Make axes in plots log scale

example/example.pip

@@ -40,8 +40,8 @@ assign_to_pippi_datastream = 'np.log10($2)-np.log10($3)':64 \
                                             ;Assign a python function or named hdf5 data stream to a particular pippi datastream index (use pippi probe to test; EFN)
 quantity_labels = 0:'multiplicity' \
                   1:'-lnlike'      \
-                  2:'$\log_{10}\left(m_0/\mathrm{TeV}\right)$' \
-                  3:'$\log_{10}\left(m_\frac12/\mathrm{TeV}\right)$' \
+                  2:'$m_0$ (TeV)' \
+                  3:'$m_\frac12$ (TeV)' \
                   4:'$A_0$ (TeV)' \
                   5:'$\tan\beta$' \
                   64:'$\log_{10}\left(m_0/m_\frac12\right)$' \
@@ -67,7 +67,8 @@ plot_colourbar_2D = {3,2} {5,4}             ;2D plots that should include colour
 
 plot_comparison = T                         ;Overplot distributions from comparisonFilename in 1D plots and contours in 2D plots
 extra_legend_lines = 'Flat priors' 'CMSSM $\mu>0$';Additional text lines to be included in any legends (EFN)
-blame = 'pippi v2.2'                        ;Credit line to be placed in top corner of all plots
+blame_text = 'pippi v2.2'                   ;Credit line to be placed in top corner of all plots
+blame_scale = 0.5                           ;Scale of credit line, default is 0.5
 yaxis_number_angle = -90                    ;Angle relative to vertical for y-axis numerical labels
 
 plot_posterior_mean_on_posterior_pdf = T    ;Indicate the posterior mean in all posterior pdf plots
@@ -77,6 +78,8 @@ plot_best_fit_on_profile_like = T           ;Indicate the best fit in all profil
 
 axis_ranges = 2:{2.0,3.5} 3:{2.05,3.6} 4:{-4,4} ;Axis ranges over which to plot parameters/observables (defaults to data_ranges if absent)
 
+custom_ticks =                              ;Parameters/observables that use custom ticks
+
 reference_point = 2:3.3 3:2.5               ;Coordinates of reference point (only plotted where one of the listed axes is present)
 reference_text = 'True value'               ;Key string to be printed for reference point
 

example/example_diver.pip

@@ -59,7 +59,8 @@ plot_colourbar_2D =                         ;2D plots that should include colour
 
 plot_comparison = F                         ;Overplot distributions from comparisonFilename in 1D plots and contours in 2D plots
 extra_legend_lines =                        ;Additional text lines to be included in any legends (EFN)
-blame = 'pippi v2.2'                        ;Credit line to be placed in top corner of all plots
+blame_text = 'pippi v2.2'                   ;Credit line to be placed in top corner of all plots
+blame_scale = 0.5                           ;Scale of credit line, default is 0.5
 yaxis_number_angle = -90                    ;Angle relative to vertical for y-axis numerical labels
 
 plot_posterior_mean_on_posterior_pdf = F    ;Indicate the posterior mean in all posterior pdf plots
@@ -69,6 +70,8 @@ plot_best_fit_on_profile_like = T           ;Indicate the best fit in all profil
 
 axis_ranges =                               ;Axis ranges over which to plot parameters/observables (defaults to data_ranges if absent)
 
+custom_ticks =                              ;Parameters/observables that use custom ticks
+
 reference_point =                           ;Coordinates of reference point (only plotted where one of the listed axes is present)
 reference_text =                            ;Key string to be printed for reference point
 

pippi

@@ -15,6 +15,7 @@
 # Originally developed: March 2012
 #############################################################
 
