def __first_compilation_attempt(self):
####### First compilation attempt ####################################
targetdir, exec_name = os.path.split(self.getInternalExecPath())
sanity_check, log_fname = os.path.split(self.__log_file_path)
assert sanity_check == targetdir
if sys.platform == 'win32':
# When there are characters like '=' in a filenme, Windows can get
# confused if the filename is not quoted.
log_fname = '"%s"' % log_fname
# Remove outdated log file
assert not os.path.exists(exec_name)
if os.path.exists(log_fname):
os.remove(log_fname)
elif not os.path.exists(targetdir):
os.makedirs(targetdir)
# Actual compilation
moresh.pushd(targetdir)
logging.debug("\nIn %s:"%os.getcwd())
if sys.platform == 'win32':
# We assume the compiler is pymake.
if self.compiler != "pymake":
raise Not_Implemented
the_compiler = "python " + \
os.path.join(ppath.ppath('PLEARNDIR'), 'scripts', 'pymake')
else:
the_compiler = self.compiler
compile_options = ""
if self.compile_options is not None:
compile_options = self.compile_options
compile_cmd= self.getCompileCommand(the_compiler, compile_options)
logging.debug(compile_cmd)
p= subprocess.Popen(compile_cmd,
shell= True,
stdout= open(log_fname, 'w'),
stderr= subprocess.STDOUT)
compile_exit_code= p.wait()
logging.debug("compile_exit_code <- %d\n"%compile_exit_code)
moresh.popd()
# Report success of fail and remember that compilation was attempted
self.__attempted_to_compile = True
if compile_exit_code!=0 and os.path.exists(self.getInternalExecPath()):
os.remove(self.getInternalExecPath())
# Strip C++ execs
if self.isCompilable() and self.compilationSucceeded():
os.system("strip %s"%self.getInternalExecPath())
return compile_exit_code==0
def cd(path=None):
"""Emulate shell's cd --- forwards the call to os.chdir().
Mainly called as cd() as a shorthand to os.chdir( os.environ.get('HOME') ).
"""
if path is None:
path = ppath.ppath('HOME')
os.chdir(path)
def cd( path = None ):
"""Emulate shell's cd --- forwards the call to os.chdir().
Mainly called as cd() as a shorthand to os.chdir( os.environ.get('HOME') ).
"""
if path is None:
path = ppath.ppath('HOME')
os.chdir( path )
#
# Imports
#
import inspect, os
from plearn.pyplearn import *
from plearn.pyplearn import _plargs_storage_readonly
from plearn_repr import plearn_repr
from PyPLearnObject import PLOption, PyPLearnObject
from plearn.utilities.Tutorial import *
#
# Global variables
#
from plearn.utilities.ppath import ppath
LINEAR_REGRESSOR_SCRIPT = os.path.join(
ppath("PLEARNDIR"),
"plearn_learners/regressors/test/LinearRegressor/linear_regressor.pyplearn"
)
def pyPLearnMagicModuleSubSection( indent = ' '*4 ):
from plearn import pyplearn
pyplearn_magic_module = pyplearn.__dict__['__pyplearn_magic_module']
module_source = inspect.getsource( pyplearn_magic_module )
module_source = module_source.replace( '\n', '\n'+(indent*2) )
doc = pyplearn_magic_module.__doc__
line1 = doc.find('\n')
return SubSection( 'L{%s<__pyplearn_magic_module>}' % doc[:line1],
doc[line1+1:] + '\n' + indent + 'Implementation::\n' +
(indent*2) + module_source
m = array([[stats[k][i] for i in range(self.width())] for k in sk])
_printMatrix(m, sk, self.fieldnames, os, pretty)
print "\nCovariance Matrix:"
_printMatrix(stats["COV"], self.fieldnames, self.fieldnames, os, pretty)
print "\nCorrelation Matrix:"
_printMatrix(stats["CORR"], self.fieldnames, self.fieldnames, os, pretty)
if __name__ == "__main__":
from plearn.vmat.readAMat import readAMat
ut,fieldnames = readAMat(
os.path.join(
ppath.ppath('PLEARNDIR'),
'examples', 'data', 'test_suite',
'top_100_test.amat'
)
)
sc = StatsCollector(fieldnames)
sc.update(ut)
sc.printStats(sys.stdout, False)
print "\nAfter accumulating some more:"
sc.update(ut)
sc.printStats(sys.stdout, False)
print "\nAfter forgetting:"
sc.forget(fieldnames)
sc.printStats(sys.stdout, False)
from plearn.pyplearn.PyPLearnObject import PLOption
# PyTest modules
import core
## Hardcoded branch management:
##
## @var plbranches: We call plearn branches the PLearn, LisaPLearn and apstatsoft libraries.
##
## The plbranches format is old and is inspired from a removed module
## (plpath). It may well be inappropriate: rethink all this when the
## branches will be moved to a config file.
plbranches = []
for mpath in ["PLEARNDIR", "APSTATSOFTDIR", "LISAPLEARNDIR"]:
try:
plbranches.append( ppath.ppath(mpath) )
except:
pass
####### Helper Functions ####################################################
def find_global_program(name):
assert name != "source", "Do not use source, run .sh files instead."
