feat: add PeakProfiles to profiles.py

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sbillinge@ucsb.edu and cadenmyers13@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
+sbillinge@ucsb.edu and cjm2304@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.

README.rst

@@ -129,7 +129,7 @@ Before contributing, please read our `Code of Conduct <https://github.com/diffpy
 Contact
 -------
 
-For more information on diffpy.cmirietveld please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu) and Caden Myers(cadenmyers13@columbia.edu)``.
+For more information on diffpy.cmirietveld please visit the project `web-page <https://diffpy.github.io/>`_ or email the maintainers ``Simon Billinge(sbillinge@ucsb.edu) and Caden Myers(cjm2304@columbia.edu)``.
 
 Acknowledgements
 ----------------

cookiecutter.json

@@ -1,8 +1,8 @@
 {
   "author_names": "Simon Billinge, Caden Myers",
-  "author_emails": "sbillinge@ucsb.edu, cadenmyers13@columbia.edu",
+  "author_emails": "sbillinge@ucsb.edu, cjm2304@columbia.edu",
   "maintainer_names": "Simon Billinge, Caden Myers",
-  "maintainer_emails": "sbillinge@ucsb.edu, cadenmyers13@columbia.edu",
+  "maintainer_emails": "sbillinge@ucsb.edu, cjm2304@columbia.edu",
   "maintainer_github_usernames": "sbillinge",
   "contributors": "Caden Myers, members of the Billinge group, and contributors to the diffpy.cmirietveld project",
   "project_name": "diffpy.cmirietveld",

news/component-parameters.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add ``Component.create_parameters_from``, which creates a component's Parameters from a pyobjcryst model, with the model's default values and its limits as bounds, and ``Component.push_parameters``, which writes the values back and raises a ``ValueError`` for a value outside the limits instead of letting ObjCryst clamp it silently.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/peak-profiles.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Add the ``PseudoVoigtProfile`` and ``TCHProfile`` peak profile components, which create their Parameters from pyobjcryst's ``ReflectionProfilePseudoVoigt`` and ``ReflectionProfilePseudoVoigtTCH`` and configure a pyobjcryst powder pattern with ``install`` and ``update``.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -7,11 +7,11 @@ name = "diffpy.cmirietveld"
 dynamic=['version', 'dependencies']
 authors = [
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
-  {name='Caden Myers', email='cadenmyers13@columbia.edu'},
+  {name='Caden Myers', email='cjm2304@columbia.edu'},
 ]
 maintainers = [
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
-  {name='Caden Myers', email='cadenmyers13@columbia.edu'},
+  {name='Caden Myers', email='cjm2304@columbia.edu'},
 ]
 description = "A pack for diffpy.cmi that allows it to do Rietveld refinement of powder diffraction data"
 keywords = ['diffraction', 'PDF', 'X-ray', 'neutron', 'Rietveld']

requirements/conda.txt

@@ -1,2 +1,3 @@
 numpy
 diffpy.srfit
+pyobjcryst

requirements/pip.txt

@@ -1,2 +1,3 @@
 numpy
 diffpy.srfit
+pyobjcryst

src/diffpy/cmirietveld/component.py

@@ -22,6 +22,7 @@
 
 __all__ = ["Component"]
 
+from diffpy.srfit.fitbase.parameter import Parameter
 from diffpy.srfit.fitbase.parameterset import ParameterSet
 
 
@@ -38,6 +39,10 @@ class Component(ParameterSet):
         The name of the component. It must be a valid attribute name.
     """
 
+    def __init__(self, name):
+        ParameterSet.__init__(self, name)
+        self._refinable_par_names = {}
+
     def install(self, pattern, diffraction):
         """Set the model up in one generator.
 
@@ -73,20 +78,81 @@ def create_parameters_from(self, refinable_obj, names):
         model.
 
         Each Parameter takes the default value of the matching
-        ``RefinablePar`` and its limits as bounds.
+        ``RefinablePar`` and its limits as bounds. ObjCryst silently clamps
+        a value outside its limits, so the bounds keep a refinement within
+        the values ObjCryst actually uses.
+
+        The Parameter names are mapped to the ``RefinablePar`` names
+        rather than copied, so the names users see are this package's,
+        independent of ObjCryst's. Some ObjCryst names are not valid
+        Parameter names (``2ThetaDispl``). The mapping keeps ObjCryst
+        parameters out of refinement scripts. The mapping is stored, so
+        ``push_parameters`` writes each value back to the same
+        ``RefinablePar``.
 
