Fixing typo and removing double copy of scripts

PythonTools/Boxcounter/README

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+The bash script processing.sh takes a pout.0 from a run and parses it so that it is in a format that reads 'level, time, boxes on this proc, total boxes'. Run using './processing.sh' in the same directory as the pout.0 and it outputs pout.0_parsed
+
+This pout.0_parsed can then be processed by running 'python extractboxes.py' to plot the total number of boxes per refinement level. Must manually set max refinement level to plot in L16. Outputs a graph for each level i which includes all levels < i, easily modifiable.

PythonTools/Boxcounter/extractboxes.py

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+import csv
+import matplotlib.pyplot as plt
+
+'''Run processing.sh with pout.0 - outputs level, time, boxes on proc 0, total boxes'''
+'''Only works on output with verbosity 0'''
+
+i=0
+
+data = open('pout.0_parsed')
+with data as csvfile:
+    filereader = csv.reader(csvfile, delimiter=',')
+    timelist = [] #col 1
+    totalboxlist = [] #col 3
+
+    '''Hardcoded max level to plot'''
+    while i < 10:
+        for row in filereader:
+            if int(row[0]) == i:
+                '''Can input max time'''
+ #              if float(row[1]) < 300:
+                timelist.append(float(row[1]))
+                totalboxlist.append(int(row[3]))
+
+        plt.plot(timelist, totalboxlist, label='%s' % i)
+        plt.legend()
+        plt.savefig('boxplot_level_%s.png' % i)
+
+        timelist.clear()
+        totalboxlist.clear()
+
+        '''Resets file loop'''
+        data.seek(0)
+
+        i+=1
+
+    print('%s' % i)
+
+

PythonTools/Boxcounter/processing.sh

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+#!/bin/bash
+
+sed -n '/GRAMRLevel::/,$p' ./pout.0 > ./pout.0_temp
+sed -e 's!GRAMRLevel::advance level !!' ./pout.0_temp > ./pout.0_temp2
+sed -r 's/ +/, /' ./pout.0_temp2 > ./pout.0_temp
+sed -e 's!at time !!' ./pout.0_temp > ./pout.0_temp2
+sed -e 's/ (.*:/,/' ./pout.0_temp2 > ./pout.0_temp
+sed -e 's/ \//,/' ./pout.0_temp > ./pout.0_parsed
+rm ./pout.0_temp ./pout.0_temp2