Fix changing r-grid issue in refine

Author: Sparks29032

docs/source/morphpy.rst

@@ -105,19 +105,26 @@ apply: bool
 exclude: str
     Exclude a manipulation from refinement by name.
 scale: float
-    Apply scale factor. This multiplies the function ordinate by scale.
+    Apply scale factor.
+
+    This multiplies the function ordinate by scale.
 stretch: float
-    Stretch function grid by a fraction stretch. Specifically, this multiplies the function grid by 1+stretch.
+    Stretch function grid by a fraction stretch.
+
+    This multiplies the function grid by 1+stretch.
 squeeze: list of float
     Squeeze function grid given a polynomial
-    p(x) = squeeze[0]+squeeze[1]*x+...+squeeze[n]*x^n. n is dependent on the number
+    p(x) = squeeze[0]+squeeze[1]*x+...+squeeze[n]*x^n.
+
+    n is dependent on the number
     of values in the user-inputted comma-separated list.
     The morph transforms the function grid from x to x+p(x).
     When this parameter is given, hshift is disabled.
     When n>1, stretch is disabled.
 smear: float
-    Smear the peaks with a Gaussian of width smear. This
-    is done by convolving the function with a Gaussian
+    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 used, only smear_pdf will be
     applied.
@@ -128,6 +135,7 @@ smear_pdf: float
     applied.
 slope: float
     Slope of the baseline used in converting from PDF to RDF.
+
     This is used with the option smear_pdf. The slope will
     be estimated if not provided.
 hshift: float
@@ -138,57 +146,119 @@ qdamp: float
     Dampen PDF by a factor qdamp.
 radius: float
     Apply characteristic function of sphere with radius
-    given by parameter radius. If pradius is also specified, instead apply
+    given by parameter radius.
+
+    If pradius is also specified, instead apply
     characteristic function of spheroid with equatorial
     radius radius and polar radius pradius.
 pradius: float
     Apply characteristic function of spheroid with
     equatorial radius given by above parameter radius and polar radius pradius.
+
     If only pradius is specified, instead apply
     characteristic function of sphere with radius pradius.
 iradius: float
     Apply inverse characteristic function of sphere with
-    radius iradius. If ipradius is also specified, instead
+    radius iradius.
+
+    If ipradius is also specified, instead
     apply inverse characteristic function of spheroid with
     equatorial radius iradius and polar radius ipradius.
 ipradius: float
     Apply inverse characteristic function of spheroid with
     equatorial radius iradius and polar radius ipradius.
+
     If only ipradius is specified, instead apply inverse
     characteristic function of sphere with radius ipradius.
 funcy: tuple (function, dict)
+    Apply a function to the y-axis of the (two-column) data.
+
     This morph applies the function funcy[0] with parameters given in funcy[1].
-    The function funcy[0] must be a function of both the abscissa and ordinate
-    (e.g. take in at least two inputs with as many additional parameters as needed).
+    The function funcy[0] take in as parameters both the abscissa and ordinate
+    (i.e. take in at least two inputs with as many additional parameters as needed).
+    The y-axis values of the data are then replaced by the return value of funcy[0].
+
     For example, let's start with a two-column table with abscissa x and ordinate y.
     let us say we want to apply the function ::
 
