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Rename PDF-specific smear option to --smear-pdf #220

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Merged
sbillinge merged 5 commits into from
Jun 24, 2025
Merged

Rename PDF-specific smear option to --smear-pdf #220

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215c5e5
Refactor smear to smear-pdf
Sparks29032 Jun 23, 2025
2d4ada8
Reformat help headers
Sparks29032 Jun 23, 2025
a5301bf
Move tests to test_morphapp
Sparks29032 Jun 23, 2025
60d381a
News
Sparks29032 Jun 23, 2025
69d45ee
Merge branch 'main' into smear-update
Sparks29032 Jun 24, 2025
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Refactor smear to smear-pdf
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@Sparks29032
Sparks29032 committed Jun 23, 2025
commit 215c5e51ac2dddefa1139342f6423721c5a4bc00
30 changes: 23 additions & 7 deletions src/diffpy/morph/morphapp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,14 +167,25 @@ def custom_error(self, msg):
"--smear",
type="float",
metavar="SMEAR",
help="Smear peaks with a Gaussian of width SMEAR.",
help="""Smear the peaks with a Guassian of width SMEAR.
This is done by convolving the function with a Gaussian with standard
deviation SMEAR. If both --smear and --smear-pdf are enabled, only
--smear-pdf will be applied.""",
)
group.add_option(
"--smear-pdf",
type="float",
metavar="SMEAR",
help="""Convert PDF to RDF. Then, smear peaks with a Gaussian of
width SMEAR. Convert back to PDF. If both --smear and --smear-pdf are
enabled, only --smear-pdf will be applied.""",
)
group.add_option(
"--slope",
type="float",
dest="baselineslope",
help="""Slope of the baseline. This is used when applying the smear
factor. It will be estimated if not provided.""",
help="""Slope of the baseline. This is used with the option --smear-pdf
to convert from the PDF to RDF. It will be estimated if not provided.""",
)
group.add_option(
"--hshift",
Expand Down Expand Up @@ -468,8 +479,8 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
config["vshift"] = vshift_in
refpars.append("vshift")
# Smear
if opts.smear is not None:
smear_in = opts.smear
if opts.smear_pdf is not None:
smear_in = opts.smear_pdf
chain.append(helpers.TransformXtalPDFtoRDF())
chain.append(morphs.MorphSmear())
chain.append(helpers.TransformXtalRDFtoPDF())
Expand All @@ -480,6 +491,11 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
if opts.baselineslope is None:
config["baselineslope"] = -0.5
refpars.append("baselineslope")
elif opts.smear is not None:
smear_in = opts.smear
chain.append(morphs.MorphSmear())
refpars.append("smear")
config["smear"] = smear_in
# Size
radii = [opts.radius, opts.pradius]
nrad = 2 - radii.count(None)
Expand Down Expand Up @@ -742,7 +758,7 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
morph_inputs = {
"scale": opts.scale,
"stretch": opts.stretch,
"smear": opts.smear,
"smear": opts.smear_pdf,
}
morph_inputs.update({"hshift": opts.hshift, "vshift": opts.vshift})

Expand Down Expand Up @@ -925,7 +941,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
morph_inputs = {
"scale": opts.scale,
"stretch": opts.stretch,
"smear": opts.smear,
"smear": opts.smear_pdf,
}
morph_inputs.update({"hshift": opts.hshift, "vshift": opts.vshift})

Expand Down