+from __future__ import print_function
 from pippi_probe  import *
 from pippi_merge  import *
 from pippi_pare   import *
@@ -37,41 +38,41 @@ def main(arguments):
       #Check if pippi has been invoked with one of the five known specific commands
       command = commandLineOptions[arguments[1]]
       if not command in [merge, pare]:
-        print
-        print 'Beginning pippi '+arguments[1]+' operation...'
+        print()
+        print('Beginning pippi '+arguments[1]+' operation...')
       try:
         command(arguments[2:])
       except BaseException as err:
-        print
-        print 'Running pippi failed in '+command.__name__+' operation, due to error:'
-        print err
-        print
+        print()
+        print('Running pippi failed in '+command.__name__+' operation, due to error:')
+        print(err)
+        print()
         sys.exit()
       if not command in [merge, pare]:
-        print
-        print 'Completed sucessfully.'
-        print
+        print()
+        print('Completed sucessfully.')
+        print()
     except KeyError:
       #Otherise check if it has been invoked with just a filename
       if os.path.isfile(arguments[1]):
-        print
-        print 'Beginning pippi parse-to-plot operation...'
+        print()
+        print('Beginning pippi parse-to-plot operation...')
         for command in [parse, script, plot]:
           try:
             command(arguments[1:])
           except BaseException as err:
-            print
-            print 'Running pippi failed in '+command.__name__+' operation.'
-            print err
-            print
+            print()
+            print('Running pippi failed in '+command.__name__+' operation.')
+            print(err)
+            print()
             sys.exit()
-        print
-        print 'Completed sucessfully.'
-        print
+        print()
+        print('Completed sucessfully.')
+        print()
       else:
         #Otherwise crack it and tell the user to get their shit in order
-        print
-        print 'Can\'t find file '+arguments[1]
+        print()
+        print('Can\'t find file '+arguments[1])
         usage()
 
   sys.exit()

pippi_colours.py

@@ -9,13 +9,15 @@
 # Originally developed: March 2012
 #############################################################
 
+from __future__ import print_function
 import re
 import copy
 
 permittedSchemes = {}
 
 def Blockshading(colour,line_code, fill_code):
   scheme = colourScheme('Blockshading_'+colour)
+  scheme.backgroundColour = '#fff'
   scheme.baseProfColourMap = '#fff--#fff(contour1)--#'+fill_code+'(contour1)--#'+fill_code
   scheme.basePostColourMap = '#fff--#fff(contour1)--#'+fill_code+'(contour1)--#'+fill_code
   scheme.mainPostContourColour2D = '\'#'+line_code+'\''
@@ -43,6 +45,7 @@ class colourScheme:
   comparisonProfColour1D = 'Grey'
   comparisonPostContourColour2D = 'Grey'
   comparisonProfContourColour2D = 'Grey'
+  backgroundColour = '#fff'
   baseProfColourMap = '#fff--#fff(contour2)--#f45(contour1)--#612'
   basePostColourMap = '#fff--#fff(contour2)--#88f(contour1)--#229'
 
@@ -122,6 +125,7 @@ def colourMap(self,contours,kind):
 
 # iceCube colour scheme
 iceCube = colourScheme('iceCube')
+iceCube.backgroundColour = '#fff'
 iceCube.baseProfColourMap = '#fff--#fff(contour2)--#292(contour1)--#f55(contour1)--#000'
 iceCube.basePostColourMap = '#fff--#fff(contour2)--#29d(contour1)--#f55(contour1)--#000'
 iceCube.baseObsColourMap = 'hls:White(contour1)--Red(contour2)--Green(contour3)'
@@ -132,6 +136,7 @@ def colourMap(self,contours,kind):
 
 # iceCube79 colour scheme
 iceCube79 = colourScheme('iceCube79')
+iceCube79.backgroundColour = '#fff'
 iceCube79.baseProfColourMap = '#fff--#fff(contour2)--#fab(contour1)--#f45'
 iceCube79.basePostColourMap = '#fff--#fff(contour2)--#ddf(contour1)--#88f'
 iceCube79.baseObsColourMap = 'hls:White(contour1)--Red(contour2)--Green(contour3)'
@@ -145,6 +150,7 @@ def colourMap(self,contours,kind):
 
