d" % scanno
savemat(outdir+'/'+outname + ".mat", {outname: subs}, do_compression=1,
oned_as='row')
def subtract_background_from_ydats(scanfile, indir, outdir, scannumber=-1, highqnorm=False):
"""Subtract backround from SAXS data in .ydat files.
If `highqnorm` is True, normalize the buffer to the sample intensity
in q-range [4.0, 5.0] 1/nm and adjust with a constant before subtracting.
"""
scans = read_yaml(scanfile)
if scannumber > 0:
scannos = [ scannumber ]
else:
scannos = scans.keys()
scannos.sort()
for scanno in scannos:
print("Scan #%03d" % scanno)
try:
bufscan = scans[scanno][0]
except TypeError:
print("Scan #%03d is a buffer" % scanno)
continue
try:
conc = scans[scanno][1]
except TypeError:
print("No concentration for scan #02d." % scanno)
conc = 1.0
print("Using concentration %g g/l." % conc)
filelist = glob.glob(indir+"/s%03d.*.fil.ydat" % scanno)
for posno in xrange(len(filelist)):
bufname = indir + "/bufs%03d.p%02d.out.ydat" % (bufscan, posno)
buf, dbuf = read_ydat(bufname, addict=1)
fname = indir + "/s%03d.p%02d.fil.ydat" % (scanno, posno)
sam, dsam = read_ydat(fname, addict=1)
outname = os.path.basename(fname)
outname = outdir+'/'+outname[:outname.find('.fil.ydat')]+'.sub.ydat'
ad = {
'samfile': [os.path.basename(fname), md5_file(fname)],
'buffile': [os.path.basename(bufname), md5_file(bufname)],
'position' : dsam.get('inputposition', "unknown"),
'q~unit' : dsam.get('q~unit', "unknown"),
'I~unit' : dsam.get('I~unit', "unknown"),
'Ierr~unit' : dsam.get('Ierr~unit', "unknown"),
}
if highqnorm:
# 1 + 0.007 1/(g/l) is the excess of scattered intensity
# in a protein sample versus buffer in the q-range
# used [4.0, 5.0] 1/nm per concentration.
scale = highq_scale(sam, buf)
bufscale = scale * 1.0/(1.0 + 0.007*conc)
print("scale: %g, bufscale: %g" % (scale, bufscale))
buf[1,:] = bufscale * buf[1,:]
buf[2,:] = bufscale * buf[2,:]
ad['normalization'] = float(bufscale)
else:
ad['normalization'] = 'transmission'
# Assumes the standard q, I, Ierr ordering in index 0 columns
sub = errsubtract(sam, buf)
sub[1:3,:] = sub[1:3,:] / conc
write_ydat(sub, outname, addict=ad, attributes=['~unit'])
print(os.path.basename(outname))
def read_experiment_conf(fname):
"""Return a dictionary with values read from YAML-format conffile.
"""
yd = read_yaml(fname)
c = {}
c['Basedir'] = yd['basedir']
c['Pilatusdir'] = c['Basedir'] + yd['pilatusdir']
c['Eigerdir'] = c['Basedir'] + yd.get('eigerdir', '')
c['Expno'] = int(yd['expno'])
c['Detno'] = int(yd['detno'])
c['Cbfext'] = yd['cbfext']
c['Specfile'] = c['Basedir'] + yd['specfile']
c['Indfile'] = c['Basedir'] + yd['indfile']
return c
def excess_ratio(scanfile, qrange=[4.0, 5.0], cnorm=True):
"""Return ratio of (sam/buf)-1 in subtractions in the `qrange` given.
Subtractions are made from data given in `scanfile` as in
'subtract_background_from_ydats()', but only the ratios of
sample / buffer intensity are returned in a list of arrays.
If `cnorm` is True (default) then the ratio is normalized to the
concentration read from the scanfile.
Results from this function can be used to calibrate high-q normalized
subtraction.
"""
scans = read_yaml(scanfile)
scannos = scans.keys()
scannos.sort()
indir = '.'
mlist = []
indlist = []
clist = []
for scanno in scannos:
try:
bufscan = scans[scanno][0]
except TypeError:
logging.warning("Scan #%03d is a buffer" % scanno)
continue
try:
conc = scans[scanno][1]
except TypeError:
print("No concentration for scan #02d." % scanno)
raise TypeError()
logging.warning("Scan #%03d" % scanno)
filelist = glob.glob(indir+"/s%03d.*.fil.ydat" % scanno)
marr= np.zeros((len(filelist)))
for posno in xrange(len(filelist)):
bufname = indir + "/bufs%03d.p%02d.out.ydat" % (bufscan, posno)
buf, dbuf = read_ydat(bufname, addict=1)
fname = indir + "/s%03d.p%02d.fil.ydat" % (scanno, posno)
sam, dsam = read_ydat(fname, addict=1)
# Assumes the standard q, I, Ierr ordering in index 0 columns
q = sam[0,:]
qind = np.logical_and(q > qrange[0], q < qrange[1])
ratio = np.mean(sam[1,qind]) / np.mean(buf[1,qind]) - 1.0
if cnorm:
ratio = ratio / conc
marr[posno] = ratio
mlist.append(marr)
indlist.append(scanno)
clist.append(conc)
return mlist, indlist, clist
def stack_files(scanfile, conffile, outdir, modulus=10, eiger=0, matfile=1, scannumber=-1):
"""Create stacks from scans read from YAML-file `scanfile`.
If `matfile` is true (default), write output stacks to a MAT-file.
Otherwise writes (slowly) to a YAML-file.
"""
if not os.path.isdir(outdir):
# FIXME: Create the directory
raise IOError("Output directory does not exist.")
conf = read_experiment_conf(conffile)
specscans = read_spec(conf['Specfile'])
radind = read_matclean(conf['Indfile'])['radind']
q = radind['q']
if scannumber > 0:
scannos = [ scannumber ]
else:
scans = read_yaml(scanfile)
scannos = scans.keys()
scannos.sort()
for scanno in scannos:
outname = "s%03d" % scanno
if eiger:
stack, fnames, dvals = \
stack_eiger(conf, scanno, specscans, radind, modulus)
else:
stack, fnames, dvals = \
stack_scan(conf, scanno, specscans, radind, modulus)
stack = stack.squeeze()
if matfile:
outfn = outdir+'/'+outname + ".mat"
savemat(outfn, {outname: stack}, do_compression=1, oned_as='row')
print("Wrote output to '%s'." % outfn)
else:
for pos in range(stack.shape[0]):
outfn = outname+'.p%02d.all.ydat' % pos
write_stack_ydat(outdir+'/'+outfn, stack[pos], fnames[pos], dvals[pos], conf)
print("Wrote output to '%s'." % outfn)