research/ellipsometry/process.py

   1 #!/usr/bin/python
   2 """
   3         Script to process ellipsometry data output by WVASE
   4         and interface to gnuplot
   5
   6         @author Sam Moore
   7 """
   8
   9 import sys
  10 import os
  11
  12 keys = ["wavelength","angle", "psi", "delta", "uncertainty_psi", "uncertainty_delta"]
  13
  14 def getData(fileName):
  15         dataFile = open(fileName, "r")
  16         #Format is
  17         #wavelength     angle   psi     delta   uncertainty_psi uncertainty_delta
  18
  19         title = dataFile.readline().strip()
  20
  21         #Skip lines before data
  22         for i in range(1,4):
  23                 dataFile.readline()
  24
  25         data = []
  26
  27         line = dataFile.readline()
  28         while line != "":
  29                 values = line.split("   ")
  30                 if len(values) != len(keys):
  31                         sys.stderr.write("Number of on line \""+line.strip() + "\" doesn't match number of keys ("+str(len(keys))+") " + str(keys) +"\n")
  32                         sys.exit(1)
  33                 #sys.stdout.write("Debug: Read line \""+line.strip()+"\"\n")
  34                 point = {}
  35                 for i in range(0, len(keys)):
  36                         point.update({keys[i]:values[i]})
  37                 data.append(point)
  38                 #data.append({"wavelength":values[0], "angle":values[1], "psi":values[2], "delta":values[3], "uncertainty_psi":values[4], "uncertainty_delta":values[4]})
  39                 line = dataFile.readline()
  40
  41         return {"title":title, "data":data}
  42
  43 def extractData(line, x, y, conditions):
  44         for condition in conditions:
  45                 [name, value] = condition.split("=")
  46                 if keys.count(name) <= 0:
  47                         sys.stderr.write("Unknown key \""+name+"\" for condition " + str(condition) + "\n")
  48                         sys.exit(1)
  49                 values = value.split(",")
  50                 match = False
  51                 for v in values:
  52                         #sys.stdout.write(line[name] + " .vs. " + str(v) + "\n")
  53                         if float(line[name]) == float(v):
  54                                 match = True
  55                                 break
  56                 if match == False:
  57                         #sys.stdout.write("Condition \""+str(condition)+"\" not satisfied ("+str(line[name]) + " .vs. " + str(values[0])+ "\n")
  58                         return None
  59                 #sys.stdout.write("Condition satisfied\n")
  60         return [line[x], line[y]]
  61
  62
  63 if __name__ == "__main__":
  64
  65
  66
  67         indexStart = 1
  68         state = "--raw"
  69         for arg in sys.argv:
  70                 if arg[0] == '-' and arg[1] == '-':
  71                         indexStart += 1
  72                         state = arg
  73         #sys.stdout.write("State is " + state + "\n")
  74
  75
  76         if len(sys.argv) - indexStart < 3:
  77                 sys.stderr.write("Usage: " +sys.argv[0] + " [options] datafile x y [conditions] outfile\n")
  78                 sys.exit(1)
  79
  80         datafile = sys.argv[indexStart]
  81         x = sys.argv[indexStart+1]
  82         y = sys.argv[indexStart+2]
  83
  84         error = False
  85         for k in [x,y]:
  86                 if keys.count(k) <= 0:
  87                         sys.stderr.write("Unknown key \""+k+"\"\n")
  88                         error = True
  89         if error:
  90                 sys.exit(1)
  91
  92
  93         conditions = sys.argv[indexStart+3:len(sys.argv)-1]
  94         sys.stdout.write("Debug: Conditions are " + str(conditions) + "\n")
  95         for condition in conditions:
  96                 sys.stdout.write("      Debug: Condition " + str(condition.split("=")) + "\n")
  97         outfile = sys.argv[len(sys.argv)-1]
  98
  99         results = getData(datafile)
 100
 101
 102         toPlot = map(lambda e : extractData(e, x,y,conditions) , results["data"])
 103         toPlot = filter(lambda e : e != None and len(e) == 2, toPlot)
 104
 105         tmpFile = open(outfile+".tmp", "w")
 106         for point in toPlot:
 107                 tmpFile.write(point[0] + "      " + point[1] + "\n")
 108         tmpFile.close()
 109
 110         if state == "--plot":
 111                 command = ""
 112                 command += "set term png size 960,480\n"
 113                 command += "set output \"" + outfile + "\"\n"
 114                 command += "set xlabel \"" + x + "\"\n"
 115                 command += "set ylabel \"" + y + "\"\n"
 116                 command += "set title \"" + results["title"] + "\"\n"
 117                 command += "set key outside right\n"
 118                 command += "plot \"" + outfile + ".tmp\" using 1:2 with points title \""+str(conditions)+"\"\n"
 119                 command += "exit\n"
 120
 121                 tmpFile = open(outfile+".tmp.plt", "w")
 122                 tmpFile.write(command)
 123                 tmpFile.close()
 124
 125                 sys.stdout.write("Calling gnuplot now...\n")
 126                 #sys.stdout.write("------------------------------------\n")
 127                 os.system("gnuplot -p "+outfile+".tmp.plt") #2>/dev/null 1>/dev/null")
 128                 #sys.stdout.write("------------------------------------\n")
 129                 sys.stdout.write("gnuplot finished.\n")
 130
 131                 os.remove(outfile+".tmp")
 132                 os.remove(outfile+".tmp.plt")
 133                 sys.stdout.write("Done!\n")
 134         elif state == "--raw":
 135                 os.system("mv " + outfile+".tmp " + outfile)
 136         sys.exit(0)
 137
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