def main():
parser = createOptionParser()
(opts, pargs) = parser.parse_args()
if len(pargs) != 2:
parser.error("You must supply FILE1 and FILE2")
# Get the PDFs
xobj, yobj = getPDFFromFile(pargs[0])
xref, yref = getPDFFromFile(pargs[1])
# Get configuration values
config = {}
config["rmin"] = opts.rmin
config["rmax"] = opts.rmax
config["rstep"] = None
if opts.rmin is not None and opts.rmax is not None and \
opts.rmax <= opts.rmin:
e = "rmin must be less than rmax"
parser.error(e)
# Set up the morphs
chain = morphs.MorphChain(config)
# Add the r-range morph, we will remove it when saving and plotting
chain.append(morphs.MorphRGrid())
refpars = []
## Scale
if opts.scale is not None:
chain.append(morphs.MorphScale())
config["scale"] = opts.scale
refpars.append("scale")
## Stretch
if opts.stretch is not None:
chain.append(morphs.MorphStretch())
config["stretch"] = opts.stretch
refpars.append("stretch")
## Smear
if opts.smear is not None:
chain.append(morphs.MorphXtalPDFtoRDF())
chain.append(morphs.MorphSmear())
chain.append(morphs.MorphXtalRDFtoPDF())
refpars.append("smear")
config["smear"] = opts.smear
config["baselineslope"] = opts.baselineslope
if opts.baselineslope is None:
refpars.append("baselineslope")
config["baselineslope"] = -0.5
## Size
radii = [opts.radius, opts.pradius]
nrad = 2 - radii.count(None)
if nrad == 1:
radii.remove(None)
config["radius"] = radii[0]
chain.append(morphs.MorphSphere())
refpars.append("radius")
elif nrad == 2:
config["radius"] = radii[0]
refpars.append("radius")
config["pradius"] = radii[1]
refpars.append("pradius")
chain.append(morphs.MorphSpheroid())
iradii = [opts.iradius, opts.ipradius]
inrad = 2 - iradii.count(None)
if inrad == 1:
iradii.remove(None)
config["iradius"] = iradii[0]
chain.append(morphs.MorphISphere())
refpars.append("iradius")
elif inrad == 2:
config["iradius"] = iradii[0]
refpars.append("iradius")
config["ipradius"] = iradii[1]
refpars.append("ipradius")
chain.append(morphs.MorphISpheroid())
## Resolution
if opts.qdamp is not None:
chain.append(morphs.MorphResolutionDamping())
refpars.append("qdamp")
config["qdamp"] = opts.qdamp
# Now remove non-refinable parameters
if opts.exclude is not None:
refpars = set(refpars) - set(opts.exclude)
refpars = list(refpars)
# Refine or execute the morph
refiner = refine.Refiner(chain, xobj, yobj, xref, yref)
if opts.pearson:
refiner.residual = refiner._pearson
if opts.addpearson:
refiner.residual = refiner._addpearson
if opts.refine and refpars:
try:
