diff --git a/devutils/prep.py b/devutils/prep.py index af3b446..9eee5e8 100644 --- a/devutils/prep.py +++ b/devutils/prep.py @@ -6,7 +6,7 @@ import re import sys -__basedir__ = os.getcwdu() +__basedir__ = os.getcwd() from numpy.compat import unicode diff --git a/doc/examples/README b/doc/examples/README.rst similarity index 100% rename from doc/examples/README rename to doc/examples/README.rst diff --git a/doc/examples/extract_single_peak.py b/doc/examples/extract_single_peak.py index b32b0be..5004172 100644 --- a/doc/examples/extract_single_peak.py +++ b/doc/examples/extract_single_peak.py @@ -28,7 +28,7 @@ import matplotlib.pyplot as plt from diffpy.srmise.applications.plot import makeplot -from diffpy.srmise.baselines import Polynomial +from diffpy.srmise.baselines.polynomial import Polynomial from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction diff --git a/doc/examples/fit_initial.py b/doc/examples/fit_initial.py index 71979e8..fa9961c 100644 --- a/doc/examples/fit_initial.py +++ b/doc/examples/fit_initial.py @@ -21,10 +21,11 @@ import matplotlib.pyplot as plt -from diffpy.srmise import PDFPeakExtraction from diffpy.srmise.applications.plot import makeplot -from diffpy.srmise.baselines import FromSequence -from diffpy.srmise.peaks import Peaks, TerminationRipples +from diffpy.srmise.baselines.fromsequence import FromSequence +from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction +from diffpy.srmise.peaks.base import Peaks +from diffpy.srmise.peaks.terminationripples import TerminationRipples def run(plot=True): diff --git a/doc/examples/multimodel_known_dG1.py b/doc/examples/multimodel_known_dG1.py index f0ceb1b..f1fe508 100644 --- a/doc/examples/multimodel_known_dG1.py +++ b/doc/examples/multimodel_known_dG1.py @@ -37,7 +37,8 @@ import numpy as np import diffpy.srmise.srmiselog as sml -from diffpy.srmise import MultimodelSelection, PDFPeakExtraction +from diffpy.srmise.multimodelselection import MultimodelSelection +from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction def run(plot=True): diff --git a/doc/examples/multimodel_known_dG2.py b/doc/examples/multimodel_known_dG2.py index e72db46..6e6fdb3 100644 --- a/doc/examples/multimodel_known_dG2.py +++ b/doc/examples/multimodel_known_dG2.py @@ -35,8 +35,8 @@ import numpy as np import diffpy.srmise.srmiselog as sml -from diffpy.srmise import MultimodelSelection from diffpy.srmise.applications.plot import makeplot +from diffpy.srmise.multimodelselection import MultimodelSelection # distances from ideal Ag (refined to PDF) dcif = np.array( diff --git a/doc/examples/multimodel_unknown_dG1.py b/doc/examples/multimodel_unknown_dG1.py index 7a6a2b8..4570f78 100644 --- a/doc/examples/multimodel_unknown_dG1.py +++ b/doc/examples/multimodel_unknown_dG1.py @@ -36,8 +36,9 @@ import numpy as np import diffpy.srmise.srmiselog as sml -from diffpy.srmise import MultimodelSelection, PDFPeakExtraction -from diffpy.srmise.baselines import FromSequence +from diffpy.srmise.baselines.fromsequence import FromSequence +from diffpy.srmise.multimodelselection import MultimodelSelection +from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction def run(plot=True): diff --git a/doc/examples/multimodel_unknown_dG2.py b/doc/examples/multimodel_unknown_dG2.py index 9a4b24a..c4bbef4 100644 --- a/doc/examples/multimodel_unknown_dG2.py +++ b/doc/examples/multimodel_unknown_dG2.py @@ -42,8 +42,8 @@ import numpy as np import diffpy.srmise.srmiselog as sml -from diffpy.srmise import MultimodelSelection from diffpy.srmise.applications.plot import makeplot +from diffpy.srmise.multimodelselection import MultimodelSelection # distances from ideal (unrefined) C60 dcif = np.array( diff --git a/doc/examples/parameter_summary.py b/doc/examples/parameter_summary.py index 1b8a195..1d4095c 100644 --- a/doc/examples/parameter_summary.py +++ b/doc/examples/parameter_summary.py @@ -29,10 +29,10 @@ import matplotlib.pyplot as plt -from diffpy.srmise import PDFPeakExtraction from diffpy.srmise.applications.plot import makeplot -from diffpy.srmise.baselines import Polynomial -from diffpy.srmise.peaks import GaussianOverR +from diffpy.srmise.baselines.polynomial import Polynomial +from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction +from diffpy.srmise.peaks.gaussianoverr import GaussianOverR def run(plot=True): diff --git a/doc/examples/query_results.py b/doc/examples/query_results.py index 8035921..c012567 100644 --- a/doc/examples/query_results.py +++ b/doc/examples/query_results.py @@ -29,7 +29,8 @@ import matplotlib.pyplot as plt import numpy as np -from diffpy.srmise import ModelCovariance, PDFPeakExtraction +from diffpy.srmise.modelcluster import ModelCovariance +from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction def run(plot=True): diff --git a/src/diffpy/srmise/multimodelselection.py b/src/diffpy/srmise/multimodelselection.py index 3fc4f5b..a10dba2 100644 --- a/src/diffpy/srmise/multimodelselection.py +++ b/src/diffpy/srmise/multimodelselection.py @@ -507,8 +507,8 @@ def plot3dclassprobs(self, **kwds): probfilter = kwds.pop("probfilter", [0.0, 1.0]) class_size = kwds.pop("class_size", "number") norm = kwds.pop("norm", "auto") - cmap = kwds.pop("cmap", cm.jet) - highlight_cmap = kwds.pop("highlight_cmap", cm.gray) + cmap = kwds.pop("cmap", cm.get_cmap("jet")) + highlight_cmap = kwds.pop("highlight_cmap", cm.get_cmap("gray")) title = kwds.pop("title", True) p_alpha = kwds.pop("p_alpha", 0.7) scale = kwds.pop("scale", 1.0) diff --git a/src/diffpy/srmise/peaks/base.py b/src/diffpy/srmise/peaks/base.py index aa7849c..44c7963 100644 --- a/src/diffpy/srmise/peaks/base.py +++ b/src/diffpy/srmise/peaks/base.py @@ -189,7 +189,7 @@ def match_at(self, x, y): return False return any_scaled - def sort(self, key="position"): + def sort(self, reverse=False, key="position"): """Sort peaks in order specified by key.""" keypars = np.array([p[key] for p in self]) order = keypars.argsort()