djmoffat@1099: #!/usr/bin/python
djmoffat@1099: 
djmoffat@1099: import sys
djmoffat@1099: import os
djmoffat@1099: import csv
djmoffat@1099: import matplotlib.pyplot as plt
djmoffat@1099: import numpy as np
djmoffat@1099: import scipy as sp
djmoffat@1099: import scipy.stats
djmoffat@1099: 
djmoffat@1099: # COMMAND LINE ARGUMENTS
djmoffat@1099: 
djmoffat@1099: #TODO: Merge, implement this functionality
djmoffat@1099: #TODO: Control by CLI arguments (plot types, save and/or show, ...) 
djmoffat@1099: 
djmoffat@1099: assert len(sys.argv)<4, "score_plot takes at most 2 command line arguments\n"+\
djmoffat@1099:                         "Use: python score_plot.py [ratings_folder_location]."+\
djmoffat@1099:                         "Type 'python score_plot.py -h' for more options"
djmoffat@1099: 
djmoffat@1099: # initialise plot types (false by default) and options
djmoffat@1099: enable_boxplot    = False     # show box plot
djmoffat@1099: enable_confidence = False     # show confidence interval
djmoffat@1099: confidence        = 0.90      # confidence value (for confidence interval plot)
djmoffat@1099: enable_individual = False     # show all individual ratings
djmoffat@1099: show_individual   = []        # show specific individuals (empty: show all individuals found)
djmoffat@1099: show_legend       = False     # show names of individuals
djmoffat@1099: 
djmoffat@1099: # DEFAULT: Looks in 'saves/ratings/' folder from 'scripts/' folder
djmoffat@1099: rating_folder = "../saves/ratings/" 
djmoffat@1099: 
djmoffat@1099: # XML results files location
djmoffat@1099: if len(sys.argv) == 1: # no extra arguments
djmoffat@1099:     enable_boxplot    = True # show box plot
djmoffat@1099:     print "Use: python score_plot.py [rating folder] [plot_type] [-l/-legend]"
djmoffat@1099:     print "Type 'python score_plot.py -h' for help."
djmoffat@1099:     print "Using default path: " + rating_folder + " with boxplot."
djmoffat@1099: else:
djmoffat@1099:     for arg in sys.argv: # go over all arguments
djmoffat@1099:         if arg == '-h':
djmoffat@1099:             # show help
djmoffat@1099:             #TODO: replace with contents of helpfile score_plot.info (or similar)
djmoffat@1099:             print "Use: python score_plot.py [rating_folder] [plot_type] [-l] [confidence]"
djmoffat@1099:             print "   rating_folder:"
djmoffat@1099:             print "            folder where output of 'score_parser' can be found, and"
djmoffat@1099:             print "            where plots will be stored."
djmoffat@1099:             print "            By default, '../saves/ratings/' is used."
djmoffat@1099:             print ""
djmoffat@1099:             print "PLOT TYPES"
djmoffat@1099:             print " Can be used in combination."
djmoffat@1099:             print "    box | boxplot | -b"
djmoffat@1099:             print "            Enables the boxplot" 
djmoffat@1099:             print "    conf | confidence | -c"
djmoffat@1099:             print "            Enables the confidence interval plot" 
djmoffat@1099:             print "    ind | individual | -i"
djmoffat@1099:             print "            Enables plot of individual ratings" 
djmoffat@1099:             print ""
djmoffat@1099:             print "PLOT OPTIONS"
djmoffat@1099:             print "    leg | legend | -l"
djmoffat@1099:             print "            For individual plot: show legend with individual file names"
djmoffat@1099:             print "    numeric value between 0 and 1, e.g. 0.95"
djmoffat@1099:             print "            For confidence interval plot: confidence value"
djmoffat@1099:             assert False, ""# stop immediately after showing help #TODO cleaner way
djmoffat@1099:             
djmoffat@1099:         # PLOT TYPES
djmoffat@1099:         elif arg == 'box' or arg == 'boxplot' or arg == '-b':
djmoffat@1099:             enable_boxplot    = True     # show box plot
djmoffat@1099:         elif arg == 'conf' or arg == 'confidence' or arg == '-c':
djmoffat@1099:             enable_confidence = True     # show confidence interval
