Reads the TIC "freq_cnt_keysight_53230A" in a directory and plots trend.

dc7c0afb · Peter Jansweijer · eb3be8aa · dc7c0afb
Commit dc7c0afb authored Jun 22, 2018 by Peter Jansweijer
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trend.py sw/insitu_alpha/trend.py +247 -0

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--- a/sw/insitu_alpha/trend.py
+++ b/sw/insitu_alpha/trend.py
+#!/usr/bin/python
+
+"""
+trend.py:
+Reads the TIC "freq_cnt_keysight_53230A" in a directory. Each file contains multiple
+measurements. The mean value is calculated and added to an array.
+A directory may contain multiple measurements, each with a set of "freq_cnt_keysight_53230A"
+files. For example, 10 measurements are done using 25 link restarts each so there
+are 250 files.
+The link restart number must be forwarded to "trend.py" such that it knows at what file
+one measurement ends and another starts.
+Outliers are reported and their values are replaced by the average values recorded so far.
+An output file is created that reports the mean values of all tic-measurement files
+per measurement (excluding outliers!)
+
+-------------------------------------------------------------------------------
+Copyright (C) 2016 Peter Jansweijer, Henk Peek
+    
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>
+-------------------------------------------------------------------------------
+
+Usage:
+  trend.py     -name dir
+  trend.py     -h | --help
+
+Options:
+  -h --help    Show this screen.
+  -name        pointer to a directory with measurement files "freq_cnt_keysight_53230A"
+  -o <dir>     optional directory for output file storage, default: "data/"
+  -r <number>  number of link restarts over which the delta_delay is averaged (default = 10)
+  -t <number>  tolerance [ps], skip outliers that are offset from the mean value
+  
+"""
+
+import os
+import sys
+import numpy
+import scipy
+import time
+import matplotlib.pyplot as plt
+
+import pdb
+
+# Add parent directory (containing 'lib') to the module search path
+lib_path = (os.path.dirname(os.path.abspath(__file__)))
+lib_path = os.path.join(lib_path,"..")
+sys.path.insert(0,lib_path)
+
+# private imports:
+import lib.Keysight_53230A as tic
+
+############################################################################
+
+def save_plot(out_file, name, nameref, measurement_str, measurement_lst, outliers):
+
+  """
+  outfile           <file> handle to outfput file
+  name              <str>  name of the input file (with fiber spool PPS skew measurements)
+  nameref           <str>  name of the input file (with reference setup PPS skew measurements)
+  measurement_str   <str>  processed measurement
+  measurement_lst   <list> list of PPS skew measurements (from multiple link restarts)
+  outliers          <int>  number of outliers encountered while processing
+  """
+
+  measurement_str_shortend = measurement_str.replace("# Selected ITU channel for ","")
+  measurement_str_shortend = measurement_str_shortend.replace("\n","")
+
+  meas_arr= numpy.array(measurement_lst)
+  mean = meas_arr.mean()
+  stdev = meas_arr.std(ddof=1)
+
+  #out_file.write("outliers: " + str(outliers) + "\n")
+  #out_file.write("mean: " + str(mean) + "\n")
+  #out_file.write("stdev: " + str(stdev) + "\n")
+  out_file.write(str(mean) + ", " + str(stdev) + ", " +str(outliers) + ", " +str(measurement_str_shortend) + "\n")
+
+  fig = plt.figure("PPS_skew_fiberspool - PPS_skew_reference [ps]")
+  ax = fig.add_subplot(111)
+  ax.set_ylabel('PPS difference [ps]')
+  ax.set_title("PPS_skew_fiberspool - PPS_skew_reference [ps]")
+  ax.set_xlabel('Link restart number')
+  fig_str = measurement_str_shortend + "\n" + "file: "+name + "\n" + "ref file: "+nameref + "\n" + "outliers: " + str(outliers) + "\n" + "mean: " + str(mean) + "\n" +"stdev: " + str(stdev)
+  ax.text(0.01, 0.70, fig_str, transform=ax.transAxes)
+  ax.plot(range(1,len(meas_arr)+1), meas_arr, color = 'blue', label='data')
+  png_name = measurement_str_shortend.replace("[","")
+  png_name = png_name.replace("]","")
+  png_name = png_name.replace("(","")
+  png_name = png_name.replace(")","")
+  png_name = png_name.replace(":","")
+  png_name = png_name.replace(",","")
+  png_name = png_name.replace(" ","_")
+  png_name = png_name.replace("->","2")
+
+  fig.savefig(output_dir+png_name+".png")
+  fig.clf() # clear figure (it was stored in a png file)
+
+  return
+
+############################################################################
+
+
+###############################################
+# Main
+###############################################
+
+"""
+Usage:
+  trend.py     -name dir
+  trend.py     -h | --help
+
+Options:
+  -h --help    Show this screen.
