def integrate_them(o):
"""
Process a series of files
o = options object
o.parfile gives name of parameter file (fit2d or poni format)
o.dark overrides to supply dark filename
o.flood overrides to supply flood filename
o.mask overrides to supply mask filename
o.backcalc asks for the back computation of the image
o.npts gives number of output points
"""
# pyFAI.load( ponifile )
integrator = AzimuthalIntegrator()
#integrator.tth = integrator.newtth
# integrator.setChiDiscAtZero()
ptype = determineparfile(o.parfile)
if ptype == "pyfai":
integrator.load(o.parfile)
if o.dark is not None:
print("Using dark from command line", o.dark)
if o.flood is not None:
print("Using dark from command line", o.flood)
elif ptype == "fit2d":
f2d = fit2dcakepars(o.parfile)
if f2d["SPATIAL DIS."][0] not in ["Y", "y"]:
# Set to None. Spatial is from parfile
f2d["SD FILE"] = None
integrator.setFit2D(float(f2d["DISTANCE"]),
float(f2d["X-BEAM CENTRE"]),
float(f2d["Y-BEAM CENTRE"]),
tilt=float(f2d["ANGLE OF TILT"]),
tiltPlanRotation=float(f2d["TILT ROTATION"]),
pixelX=float(f2d["X-PIXEL SIZE"]),
pixelY=float(f2d["Y-BEAM CENTRE"]),
splineFile=f2d["SD FILE"])
integrator.rot3 = 0
integrator.reset()
print(integrator.param, integrator.detector.pixel1)
# First choice is command line. Then from pars if supplied
if o.dark is None:
if f2d["DARK CURRENT"][0] in ["Y", "y"]:
o.dark = f2d["DC FILE"]
print("Using dark from fit2d parameter file", o.dark)
else:
print("Using dark from command line", o.dark)
if o.flood is None:
if f2d["FLAT-FIELD"][0] in ["Y", "y"]:
o.flood = f2d["FF FILE"]
print("Using flood from fit2d parameter file", o.flood)
else:
print("Using flood from command line", o.flood)
# Should be in fabio utilities
df = darkflood(o.dark, o.flood)
# Should be in fabio
fs = edffilenameseries(o.stem, o.first, o.last, o.glob, o.extn)
# integrator.polarization( factor = 1, shape=(2048,2048) )
# Command line is first priority for make
if o.mask is not None:
mask = fabio.open(o.mask).data
print("Using mask", o.mask)
# assume poni file deals with this independently?
elif ptype == "fit2d": # try in fit2d parfile
if f2d["USE MASK"][0] in ['y', 'Y']:
mask = fabio.open(f2d["MASK FILE"]).data
print("Using mask", f2d["MASK FILE"])
else:
mask = None
if mask is not None:
print("mask mean:", mask.mean())
integrator.write(os.path.splitext(o.parfile)[0] + ".poni")
for f in fs:
print("Processing", f, end=' ')
try:
fo = df.correct(fabio.open(f))
except:
continue
if ptype == "fit2d":
outFile = f.replace(f2d["input_extn"], f2d["output_extn"])
else:
outFile = f.replace(o.extn, ".dat")
global SOLID_ANGLE
if 0:
from matplotlib.pylab import imshow, figure, show, log, plot
#imshow(log(fo.data))
#figure()
if mask is not None:
imshow(log(fo.data * (1 - mask)),
vmin=log(10),
vmax=log(30000))
else:
imshow(log(fo.data), vmin=log(100), vmax=log(3000))
# show()
if o.npts is None:
npts = min(fo.data.shape)
else:
npts = int(o.npts)
tth, I = integrator.integrate1d(
fo.data,
nbPt=npts,
filename=outFile,
correctSolidAngle=SOLID_ANGLE,
mask=mask, # 1 for valid
unit="q_A^-1",
#dummy=dummy, # mask pixels == dummy
#delta_dummy=delta_dummy # precision of dummy
)
print("wrote", outFile)
if o.backcalc:
calcimage = calcfrom1d(integrator, tth, I,
fo.data.shape) * integrator._polarization
err = (calcimage - fo.data) * (1 - mask) / (calcimage + mask)
e = fabio.edfimage.edfimage(data=err.astype(numpy.float32))
e.write(outFile + ".edf")
fitcen(fo.data, calcimage, (1 - mask))
# from matplotlib.pylab import imshow, show
# imshow( integrator._polarization )
# show()
if o.display:
if mask is not None:
display(tth, I,
(calcimage - fo.data) * (1 - mask) / (calcimage + 1))
else:
display(tth, I, (calcimage - fo.data) / (calcimage + 1))