djmoffat@1099:             #TODO add confidence value input
djmoffat@1099:         elif arg == 'ind' or arg == 'individual' or arg == '-i':
djmoffat@1099:             enable_individual = True     # show all individual ratings
djmoffat@1099:             
djmoffat@1099:         # PLOT OPTIONS
djmoffat@1099:         elif arg == 'leg' or arg == 'legend' or arg == '-l':
djmoffat@1099:             if not enable_individual: 
djmoffat@1099:                 print "WARNING: The 'legend' option is only relevant to plots of "+\
djmoffat@1099:                       "individual ratings"
djmoffat@1099:             show_legend = True     # show all individual ratings
djmoffat@1099:         elif arg.isdigit():
djmoffat@1099:             if not enable_confidence: 
djmoffat@1099:                 print "WARNING: The numeric confidence value is only relevant when "+\
djmoffat@1099:                       "confidence plot is enabled"
djmoffat@1099:             if float(arg)>0 and float(arg)<1:
djmoffat@1099:                 confidence = float(arg)
djmoffat@1099:             else: 
djmoffat@1099:                 print "WARNING: The confidence value needs to be between 0 and 1"
djmoffat@1099:         
djmoffat@1099:         # FOLDER NAME
djmoffat@1099:         else: 
djmoffat@1099:              # assume it's the folder name
djmoffat@1099:              rating_folder = arg
djmoffat@1099: 
djmoffat@1099: # at least one plot type should be selected: box plot by default
djmoffat@1099: if not enable_boxplot and not enable_confidence and not enable_individual:
djmoffat@1099:     enable_boxplot = True
djmoffat@1099: 
djmoffat@1099: # check if folder_name exists
djmoffat@1099: if not os.path.exists(rating_folder):
djmoffat@1099:     #the file is not there
djmoffat@1099:     print "Folder '"+rating_folder+"' does not exist."
djmoffat@1099:     sys.exit() # terminate script execution
djmoffat@1099: elif not os.access(os.path.dirname(rating_folder), os.W_OK):
djmoffat@1099:     #the file does exist but write rating_folder are not given
djmoffat@1099:     print "No write privileges in folder '"+rating_folder+"'."
djmoffat@1099: 
djmoffat@1099: 
djmoffat@1099: # CONFIGURATION
djmoffat@1099: 
djmoffat@1099: # Font settings
djmoffat@1099: font = {'weight' : 'bold',
djmoffat@1099:         'size'   : 10}
djmoffat@1099: plt.rc('font', **font)
djmoffat@1099: 
djmoffat@1099: 
djmoffat@1099: # CODE
djmoffat@1099: 
djmoffat@1099: # get every csv file in folder
djmoffat@1099: for file in os.listdir(rating_folder):
djmoffat@1099:     if file.endswith(".csv"):
djmoffat@1099:         page_name = file[:-4] # file name (without extension) is page ID
djmoffat@1099: 
djmoffat@1099:         # get header
djmoffat@1099:         with open(rating_folder+file, 'rb') as readfile: # read this csv file
djmoffat@1099:             filereader = csv.reader(readfile, delimiter=',')
djmoffat@1099:             headerrow = filereader.next() # use headerrow as X-axis
djmoffat@1099:             headerrow = headerrow[1:]
djmoffat@1099: 
djmoffat@1099:         # read ratings into matrix
djmoffat@1099: #         ratings = np.loadtxt(open(rating_folder+file,"rb"),
djmoffat@1099: #                             delimiter=",",
djmoffat@1099: #                             skiprows=1,
djmoffat@1099: #                             usecols=range(1,len(headerrow)+1)
djmoffat@1099: #                             )
djmoffat@1099:             ratings = np.genfromtxt(readfile,
djmoffat@1099:                                    delimiter=",",
djmoffat@1099:                                    #skip_header = 1,
djmoffat@1099:                                    converters = {3: lambda s: float(s or 'Nan')},
djmoffat@1099:                                    usecols=range(1,len(headerrow)+1)
djmoffat@1099:                                    )
djmoffat@1099:         
djmoffat@1099:         # assert at least 2 subjects (move on to next file if violated)
djmoffat@1099:         if ratings.shape[0]<2:
djmoffat@1099:             print "WARNING: Just one subject for " + page_name + ". Moving on to next file."