 # iceCube3sig colour scheme
 iceCube3sig = colourScheme('iceCube3sig')
+iceCube3sig.backgroundColour = '#fff'
 iceCube3sig.baseProfColourMap = '#fff--#fff(contour3)--#292(contour2)--#fff(contour2)--#929(contour1)--#f55(contour1)--#000'
 iceCube3sig.basePostColourMap = '#fff--#fff(contour3)--#29d(contour2)--#fff(contour2)--#929(contour1)--#f55(contour1)--#000'
 iceCube3sig.baseObsColourMap = 'hls:White(contour1)--Red(contour2)--Green(contour3)'
@@ -155,6 +161,7 @@ def colourMap(self,contours,kind):
 
 # SBClassic colour scheme
 SBClassic = colourScheme('SBClassic')
+SBClassic.backgroundColour = '#fff'
 SBClassic.baseProfColourMap = '#fff--#fff(contour2)--#2f2(contour1)--#f33(0.5)--#000'
 SBClassic.basePostColourMap = '#fff--#fff(contour2)--#95d(contour1)--#f33(0.5)--#000'
 SBClassic.baseObsColourMap = 'hls:White(contour1)--Red(contour2)--Green(contour3)'
@@ -165,6 +172,7 @@ def colourMap(self,contours,kind):
 
 # BlueGold colour scheme
 BlueGold = colourScheme('BlueGold')
+BlueGold.backgroundColour = '#fff'
 BlueGold.baseProfColourMap = '#fff--#fff(contour2)--#f44(contour2)--#f44(contour1)--#ece(contour1)--#ece'
 BlueGold.basePostColourMap = '#fff--#fff(contour2)--#44f(contour2)--#44f(contour1)--#fc0(contour1)--#fc0'
 BlueGold.baseObsColourMap = 'hls:White(contour1)--Red(contour2)--Green(contour3)'
@@ -178,6 +186,7 @@ def colourMap(self,contours,kind):
 
 # nightOfTheAllanachs colour scheme
 nightOfTheAllanachs = colourScheme('nightOfTheAllanachs')
+nightOfTheAllanachs.backgroundColour = '#000'
 nightOfTheAllanachs.basePostColourMap = '#000--#000(contour2)--#808(contour1)--#f33(0.5)--#ff0'
 nightOfTheAllanachs.baseProfColourMap = '#000--#000(contour2)--#33f(contour1)--#0ff(0.5)--#ff0'
 nightOfTheAllanachs.baseObsColourMap = 'Black(contour1)--Red(contour2)--Green(contour3)'
@@ -195,6 +204,7 @@ def colourMap(self,contours,kind):
 
 # nightOfTheAllanachs2 colour scheme
 nightOfTheAllanachs2 = colourScheme('nightOfTheAllanachs2')
+nightOfTheAllanachs2.backgroundColour = '#000'
 nightOfTheAllanachs2.basePostColourMap = '#000--#000(contour2)--#808(contour1)--#f33(0.5)--#ff0'
 nightOfTheAllanachs2.baseProfColourMap = '#000--#000(contour2)--#33f(contour1)--#0ff(0.5)--#ff0'
 nightOfTheAllanachs2.baseObsColourMap = 'Black(contour1)--Red(contour2)--#00FFFF(contour3)'
@@ -214,6 +224,7 @@ def colourMap(self,contours,kind):
 
 # nightOfTheAllanachs3 colour scheme
 nightOfTheAllanachs3 = colourScheme('nightOfTheAllanachs3')
+nightOfTheAllanachs3.backgroundcolour = '#000'
 nightOfTheAllanachs3.basePostColourMap = '#000--#000(contour2)--#808(contour1)--#f33(0.5)--#ff0'
 nightOfTheAllanachs3.baseProfColourMap = '#000--#000(contour2)--#33f(contour1)--#0ff(0.5)--#ff0'
 nightOfTheAllanachs3.baseObsColourMap = 'Black(contour1)--Blue(contour2)--Orange(contour3)'

pippi_merge.py

@@ -30,11 +30,11 @@ def merge(filenames):
     import h5py
     f = h5py.File(filenames[0],'r')
     h5merge = True
-    print
-    print "Files identified as hdf5.  Interpreting final argument as output filename."
-    print
-    print "Concatenating common datasets and outputting to {0}...".format(filenames[-1])
-    print
+    print()
+    print("Files identified as hdf5.  Interpreting final argument as output filename.")
+    print()
+    print("Concatenating common datasets and outputting to {0}...".format(filenames[-1]))
+    print()
   except:
     h5merge = False
 
