conversion from python2 to python3 language

Author: stevenhua0320

Diff for: diffpy/srmise/applications/extract.py

@@ -277,21 +277,21 @@ def main():
         from diffpy.srmise import peaks
         try:
             options.peakfunction = eval("peaks."+options.peakfunction)
-        except Exception, err:
-            print err
-            print "Could not create peak function '%s'. Exiting." \
-                  %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,  err:
-            print err
-            print "Could not find ModelEvaluator '%s'. Exiting." \
-                  %options.modelevaluator
+        except Exception as err:
+            print(err)
+            print ("Could not find ModelEvaluator '%s'. Exiting." \
+                  %options.modelevaluator)
             return
 
     if options.bcrystal is not None:
@@ -328,9 +328,9 @@ def main():
         from diffpy.srmise import baselines
         try:
             options.baseline = eval("baselines."+options.baseline)
-        except Exception, err:
-            print err
-            print "Could not create baseline '%s'. Exiting." %options.baseline
+        except Exception as err:
+            print(err)
+            print("Could not create baseline '%s'. Exiting." %options.baseline)
             return
 
     filename = args[0]
@@ -392,22 +392,22 @@ def main():
         if options.savefile is not None:
             try:
                 ext.write(options.savefile)
-            except SrMiseFileError, err:
-                print err
-                print "Could not save result to '%s'." %options.savefile
+            except SrMiseFileError as err:
+                print(err)
+                print("Could not save result to '%s'." %options.savefile)
 
 
         if options.pwafile is not None:
             try:
                 ext.writepwa(options.pwafile)
-            except SrMiseFileError, err:
-                print err
-                print "Could not save pwa summary to '%s'." %options.pwafile
+            except SrMiseFileError as err:
+                print(err)
+                print("Could not save pwa summary to '%s'." %options.pwafile)
 
 
-        print ext
+        print(ext)
         if cov is not None:
-            print cov
+            print(cov)
 
         if options.plot:
             from diffpy.srmise.applications.plot import makeplot

Diff for: diffpy/srmise/applications/plot.py

@@ -16,6 +16,7 @@
 import sys
 
 import matplotlib.pyplot as plt
+from matplotlib.pyplot import MultipleLocator
 import mpl_toolkits.axisartist as AA
 import numpy as np
 from mpl_toolkits.axes_grid1 import make_axes_locatable
@@ -147,7 +148,7 @@ def labelallsubplots():
         s = "(%s)" % c
         ht = plt.text(0.04, 0.95, s,
                 horizontalalignment='left', verticalalignment='top',
-                transform=gca().transAxes, weight='bold')
+                transform=plt.gca().transAxes, weight='bold')
         rv.append(ht)
     return rv
 
@@ -478,7 +479,7 @@ def readcompare(filename):
     # TODO: Make this safer
     try:
         datastring = open(filename,'rb').read()
-    except Exception, err:
+    except Exception as err:
         raise err
 
     import re
@@ -491,8 +492,8 @@ def readcompare(filename):
     try:
         for line in datastring.split("\n"):
             distances.append(float(line))
-    except (ValueError, IndexError), err:
-        print "Could not read distances from '%s'. Ignoring file." %filename
+    except (ValueError, IndexError) as err:
+        print("Could not read distances from '%s'. Ignoring file." %filename)
 
     if len(distances) == 0:
         return None
@@ -539,14 +540,14 @@ def main():
             try:
                 toplot.load(filename)
             except Exception:
-                print "File '%s' is not a .srmise or PeakStability data file." %filename
+                print("File '%s' is not a .srmise or PeakStability data file." %filename)
                 return
 
     if opts.model is not None:
         try:
             toplot.setcurrent(opts.model)
         except (Exception):
-            print "Ignoring model, %s is not a PeakStability file." %filename
+            print("Ignoring model, %s is not a PeakStability file." %filename)
 
     distances = None
     if opts.compare is not None:

Diff for: diffpy/srmise/basefunction.py

@@ -15,7 +15,7 @@
 import logging
 import re
 import sys
-
+from fontTools.unicode import Unicode
 import numpy as np
 
 from diffpy.srmise.modelparts import ModelPart, ModelParts
@@ -90,7 +90,7 @@ def __init__(self, parameterdict, parformats, default_formats, metadict, base=No
         # arbitrary types, parameters are indexed by these keys as well as
         # integer indices.  Restricting keys to strings keeps things sane.
         for p in self.parameterdict.keys():
-            if type(p) not in (str, unicode):
+            if type(p) not in (str, Unicode):
                 emsg = "Argument parameterdict's keys must be strings."
                 raise ValueError(emsg)
         vals = self.parameterdict.values()
@@ -377,7 +377,7 @@ def factory(functionstr, baselist):
         for (k, v) in ddict.items():
             try:
                 pdict[k] = eval(v)
-            except Exception, e:
+            except Exception as e:
                 logger.exception(e)
                 emsg = ("Invalid parameter: %s=%s" %(k,v))
                 raise SrMiseDataFormatError(emsg)
@@ -451,7 +451,7 @@ def safefunction(f, fsafe):
 
