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Merge branch 'Cookie' of github.com:diffpy/diffpy.srmise into Cookie
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@sbillinge
sbillinge committed Jul 30, 2024
2 parents 166e726 + 30d0909 commit 5249bf2
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26 changes: 2 additions & 24 deletions diffpy/srmise/__init__.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
Expand All @@ -13,28 +14,5 @@

"""Tools for peak extraction from PDF."""

__all__ = [
"basefunction",
"srmiseerrors",
"srmiselog",
"dataclusters",
"modelcluster",
"modelparts",
"pdfdataset",
"pdfpeakextraction",
"peakextraction",
"peakstability",
"multimodelselection",
]

from basefunction import BaseFunction
from dataclusters import DataClusters
from modelcluster import ModelCluster, ModelCovariance
from modelparts import ModelPart, ModelParts
from multimodelselection import MultimodelSelection
from pdfdataset import PDFDataSet
from pdfpeakextraction import PDFPeakExtraction
from peakextraction import PeakExtraction
from peakstability import PeakStability

from diffpy.srmise.version import __version__
3 changes: 2 additions & 1 deletion diffpy/srmise/applications/__init__.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/applications/plot.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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4 changes: 3 additions & 1 deletion diffpy/srmise/basefunction.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (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
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/__init__.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/arbitrary.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/base.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/fromsequence.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/nanospherical.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/baselines/polynomial.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/dataclusters.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/modelcluster.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/modelevaluators/__init__.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/modelevaluators/aic.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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3 changes: 2 additions & 1 deletion diffpy/srmise/modelevaluators/aicc.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
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26 changes: 12 additions & 14 deletions diffpy/srmise/modelevaluators/base.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
Expand Down Expand Up @@ -43,9 +44,6 @@

import numpy as np

import diffpy.srmise.srmiselog
from diffpy.srmise.srmiseerrors import SrMiseModelEvaluatorError

logger = logging.getLogger("diffpy.srmise")


Expand All @@ -68,9 +66,9 @@ def __lt__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

if self.higher_is_better:
if self.higher_is_better is not None:
return self.stat < other.stat
else:
return other.stat < self.stat
Expand All @@ -79,9 +77,9 @@ def __le__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

if self.higher_is_better:
if self.higher_is_better is not None:
return self.stat <= other.stat
else:
return other.stat <= self.stat
Expand All @@ -90,25 +88,25 @@ def __eq__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

return self.stat == other.stat

def __ne__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

return self.stat != other.stat

def __gt__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

if self.higher_is_better:
if self.higher_is_better is not None:
return self.stat > other.stat
else:
return other.stat > self.stat
Expand All @@ -117,9 +115,9 @@ def __ge__(self, other):
""" """

assert self.method == other.method # Comparison between same types required
assert self.stat != None and other.stat != None # The statistic must already be calculated
assert self.stat is not None and other.stat is not None # The statistic must already be calculated

if self.higher_is_better:
if self.higher_is_better is not None:
return self.stat >= other.stat
else:
return other.stat >= self.stat
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5 changes: 3 additions & 2 deletions diffpy/srmise/modelparts.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
Expand Down Expand Up @@ -207,7 +208,7 @@ def fit(

return

#### Notes on the fit f
# # Notes on the fit f
# f[0] = solution
# f[1] = Uses the fjac and ipvt optional outputs to construct an estimate of the jacobian around the solution.
# None if a singular matrix encountered (indicates very flat curvature in some direction).
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5 changes: 3 additions & 2 deletions diffpy/srmise/multimodelselection.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
Expand Down Expand Up @@ -527,7 +528,7 @@ def plot3dclassprobs(self, **kwds):
verts.append(np.concatenate([[p0], zip(xs, ys), [p1], [p0]]))
zlabels.append(i)

### Define face colors
# Define face colors
fc = np.array([len(self.classes[z]) for z in zlabels])
if class_size is "fraction":
fc = fc / float(len(self.results))
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3 changes: 2 additions & 1 deletion diffpy/srmise/pdfpeakextraction.py
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##############################################################################
#
# SrMise by Luke Granlund
# (c) 2014 trustees of the Michigan State University.
# (c) 2014 trustees of the Michigan State University
# (c) 2024 trustees of Columia University in the City of New York
# All rights reserved.
#
# File coded by: Luke Granlund
Expand Down
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