diff scripts/score_plot.py @ 1478:82f43919f385

Paper: Added interface screenshot and box plot example

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/score_plot.py	Thu Oct 15 20:10:00 2015 +0100
@@ -0,0 +1,233 @@
+#!/usr/bin/python
+
+import sys
+import os
+import csv
+import matplotlib.pyplot as plt
+import numpy as np
+import scipy as sp
+import scipy.stats
+
+# COMMAND LINE ARGUMENTS
+
+#TODO: Merge, implement this functionality
+#TODO: Control by CLI arguments (plot types, save and/or show, ...) 
+
+assert len(sys.argv)<4, "score_plot takes at most 2 command line arguments\n"+\
+                        "Use: python score_plot.py [ratings_folder_location]."+\
+                        "Type 'python score_plot.py -h' for more options"
+
+# initialise plot types (false by default) and options
+enable_boxplot    = False     # show box plot
+enable_confidence = False     # show confidence interval
+confidence        = 0.90      # confidence value (for confidence interval plot)
+enable_individual = False     # show all individual ratings
+show_individual   = []        # show specific individuals (empty: show all individuals found)
+show_legend       = False     # show names of individuals
+
+# DEFAULT: Looks in 'saves/ratings/' folder from 'scripts/' folder
+rating_folder = "../saves/ratings/" 
+
+# XML results files location
+if len(sys.argv) == 1: # no extra arguments
+    enable_boxplot    = True # show box plot
+    print "Use: python score_plot.py [rating folder] [plot_type] [-l/-legend]"
+    print "Type 'python score_plot.py -h' for help."
+    print "Using default path: " + rating_folder + " with boxplot."
+else:
+    for arg in sys.argv: # go over all arguments
+        if arg == '-h':
+            # show help
+            #TODO: replace with contents of helpfile score_plot.info (or similar)
+            print "Use: python score_plot.py [rating_folder] [plot_type] [-l] [confidence]"
+            print "   rating_folder:"
+            print "            folder where output of 'score_parser' can be found, and"
+            print "            where plots will be stored."
+            print "            By default, '../saves/ratings/' is used."
+            print ""
+            print "PLOT TYPES"
+            print " Can be used in combination."
+            print "    box | boxplot | -b"
+            print "            Enables the boxplot" 
+            print "    conf | confidence | -c"
+            print "            Enables the confidence interval plot" 
+            print "    ind | individual | -i"
+            print "            Enables plot of individual ratings" 
+            print ""
+            print "PLOT OPTIONS"
+            print "    leg | legend | -l"
+            print "            For individual plot: show legend with individual file names"
+            print "    numeric value between 0 and 1, e.g. 0.95"
+            print "            For confidence interval plot: confidence value"
+            assert False, ""# stop immediately after showing help #TODO cleaner way
+            
+        # PLOT TYPES
+        elif arg == 'box' or arg == 'boxplot' or arg == '-b':
+            enable_boxplot    = True     # show box plot
+        elif arg == 'conf' or arg == 'confidence' or arg == '-c':
+            enable_confidence = True     # show confidence interval
+            #TODO add confidence value input
+        elif arg == 'ind' or arg == 'individual' or arg == '-i':
+            enable_individual = True     # show all individual ratings
+            
+        # PLOT OPTIONS
+        elif arg == 'leg' or arg == 'legend' or arg == '-l':
+            if not enable_individual: 
+                print "WARNING: The 'legend' option is only relevant to plots of "+\
+                      "individual ratings"
+            show_legend = True     # show all individual ratings
+        elif arg.isdigit():
+            if not enable_confidence: 
+                print "WARNING: The numeric confidence value is only relevant when "+\
+                      "confidence plot is enabled"
+            if float(arg)>0 and float(arg)<1:
+                confidence = float(arg)
+            else: 
+                print "WARNING: The confidence value needs to be between 0 and 1"
+        
+        # FOLDER NAME
+        else: 
+             # assume it's the folder name
+             rating_folder = arg
+
+# at least one plot type should be selected: box plot by default
+if not enable_boxplot and not enable_confidence and not enable_individual:
+    enable_boxplot = True
+
+# check if folder_name exists
+if not os.path.exists(rating_folder):
+    #the file is not there
+    print "Folder '"+rating_folder+"' does not exist."
+    sys.exit() # terminate script execution
+elif not os.access(os.path.dirname(rating_folder), os.W_OK):
+    #the file does exist but write rating_folder are not given
+    print "No write privileges in folder '"+rating_folder+"'."
