[mlpack-svn] r15476 - mlpack/conf/jenkins-conf/benchmark/methods/matlab
fastlab-svn at coffeetalk-1.cc.gatech.edu
fastlab-svn at coffeetalk-1.cc.gatech.edu
Tue Jul 16 12:47:03 EDT 2013
Author: marcus
Date: Tue Jul 16 12:47:02 2013
New Revision: 15476
Log:
Add matlab linear regression method and benchmarl script.
Added:
mlpack/conf/jenkins-conf/benchmark/methods/matlab/LINEAR_REGRESSION.m
mlpack/conf/jenkins-conf/benchmark/methods/matlab/linear_regression.py
Added: mlpack/conf/jenkins-conf/benchmark/methods/matlab/LINEAR_REGRESSION.m
==============================================================================
--- (empty file)
+++ mlpack/conf/jenkins-conf/benchmark/methods/matlab/LINEAR_REGRESSION.m Tue Jul 16 12:47:02 2013
@@ -0,0 +1,35 @@
+% @file LINEAR_REGRESSION.m
+% @author Marcus Edel
+%
+% Linear Regression with matlab.
+
+function linear_regression(cmd)
+% Simple Linear Regression Prediction
+%
+% Required options:
+% (-i) [string] File containing X (regressors).
+%
+% Options:
+% (-r) [string] File containing y (responses). If not given, the
+% responses are assumed to be the last row of the
+% input file.
+
+% Load input dataset.
+regressorsFile = regexp(cmd, '.*?-i ([^\s]+)', 'tokens', 'once');
+responsesFile = regexp(cmd, '.*?-r ([^\s]+)', 'tokens', 'once');
+
+X = csvread(regressorsFile{:});
+
+if isempty(responsesFile)
+ y = X(:,end);
+ X = X(:,1:end-1);
+else
+ y = csvread(responsesFile{:});
+end
+
+% Perform linear regression.
+total_time = tic;
+b = regress(y, X);
+disp(sprintf('[INFO ] total_time: %fs', toc(total_time)))
+
+end
Added: mlpack/conf/jenkins-conf/benchmark/methods/matlab/linear_regression.py
==============================================================================
--- (empty file)
+++ mlpack/conf/jenkins-conf/benchmark/methods/matlab/linear_regression.py Tue Jul 16 12:47:02 2013
@@ -0,0 +1,121 @@
+'''
+ @file linear_regression.py
+ @author Marcus Edel
+
+ Class to benchmark the matlab Linear Regression 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 *
+from profiler import *
+
+import shlex
+import subprocess
+import re
+import collections
+
+'''
+This class implements the Linear Regression benchmark.
+'''
+class LinearRegression(object):
+
+ '''
+ Create the Linear Regression benchmark instance.
+
+ @param dataset - Input dataset to perform Linear Regression on.
+ @param path - Path to the mlpack executable.
+ @param verbose - Display informational messages.
+ '''
+ def __init__(self, dataset, path=os.environ["MATLAB_BIN"], verbose = True):
+ self.verbose = verbose
+ self.dataset = dataset
+ self.path = path
+
+ '''
+ Destructor to clean up at the end.
+ '''
+ def __del__(self):
+ pass
+
+ '''
+ Linear Regression benchmark instance. 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 Linear Regression.", self.verbose)
+
+ # If the dataset contains two files then the second file is the responses
+ # file. In this case we add this to the command line.
+ if len(self.dataset) == 2:
+ inputCmd = "-i " + self.dataset[0] + " -r " + self.dataset[1] + " " + options
+ else:
+ inputCmd = "-i " + self.dataset + " " + options
+
+ # Split the command using shell-like syntax.
+ cmd = shlex.split(self.path + "matlab -nodisplay -nosplash -r \"try, " +
+ "LINEAR_REGRESSION('" + inputCmd + "'), catch, exit(1), end, exit(0)\"")
+
+ # 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:
+ 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"""
+ .*?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", ["total_time"])
+
+ return timer(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
+ return time
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