def extractdata(paths, param):
wanted = param.features
ncrmode = param.ncrmode
# TODO: this dependency on the "antibody" parameter is entirely
# superfluous at this point, and should be factored out
antibody = param.antibody
rawdata = sdc_extract._extract_wells_data(paths, wanted)
warnings = None
if ncrmode:
ks = rawdata.keys()
vs = rawdata.values()
def _cull_zeros(d):
assert d.shape[1] == 2
ret = d[d[:, 1] > 0.]
return ret, len(d) - len(ret)
cvs, nculled = zip(*map(_cull_zeros, vs))
tot = sum(nculled)
if tot > 0:
ss = ' + '.join(map(str, nculled))
warnings = ['data for %s = %d cells had to be culled '
'to prevent division by zero' % (ss, tot)]
nvs = [d[:, 0]/d[:, 1] for d in cvs]
data = dict(zip(ks, nvs))
else:
data = rawdata
return (dict([(k + (antibody,), v.reshape((v.size, 1)))
for k, v in data.items()]), warnings)
def get_rawdata(sdc_paths, wanted_features):
d = _extract_wells_data(sdc_paths, wanted_features)
return np.vstack([v for k, v in sorted(d.items())])