djmoffat@1099:             break
djmoffat@1099: 
djmoffat@1099:         # BOXPLOT
djmoffat@1099:         if enable_boxplot:
djmoffat@1099:             plt.boxplot(ratings)
djmoffat@1099:             
djmoffat@1099:         # CONFIDENCE INTERVAL
djmoffat@1099:         if enable_confidence:
djmoffat@1099:             iterator = 0
djmoffat@1099:             for column in ratings.T: # iterate over transposed matrix
djmoffat@1099:                 # remove all 'Nan's from column
djmoffat@1099:                 column = column[~np.isnan(column)]
djmoffat@1099:             
djmoffat@1099:                 # get number of non-Nan ratings (= #subjects)
djmoffat@1099:                 n = column.size
djmoffat@1099:         
djmoffat@1099:                 # get mean
djmoffat@1099:                 mean_rating = np.mean(column)
djmoffat@1099:         
djmoffat@1099:                 # get errors
djmoffat@1099:                 err = scipy.stats.sem(column)* sp.stats.t._ppf((1+confidence)/2., n-1)
djmoffat@1099:         
djmoffat@1099:                 # draw plot
djmoffat@1099:                 plt.errorbar(iterator+1, 
djmoffat@1099:                             mean_rating, 
djmoffat@1099:                             yerr=err,
djmoffat@1099:                             marker="x",
djmoffat@1099:                             color ="k",
djmoffat@1099:                             markersize=12,
djmoffat@1099:                             linestyle='None')
djmoffat@1099:                             
djmoffat@1099:                 iterator += 1 # increase counter
djmoffat@1099:     
djmoffat@1099:     
djmoffat@1099:         # INDIVIDUAL PLOT
djmoffat@1099:         if enable_individual or show_individual:
djmoffat@1099:             # marker list and color map to cycle through
djmoffat@1099:             markerlist = ["x", ".", "o", "*", "+", "v", ">", "<", "8", "s", "p"]
djmoffat@1099:             colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k'] 
djmoffat@1099:             increment = 0
djmoffat@1099:             linehandles = []
djmoffat@1099:             legendnames = []
djmoffat@1099:             with open(rating_folder+file, 'rb') as readfile: # read this csv file
djmoffat@1099:                 filereader = csv.reader(readfile, delimiter=',')
djmoffat@1099:                 headerrow = filereader.next() # use headerrow as X-axis
djmoffat@1099:                 headerrow = headerrow[1:]
djmoffat@1099:                 for row in filereader:
djmoffat@1099:                     subject_id = row[0][:-4] # read from beginning of line
djmoffat@1099:                     # assume plotting all individuals if no individual(s) specified
djmoffat@1099:                     if not show_individual or subject_id in show_individual:
djmoffat@1099:                         plothandle, = plt.plot(range(1,len(row)), # x-values
djmoffat@1099:                                  ratings[increment,:],#row[1:], # y-values: csv values except subject name
djmoffat@1099:                                  color=colormap[increment%len(colormap)],
djmoffat@1099:                                  marker=markerlist[increment%len(markerlist)],
djmoffat@1099:                                  markersize=10,
djmoffat@1099:                                  linestyle='None',
djmoffat@1099:                                  label=subject_id
djmoffat@1099:                                 )
djmoffat@1099:                         linehandles.append(plothandle)
djmoffat@1099:                         legendnames.append(subject_id)
djmoffat@1099:                         if show_legend:
djmoffat@1099:                             plt.legend(linehandles, legendnames,
djmoffat@1099:                                        loc='upper right',
djmoffat@1099:                                        bbox_to_anchor=(1.1, 1),
djmoffat@1099:                                        borderaxespad=0.,
djmoffat@1099:                                        numpoints=1 # remove extra marker
djmoffat@1099:                                        )
djmoffat@1099:                     increment += 1 # increase counter
djmoffat@1099: 
djmoffat@1099:         # TITLE, AXIS LABELS AND LIMITS
djmoffat@1099:         plt.title(page_name)
djmoffat@1099:         plt.xlabel('Fragment')
djmoffat@1099:         plt.xlim(0, len(headerrow)+1) # only show relevant region, leave space left & right)
djmoffat@1099:         plt.xticks(range(1, len(headerrow)+1), headerrow, rotation=90) # show fragment names
djmoffat@1099:         plt.ylabel('Rating')
djmoffat@1099:         plt.ylim(0,1)
djmoffat@1099:         
djmoffat@1099:         
djmoffat@1099: 
djmoffat@1099:         # SHOW PLOT
djmoffat@1099:         #plt.show()
djmoffat@1099:         #exit()
djmoffat@1099:     
djmoffat@1099:         # SAVE PLOT
djmoffat@1099:         # automatically 
djmoffat@1099:         plot_type = ("-box" if enable_boxplot else "") + \
djmoffat@1099:                     ("-conf" if enable_confidence else "") + \
djmoffat@1099:                     ("-ind" if enable_individual else "")
djmoffat@1099:         plt.savefig(rating_folder+page_name+plot_type+".pdf", bbox_inches='tight')
djmoffat@1099:         plt.close()