         Parameters
         ----------
         refinable_obj : pyobjcryst.refinableobj.RefinableObj
             A fresh instance of the pyobjcryst model.
         names : dict of str to str
-            The ``RefinablePar`` name for each Parameter name.
+            The ``RefinablePar`` name for each Parameter name, for example
+            ``{"eta0": "Eta0"}``. Only the named ``RefinablePar``s get a
+            Parameter.
+
+        Raises
+        ------
+        ValueError
+            If the model has no ``RefinablePar`` with one of the names.
+
+        Examples
+        --------
+        In the ``__init__`` of a peak profile:
+
+        >>> self.create_parameters_from(
+        ...     ReflectionProfilePseudoVoigt(),
+        ...     {"U": "U", "V": "V", "W": "W", "eta0": "Eta0"},
+        ... )
         """
-        raise NotImplementedError
+        available_names = [
+            refinable_obj.GetPar(index).GetName()
+            for index in range(refinable_obj.GetNbPar())
+        ]
+        for refinable_par_name in names.values():
+            if refinable_par_name not in available_names:
+                raise ValueError(
+                    f"{type(refinable_obj).__name__} has no refinable "
+                    f"parameter named '{refinable_par_name}'. Please use one "
+                    f"of its parameter names: {', '.join(available_names)}."
+                )
+        for parameter_name, refinable_par_name in names.items():
+            refinable_par = refinable_obj.GetPar(refinable_par_name)
+            parameter = Parameter(
+                parameter_name, refinable_par.GetHumanValue()
+            )
+            if refinable_par.IsLimited():
+                parameter.bound_range(
+                    refinable_par.GetHumanMin(), refinable_par.GetHumanMax()
+                )
+            self.add_parameter(parameter)
+        self._refinable_par_names.update(names)
 
     def push_parameters(self, refinable_obj):
         """Push the Parameter values into a pyobjcryst model.
 
+        Each value is written to the ``RefinablePar`` that
+        ``create_parameters_from`` mapped it to.
+
+        A value outside the limits of its ``RefinablePar`` raises an error
+        instead of being clamped, because ObjCryst would otherwise use a
+        different value from the one the Parameter reports. The check uses
+        ObjCryst's limits, not the Parameter's bounds: a value outside
+        narrowed bounds is still pushed, and widened bounds don't let a
+        value past a limit. An optimizer run without the recipe's bounds
+        stops with this error the first time it steps past a limit.
+
+        All the values are checked before any is pushed, so an error
+        leaves the model unchanged rather than half updated.
+
         Parameters
         ----------
         refinable_obj : pyobjcryst.refinableobj.RefinableObj
@@ -95,9 +161,38 @@ def push_parameters(self, refinable_obj):
         Raises
         ------
         ValueError
-            If a Parameter value is outside its bounds.
+            If a Parameter value is outside the limits of its
+            ``RefinablePar``.
         """
-        raise NotImplementedError
+        values = {
+            parameter_name: self.get(parameter_name).value
+            for parameter_name in self._refinable_par_names
+        }
+        refinable_pars = {
+            parameter_name: refinable_obj.GetPar(refinable_par_name)
+            for parameter_name, refinable_par_name in (
+                self._refinable_par_names.items()
+            )
+        }
+        for parameter_name, refinable_par in refinable_pars.items():
+            if not refinable_par.IsLimited():
+                continue
+            value = values[parameter_name]
+            lower_limit = refinable_par.GetHumanMin()
+            upper_limit = refinable_par.GetHumanMax()
+            if not lower_limit <= value <= upper_limit:
+                used_value = min(max(value, lower_limit), upper_limit)
+                raise ValueError(
+                    f"The value of '{parameter_name}', {value}, is outside "
+                    f"its limits [{lower_limit}, {upper_limit}]. ObjCryst "
+                    f"would silently use {used_value} instead, so the refined "
+                    "value would not be the one used to calculate the "
+                    "pattern. Please keep the value within the limits, for "
+                    "example by passing the recipe's bounds to the optimizer: "
+                    "least_squares(..., bounds=recipe.get_bounds_array())."
+                )
+        for parameter_name, refinable_par in refinable_pars.items():
+            refinable_par.SetHumanValue(values[parameter_name])
 
 
 # End of file

src/diffpy/cmirietveld/profiles.py

@@ -21,6 +21,11 @@
     "BackToBackExponentialProfile",
 ]
 
