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Fixes 491: updates recording to handle individual cells as PopulationView #492

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Fixes 491: updates recording to handle individual cells as PopulationView #492

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10 changes: 9 additions & 1 deletion pyNN/common/populations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -477,8 +477,11 @@ def write_data(self, io, variables='all', gather=True, clear=False, annotations=
file as metadata.
"""
logger.debug("Population %s is writing %s to %s [gather=%s, clear=%s]" % (self.label, variables, io, gather, clear))
# ignoring the method parameter 'annotations', and using class attribute 'self.annotations'
# seems ok as this method parameter does not seem to be used within pynn currently.
# TODO: decide whether this method parameter needs to be retained.
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@appukuttan-shailesh appukuttan-shailesh Jun 27, 2017 •
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@apdavison : Does this method require to accept 'annotations' as an input parameter? From a quick grep in the pynn directory, it appeared as if none of the function calls pass this parameter to the method.

self.recorder.write(variables, io, gather, self._record_filter, clear=clear,
annotations=annotations)
annotations=self.annotations)

def get_data(self, variables='all', gather=True, clear=False):
"""
Expand Down Expand Up @@ -828,6 +831,7 @@ def __init__(self, parent, selector, label=None):
self.local_cells = self.all_cells[self._mask_local]
self.first_id = numpy.min(self.all_cells) # only works if we assume all_cells is sorted, otherwise could use min()
self.last_id = numpy.max(self.all_cells)
self.annotations = {}
self.recorder = self.parent.recorder
self._record_filter = self.all_cells

Expand Down Expand Up @@ -909,6 +913,9 @@ def index_in_grandparent(self, indices):
else:
return indices_in_parent

def annotate(self, **annotations):
self.annotations.update(annotations)

def describe(self, template='populationview_default.txt', engine='default'):
"""
Returns a human-readable description of the population view.
Expand All @@ -923,6 +930,7 @@ def describe(self, template='populationview_default.txt', engine='default'):
"parent": self.parent.label,
"mask": self.mask,
"size": self.size}
context.update(self.annotations)
return descriptions.render(engine, template, context)


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6 changes: 5 additions & 1 deletion pyNN/common/procedural_api.py
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Expand Up @@ -74,7 +74,11 @@ def record(variables, source, filename, sampling_interval=None, annotations=None
# would actually like to be able to record to an array and choose later
# whether to write to a file.
if not isinstance(source, (BasePopulation, Assembly)):
source = source.parent
if isinstance(source, (IDMixin)):
source = source.as_view()
else:
# not sure when this would be used; retaining earlier code
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@apdavison : do you see any scenario where this would be used? should we remove it?

source = source.parent
source.record(variables, to_file=filename, sampling_interval=sampling_interval)
if annotations:
source.annotate(**annotations)
Expand Down