         def linear(x, y, a, b, c):
             return a * x + b * y + c
 
-    This function takes in both the abscissa and ordinate on top of three additional
-    parameters a, b, and c. To use the funcy parameter with initial guesses
-    a=1.0, b=2.0, c=3.0, we would pass ``funcy=(linear, {a: 1.0, b: 2.0, c: 3.0})``.
-    For an example use-case, see the Python-Specific Morphs section below.
+    This example function above takes in both the abscissa and ordinate on top of
+    three additional parameters a, b, and c.
+    To use the funcy parameter with parameter values a=1.0, b=2.0, and c=3.0,
+    we would pass ``funcy=(linear, {"a": 1.0, "b": 2.0, "c": 3.0})``.
+    For an explicit example, see the Python-Specific Morphs section below.
+funcx: tuple (function, dict)
+    Apply a function to the x-axis of the (two-column) data.
+
+    This morph applies the function funcx[0] with parameters given in funcx[1].
+    The function funcx[0] take in as parameters both the abscissa and ordinate
+    (i.e. take in at least two inputs with as many additional parameters as needed).
+    The x-axis values of the data are then replaced by the return value of funcx[0].
+    Note that diffpy.morph requires the x-axis be monotonic increasing
+    (i.e. for i < j, x[i] < x[j]): as such,
+    if funcx[0] is not a monotonic increasing function of the provided x-axis data,
+    the error ``x must be a strictly increasing sequence`` will be thrown.
 
+    For example, let's start with a two-column table with abscissa x and ordinate y.
+    let us say we want to apply the function ::
+
+        def exponential(x, y, amp, decay):
+            return abs(amp) * (1 - 2**(-decay * x))
+
+    This example function above takes in both the abscissa and ordinate on top of
+    three additional parameters amp and decay.
+    (Even though the ordinate is not used in the function,
+    it is still required that the function take in both acscissa and ordinate.)
+    To use the funcx parameter with parameter values amp=1.0 and decay=2.0,
+    we would pass ``funcx=(exponential, {"amp": 1.0, "decay:: 2.0})``.
+    For an explicit example, see the Python-Specific Morphs section below.
+funcxy: tuple (function, dict)
+    Apply a function the (two-column) data.
+
+    This morph applies the function funcxy[0] with parameters given in funcxy[1].
+    The function funcxy[0] take in as parameters both the abscissa and ordinate
+    (i.e. take in at least two inputs with as many additional parameters as needed).
+    The two columns of the data are then replaced by the two return values of funcxy[0].
+
+    For example, let's start with a two-column table with abscissa x and ordinate y.
+    let us say we want to apply the function ::
+
+        def shift(x, y, hshift, vshift):
+            return x + hshift, y + vshift
+
+    This example function above takes in both the abscissa and ordinate on top of
+    two additional parameters hshift and vshift.
+    To use the funcy parameter with parameter values hshift=1.0 and vshift=2.0,
+    we would pass ``funcy=(shift, {"hshift": 1.0, "vshift": 1.0})``.
+    For an example use-case, see the Python-Specific Morphs section below.
 
 Python-Specific Morphs
 ======================
 
 Some morphs in ``diffpy.morph`` are supported only in Python. Here, we detail
 how they are used and how to call them.
 
-MorphFuncy: Applying custom functions
+MorphFunc: Applying custom functions
 -------------------------------------
 
+In these tutorial, we walk through how to use the ``MorphFunc`` morphs
+(``MorphFuncy``, ``MorphFuncx``, ``MorphFuncxy``)
+with some example transformations.
+
+Unlike other morphs that can be run from the command line,
+``MorphFunc`` moprhs require a Python function and is therefore
+intended to be used through Python scripting.
+
+MorphFuncy:
+^^^^^^^^^^^
+
 The ``MorphFuncy`` morph allows users to apply a custom Python function
 to the y-axis values of a dataset, enabling flexible and user-defined
 transformations.
 
-In this tutorial, we walk through how to use ``MorphFuncy`` with an example
-transformation. Unlike other morphs that can be run from the command line,
-``MorphFuncy`` requires a Python function and is therefore intended to be used
-through Python scripting.
+Let's try out this morph!
 
     1. Import the necessary modules into your Python script:
 
@@ -229,7 +299,7 @@ through Python scripting.
 