+from pyobjcryst.reflectionprofile import (
+    ReflectionProfilePseudoVoigt,
+    ReflectionProfilePseudoVoigtTCH,
+)
+
 from diffpy.cmirietveld.component import Component
 
 
@@ -52,6 +57,62 @@ class PseudoVoigtProfile(PeakProfile):
         The peak asymmetry terms.
     """
 
+    def __init__(self):
+        PeakProfile.__init__(self)
+        self.create_parameters_from(
+            ReflectionProfilePseudoVoigt(),
+            {
+                "U": "U",
+                "V": "V",
+                "W": "W",
+                "eta0": "Eta0",
+                "eta1": "Eta1",
+                "asym0": "Asym0",
+                "asym1": "Asym1",
+                "asym2": "Asym2",
+            },
+        )
+
+    def install(self, pattern, diffraction):
+        """Install a fresh pyobjcryst pseudo-Voigt profile in one
+        generator.
+
+        The diffraction component gets a new
+        ``ReflectionProfilePseudoVoigt``, replacing the profile installed
+        before. Its values are set by ``update``.
+
+        Parameters
+        ----------
+        pattern : pyobjcryst.powderpattern.PowderPattern
+            The pattern of the generator.
+        diffraction : pyobjcryst.powderpattern.PowderPatternDiffraction
+            The diffraction component of the generator's structure.
+        """
+        diffraction.SetProfile(ReflectionProfilePseudoVoigt())
+
+    def update(self, pattern, diffraction):
+        """Push the Parameter values into the installed pseudo-Voigt
+        profile.
+
+        ``SetProfile`` installs a copy, so the values are written into
+        ``diffraction.GetProfile()``, not into the profile given to
+        ``SetProfile``.
+
+        Parameters
+        ----------
+        pattern : pyobjcryst.powderpattern.PowderPattern
+            The pattern of the generator.
+        diffraction : pyobjcryst.powderpattern.PowderPatternDiffraction
+            The diffraction component of the generator's structure.
+
+        Raises
+        ------
+        ValueError
+            If a Parameter value is outside the limits of its
+            ``RefinablePar``.
+        """
+        self.push_parameters(diffraction.GetProfile())
+
 
 class TCHProfile(PeakProfile):
     """Symmetric Thompson-Cox-Hastings pseudo-Voigt peak profile.
@@ -71,6 +132,60 @@ class TCHProfile(PeakProfile):
         The mixing of the Gaussian and Lorentzian size broadening.
     """
 
+    def __init__(self):
+        PeakProfile.__init__(self)
+        self.create_parameters_from(
+            ReflectionProfilePseudoVoigtTCH(),
+            {
+                "U": "U",
+                "V": "V",
+                "W": "W",
+                "X": "X",
+                "Y": "Y",
+                "Z": "Z",
+                "P": "P",
+                "LGmix": "LGmix",
+            },
+        )
+
+    def install(self, pattern, diffraction):
+        """Install a fresh pyobjcryst TCH profile in one generator.
+
+        The diffraction component gets a new
+        ``ReflectionProfilePseudoVoigtTCH``, replacing the profile installed
+        before. Its values are set by ``update``.
+
+        Parameters
+        ----------
+        pattern : pyobjcryst.powderpattern.PowderPattern
+            The pattern of the generator.
+        diffraction : pyobjcryst.powderpattern.PowderPatternDiffraction
+            The diffraction component of the generator's structure.
+        """
+        diffraction.SetProfile(ReflectionProfilePseudoVoigtTCH())
+
+    def update(self, pattern, diffraction):
+        """Push the Parameter values into the installed TCH profile.
+
+        ``SetProfile`` installs a copy, so the values are written into
+        ``diffraction.GetProfile()``, not into the profile given to
+        ``SetProfile``.
+
+        Parameters
+        ----------
+        pattern : pyobjcryst.powderpattern.PowderPattern
+            The pattern of the generator.
+        diffraction : pyobjcryst.powderpattern.PowderPatternDiffraction
+            The diffraction component of the generator's structure.
+
+        Raises
+        ------
+        ValueError
+            If a Parameter value is outside the limits of its
+            ``RefinablePar``.
+        """
+        self.push_parameters(diffraction.GetProfile())
+
 
 class BackToBackExponentialProfile(PeakProfile):
     """Peak profile of a time-of-flight pattern.