[mlpack-svn] r15489 - mlpack/conf/jenkins-conf/benchmark/methods/mlpack
fastlab-svn at coffeetalk-1.cc.gatech.edu
fastlab-svn at coffeetalk-1.cc.gatech.edu
Wed Jul 17 13:11:42 EDT 2013
Author: marcus
Date: Wed Jul 17 13:11:41 2013
New Revision: 15489
Log:
Add mlpack ICA benchmark script.
Added:
mlpack/conf/jenkins-conf/benchmark/methods/mlpack/ica.py
Added: mlpack/conf/jenkins-conf/benchmark/methods/mlpack/ica.py
==============================================================================
--- (empty file)
+++ mlpack/conf/jenkins-conf/benchmark/methods/mlpack/ica.py Wed Jul 17 13:11:41 2013
@@ -0,0 +1,145 @@
+'''
+ @file ica.py
+ @author Marcus Edel
+
+ Class to benchmark the mlpack independent component analysis method.
+'''
+
+import os
+import sys
+import inspect
+
+# Import the util path, this method even works if the path contains symlinks to
+# modules.
+cmd_subfolder = os.path.realpath(os.path.abspath(os.path.join(
+ os.path.split(inspect.getfile(inspect.currentframe()))[0], "../../util")))
+if cmd_subfolder not in sys.path:
+ sys.path.insert(0, cmd_subfolder)
+
+from log import *
+
+import shlex
+import subprocess
+import re
+import collections
+
+'''
+This class implements the independent component analysis benchmark.
+'''
+class ICA(object):
+
+ '''
+ Create the independent component analysis benchmark instance, show some
+ informations and return the instance.
+
+ @param dataset - Input dataset to perform ICA on.
+ @param path - Path to the mlpack executable.
+ @param verbose - Display informational messages.
+ '''
+ def __init__(self, dataset, path=os.environ["MLPACK_BIN"], verbose=True):
+ self.verbose = verbose
+ self.dataset = dataset
+ self.path = path
+
+ # Get description from executable.
+ cmd = shlex.split(self.path + "radical -h")
+ try:
+ s = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=False)
+ except Exception, e:
+ Log.Fatal("Could not execute command: " + str(cmd))
+ return -1
+
+ # Use regular expression pattern to get the description.
+ pattern = re.compile(r"""(.*?)Required.*?options:""",
+ re.VERBOSE|re.MULTILINE|re.DOTALL)
+
+ match = pattern.match(s)
+ if not match:
+ Log.Warn("Can't parse description", self.verbose)
+ description = ""
+ else:
+ description = match.group(1)
+
+ self.description = description
+
+ '''
+ Destructor to clean up at the end. Use this method to remove created files.
+ '''
+ def __del__(self):
+ Log.Info("Clean up.", self.verbose)
+ filelist = ["gmon.out", "output_unmixing.csv", "output_ic.csv"]
+ for f in filelist:
+ if os.path.isfile(f):
+ os.remove(f)
+
+ '''
+ Perform independent component analysis. If the method has been successfully
+ completed return the elapsed time in seconds.
+
+ @param options - Extra options for the method.
+ @return - Elapsed time in seconds or -1 if the method was not successful.
+ '''
+ def RunMethod(self, options):
+ Log.Info("Perform ICA.", self.verbose)
+
+ # Split the command using shell-like syntax.
+ cmd = shlex.split(self.path + "radical -i " + self.dataset + " -v "
+ + options)
+
+ # Run command with the nessecary arguments and return its output as a byte
+ # string. We have untrusted input so we disables all shell based features.
+ try:
+ s = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=False)
+ except Exception, e:
+ Log.Fatal("Could not execute command: " + str(cmd))
+ return -1
+
+ # Return the elapsed time.
+ timer = self.parseTimer(s)
+ if not timer:
+ Log.Fatal("Can't parse the timer")
+ return -1
+ else:
+ time = self.GetTime(timer)
+ Log.Info(("total time: %fs" % (time)), self.verbose)
+
+ return time
+
+ '''
+ Parse the timer data form a given string.
+
+ @param data - String to parse timer data from.
+ @return - Namedtuple that contains the timer data.
+ '''
+ def parseTimer(self, data):
+ # Compile the regular expression pattern into a regular expression object to
+ # parse the timer data.
+ pattern = re.compile(r"""
+ .*?loading_data: (?P<loading_data>.*?)s.*?
+ .*?saving_data: (?P<saving_data>.*?)s.*?
+ .*?total_time: (?P<total_time>.*?)s.*?
+ """, re.VERBOSE|re.MULTILINE|re.DOTALL)
+
+ match = pattern.match(data)
+
+ if not match:
+ Log.Fatal("Can't parse the data: wrong format")
+ return -1
+ else:
+ # Create a namedtuple and return the timer data.
+ timer = collections.namedtuple("timer", ["loading_data", "saving_data",
+ "total_time"])
+
+ return timer(float(match.group("loading_data")),
+ float(match.group("saving_data")),
+ float(match.group("total_time")))
+
+ '''
+ Return the elapsed time in seconds.
+
+ @param timer - Namedtuple that contains the timer data.
+ @return Elapsed time in seconds.
+ '''
+ def GetTime(self, timer):
+ time = timer.total_time - timer.loading_data - timer.saving_data
+ return time
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