     pt = TerminationRipples(p, 20)
     outstr2 = pt.writestr([p])
-    print outstr
+    print(outstr)
 
     pt2 = BaseFunction.factory(outstr2, [p])
-    print type(pt2)
+    print(type(pt2))

Diff for: diffpy/srmise/dataclusters.py

@@ -376,6 +376,11 @@ def animate(self):
         status = self.status
         self.reset_clusters()
 
+        fig, ax = plt.subplots()
+        canvas = fig.canvas
+        background = canvas.copy_from_bbox(ax.bbox)
+        ymin, ymax = ax.get_ylim()
+
         all_lines = []
         for i in self:
             canvas.restore_region(background)
@@ -411,9 +416,9 @@ def animate(self):
     testcluster = DataClusters(x, y, .1)
     testcluster.makeclusters()
 
-    print testcluster.clusters
+    print(testcluster.clusters)
     adj = testcluster.find_adjacent_clusters()
-    print adj
+    print(adj)
     if len(adj) >0:
         testcluster.combine_clusters(adj)
-    print testcluster.clusters
+    print(testcluster.clusters)

Diff for: diffpy/srmise/modelcluster.py

@@ -666,7 +666,7 @@ def factory(mcstr, **kwds):
                     emsg = ("Number of value fields does not match that given by '%s'" %start_data_info)
                 for a, v in zip(arrays, line.split()):
                     a.append(float(v))
-        except (ValueError, IndexError), err:
+        except (ValueError, IndexError) as err:
             raise SrMiseDataFormatError(err)
         if hasr:
             r_data = np.array(r_data)
@@ -875,7 +875,7 @@ def fit(self, justify=False, ntrials=0, fitbaseline=False, estimate=True, cov=No
             if estimate:
                 try:
                     self.estimatepeak()
-                except SrMiseEstimationError, e:
+                except SrMiseEstimationError as e:
                     logger.info("Fit: No model to fit, estimation not possible.")
                     return
             else:
@@ -906,7 +906,7 @@ def fit(self, justify=False, ntrials=0, fitbaseline=False, estimate=True, cov=No
                        ntrials,
                        cov,
                        cov_format)
-        except SrMiseFitError, e:
+        except SrMiseFitError as e:
             logger.debug("Error while fitting cluster: %s\nReverting to original model.", e)
             self.model = orig_model
             self.baseline = orig_baseline
@@ -1413,13 +1413,13 @@ def prune(self):
     guess_peaks = Peaks([pf.actualize(p, "pwa") for p in guesspars])
     cluster = ModelCluster(guess_peaks, None, r, y, err, None, AICc, [pf])
 
-    print "--- Actual Peak parameters ---"
-    print ideal_peaks
+    print("--- Actual Peak parameters ---")
+    print(ideal_peaks)
 
-    print "\n--- Before fit ---"
-    print cluster
+    print("\n--- Before fit ---")
+    print(cluster)
 
     cluster.fit()
 
-    print "\n--- After fit ---"
-    print cluster
+    print("\n--- After fit ---")
+    print(cluster)

Diff for: diffpy/srmise/modelparts.py

@@ -150,8 +150,8 @@ def fit(self, r, y, y_error, range=None, ntrials=0, cov=None, cov_format="defaul
             plt.draw()
 
             if srmiselog.wait:
-                print "Press 'Enter' to continue...",
-                raw_input()
+                print("Press 'Enter' to continue...",)
+                input()
 
         if f[4] not in (1,2,3,4):
             emsg = "Fit did not succeed -- " + str(f[3])

Diff for: diffpy/srmise/multimodelselection.py

@@ -27,7 +27,7 @@ def eatkwds(*args, **kwds):
     """Convenience function to remove all keywords in args from kwds."""
     for k in args:
         if k in kwds:
-            print "Keyword %s=%s ignored." %(k, kwds.pop(k))
+            print("Keyword %s=%s ignored." %(k, kwds.pop(k)))
     return kwds
 
 class MultimodelSelection(PeakStability):
@@ -77,7 +77,7 @@ def makeaics(self, dgs, dr, filename=None):
         (r, y, dr, dy) = self.ppe.resampledata(dr)
 
         for model_idx in range(len(self.results)):
-            print "Testing model %s of %s." %(model_idx, len(self.results))
+            print("Testing model %s of %s." %(model_idx, len(self.results)))
 
             result = self.results[model_idx]
             em = self.ppe.error_method
@@ -208,7 +208,7 @@ def animate_probs(self, step=False, duration=0., **kwds):
             plt.ion()
             plt.draw()
             if step:
-                raw_input()
+                input()
             if duration > 0:
                 time.sleep(sleeptime)
 