+  -name        pointer to a directory with measurement files "freq_cnt_keysight_53230A"
+  -o <dir>     optional directory for output file storage, default: "data/"
+  -r <number>  number of link restarts over which the delta_delay is averaged (default = 10)
+  -t <number>  tolerance [ps], skip outliers that are offset from the mean value
+
+"""
+if __name__ == "__main__":
+  
+  #arguments = docopt(__doc__,version='White Rabbit controled via serial port')
+  import argparse
+  parser = argparse.ArgumentParser()
+  parser.add_argument("name", help="directory containing measurement files freq_cnt_keysight_53230A")
+  parser.add_argument("-output_dir", default="data")
+  parser.add_argument("-r", default=10)
+  parser.add_argument("-t", default=200)
+  args = parser.parse_args()
+
+  name = args.name
+  restarts = int(args.r)
+  tolerance = int(args.t)
+  print("Used directory: ",name)
+  print("Output directory: ",args.output_dir)
+  print("link restarts: ",restarts)
+  print("tolerance: " + str(tolerance) + " [ps]")
+  tolerance = tolerance * 1e-12 # tolerance in [ps]!
+
+  files = []
+
+  # Figure out if the input is a single measurement file or a directory with files
+  if os.path.exists(name) == True:
+    if os.path.isdir(name) == True:
+      print(name+": is a directory")
+
+      # Any result files already there will be removed
+      if os.path.isfile(os.path.join(name,"result.txt")) == True:
+        os.remove(os.path.join(name, "result.txt"))
+
+      # Get a file list (exclude files with extensions!)
+      for file_name in os.listdir(name):
+        if len(file_name.split('.')) <= 1:
+          files.append(os.path.join(name, file_name))
+
+    else:
+      print(name+": is a file, not a directory.")
+      sys.exit()
+
+  else:
+    print(name+": directory does not exist")
+  
+  # add trailing slash if not present
+  output_dir = os.path.join(args.output_dir,'')
+  if os.path.exists(output_dir) != True:
+    os.mkdir(output_dir)
+    print("Output directory does not exist => created: "+output_dir)
+  
+  timestamp = time.localtime()
+
+  filename=output_dir+time.strftime(format("%y%m%d_%H_%M_%S"),timestamp)+"_PPS_skew_mean_values"
+  print("save PPS-Skew measurements average values into file:",filename)
+
+  out_file = open(filename,"w")
+  out_file.write("# PPS-Skew measurements average values\n")
+  out_file.write("# date:"+time.strftime(format("%d %b %Y"),timestamp)+"\n")
+  out_file.write("# time:"+time.strftime(format("%H:%M:%S"),timestamp)+"\n")
+  out_file.write("# mean, StdDev, outliers\n")
+  
+  cnt_restart = 0
+  file_average = []
+  outlier_cnt = 0
+  outlier_in_meas = 0
+  
+  fig = plt.figure("Trend")
+  ax = fig.add_subplot(111)
+  ax.set_ylabel('PPS difference [ps]')
+  ax.set_title("PPS_skew Trend[ps]")
+  ax.set_xlabel('measurement number')
+  ax.text(0.01, 0.95, str(name), transform=ax.transAxes)
+
+  for tic_file in sorted(files):
+    try:
+      #print(tic_file+"\n")
+      data_file = open(tic_file,"r")
+      line = data_file.readline()
+      data_file.close()
+      if line.strip() == "#MeasurementData:Keysight 53230A":
+        tic_meas = tic.file_to_scipy_array(tic_file)
+        tic_mean = tic_meas[1].mean()    # the average value of all measurements in this file
+
+        if len(file_average) > 0:
+          dirty_arr = numpy.array(file_average)  # Take the average of all values up to now
+          dirty_mean = dirty_arr.mean()
+          
+          if abs(tic_mean - dirty_mean) > tolerance:
+            outlier_cnt = outlier_cnt + 1
+            outlier_in_meas = outlier_in_meas + 1
+            print("outlier? " + tic_file)
+            print("average = " + str(tic_mean) + "\n")
+            dirty_arr = numpy.array(file_average)  # Take the average of all values up to now
+            file_average.append(dirty_arr.mean())  # and replace the outlier by this mean value.
+          else:
+            file_average.append(tic_mean)
+        else:
+          file_average.append(tic_mean)
+       
+        cnt_restart = cnt_restart + 1
+    except:
+      print (tic_file + ": wrong file type")
+      continue
+    if cnt_restart == restarts:
+      # Keep track of statistics per measurement
+      file_average_arr = numpy.array(file_average)
+      out_file.write(str(file_average_arr.mean()) + ", " + str(file_average_arr.std(ddof=1)) + ", " + str(outlier_in_meas) + "\n")
+      cnt_restart = 0
+      file_average = []
+      outlier_in_meas = 0
+      ax.plot(range(len(file_average_arr)), file_average_arr)
+      #print(len(file_average_arr))
+
+  ax.text(0.01, 0.90, "tolerance: " + str(tolerance) + "; outliers: " + str(outlier_cnt), transform=ax.transAxes)
+  plt.draw()
+  plt.show()
+  out_file.close()
+
+  sys.exit()