add news and more tests

Author: yucongalicechen

news/scaleto.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* functionality to rescale diffraction objects, placing one on top of another at a specified point
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/utils/diffraction_objects.py

@@ -364,41 +364,43 @@ def on_tth(self):
     def on_d(self):
         return [self.all_arrays[:, 3], self.all_arrays[:, 0]]
 
-    def scale_to(self, target_diff_object, xtype=None, xvalue=None):
-        f"""
+    def scale_to(self, target_diff_object, q=None, tth=None, d=None, offset=0):
+        """
         returns a new diffraction object which is the current object but rescaled in y to the target
 
+        The y-value in the target at the closest specified x-value will be used as the factor to scale to.
+        The entire array is scaled by this factor so that one object places on top of the other at that point.
+        If multiple values of `q`, `tth`, or `d` are provided, the priority is `q` > `tth` > `d`.
+        If none are provided, the midpoint of the current object's `q`-array will be used.
+
         Parameters
         ----------
         target_diff_object: DiffractionObject
-          the diffraction object you want to scale the current one on to
-        xtype: string, optional.  Default is Q
-          the xtype, from {XQUANTITIES}, that you will specify a point from to scale to
-        xvalue: float. Default is the midpoint of the array
-          the y-value in the target at this x-value will be used as the factor to scale to.
-          The entire array is scaled be the factor that places on on top of the other at that point.
-          xvalue does not have to be in the x-array, the point closest to this point will be used for the scaling.
+            the diffraction object you want to scale the current one onto
+
+        q, tth, d : float, optional, default is the midpoint of the current object's `q`-array
+            the xvalue (in `q`, `tth`, or `d` space) to align the current and target objects
+
+        offset : float, optional, default is 0
+            an offset to add to the scaled y-values
 
         Returns
         -------
         the rescaled DiffractionObject as a new object
-
         """
         scaled = deepcopy(self)
-        if xtype is None:
-            xtype = "q"
+        xtype = "q" if q is not None else "tth" if tth is not None else "d" if d is not None else "q"
+        data, target = self.on_xtype(xtype), target_diff_object.on_xtype(xtype)
+        if len(data[0]) == 0 or len(target[0]) == 0:
+            raise ValueError("I cannot scale diffraction objects with empty arrays.")
 
-        data = self.on_xtype(xtype)
-        target = target_diff_object.on_xtype(xtype)
-        if len(data[0]) == 0 or len(target[0]) == 0 or len(data[0]) != len(target[0]):
-            raise ValueError("I cannot scale two diffraction objects with empty or different lengths.")
+        xvalue = q if xtype == "q" else tth if xtype == "tth" else d
         if xvalue is None:
-            xvalue = data[0][0] + (data[0][-1] - data[0][0]) / 2.0
+            xvalue = (data[0][0] + data[0][-1]) / 2.0
 
-        xindex = (np.abs(data[0] - xvalue)).argmin()
-        ytarget = target[1][xindex]
-        yself = data[1][xindex]
-        scaled._all_arrays[:, 0] = data[1] * ytarget / yself
+        x_data, x_target = (np.abs(data[0] - xvalue)).argmin(), (np.abs(target[0] - xvalue)).argmin()
+        y_data, y_target = data[1][x_data], target[1][x_target]
+        scaled._all_arrays[:, 0] = data[1] * y_target / y_data + offset
         return scaled
 
     def on_xtype(self, xtype):

tests/test_diffraction_objects.py

@@ -224,96 +224,126 @@ def test_on_xtype_bad():
 