+
+
+# CONFIGURATION
+
+# Font settings
+font = {'weight' : 'bold',
+        'size'   : 10}
+plt.rc('font', **font)
+
+
+# CODE
+
+# get every csv file in folder
+for file in os.listdir(rating_folder): # You have to put this in folder where rating csv files are.
+    if file.endswith(".csv"):
+        page_name = file[:-4] # file name (without extension) is page ID
+
+        # get header
+        with open(rating_folder+file, 'rb') as readfile: # read this csv file
+            filereader = csv.reader(readfile, delimiter=',')
+            headerrow = filereader.next() # use headerrow as X-axis
+            headerrow = headerrow[1:]
+
+        # read ratings into matrix
+#         ratings = np.loadtxt(open(rating_folder+file,"rb"),
+#                             delimiter=",",
+#                             skiprows=1,
+#                             usecols=range(1,len(headerrow)+1)
+#                             )
+            ratings = np.genfromtxt(readfile,
+                                   delimiter=",",
+                                   #skip_header = 1,
+                                   converters = {3: lambda s: float(s or 'Nan')},
+                                   usecols=range(1,len(headerrow)+1)
+                                   )
+        
+        # assert at least 2 subjects (move on to next file if violated)
+        if ratings.shape[0]<2:
+            print "WARNING: Just one subject for " + page_name + ". Moving on to next file."
+            break
+
+        # BOXPLOT
+        if enable_boxplot:
+            plt.boxplot(ratings)
+            
+        # CONFIDENCE INTERVAL
+        if enable_confidence:
+            iterator = 0
+            for column in ratings.T: # iterate over transposed matrix
+                # remove all 'Nan's from column
+                column = column[~np.isnan(column)]
+            
+                # get number of non-Nan ratings (= #subjects)
+                n = column.size
+        
+                # get mean
+                mean_rating = np.mean(column)
+        
+                # get errors
+                err = scipy.stats.sem(column)* sp.stats.t._ppf((1+confidence)/2., n-1)
+        
+                # draw plot
+                plt.errorbar(iterator+1, 
+                            mean_rating, 
+                            yerr=err,
+                            marker="x",
+                            color ="k",
+                            markersize=12,
+                            linestyle='None')
+                            
+                iterator += 1 # increase counter
+    
+    
+        # INDIVIDUAL PLOT
+        if enable_individual or show_individual:
+            # marker list and color map to cycle through
+            markerlist = ["x", ".", "o", "*", "+", "v", ">", "<", "8", "s", "p"]
+            colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k'] 
+            increment = 0
+            linehandles = []
+            legendnames = []
+            with open(rating_folder+file, 'rb') as readfile: # read this csv file
+                filereader = csv.reader(readfile, delimiter=',')
+                headerrow = filereader.next() # use headerrow as X-axis
+                headerrow = headerrow[1:]
+                for row in filereader:
+                    subject_id = row[0][:-4] # read from beginning of line
+                    # assume plotting all individuals if no individual(s) specified
+                    if not show_individual or subject_id in show_individual:
+                        plothandle, = plt.plot(range(1,len(row)), # x-values
+                                 ratings[increment,:],#row[1:], # y-values: csv values except subject name
+                                 color=colormap[increment%len(colormap)],
+                                 marker=markerlist[increment%len(markerlist)],
+                                 markersize=10,
+                                 linestyle='None',
+                                 label=subject_id
+                                )
+                        linehandles.append(plothandle)
+                        legendnames.append(subject_id)
+                        if show_legend:
+                            plt.legend(linehandles, legendnames,
+                                       loc='upper right',
+                                       bbox_to_anchor=(1.1, 1),
+                                       borderaxespad=0.,
+                                       numpoints=1 # remove extra marker
+                                       )
+                    increment += 1 # increase counter
+
+        # TITLE, AXIS LABELS AND LIMITS
+        plt.title(page_name)
+        plt.xlabel('Fragment')
+        plt.xlim(0, len(headerrow)+1) # only show relevant region, leave space left & right)
+        plt.xticks(range(1, len(headerrow)+1), headerrow, rotation=90) # show fragment names
+        plt.ylabel('Rating')
+        plt.ylim(0,1)
+        
+        
+
+        # SHOW PLOT
+        #plt.show()
+        #exit()
+    
+        # SAVE PLOT
+        # automatically 
+        plot_type = ("-box" if enable_boxplot else "") + \
+                    ("-conf" if enable_confidence else "") + \
+                    ("-ind" if enable_individual else "")
+        plt.savefig(rating_folder+page_name+plot_type+".pdf", bbox_inches='tight')
+        plt.close()