def _call(self, ds):
# local binding
generator = self._generator
node = self._node
ca = self.ca
space = self.get_space()
concat_as = self._concat_as
if self.ca.is_enabled("stats") and (not node.ca.has_key("stats") or
not node.ca.is_enabled("stats")):
warning("'stats' conditional attribute was enabled, but "
"the assigned node '%s' either doesn't support it, "
"or it is disabled" % node)
# precharge conditional attributes
ca.datasets = []
# run the node an all generated datasets
results = []
for i, sds in enumerate(generator.generate(ds)):
if ca.is_enabled("datasets"):
# store dataset in ca
ca.datasets.append(sds)
# run the beast
result = node(sds)
# callback
if not self._callback is None:
self._callback(data=sds, node=node, result=result)
# subclass postprocessing
result = self._repetition_postcall(sds, node, result)
if space:
# XXX maybe try to get something more informative from the
# processing node (e.g. in 0.5 it used to be 'chunks'->'chunks'
# to indicate what was trained and what was tested. Now it is
# more tricky, because `node` could be anything
result.set_attr(space, (i,))
# store
results.append(result)
if ca.is_enabled("stats") and node.ca.has_key("stats") \
and node.ca.is_enabled("stats"):
if not ca.is_set('stats'):
# create empty stats container of matching type
ca.stats = node.ca['stats'].value.__class__()
# harvest summary stats
ca['stats'].value.__iadd__(node.ca['stats'].value)
# charge condition attribute
self.ca.repetition_results = results
# stack all results into a single Dataset
if concat_as == 'samples':
results = vstack(results)
elif concat_as == 'features':
results = hstack(results)
else:
raise ValueError("Unkown concatenation mode '%s'" % concat_as)
# no need to store the raw results, since the Measure class will
# automatically store them in a CA
return results
def _sl_call(self, dataset, roi_ids, nproc):
"""Classical generic searchlight implementation
"""
# compute
if nproc > 1:
# split all target ROIs centers into `nproc` equally sized blocks
nproc_needed = min(len(roi_ids), nproc)
roi_blocks = np.array_split(roi_ids, nproc_needed)
# the next block sets up the infrastructure for parallel computing
# this can easily be changed into a ParallelPython loop, if we
# decide to have a PP job server in PyMVPA
import pprocess
p_results = pprocess.Map(limit=nproc_needed)
if __debug__:
debug('SLC', "Starting off child processes for nproc=%i"
% nproc_needed)
compute = p_results.manage(
pprocess.MakeParallel(self._proc_block))
for block in roi_blocks:
# should we maybe deepcopy the measure to have a unique and
# independent one per process?
compute(block, dataset, copy.copy(self.__datameasure))
# collect results
results = []
if self.ca.is_enabled('roi_sizes'):
roi_sizes = []
else:
roi_sizes = None
for r, rsizes in p_results:
results += r
if not roi_sizes is None:
roi_sizes += rsizes
else:
# otherwise collect the results in a list
results, roi_sizes = \
self._proc_block(roi_ids, dataset, self.__datameasure)
if __debug__ and 'SLC' in debug.active:
debug('SLC', '') # just newline
resshape = len(results) and np.asanyarray(results[0]).shape or 'N/A'
debug('SLC', ' hstacking %d results of shape %s'
% (len(results), resshape))
# but be careful: this call also serves as conversion from parallel maps
# to regular lists!
# this uses the Dataset-hstack
results = hstack(results)
if __debug__:
debug('SLC', " hstacked shape %s" % (results.shape,))
return results, roi_sizes
def _sl_call(self, dataset, roi_ids, nproc):
"""Classical generic searchlight implementation
"""
# compute
if nproc > 1:
# split all target ROIs centers into `nproc` equally sized blocks
roi_blocks = np.array_split(roi_ids, nproc)
# the next block sets up the infrastructure for parallel computing
# this can easily be changed into a ParallelPython loop, if we
# decide to have a PP job server in PyMVPA
import pprocess
p_results = pprocess.Map(limit=nproc)
if __debug__:
debug("SLC", "Starting off child processes for nproc=%i" % nproc)
compute = p_results.manage(pprocess.MakeParallel(self._proc_block))
for block in roi_blocks:
# should we maybe deepcopy the measure to have a unique and
# independent one per process?
compute(block, dataset, copy.copy(self.__datameasure))
# collect results
results = []
if self.ca.is_enabled("roi_sizes"):
roi_sizes = []
else:
roi_sizes = None
for r, rsizes in p_results:
results += r
if not roi_sizes is None:
roi_sizes += rsizes
else:
# otherwise collect the results in a list
results, roi_sizes = self._proc_block(roi_ids, dataset, self.__datameasure)
if __debug__:
debug("SLC", "")
# but be careful: this call also serves as conversion from parallel maps
# to regular lists!
# this uses the Dataset-hstack
results = hstack(results)
return results, roi_sizes
def _call(self, dataset):
"""Perform the ROI search.
"""
# local binding
nproc = self.__nproc
if nproc is None and externals.exists('pprocess'):
import pprocess
try:
nproc = pprocess.get_number_of_cores() or 1
except AttributeError:
warning("pprocess version %s has no API to figure out maximal "
"number of cores. Using 1" % externals.versions['pprocess'])
nproc = 1
# train the queryengine
self.__qe.train(dataset)
# decide whether to run on all possible center coords or just a provided
# subset
if self.__center_ids is not None:
roi_ids = self.__center_ids
# safeguard against stupidity
if __debug__:
if max(roi_ids) >= dataset.nfeatures:
raise IndexError, \
"Maximal center_id found is %s whenever given " \
"dataset has only %d features" \
% (max(roi_ids), dataset.nfeatures)
else:
roi_ids = np.arange(dataset.nfeatures)
# compute
if nproc > 1:
# split all target ROIs centers into `nproc` equally sized blocks
roi_blocks = np.array_split(roi_ids, nproc)
# the next block sets up the infrastructure for parallel computing
# this can easily be changed into a ParallelPython loop, if we
# decide to have a PP job server in PyMVPA
import pprocess
p_results = pprocess.Map(limit=nproc)
compute = p_results.manage(
pprocess.MakeParallel(self._proc_block))
for block in roi_blocks:
# should we maybe deepcopy the measure to have a unique and
# independent one per process?
compute(block, dataset, copy.copy(self.__datameasure))
# collect results
results = []
if self.ca.is_enabled('roisizes'):
roisizes = []
else:
roisizes = None
for r, rsizes in p_results:
results += r
if not roisizes is None:
roisizes += rsizes
else:
# otherwise collect the results in a list
results, roisizes = \
self._proc_block(roi_ids, dataset, self.__datameasure)
if not roisizes is None:
self.ca.roisizes = roisizes
if __debug__:
debug('SLC', '')
# but be careful: this call also serves as conversion from parallel maps
# to regular lists!
# this uses the Dataset-hstack
results = hstack(results)
if 'mapper' in dataset.a:
# since we know the space we can stick the original mapper into the
# results as well
if self.__center_ids is None:
results.a['mapper'] = copy.copy(dataset.a.mapper)
else:
# there is an additional selection step that needs to be
# expressed by another mapper
mapper = copy.copy(dataset.a.mapper)
mapper.append(FeatureSliceMapper(self.__center_ids,
dshape=dataset.shape[1:]))
results.a['mapper'] = mapper
# charge state
self.ca.raw_results = results
# return raw results, base-class will take care of transformations
return results