Reduce warnings (#252)

Author: Sparks29032

news/reduce-warns.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Only give user extrapolation warning after refinement.
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morph_io.py

@@ -18,6 +18,7 @@
 
 import inspect
 import sys
+import warnings
 from pathlib import Path
 
 import numpy
@@ -26,6 +27,13 @@
 from diffpy.morph import __save_morph_as__
 
 
+def custom_formatwarning(msg, *args, **kwargs):
+    return f"{msg}\n"
+
+
+warnings.formatwarning = custom_formatwarning
+
+
 def single_morph_output(
     morph_inputs,
     morph_results,
@@ -398,3 +406,34 @@ def tabulate_results(multiple_morph_results):
             }
         )
     return tabulated_results
+
+
+def handle_warnings(squeeze_morph):
+    if squeeze_morph is not None:
+        eil = squeeze_morph.extrap_index_low
+        eih = squeeze_morph.extrap_index_high
+
+        if eil is not None or eih is not None:
+            if eih is None:
+                wmsg = (
+                    "Warning: points with grid value below "
+                    f"{squeeze_morph.squeeze_cutoff_low} "
+                    f"will be extrapolated."
+                )
+            elif eil is None:
+                wmsg = (
+                    "Warning: points with grid value above "
+                    f"{squeeze_morph.squeeze_cutoff_high} "
+                    f"will be extrapolated."
+                )
+            else:
+                wmsg = (
+                    "Warning: points with grid value below "
+                    f"{squeeze_morph.squeeze_cutoff_low} and above "
+                    f"{squeeze_morph.squeeze_cutoff_high} "
+                    f"will be extrapolated."
+                )
+            warnings.warn(
+                wmsg,
+                UserWarning,
+            )

src/diffpy/morph/morphapp.py

@@ -546,6 +546,7 @@ def single_morph(
     # Squeeze
     squeeze_poly_deg = -1
     squeeze_dict_in = {}
+    squeeze_morph = None
     if opts.squeeze is not None:
         # Handles both list and csv input
         if (
@@ -570,7 +571,8 @@ def single_morph(
                 except ValueError:
                     parser.error(f"{coeff} could not be converted to float.")
         squeeze_poly_deg = len(squeeze_dict_in.keys())
-        chain.append(morphs.MorphSqueeze())
+        squeeze_morph = morphs.MorphSqueeze()
+        chain.append(squeeze_morph)
         config["squeeze"] = squeeze_dict_in
         # config["extrap_index_low"] = None
         # config["extrap_index_high"] = None
@@ -696,6 +698,9 @@ def single_morph(
     else:
         chain(x_morph, y_morph, x_target, y_target)
 
+    # THROW ANY WARNINGS HERE
+    io.handle_warnings(squeeze_morph)
+
     # Get Rw for the morph range
     rw = tools.getRw(chain)
     pcc = tools.get_pearson(chain)

src/diffpy/morph/morphs/morphsqueeze.py

@@ -1,22 +1,13 @@
 """Class MorphSqueeze -- Apply a polynomial to squeeze the morph
 function."""
 
-import warnings
-
 import numpy as np
 from numpy.polynomial import Polynomial
 from scipy.interpolate import CubicSpline
 
 from diffpy.morph.morphs.morph import LABEL_GR, LABEL_RA, Morph
 
 
-def custom_formatwarning(msg, *args, **kwargs):
-    return f"{msg}\n"
-
-
-warnings.formatwarning = custom_formatwarning
-
-
 class MorphSqueeze(Morph):
     """Squeeze the morph function.
 
@@ -75,6 +66,11 @@ class MorphSqueeze(Morph):
     # extrap_index_high: first index after interpolation region
     extrap_index_low = None
     extrap_index_high = None
+    squeeze_cutoff_low = None
+    squeeze_cutoff_high = None
+
+    def __init__(self, config=None):
+        super().__init__(config)
 
     def morph(self, x_morph, y_morph, x_target, y_target):
         """Apply a polynomial to squeeze the morph function.
@@ -87,34 +83,14 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         coeffs = [self.squeeze[f"a{i}"] for i in range(len(self.squeeze))]
         squeeze_polynomial = Polynomial(coeffs)
         x_squeezed = self.x_morph_in + squeeze_polynomial(self.x_morph_in)
+        self.squeeze_cutoff_low = min(x_squeezed)
+        self.squeeze_cutoff_high = max(x_squeezed)
         self.y_morph_out = CubicSpline(x_squeezed, self.y_morph_in)(
             self.x_morph_in
         )
-        low_extrap = np.where(self.x_morph_in < x_squeezed[0])[0]
-        high_extrap = np.where(self.x_morph_in > x_squeezed[-1])[0]
+        low_extrap = np.where(self.x_morph_in < self.squeeze_cutoff_low)[0]
+        high_extrap = np.where(self.x_morph_in > self.squeeze_cutoff_high)[0]
         self.extrap_index_low = low_extrap[-1] if low_extrap.size else None
         self.extrap_index_high = high_extrap[0] if high_extrap.size else None
-        below_extrap = min(x_morph) < min(x_squeezed)
-        above_extrap = max(x_morph) > max(x_squeezed)
-        if below_extrap or above_extrap:
-            if not above_extrap:
-                wmsg = (
-                    "Warning: points with grid value below "
-                    f"{min(x_squeezed)} will be extrapolated."
-                )
-            elif not below_extrap:
-                wmsg = (
-                    "Warning: points with grid value above "
-                    f"{max(x_squeezed)} will be extrapolated."
-                )
-            else:
-                wmsg = (
-                    "Warning: points with grid value below "
-                    f"{min(x_squeezed)} and above {max(x_squeezed)} will be "
-                    "extrapolated."
-                )
-            warnings.warn(
-                wmsg,
-                UserWarning,
-            )
+
         return self.xyallout

tests/test_morphsqueeze.py

@@ -2,6 +2,7 @@
 import pytest
 from numpy.polynomial import Polynomial
 
+import diffpy.morph.morphpy as morphpy
 from diffpy.morph.morphapp import create_option_parser, single_morph
 from diffpy.morph.morphs.morphsqueeze import MorphSqueeze
 
@@ -123,16 +124,19 @@ def test_morphsqueeze_extrapolate(
 ):
     x_morph = np.linspace(0, 10, 101)
     y_morph = np.sin(x_morph)
-    x_target = x_morph
-    y_target = y_morph
+    x_target = x_morph.copy()
+    y_target = y_morph.copy()
     morph = MorphSqueeze()
     morph.squeeze = squeeze_coeffs
     coeffs = [squeeze_coeffs[f"a{i}"] for i in range(len(squeeze_coeffs))]
     squeeze_polynomial = Polynomial(coeffs)
     x_squeezed = x_morph + squeeze_polynomial(x_morph)
     with pytest.warns() as w:
-        x_morph_actual, y_morph_actual, x_target_actual, y_target_actual = (
-            morph(x_morph, y_morph, x_target, y_target)
+        morphpy.morph_arrays(
+            np.array([x_morph, y_morph]).T,
+            np.array([x_target, y_target]).T,
+            squeeze=coeffs,
+            apply=True,
         )
         assert len(w) == 1
         assert w[0].category is UserWarning
@@ -152,6 +156,7 @@ def test_morphsqueeze_extrapolate(
             ",".join(map(str, coeffs)),
             f"{morph_file.as_posix()}",
             f"{target_file.as_posix()}",
+            "--apply",
             "-n",
         ]
     )