program_path = plcommand(name)
if program_path is None:
wlines = toolkit.command_output( "which %s"%name )
if len(wlines) != 1:
raise core.PyTestUsageError(
"The only global programs currently supported are those found by 'which' "
"or those found in a <plearn_branch>/commands/. Call 'which %s' resulted "
def pushd(path=None):
if path is None:
path = ppath.ppath('HOME')
DIR_STACK.append(os.getcwd())
os.chdir(path)
def __first_compilation_attempt(self):
####### First compilation attempt ####################################
targetdir, exec_name = os.path.split(self.getInternalExecPath())
sanity_check, log_fname = os.path.split(self.__log_file_path)
assert sanity_check == targetdir
if sys.platform == 'win32':
# When there are characters like '=' in a filenme, Windows can get
# confused if the filename is not quoted.
log_fname = '"%s"' % log_fname
# Remove outdated log file
assert not os.path.exists(exec_name)
if os.path.exists(log_fname):
os.remove(log_fname)
elif not os.path.exists(targetdir):
os.makedirs(targetdir)
# Actual compilation
moresh.pushd(targetdir)
logging.debug("\nIn %s:" % os.getcwd())
if sys.platform == 'win32':
# We assume the compiler is pymake.
if self.compiler != "pymake":
raise Not_Implemented
the_compiler = "python " + \
os.path.join(ppath.ppath('PLEARNDIR'), 'scripts', 'pymake')
else:
the_compiler = self.compiler
compile_options = ""
if self.compile_options is not None:
compile_options = self.compile_options
compile_cmd = self.getCompileCommand(the_compiler, compile_options)
logging.debug(compile_cmd)
p = subprocess.Popen(compile_cmd,
shell=True,
stdout=open(log_fname, 'w'),
stderr=subprocess.STDOUT)
compile_exit_code = p.wait()
logging.debug("compile_exit_code <- %d\n" % compile_exit_code)
moresh.popd()
# Report success of fail and remember that compilation was attempted
self.__attempted_to_compile = True
if compile_exit_code != 0 and os.path.exists(
self.getInternalExecPath()):
os.remove(self.getInternalExecPath())
# Strip C++ execs
if self.isCompilable() and self.compilationSucceeded():
os.system("strip %s" % self.getInternalExecPath())
return compile_exit_code == 0
from plearn.pyplearn.PyPLearnObject import PLOption
# PyTest modules
import core
## Hardcoded branch management:
##
## @var plbranches: We call plearn branches the PLearn, LisaPLearn and apstatsoft libraries.
##
## The plbranches format is old and is inspired from a removed module
## (plpath). It may well be inappropriate: rethink all this when the
## branches will be moved to a config file.
plbranches = []
for mpath in ["PLEARNDIR", "APSTATSOFTDIR", "LISAPLEARNDIR"]:
try:
plbranches.append(ppath.ppath(mpath))
except:
pass
####### Helper Functions ####################################################
def find_global_program(name):
assert name != "source", "Do not use source, run .sh files instead."
program_path = plcommand(name)
if program_path is None:
wlines = toolkit.command_output("which %s" % name)
if len(wlines) != 1:
raise core.PyTestUsageError(
"The only global programs currently supported are those found by 'which' "
#
# Imports
#
import inspect, os
from plearn.pyplearn import *
from plearn.pyplearn import _plargs_storage_readonly
from plearn_repr import plearn_repr
from PyPLearnObject import PLOption, PyPLearnObject
from plearn.utilities.Tutorial import *
#
# Global variables
#
from plearn.utilities.ppath import ppath
LINEAR_REGRESSOR_SCRIPT = os.path.join(
ppath("PLEARNDIR"),
"plearn_learners/regressors/test/LinearRegressor/linear_regressor.pyplearn"
)
def pyPLearnMagicModuleSubSection(indent=' ' * 4):
from plearn import pyplearn
pyplearn_magic_module = pyplearn.__dict__['__pyplearn_magic_module']
module_source = inspect.getsource(pyplearn_magic_module)
module_source = module_source.replace('\n', '\n' + (indent * 2))
doc = pyplearn_magic_module.__doc__
line1 = doc.find('\n')
return SubSection(
'L{%s<__pyplearn_magic_module>}' % doc[:line1], doc[line1 + 1:] +
def pushd( path = None ):
if path is None:
path = ppath.ppath('HOME')
DIR_STACK.append( os.getcwd() )
os.chdir( path )
"N", "NMISSING", "NNONMISSING", "E", "V", "STDDEV", "STDERR",
"SUM", "SUMSQ", "MIN", "ARGMIN", "MAX", "ARGMAX"
]
m = array([[stats[k][i] for i in range(self.width())] for k in sk])
_printMatrix(m, sk, self.fieldnames, os, pretty)
print "\nCovariance Matrix:"
_printMatrix(stats["COV"], self.fieldnames, self.fieldnames, os,
pretty)
print "\nCorrelation Matrix:"
_printMatrix(stats["CORR"], self.fieldnames, self.fieldnames, os,
pretty)
if __name__ == "__main__":
from plearn.vmat.readAMat import readAMat
ut, fieldnames = readAMat(
os.path.join(ppath.ppath('PLEARNDIR'), 'examples', 'data',
'test_suite', 'top_100_test.amat'))
sc = StatsCollector(fieldnames)
sc.update(ut)
sc.printStats(sys.stdout, False)
print "\nAfter accumulating some more:"
sc.update(ut)
sc.printStats(sys.stdout, False)
print "\nAfter forgetting:"
sc.forget(fieldnames)
sc.printStats(sys.stdout, False)