# This works better when we adjust scale and smear first.
if "smear" in refpars:
rptemp = ["smear"]
if "scale" in refpars:
rptemp.append("scale")
refiner.refine(*rptemp)
refiner.refine(*refpars)
except ValueError as e:
parser.error(str(e))
elif "smear" in refpars and opts.baselineslope is None:
try:
refiner.refine("baselineslope", baselineslope=-0.5)
except ValueError as e:
parser.error(str(e))
else:
chain(xobj, yobj, xref, yref)
# Get Rw for the morph range
rw = tools.getRw(chain)
pcc = tools.getPearson(chain)
# Replace the MorphRGrid with Morph identity
chain[0] = morphs.Morph()
chain(xobj, yobj, xref, yref)
items = list(config.items())
items.sort()
output = "\n".join("# %s = %f" % i for i in items)
output += "\n# Rw = %f" % rw
output += "\n# Pearson = %f" % pcc
print(output)
if opts.savefile is not None:
header = "# PDF created by pdfmorph\n"
header += "# from %s\n" % os.path.abspath(pargs[0])
header += output
if opts.savefile == "-":
outfile = sys.stdout
else:
outfile = open(opts.savefile, 'w')
print(header, file=outfile)
import numpy
numpy.savetxt(outfile, zip(chain.xobjout, chain.yobjout))
outfile.close()
if opts.plot:
pairlist = [chain.xyobjout, chain.xyrefout]
labels = ["objective", "reference"]
# Plot extent defaults to calculation extent
pmin = opts.pmin if opts.pmin is not None else opts.rmin
pmax = opts.pmax if opts.pmax is not None else opts.rmax
maglim = opts.maglim
mag = opts.mag
pdfplot.comparePDFs(pairlist,
labels,
rmin=pmin,
rmax=pmax,
maglim=maglim,
mag=mag,
rw=rw)
return
def main():
parser = createOptionParser()
(opts, pargs) = parser.parse_args()
if len(pargs) != 2:
parser.error("You must supply FILE1 and FILE2")
# Get the PDFs
xobj, yobj = getPDFFromFile(pargs[0])
xref, yref = getPDFFromFile(pargs[1])
# Get configuration values
config = {}
config["rmin"] = opts.rmin
config["rmax"] = opts.rmax
config["rstep"] = None
if opts.rmin is not None and opts.rmax is not None and \
opts.rmax <= opts.rmin:
e = "rmin must be less than rmax"
parser.error(e)
# Set up the morphs
chain = morphs.MorphChain(config)
# Add the r-range morph, we will remove it when saving and plotting
chain.append( morphs.MorphRGrid() )
refpars = []
## Scale
if opts.scale is not None:
chain.append( morphs.MorphScale() )
config["scale"] = opts.scale
refpars.append("scale")
## Stretch
if opts.stretch is not None:
chain.append( morphs.MorphStretch() )
config["stretch"] = opts.stretch
refpars.append("stretch")
## Smear
if opts.smear is not None:
chain.append( morphs.MorphXtalPDFtoRDF() )
chain.append( morphs.MorphSmear() )
chain.append( morphs.MorphXtalRDFtoPDF() )
refpars.append("smear")
config["smear"] = opts.smear
config["baselineslope"] = opts.baselineslope
if opts.baselineslope is None:
refpars.append("baselineslope")
config["baselineslope"] = -0.5
## Size
radii = [opts.radius, opts.pradius]
nrad = 2 - radii.count(None)
if nrad == 1:
radii.remove(None)
config["radius"] = radii[0]
chain.append( morphs.MorphSphere() )
refpars.append("radius")
elif nrad == 2:
config["radius"] = radii[0]
refpars.append("radius")
config["pradius"] = radii[1]
refpars.append("pradius")
chain.append( morphs.MorphSpheroid() )
iradii = [opts.iradius, opts.ipradius]
inrad = 2 - iradii.count(None)
if inrad == 1:
iradii.remove(None)
config["iradius"] = iradii[0]
chain.append( morphs.MorphISphere() )
refpars.append("iradius")
elif inrad == 2:
config["iradius"] = iradii[0]
refpars.append("iradius")
config["ipradius"] = iradii[1]
refpars.append("ipradius")
chain.append( morphs.MorphISpheroid() )
## Resolution
if opts.qdamp is not None:
chain.append( morphs.MorphResolutionDamping() )
refpars.append("qdamp")
config["qdamp"] = opts.qdamp
# Now remove non-refinable parameters
if opts.exclude is not None:
refpars = set(refpars) - set(opts.exclude)
refpars = list(refpars)
# Refine or execute the morph
refiner = refine.Refiner(chain, xobj, yobj, xref, yref)
if opts.pearson:
refiner.residual = refiner._pearson
if opts.addpearson:
refiner.residual = refiner._addpearson
if opts.refine and refpars:
try:
# This works better when we adjust scale and smear first.
if "smear" in refpars:
rptemp = ["smear"]
if "scale" in refpars:
rptemp.append("scale")
refiner.refine(*rptemp)
refiner.refine(*refpars)
except ValueError, e:
parser.error(str(e))