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

* Refactor smear to smear-pdf

* Reformat help headers

* Move tests to test_morphapp

* News

Author: Sparks29032

news/smear-update.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* New --smear option applies the smear morph directly to the function (without transforming to RDF).
+
+**Changed:**
+
+* Former --smear option renamed to --smear-pdf (converts PDF to RDF before applying the smear morph).
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -196,16 +196,31 @@ def custom_error(self, msg):
         type="float",
         metavar="SMEAR",
         help=(
-            "Smear peaks with a Gaussian of width SMEAR. "
-            "This convolves the function with a Gaussian of width SMEAR."
+            "Smear the peaks with a Gaussian 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",
@@ -520,8 +535,8 @@ 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())
@@ -532,6 +547,11 @@ 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)
@@ -806,7 +826,7 @@ 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})
 
@@ -989,7 +1009,7 @@ 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})
 

tests/test_morphapp.py

@@ -2,6 +2,7 @@
 
 from pathlib import Path
 
+import numpy as np
 import pytest
 
 from diffpy.morph.morphapp import (
@@ -255,6 +256,68 @@ def test_morphsequence(self, setup_morphsequence):
         )
         assert s_sequence_results == sequence_results
 
+    def test_morphsmear(self, setup_parser, tmp_path):
+        def gaussian(x, mu, sigma):
+            return np.exp(-((x - mu) ** 2) / (2 * sigma**2)) / (
+                sigma * np.sqrt(2 * np.pi)
+            )
+
+        # Generate the test files
+        x_grid = np.linspace(1, 101, 1001)
+        # Gaussian with STD 3 (morph)
+        g2 = gaussian(x_grid, 51, 3)
+        mf = tmp_path / "morph.txt"
+        with open(mf, "w") as f:
+            np.savetxt(f, np.array([x_grid, g2]).T)
+        # Gaussian with STD 5 (target)
+        g3 = gaussian(x_grid, 51, 5)
+        tf = tmp_path / "target.txt"
+        with open(tf, "w") as f:
+            np.savetxt(f, np.array([x_grid, g3]).T)
+        # Gaussian with STD 3 and baseline slope -0.5 (PDF morph)
+        g2_bl = gaussian(x_grid, 51, 3) / x_grid - 0.5 * x_grid
+        pmf = tmp_path / "pdf_morph.txt"
+        with open(pmf, "w") as f:
+            np.savetxt(f, np.array([x_grid, g2_bl]).T)
+        # Gaussian with STD 5 with baseline slope -0.5 (PDF target)
+        g3_bl = gaussian(x_grid, 51, 5) / x_grid - 0.5 * x_grid
+        ptf = tmp_path / "pdf_target.txt"
+        with open(ptf, "w") as f:
+            np.savetxt(f, np.array([x_grid, g3_bl]).T)
+
+        # No PDF smear (should not activate baseline slope)
+        (opts, _) = self.parser.parse_args(
+            [
+                "--smear",
+                "1",
+                "-n",
+            ]
+        )
+        pargs = [mf, tf]
+        smear_results = single_morph(
+            self.parser, opts, pargs, stdout_flag=False
+        )
+        # Variances add, and 3^2+4^2=5^2
+        assert pytest.approx(abs(smear_results["smear"])) == 4.0
+        assert pytest.approx(smear_results["Rw"]) == 0.0
+
+        # PDF-specific smear (should activate baseline slope)
+        (opts, _) = self.parser.parse_args(
+            [
+                "--smear",
+                "100",
+                "--smear-pdf",
+                "1",
+                "-n",
+            ]
+        )
+        pargs = [pmf, ptf]
+        pdf_smear_results = single_morph(
+            self.parser, opts, pargs, stdout_flag=False
+        )
+        assert pytest.approx(abs(pdf_smear_results["smear"])) == 4.0
+        assert pytest.approx(pdf_smear_results["Rw"]) == 0.0
+
 
 if __name__ == "__main__":
     TestApp()