 
 params_scale_to = [
-    # UC1: xvalue exact match
+    # UC1: same x-array and y-array, check offset
     (
         [
             np.array([10, 15, 25, 30, 60, 140]),
-            np.array([10, 20, 25, 30, 60, 100]),
+            np.array([2, 3, 4, 5, 6, 7]),
             "tth",
             2 * np.pi,
             np.array([10, 15, 25, 30, 60, 140]),
             np.array([2, 3, 4, 5, 6, 7]),
             "tth",
             2 * np.pi,
+            None,
+            60,
+            None,
+            2.1,
+        ],
+        ["tth", np.array([4.1, 5.1, 6.1, 7.1, 8.1, 9.1])],
+    ),
+    # UC2: same length x-arrays with exact x-value match
+    (
+        [
+            np.array([10, 15, 25, 30, 60, 140]),
+            np.array([10, 20, 25, 30, 60, 100]),
+            "tth",
+            2 * np.pi,
+            np.array([10, 20, 25, 30, 60, 140]),
+            np.array([2, 3, 4, 5, 6, 7]),
             "tth",
+            2 * np.pi,
+            None,
             60,
+            None,
+            0,
         ],
-        [np.array([1, 2, 2.5, 3, 6, 10])],
+        ["tth", np.array([1, 2, 2.5, 3, 6, 10])],
     ),
-    # UC2: xvalue approximate match
+    # UC3: same length x-arrays with approximate x-value match
     (
         [
-            np.array([0.11, 0.24, 0.31, 0.4]),
+            np.array([0.12, 0.24, 0.31, 0.4]),
             np.array([10, 20, 40, 60]),
             "q",
             2 * np.pi,
-            np.array([0.11, 0.24, 0.31, 0.4]),
+            np.array([0.14, 0.24, 0.31, 0.4]),
             np.array([1, 3, 4, 5]),
             "q",
             2 * np.pi,
-            "q",
             0.1,
+            None,
+            None,
+            0,
         ],
-        [np.array([1, 2, 4, 6])],
+        ["q", np.array([1, 2, 4, 6])],
     ),
-]
-
-
-@pytest.mark.parametrize("inputs, expected", params_scale_to)
-def test_scale_to(inputs, expected):
-    orig_diff_object = DiffractionObject(xarray=inputs[0], yarray=inputs[1], xtype=inputs[2], wavelength=inputs[3])
-    target_diff_object = DiffractionObject(
-        xarray=inputs[4], yarray=inputs[5], xtype=inputs[6], wavelength=inputs[7]
-    )
-    scaled_diff_object = orig_diff_object.scale_to(target_diff_object, xtype=inputs[8], xvalue=inputs[9])
-    # Check the intensity data is same as expected
-    assert np.allclose(scaled_diff_object.on_xtype(inputs[8])[1], expected[0])
-
-
-params_scale_to_bad = [
-    # UC1: at least one of the y-arrays is empty
+    # UC4: different x-array lengths with approximate x-value match
     (
         [
-            np.array([]),
-            np.array([]),
+            np.array([10, 25, 30.1, 40.2, 61, 120, 140]),
+            np.array([10, 20, 30, 40, 50, 60, 100]),
             "tth",
             2 * np.pi,
-            np.array([11, 14, 16, 20, 25, 30]),
-            np.array([2, 3, 4, 5, 6, 7]),
+            np.array([20, 25.5, 32, 45, 50, 62, 100, 125, 140]),
+            np.array([1.1, 2, 3, 3.5, 4, 5, 10, 12, 13]),
             "tth",
             2 * np.pi,
-            "tth",
+            None,
             60,
-        ]
+            None,
+            0,
+        ],
+        # scaling factor is calculated at index = 5 for self and index = 6 for target
+        ["tth", np.array([1, 2, 3, 4, 5, 6, 10])],
     ),
-    # UC2: diffraction objects with different array lengths
+    # UC5: user specified multiple x-values, prioritize q > tth > d
     (
         [
-            np.array([0.11, 0.24, 0.31, 0.4, 0.5]),
-            np.array([10, 20, 40, 50, 60]),
-            "q",
+            np.array([10, 25, 30.1, 40.2, 61, 120, 140]),
+            np.array([10, 20, 30, 40, 50, 60, 100]),
+            "tth",
             2 * np.pi,
-            np.array([0.1, 0.15, 0.3, 0.4]),
-            np.array([1, 3, 4, 5]),
-            "q",
+            np.array([20, 25.5, 32, 45, 50, 62, 100, 125, 140]),
+            np.array([1.1, 2, 3, 3.5, 4, 5, 10, 12, 13]),
+            "tth",
             2 * np.pi,
-            "q",
-            0.1,
-        ]
+            None,
+            60,
+            10,
+            0,
+        ],
+        ["tth", np.array([1, 2, 3, 4, 5, 6, 10])],
     ),
 ]
 
 
-@pytest.mark.parametrize("inputs", params_scale_to_bad)
-def test_scale_to_bad(inputs):
+@pytest.mark.parametrize("inputs, expected", params_scale_to)
+def test_scale_to(inputs, expected):
     orig_diff_object = DiffractionObject(xarray=inputs[0], yarray=inputs[1], xtype=inputs[2], wavelength=inputs[3])
     target_diff_object = DiffractionObject(
         xarray=inputs[4], yarray=inputs[5], xtype=inputs[6], wavelength=inputs[7]
     )
-    with pytest.raises(
-        ValueError, match="I cannot scale two diffraction objects with empty or different lengths."
-    ):
-        orig_diff_object.scale_to(target_diff_object, xtype=inputs[8], xvalue=inputs[9])
+    scaled_diff_object = orig_diff_object.scale_to(
+        target_diff_object, q=inputs[8], tth=inputs[9], d=inputs[10], offset=inputs[11]
+    )
+    # Check the intensity data is same as expected
+    assert np.allclose(scaled_diff_object.on_xtype(expected[0])[1], expected[1])
+
+
+def test_scale_to_bad():
+    # UC1: at least one of the y-arrays is empty
+    orig_diff_object = DiffractionObject(
+        xarray=np.array([]), yarray=np.array([]), xtype="tth", wavelength=2 * np.pi
+    )
+    target_diff_object = DiffractionObject(
+        xarray=np.array([11, 14, 16, 20, 25, 30]),
+        yarray=np.array([2, 3, 4, 5, 6, 7]),
+        xtype="tth",
+        wavelength=2 * np.pi,
+    )
+    with pytest.raises(ValueError, match="I cannot scale diffraction objects with empty arrays."):
+        orig_diff_object.scale_to(target_diff_object, tth=20)
 
 
 params_index = [