@@ -49,19 +49,19 @@ def merge(filenames):
     try:
       fout = h5py.File(filenames[-1],'w-')
     except:
-      print "Could not create output file {0}!".format(filenames[-1])
-      print "Please make sure it does not exist already."
-      print
+      print("Could not create output file {0}!".format(filenames[-1]))
+      print("Please make sure it does not exist already.")
+      print()
       return
 
-    print "  Determining common datasets..."
+    print("  Determining common datasets...")
     for fname in filenames[0:-1]:
-      print "    Opening: {0}".format(fname)
+      print("    Opening: {0}".format(fname))
       try:
         f = h5py.File(fname,'r')
       except:
-        print "Could not open file {0}!".format(fname)
-        print
+        print("Could not open file {0}!".format(fname))
+        print()
         return
       files[fname] = f
       datasets = {}
@@ -77,35 +77,35 @@ def merge(filenames):
       datashape = dataset_collection[0][x].shape
       if all(f[x].dtype == datatype and f[x].shape[1:] == datashape[1:] for f in dataset_collection):
         common_datasets.add(x)
-    print
-    print "  Common datasets: "
-    for x in common_datasets: print "    {0}".format(x)
-    print
+    print()
+    print("  Common datasets: ")
+    for x in common_datasets: print("    {0}".format(x))
+    print()
 
     #Find the length of each dataset and create it (empty) in the new file
-    print "  Creating empty datasets of required lengths in {0}...".format(filenames[-1])
+    print("  Creating empty datasets of required lengths in {0}...".format(filenames[-1]))
     out_dsets = {}
     for ds in common_datasets:
       length = 0
       for f in dataset_collection: length += f[ds].len()
       datatype = dataset_collection[0][ds].dtype
       datashape = (length,) + dataset_collection[0][ds].shape[1:]
       out_dsets[ds] = fout.create_dataset(ds, datashape, dtype=datatype)
-    print
+    print()
 
     #Copy the data over to the new file
-    print "  Adding data to empty datasets in {0}...".format(filenames[-1])
+    print("  Adding data to empty datasets in {0}...".format(filenames[-1]))
     for ds in common_datasets:
-      print "    Populating {0}".format(ds)
+      print("    Populating {0}".format(ds))
       index_low = 0
       for f in dataset_collection:
         index_high = index_low + f[ds].len()
         out_dsets[ds][index_low:index_high,...] = f[ds][...]
         index_low = index_high
 
-    print
-    print "Done."
-    print
+    print()
+    print("Done.")
+    print()
 
 
   else:    # We are doing an ASCII merge
@@ -137,7 +137,7 @@ def merge(filenames):
             #Crash if a later chain or line has a different number of columns to the first one
             sys.exit('Error: chains do not match (number of columns differ).  Quitting...')
           #Output the current line to stdout and get the next one
-          print line.rstrip('\n')
+          print(line.rstrip('\n'))
           #Read the next line
           line = infile.readline()
           #Work out the number of columns in the next line
@@ -150,6 +150,6 @@ def merge(filenames):
 
 def get_datasets(g,datasets):
   import h5py
-  for name, item in g.iteritems():
+  for name, item in g.items():
     if isinstance(item,h5py.Group): get_datasets(item,datasets)
     if isinstance(item,h5py.Dataset): datasets[item.name] = item

pippi_pare.py

@@ -45,6 +45,6 @@ def pare(argstring):
 
   # Pump it through the user-supplied function, printing each new point to stdout
   for i in range(chainArray.shape[0]):
-    print '\t'.join([str(x) for x in pareFunc(chainArray[i,:])])
+    print('\t'.join([str(x) for x in pareFunc(chainArray[i,:])]))