        .. code-block:: python
 
-            morph_params, morph_table = morph_arrays(np.array([x_morph, y_morph]).T,np.array([x_target, y_target]).T,
+            morph_params, morph_table = morph_arrays(np.array([x_morph, y_morph]).T, np.array([x_target, y_target]).T,
             funcy=(linear_function,{'scale': 1.2, 'offset': 0.1}))
 
     5. Extract the fitted parameters from the result:
@@ -245,3 +315,85 @@ to generate the target (scale=20 & offset=0.8). This example shows how
 ``MorphFuncy`` can be used to fit and apply custom transformations. Now
 it's your turn to experiment with other custom functions that may be useful
 for analyzing your data.
+
+MorphFuncx:
+^^^^^^^^^^^
+
+The ``MorphFuncx`` morph allows users to apply a custom Python function
+to the x-axis values of a dataset, similar to the ``MorphFuncy`` morph.
+
+One caveat to this morph is that the x-axis values must remain monotonic
+increasing, so it is possible to run into errors when applying this morph.
+For example, if your initial grid is ``[-1, 0, 1]``, and your function is
+``lambda x, y: x**2``, the grid after the function is applied will be
+``[1, 0, 1]``, which is no longer monotonic increasing.
+In this case, the error ``x must be a strictly increasing sequence``
+will be thrown.
+
+Let's try out this morph!
+
+    1. Import the necessary modules into your Python script:
+
+       .. code-block:: python
+
+            from diffpy.morph.morphpy import morph_arrays
+            import numpy as np
+
+    2. Define a custom Python function to apply a transformation to the data.
+       The function must take ``x`` and ``y`` (1D arrays of the same length)
+       along with named parameters, and return a transformed ``x`` array of the
+       same length. Recall that this function must maintain the monotonic
+       increasing nature of the ``x`` array.
+
+       For this example, we will use a simple exponential function transformation that
+       greatly modifies the input:
+
+       .. code-block:: python
+
+            def exp_function(x, y, scale, rate):
+                return np.abs(scale) * np.exp(np.abs(rate) * x)
+
+       Notice that, though the function only uses the ``x`` input,
+       the function signature takes in both ``x`` and ``y``.
+
+    3. Like in the previous example, we will use a sine function for the morph
+       data and generate the target data by applying the decay transfomration
+       with a known scale and rate:
+
+       .. code-block:: python
+
+            x_morph = np.linspace(0, 10, 1001)
+            y_morph = np.sin(x_morph)
+            x_target = x_target = 20 * np.exp(0.8 * x_morph)
+            y_target = y_morph.copy()
+
+    4. Setup and run the morph using the ``morph_arrays(...)``.
+       ``morph_arrays`` expects the morph and target data as **2D arrays** in
+       *two-column* format ``[[x0, y0], [x1, y1], ...]``. This will apply
+       the user-defined function and refine the parameters to best align the
+       morph data with the target data. This includes both the transformation
+       parameters (our initial guess) and the transformation function itself:
+
+       .. code-block:: python
+
+            morph_params, morph_table = morph_arrays(np.array([x_morph, y_morph]).T, np.array([x_target, y_target]).T,
+            funcx=(decay_function, {'scale': 1.2, 'rate': 1.0}))
+
+    5. Extract the fitted parameters from the result:
+
+       .. code-block:: python
+
+            fitted_params = morph_params["funcx"]
+            print(f"Fitted scale: {fitted_params['scale']}")
+            print(f"Fitted rate: {fitted_params['rate']}")
+
+Again, we should see that the fitted scale and offset values match the ones used
+to generate the target (scale=20 & rate=0.8).
+
+For fun, you can plot the original function to the morphed function to see
+how much the
+
+MorphFuncxy:
+^^^^^^^^^^^^
+The ``MorphFuncxy`` morph allows users to apply a custom Python function
+to a dataset, ***.

src/diffpy/morph/morphs/morphfuncx.py

@@ -41,15 +41,15 @@ class MorphFuncx(Morph):
     Define or import the user-supplied transformation function:
 
         >>> import numpy as np
-        >>> def exp_function(x, y, amplitude, decay):
-        >>>     return abs(amplitude) * (1 - np.exp(-abs(decay) * x))
+        >>> def exp_function(x, y, scale, rate):
+        >>>     return abs(scale) * np.exp(rate * x)
 
     Note that this transformation is monotonic increasing, so will preserve
     the monotonic increasing nature of the provided grid.
 
