Merge branch 'Cookie' of github.com:diffpy/diffpy.srmise into Cookie

sbillinge · Jul 30, 2024 · b44c264 · b44c264
2 parents 5249bf2 + 978dca1
commit b44c264
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Showing 22 changed files with 101 additions and 120 deletions.
diff --git a/diffpy/srmise/applications/extract.py b/diffpy/srmise/applications/extract.py
@@ -419,25 +419,19 @@ def main():
     from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction
     from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
-    if options.peakfunction is not None:
-        from diffpy.srmise import peaks
-
-        try:
-            options.peakfunction = eval("peaks." + options.peakfunction)
-        except Exception as err:
-            print(err)
-            print("Could not create peak function '%s'. Exiting." % options.peakfunction)
-            return
-
-    if options.modelevaluator is not None:
-        from diffpy.srmise import modelevaluators
-
-        try:
-            options.modelevaluator = eval("modelevaluators." + options.modelevaluator)
-        except Exception as err:
-            print(err)
-            print("Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator)
-            return
+    try:
+        options.peakfunction = eval("peaks." + options.peakfunction)
+    except Exception as err:
+        print(err)
+        print("Could not create peak function '%s'. Exiting." % options.peakfunction)
+        return
+
+    try:
+        options.modelevaluator = eval("modelevaluators." + options.modelevaluator)
+    except Exception as err:
+        print(err)
+        print("Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator)
+        return
 
     if options.bcrystal is not None:
         from diffpy.srmise.baselines import Polynomial
@@ -475,8 +469,6 @@ def main():
 
         bl = NanoSpherical()
         options.baseline = parsepars(bl, options.bspherical)
-    elif options.baseline is not None:
-        from diffpy.srmise import baselines
 
         try:
             options.baseline = eval("baselines." + options.baseline)

diff --git a/diffpy/srmise/basefunction.py b/diffpy/srmise/basefunction.py
@@ -3,8 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/baselines/arbitrary.py b/diffpy/srmise/baselines/arbitrary.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund
@@ -89,11 +89,12 @@ def __init__(self, npars, valuef, jacobianf=None, estimatef=None, Cache=None):
 
         # TODO: figure out how the metadict can be used to save the functions
         # and use them again when a file is loaded...
-        metadict = {}
-        metadict["npars"] = (npars, repr)
-        metadict["valuef"] = (valuef, repr)
-        metadict["jacobianf"] = (jacobianf, repr)
-        metadict["estimatef"] = (estimatef, repr)
+        metadict = {
+            "npars": (npars, repr),
+            "valuef": (valuef, repr),
+            "jacobianf": (jacobianf, repr),
+            "estimatef": (estimatef, repr),
+        }
         BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache)
 
     # Methods required by BaselineFunction ####
@@ -182,7 +183,6 @@ def _transform_parametersraw(self, pars, in_format, out_format):
     def _valueraw(self, pars, r):
         """Return value of polynomial for the given parameters and r values.
 
-        Parameters
         Parameters
         pars: Sequence of parameters
             pars[0] = a_0

diff --git a/diffpy/srmise/baselines/base.py b/diffpy/srmise/baselines/base.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/baselines/fromsequence.py b/diffpy/srmise/baselines/fromsequence.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/baselines/nanospherical.py b/diffpy/srmise/baselines/nanospherical.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund
@@ -35,7 +35,7 @@ class NanoSpherical(BaselineFunction):
     scale factor is 4*pi*rho_0, where rho_r is the nanoparticle density.
 
     gamma_0(r) Reference:
-    Guinier et. al. (1955). Small-angle Scattering from X-rays. New York: John Wiley & Sons, Inc.
+    Guinier et al. (1955). Small-angle Scattering from X-rays. New York: John Wiley & Sons, Inc.
     """
 
     def __init__(self, Cache=None):

diff --git a/diffpy/srmise/baselines/polynomial.py b/diffpy/srmise/baselines/polynomial.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund
@@ -49,8 +49,7 @@ def __init__(self, degree, Cache=None):
             parameterdict["a_" + str(d)] = self.degree - d
         formats = ["internal"]
         default_formats = {"default_input": "internal", "default_output": "internal"}
-        metadict = {}
-        metadict["degree"] = (degree, repr)
+        metadict = {"degree": (degree, repr)}
         BaselineFunction.__init__(self, parameterdict, formats, default_formats, metadict, None, Cache)
 
     # Methods required by BaselineFunction ####
@@ -95,12 +94,11 @@ def estimate_parameters(self, r, y):
 
                 import numpy.linalg as la
 
-                A = np.array([r[cut_idx]]).T
-                slope = la.lstsq(A, y[cut_idx])[0][0]
+                a = np.array([r[cut_idx]]).T
+                slope = la.lstsq(a, y[cut_idx])[0][0]
                 return np.array([slope, 0.0])
             except Exception as e:
                 emsg = "Error during estimation -- " + str(e)
-                raise
                 raise SrMiseEstimationError(emsg)
 
     def _jacobianraw(self, pars, r, free):

diff --git a/diffpy/srmise/dataclusters.py b/diffpy/srmise/dataclusters.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/modelcluster.py b/diffpy/srmise/modelcluster.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/modelevaluators/aic.py b/diffpy/srmise/modelevaluators/aic.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund
@@ -16,7 +16,6 @@
 
 import numpy as np
 
-import diffpy.srmise.srmiselog
 from diffpy.srmise.modelevaluators.base import ModelEvaluator
 from diffpy.srmise.srmiseerrors import SrMiseModelEvaluatorError
 
@@ -72,7 +71,7 @@ def evaluate(self, fit, count_fixed=False, kshift=0):
             logger.warn("AIC.evaluate(): too few data to evaluate quality reliably.")
             n = self.minpoints(k)
 
-        if self.chisq == None:
+        if self.chisq is None:
             self.chisq = self.chi_squared(fit.value(), fit.y_cluster, fit.error_cluster)
 
         self.stat = self.chisq + self.parpenalty(k, n)
@@ -94,10 +93,12 @@ def parpenalty(self, k, n):
         return (2 * k) * fudgefactor
 
     def growth_justified(self, fit, k_prime):
-        """Returns whether adding k_prime parameters to the given model (ModelCluster) is justified given the current quality of the fit.
-        The assumption is that adding k_prime parameters will result in "effectively 0" chiSquared cost, and so adding it is justified
-        if the cost of adding these parameters is less than the current chiSquared cost.  The validity of this assumption (which
-        depends on an unknown chiSquared value) and the impact of the errors used should be examined more thoroughly in the future.
+        """Returns whether adding k_prime parameters to the given model (ModelCluster) is justified
+        given the current quality of the fit. The assumption is that adding k_prime parameters will
+        result in "effectively 0" chiSquared cost, and so adding it is justified if the cost of adding
+        these parameters is less than the current chiSquared cost.
+        The validity of this assumption (which depends on an unknown chiSquared value)
+        and the impact of the errors used should be examined more thoroughly in the future.
         """
 
         if self.chisq is None:

diff --git a/diffpy/srmise/modelevaluators/aicc.py b/diffpy/srmise/modelevaluators/aicc.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund

diff --git a/diffpy/srmise/modelevaluators/base.py b/diffpy/srmise/modelevaluators/base.py
@@ -3,7 +3,7 @@
 #
 # SrMise            by Luke Granlund
 #                   (c) 2014 trustees of the Michigan State University
-#                   (c) 2024 trustees of Columia University in the City of New York
+#                   (c) 2024 trustees of Columbia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund