def validate(self, x, y, classifier_kwargs={}, extra=None, parallel=True):
'''
Runs crossvalidation on the provided data. The length of the :py:obj:`x` array should be identical to :py:obj:`y`
and will be used to partition the lists by index.
:param x: observations, needs to implement __len__ and __getitem__ aka len(x), x[i]
:param y: expected output, needs to implement __getitem__, aka y[i]
:param classifier_kwargs: a dictionary of parameters to pass to the classifier
:param extra: @todo extra information to pull out of the classifier
:returns: @todo figure this out
'''
if extra is not None:
if not isinstance(extra, str) and \
not isinstance(extra, types.MethodType) and \
not isinstance(extra, types.FunctionType):
raise ValueError('the `extra\' argument takes either a string or a method.')
if isinstance(extra, types.MethodType):
extra = extra.__name__
assert(hasattr(self.classifier_cls, extra))
log = logging.getLogger(PYXVAL_LOGGER)
log.debug('beginning %d-fold crossvalidation' % self.folds)
partition = CrossValidator.__partition(len(x), self.folds)
# log.debug('partition assignments: %s' % str(partition))
kwargs = deepcopy(self.classifier_kwargs)
kwargs.update(classifier_kwargs)
results = farmout(
num=self.folds,
setup=lambda f: (_folder, f, partition, x, y, self.classifier_cls(**kwargs), extra),
worker=farmworker,
isresult=lambda r: isinstance(r, tuple) and len(r) == 5,
attempts=3,
pickletest=self if parallel else False
)
stats = self.scorer_cls(**self.scorer_kwargs)
lret = []
xtra = []
for l, x, t, p, w in results:
if l is not None:
lret.append(l)
if x is not None:
xtra.append(x)
stats.append(t, p, w)
log.debug('finished %d-fold crossvalidation, performance stats: %s' % (self.folds, stats))
return ValidationResult(
lret if len(lret) else None,
stats,
xtra if len(xtra) else None
)
def map(self, argslist, globalvars={}, quiet=True):
numjobs = len(argslist)
if self._mpi:
# message passing interface
# don't f**k with the number of backslashes.
# Seriously. You don't know what you're doing.
cmds = dedent('''\
GLOBAL_FPRINTF_REDIRECT = "/dev/null";
_job = 0;
%(jobopts)s
_jobvals = {};
_nodestates = { MPI_NODE_COUNT-1, 2 };
_received = 0;
while ( _received < %(numjobs)d ) {
_recvjob = 1;
if ( _job < %(numjobs)d ) {
for ( _node = 0; _node < MPI_NODE_COUNT-1; _node += 1 ) {
if ( _nodestates[ _node ][ 0 ] == 0 ) {
_recvjob = 0;
break;
}
}
if ( ! _recvjob ) {
_mpicmds = "";
_mpicmds * 256;
_mpicmds * ( "%(globalvars)s" );
_mpicmds * ( "MESSAGE_LOGGING = 0;" );
_mpicmds * ( "_options = " + _jobopts[ _job ] + ";" );
_mpicmds * ( "ExecuteAFile( "{1}%(batchfile)s"{1}, _options );" );
_mpicmds * ( "_retstr = "{1}"{1};" );
_mpicmds * ( "_retstr * 128;" );
_mpicmds * ( "_retstr * ( "{1}_retjob = "{1} + " + _job + " + "{1};"{1} );" );
_mpicmds * ( "_retstr * ( "{1}_retval = "{2}"{1} + ( %(retvar)s ^ {{ "{1}"{2}"{1}, "{1}"{3}"{1} }} ) + "{1}"{2};"{1} );" );
_mpicmds * ( "_retstr * 0;" );
_mpicmds * ( "return _retstr;" );
_mpicmds * 0;
MPISend( _node + 1, _mpicmds );
_nodestates[ _node ][ 0 ] = 1;
_nodestates[ _node ][ 1 ] = Time(0);
_job += 1;
}
}
if ( _recvjob ) {
MPIReceive( -1, _null, _retstr );
ExecuteCommands( _retstr );
_jobvals[ _retjob ] = _retval;
_received += 1;
}
}
GLOBAL_FPRINTF_REDIRECT = "";
fprintf( stdout, "[" + _jobvals[ 0 ] );
for ( _job = 1; _job < %(numjobs)d; _job += 1 ) {
fprintf ( stdout, "," + _jobvals[ _job ] );
}
fprintf( stdout, "]" );
''') % {
'batchfile': self._batchfile,
'globalvars': _globalvars(globalvars).replace('\n', '\\n').replace('"', '\\"'),
'numjobs': numjobs,
'retvar': self._retvar,
'jobopts': _jobopts(argslist),
}
# this facility helps us write code that doesn't break
# by allowing us to escape quotations appropriately:
# by depth
digits = set()
for m in finditer(r'"{(\d+)}', cmds):
digits.add(int(m.group(1)))
for nslash in digits:
pwr = 2 ** nslash - 1
cmds = cmds.replace('"{%d}' % nslash, ('\\' * pwr) + '"')
retcode, pout, perr = _runhyphympi(cmds)
# the following no longer makes sense given the child process nature
# of how we call hyphympi
# if not quiet:
# if pout != '':
# print(pout, file=stderr)
if perr != '':
raise RuntimeError(perr)
# this is a hideous parser for the outermost
# json-esque array that the script above outputs
# start at 1 because the first char is a '['
i = 1
nb = 0
retarr = []
for j, c in enumerate(pout):
# every time we encounter a '[', increment nb
if c == '[':
nb += 1
# likewise, if we encounter a closing bracket, decrement
if c == ']':
nb -= 1
# if we're at a comma and nb == 1, we're in the outer list
# so split from the last time we split to j-1
if c == ',' and nb == 1:
retarr.append(pout[i:j])
i = j + 1
# don't forget the final piece
retarr.append(pout[i:(j + nb)])
return retarr
else:
# multiprocessing
numjobs = len(argslist)
globals = _globalvars(globalvars)
results = farmout(
num=numjobs,
setup=lambda i: (
_jobdispatch,
self._batchfile,
self._retvar,
globals,
(argslist[i],),
quiet
),
worker=farmworker,
isresult=lambda r: isinstance(r, list),
attempts=3
)
return list(chain(*results))
def map(self, argslist, globalvars={}, quiet=True):
numjobs = len(argslist)
if self._mpi:
# message passing interface
# don't f**k with the number of backslashes.
# Seriously. You don't know what you're doing.
cmds = dedent('''\
GLOBAL_FPRINTF_REDIRECT = "/dev/null";
_job = 0;
%(jobopts)s
_jobvals = {};
_nodestates = { MPI_NODE_COUNT-1, 2 };
_received = 0;
while ( _received < %(numjobs)d ) {
_recvjob = 1;
if ( _job < %(numjobs)d ) {
for ( _node = 0; _node < MPI_NODE_COUNT-1; _node += 1 ) {
if ( _nodestates[ _node ][ 0 ] == 0 ) {
_recvjob = 0;
break;
}
}
if ( ! _recvjob ) {
_mpicmds = "";
_mpicmds * 256;
_mpicmds * ( "%(globalvars)s" );
_mpicmds * ( "MESSAGE_LOGGING = 0;" );
_mpicmds * ( "_options = " + _jobopts[ _job ] + ";" );
_mpicmds * ( "ExecuteAFile( "{1}%(batchfile)s"{1}, _options );" );
_mpicmds * ( "_retstr = "{1}"{1};" );
_mpicmds * ( "_retstr * 128;" );
_mpicmds * ( "_retstr * ( "{1}_retjob = "{1} + " + _job + " + "{1};"{1} );" );
_mpicmds * ( "_retstr * ( "{1}_retval = "{2}"{1} + ( %(retvar)s ^ {{ "{1}"{2}"{1}, "{1}"{3}"{1} }} ) + "{1}"{2};"{1} );" );
_mpicmds * ( "_retstr * 0;" );
_mpicmds * ( "return _retstr;" );
_mpicmds * 0;
MPISend( _node + 1, _mpicmds );
_nodestates[ _node ][ 0 ] = 1;
_nodestates[ _node ][ 1 ] = Time(0);
_job += 1;
}
}
if ( _recvjob ) {
MPIReceive( -1, _null, _retstr );
ExecuteCommands( _retstr );
_jobvals[ _retjob ] = _retval;
_received += 1;
}
}
GLOBAL_FPRINTF_REDIRECT = "";
fprintf( stdout, "[" + _jobvals[ 0 ] );
for ( _job = 1; _job < %(numjobs)d; _job += 1 ) {
fprintf ( stdout, "," + _jobvals[ _job ] );
}
fprintf( stdout, "]" );
''') % {
'batchfile':
self._batchfile,
'globalvars':
_globalvars(globalvars).replace('\n', '\\n').replace(
'"', '\\"'),
'numjobs':
numjobs,
'retvar':
self._retvar,
'jobopts':
_jobopts(argslist),
}
# this facility helps us write code that doesn't break
# by allowing us to escape quotations appropriately:
# by depth
digits = set()
for m in finditer(r'"{(\d+)}', cmds):
digits.add(int(m.group(1)))
for nslash in digits:
pwr = 2**nslash - 1
cmds = cmds.replace('"{%d}' % nslash, ('\\' * pwr) + '"')
retcode, pout, perr = _runhyphympi(cmds)
# the following no longer makes sense given the child process nature
# of how we call hyphympi
# if not quiet:
# if pout != '':
# print(pout, file=stderr)
if perr != '':
raise RuntimeError(perr)
# this is a hideous parser for the outermost
# json-esque array that the script above outputs
# start at 1 because the first char is a '['
i = 1
nb = 0
retarr = []
for j, c in enumerate(pout):
# every time we encounter a '[', increment nb
if c == '[':
nb += 1
# likewise, if we encounter a closing bracket, decrement
if c == ']':
nb -= 1
# if we're at a comma and nb == 1, we're in the outer list
# so split from the last time we split to j-1
if c == ',' and nb == 1:
retarr.append(pout[i:j])
i = j + 1
# don't forget the final piece
retarr.append(pout[i:(j + nb)])
return retarr
else:
# multiprocessing
numjobs = len(argslist)
globals = _globalvars(globalvars)
results = farmout(
num=numjobs,
setup=lambda i:
(_jobdispatch, self._batchfile, self._retvar, globals,
(argslist[i], ), quiet),
worker=farmworker,
isresult=lambda r: isinstance(r, list),
attempts=3)
return list(chain(*results))