Merge pull request #155 from Sparks29032/morphshift

Add shifting morph

Author: sbillinge

Diff for: news/morphshift.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Shifting morph for vertical and horizontal shifts.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

Diff for: src/diffpy/pdfmorph/morphs/morphshift.py

@@ -47,10 +47,19 @@ class MorphShift(Morph):
 
     def morph(self, x_morph, y_morph, x_target, y_target):
         """Apply the shifts."""
+        try:
+            hshift = self.hshift
+        except AttributeError:
+            hshift = 0
+        try:
+            vshift = self.vshift
+        except AttributeError:
+            vshift = 0
+
         Morph.morph(self, x_morph, y_morph, x_target, y_target)
-        r = self.x_morph_in - self.hshift
+        r = self.x_morph_in - hshift
         self.y_morph_out = numpy.interp(r, self.x_morph_in, self.y_morph_in)
-        self.y_morph_out += self.vshift
+        self.y_morph_out += vshift
         return self.xyallout
 
 

Diff for: src/diffpy/pdfmorph/pdfmorphapp.py

@@ -121,26 +121,43 @@ def custom_error(self, msg):
         help="""Exclude a manipulation from refinement by name. This can
  appear multiple times.""",
     )
-    group.add_option("--scale", type="float", metavar="SCALE", help="Apply scale factor SCALE.")
     group.add_option(
-        "--smear",
+        "--scale",
         type="float",
-        metavar="SMEAR",
-        help="Smear peaks with a Gaussian of width SMEAR.",
+        metavar="SCALE",
+        help="Apply scale factor SCALE.",
     )
     group.add_option(
         "--stretch",
         type="float",
         metavar="STRETCH",
         help="Stretch PDF by a fraction STRETCH.",
     )
+    group.add_option(
+        "--smear",
+        type="float",
+        metavar="SMEAR",
+        help="Smear peaks with a Gaussian of width SMEAR.",
+    )
     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.""",
     )
+    group.add_option(
+        "--hshift",
+        type="float",
+        metavar="HSHIFT",
+        help="Shift the PDF horizontally by HSHIFT to the right.",
+    )
+    group.add_option(
+        "--vshift",
+        type="float",
+        metavar="VSHIFT",
+        help="Shift the PDF vertically by VSHIFT upward.",
+    )
     group.add_option(
         "--qdamp",
         type="float",
@@ -318,6 +335,8 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
     scale_in = "None"
     stretch_in = "None"
     smear_in = "None"
+    hshift_in = "None"
+    vshift_in = "None"
     config = {}
     config["rmin"] = opts.rmin
     config["rmax"] = opts.rmax
@@ -336,22 +355,33 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
     if opts.scale is not None:
         scale_in = opts.scale
         chain.append(morphs.MorphScale())
-        config["scale"] = opts.scale
+        config["scale"] = scale_in
         refpars.append("scale")
     # Stretch
     if opts.stretch is not None:
         stretch_in = opts.stretch
         chain.append(morphs.MorphStretch())
-        config["stretch"] = opts.stretch
+        config["stretch"] = stretch_in
         refpars.append("stretch")
+    # Shift
+    if opts.hshift is not None or opts.vshift is not None:
+        chain.append(morphs.MorphShift())
+    if opts.hshift is not None:
+        hshift_in = opts.hshift
+        config["hshift"] = hshift_in
+        refpars.append("hshift")
+    if opts.vshift is not None:
+        vshift_in = opts.vshift
+        config["vshift"] = vshift_in
+        refpars.append("vshift")
     # Smear
     if opts.smear is not None:
         smear_in = opts.smear
         chain.append(helpers.TransformXtalPDFtoRDF())
         chain.append(morphs.MorphSmear())
         chain.append(helpers.TransformXtalRDFtoPDF())
         refpars.append("smear")
-        config["smear"] = opts.smear
+        config["smear"] = smear_in
         # Set baselineslope if not given
         config["baselineslope"] = opts.baselineslope
         if opts.baselineslope is None:
@@ -432,6 +462,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
 
     # Input morph parameters
     morph_inputs = {"scale": scale_in, "stretch": stretch_in, "smear": smear_in}
+    morph_inputs.update({"hshift": hshift_in, "vshift": vshift_in})
 
     # Output morph parameters
     morph_results = dict(config.items())
@@ -580,6 +611,7 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
         target_file_names.append(key)
 
     morph_inputs = {"scale": opts.scale, "stretch": opts.stretch, "smear": opts.smear}
+    morph_inputs.update({"hshift": opts.hshift, "vshift": opts.vshift})
 
     try:
         # Print summary of morphs to terminal and to file (if requested)
@@ -724,6 +756,7 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
         morph_file_names.append(key)
 
     morph_inputs = {"scale": opts.scale, "stretch": opts.stretch, "smear": opts.smear}
+    morph_inputs.update({"hshift": opts.hshift, "vshift": opts.vshift})
 
     try:
         # Print summary of morphs to terminal and to file (if requested)

Diff for: tests/test_morphshift.py

@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+
+import os
+
+import numpy
+import pytest
+
+from diffpy.pdfmorph.morphs.morphshift import MorphShift
+
+# useful variables
+thisfile = locals().get("__file__", "file.py")
+tests_dir = os.path.dirname(os.path.abspath(thisfile))
+# testdata_dir = os.path.join(tests_dir, 'testdata')
+
+
+class TestMorphShift:
+    @pytest.fixture
+    def setup(self):
+        self.hshift = 2.0
+        self.vshift = 3.0
+
+        # Original dataset goes from 0.1 to 5.0
+        self.x_morph = numpy.arange(0.01, 5 + self.hshift, 0.01)
+        self.y_morph = numpy.arange(0.01, 5 + self.hshift, 0.01)
+
+        # New dataset is moved to the right by 2.0 and upward by 3.0
+        self.x_target = numpy.arange(0.01 + self.hshift, 5 + self.hshift, 0.01)
+        self.y_target = numpy.arange(0.01 + self.vshift, 5 + self.vshift, 0.01)
+        return
+
+    def test_morph(self, setup):
+        """check MorphScale.morph()"""
+        config = {"hshift": self.hshift, "vshift": self.vshift}
+        morph = MorphShift(config)
+
+        x_morph, y_morph, x_target, y_target = morph(self.x_morph, self.y_morph, self.x_target, self.y_target)
+
+        # Only care about the shifted data past the shift
+        # Everything to left of shift is outside our input data domain
+        assert numpy.allclose(y_morph[x_morph > self.hshift], y_target)
+        assert numpy.allclose(self.x_target, x_target)
+        assert numpy.allclose(self.y_target, y_target)
+        return
+
+
+# End of class TestMorphScale
+
+if __name__ == "__main__":
+    TestMorphShift()
+
+# End of file

Diff for: tests/testdata/testsaving/succinct/Morph_Reference_Table.txt

@@ -6,6 +6,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Labels: [Target] [Temperature] [Pearson] [Rw]
 f_180K.gr 180.0 0.999810 0.020141

Diff for: tests/testdata/testsaving/verbose/Morph_Reference_Table.txt

@@ -6,6 +6,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Target: f_180K.gr
 # Optimized morphing parameters:

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_a.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_b.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_c.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_d.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_e.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/Morphs/mwt_f.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000

Diff for: tests/testdata/testsaving/verbose/single_verbose_morph.cgr

@@ -5,6 +5,8 @@
 # scale = None
 # stretch = None
 # smear = None
+# hshift = None
+# vshift = None
 
 # Optimized morphing parameters:
 # rmin = 0.000000