@@ -269,7 +269,7 @@ def animate_classprobs(self, step=False, duration=0., **kwds):
             plt.ion()
             plt.draw()
             if step:
-                raw_input()
+                input()
             if duration > 0:
                 time.sleep(sleeptime)
 

Diff for: diffpy/srmise/pdfdataset.py

@@ -150,7 +150,7 @@ def read(self, filename):
         """
         try:
             self.readStr(open(filename,'rb').read())
-        except PDFDataFormatError, err:
+        except PDFDataFormatError as err:
             basename = os.path.basename(filename)
             emsg = ("Could not open '%s' due to unsupported file format " +
                 "or corrupted data. [%s]") % (basename, err)
@@ -274,7 +274,7 @@ def readStr(self, datastring):
                 self.drobs = len(self.robs) * [0.0]
             if not has_dGobs:
                 self.dGobs = len(self.robs) * [0.0]
-        except (ValueError, IndexError), err:
+        except (ValueError, IndexError) as err:
             raise PDFDataFormatError(err)
         self.rmin = self.robs[0]
         self.rmax = self.robs[-1]
@@ -378,21 +378,21 @@ class PDFDataFormatError(Exception):
     filename = sys.argv[1]
     dataset = PDFDataSet("test")
     dataset.read(filename)
-    print "== metadata =="
+    print("== metadata ==")
     for k, v in dataset.metadata.iteritems():
-        print k, "=", v
-    print "== data members =="
+        print(k, "=", v)
+    print("== data members ==")
     for k, v in dataset.__dict__.iteritems():
         if k in ('metadata', 'robs', 'Gobs', 'drobs', 'dGobs') or k[0] == "_":
             continue
-        print k, "=", v
-    print "== robs Gobs drobs dGobs =="
+        print(k, "=", v)
+    print("== robs Gobs drobs dGobs ==")
     for i in range(len(dataset.robs)):
-        print dataset.robs[i], dataset.Gobs[i], dataset.drobs[i], dataset.dGobs[i]
-    print "== writeStr() =="
-    print dataset.writeStr()
-    print "== datasetcopy.writeStr() =="
+        print(dataset.robs[i], dataset.Gobs[i], dataset.drobs[i], dataset.dGobs[i])
+    print("== writeStr() ==")
+    print(dataset.writeStr())
+    print("== datasetcopy.writeStr() ==")
     datasetcopy = dataset.copy()
-    print datasetcopy.writeStr()
+    print(datasetcopy.writeStr())
 
 # End of file

Diff for: diffpy/srmise/pdfpeakextraction.py

@@ -913,7 +913,7 @@ def find_qmax(r, y, showgraphs=False):
 
         plt.show()
         plt.ioff()
-        raw_input()
+        input()
 
     return (qmax, dq)
 

Diff for: diffpy/srmise/peakextraction.py

@@ -255,7 +255,7 @@ def read(self, filename):
         """
         try:
             self.readstr(open(filename,'rb').read())
-        except SrMiseDataFormatError, err:
+        except SrMiseDataFormatError as err:
             logger.exception("")
             basename = os.path.basename(filename)
             emsg = ("Could not open '%s' due to unsupported file format " +
@@ -443,7 +443,7 @@ def readstr(self, datastring):
                     emsg = ("Number of value fields does not match that given by '%s'" %start_data_info)
                 for a, v in zip(arrays, line.split()):
                     a.append(float(v))
-        except (ValueError, IndexError), err:
+        except (ValueError, IndexError) as err:
             raise SrMiseDataFormatError(str(err))
         if hasx:
             self.x = np.array(self.x)
@@ -1212,11 +1212,11 @@ def fit_single(self):
     te.setvars(rng=[1.51,10.], pf=[pf], cres=.1, effective_dy = 1.5*err)
     te.extract_single()
 
-    print "--- Actual Peak parameters ---"
-    print ideal_peaks
+    print("--- Actual Peak parameters ---")
+    print(ideal_peaks)
 
-    print "\n--- After extraction ---"
-    print te
+    print("\n--- After extraction ---")
+    print(te)
 
     te.plot()
-    raw_input()
+    input()