     Provide initial guess for parameters:
 
-        >>> parameters = {'amplitude': 1, 'frequency': 1}
+        >>> parameters = {'scale': 1, 'rate': 1}
 
     Run the funcy morph given input morph array (x_morph, y_morph)and target
     array (x_target, y_target):

src/diffpy/morph/morphs/morphfuncxy.py

@@ -5,16 +5,21 @@
 
 
 class MorphFuncxy(Morph):
-    """Apply a custom function to the y-axis of the morph function.
+    """Apply a custom function to the morph function.
 
     General morph function that applies a user-supplied function to the
-    y-coordinates of morph data to make it align with a target.
+    morph data to make it align with a target.
+
+    This function may modify both the grid (x-axis) and function (y-axis)
+    of the morph data.
+
+    The user-provided function must return a two-column 1D function.
 
     Configuration Variables
     -----------------------
     function: callable
         The user-supplied function that applies a transformation to the
-        y-coordinates of the data.
+        grid (x-axis) and morph function (y-axis).
 
     parameters: dict
         A dictionary of parameters to pass to the function.
@@ -28,24 +33,25 @@ class MorphFuncxy(Morph):
 
     Example (EDIT)
     -------
-    Import the funcy morph function:
+    Import the funcxy morph function:
 
         >>> from diffpy.morph.morphs.morphfuncxy import MorphFuncxy
 
     Define or import the user-supplied transformation function:
 
-        >>> def sine_function(x, y, amplitude, frequency):
-        >>>     return amplitude * np.sin(frequency * x) * y
+        >>> import numpy as np
+        >>> def shift_function(x, y, hshift, vshift):
+        >>>     return x + hshift, y + vshift
 
     Provide initial guess for parameters:
 
-        >>> parameters = {'amplitude': 2, 'frequency': 2}
+        >>> parameters = {'hshift': 1, 'vshift': 1}
 
     Run the funcy morph given input morph array (x_morph, y_morph)and target
     array (x_target, y_target):
 
-        >>> morph = MorphFuncy()
-        >>> morph.function = sine_function
+        >>> morph = MorphFuncxy()
+        >>> morph.function = shift_function
         >>> morph.funcy = parameters
         >>> x_morph_out, y_morph_out, x_target_out, y_target_out =
         ... morph.morph(x_morph, y_morph, x_target, y_target)
@@ -60,7 +66,9 @@ class MorphFuncxy(Morph):
     """
 
     # Define input output types
-    summary = "Apply a Python function to the y-axis data"
+    summary = (
+        "Apply a Python function to the data (y-axis) and data grid (x-axis)"
+    )
     xinlabel = LABEL_RA
     yinlabel = LABEL_GR
     xoutlabel = LABEL_RA

src/diffpy/morph/morphs/morphrgrid.py

@@ -58,8 +58,12 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         """Resample arrays onto specified grid."""
         Morph.morph(self, x_morph, y_morph, x_target, y_target)
         rmininc = max(self.x_target_in[0], self.x_morph_in[0])
-        r_step_target = self.x_target_in[1] - self.x_target_in[0]
-        r_step_morph = self.x_morph_in[1] - self.x_morph_in[0]
+        r_step_target = (self.x_target_in[-1] - self.x_target_in[0]) / (
+            len(self.x_target_in) - 1
+        )
+        r_step_morph = (self.x_morph_in[-1] - self.x_morph_in[0]) / (
+            len(self.x_morph_in) - 1
+        )
         rstepinc = max(r_step_target, r_step_morph)
         rmaxinc = min(
             self.x_target_in[-1] + r_step_target,