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Eliminate Python overhead from synapses_create_array and synapses_create_generator templates _resize() and _update_synapse_numbers() methods #1717

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Eliminate Python overhead from synapses_create_array and synapses_create_generator templates _resize() and _update_synapse_numbers() methods #1717

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32 changes: 27 additions & 5 deletions brian2/codegen/runtime/cython_rt/templates/synapses_create_array.pyx
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Original file line number Diff line number Diff line change
@@ -1,31 +1,53 @@
{# USES_VARIABLES { _synaptic_pre, _synaptic_post, sources, targets, N,
N_pre, N_post, _source_offset, _target_offset }
N_incoming, N_outgoing, N_pre, N_post, _source_offset, _target_offset }
#}
{# WRITES_TO_READ_ONLY_VARIABLES { _synaptic_pre, _synaptic_post, N}
{# WRITES_TO_READ_ONLY_VARIABLES { _synaptic_pre, _synaptic_post, N ,N_incoming, N_outgoing }
#}
{% extends 'common_group.pyx' %}

{% block maincode %}
cdef size_t _old_num_synapses = {{N}}
cdef size_t _new_num_synapses = _old_num_synapses + _num{{sources}}

# Resize the main synaptic connection arrays
{{_dynamic__synaptic_pre}}.resize(_new_num_synapses)
{{_dynamic__synaptic_post}}.resize(_new_num_synapses)
# Get the potentially newly created underlying data arrays
cdef int32_t[:] _synaptic_pre_data = {{_dynamic__synaptic_pre}}.data
cdef int32_t[:] _synaptic_post_data = {{_dynamic__synaptic_post}}.data

# Get N_pre and N_post (handles both constants and scalar arrays)
cdef size_t _N_pre = {{constant_or_scalar('N_pre', variables['N_pre'])}}
cdef size_t _N_post = {{constant_or_scalar('N_post', variables['N_post'])}}

# Resize N_incoming and N_outgoing statistics arrays
{{_dynamic_N_incoming}}.resize(_N_post + _target_offset)
{{_dynamic_N_outgoing}}.resize(_N_pre + _source_offset)

# Get raw pointers to statistics arrays
cdef int32_t* _N_incoming_data = {{_dynamic_N_incoming}}.get_data_ptr()
cdef int32_t* _N_outgoing_data = {{_dynamic_N_outgoing}}.get_data_ptr()

for _idx in range(_num{{sources}}):
# After this code has been executed, the arrays _real_sources and
# _real_variables contain the final indices. Having any code here it all is
# only necessary for supporting subgroups
{{ vector_code | autoindent }}
_synaptic_pre_data[_idx + _old_num_synapses] = _real_sources
_synaptic_post_data[_idx + _old_num_synapses] = _real_targets


# Update connection counts
_N_outgoing_data[_real_sources] += 1
_N_incoming_data[_real_targets] += 1

# now we need to resize all registered variables and set the total number
# of synapses (via Python)
_owner._resize(_new_num_synapses)
# of synapses
{% for varname in owner._registered_variables | variables_to_array_names(access_data=False) | sort %}
{{varname}}_ptr.resize(newsize)
{% endfor %}

# Update the total number of synapses
{{N}} = newsize

# And update N_incoming, N_outgoing and synapse_number
_owner._update_synapse_numbers(_old_num_synapses)
Expand Down
15 changes: 14 additions & 1 deletion brian2/synapses/synapses.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1850,11 +1850,12 @@ def _get_multisynaptic_indices(self):
def _add_synapses_from_arrays(self, sources, targets, n, p, namespace=None):
template_kwds, needed_variables = self._get_multisynaptic_indices()

template_kwds["_registered_variables"] = self._registered_variables
variables = Variables(self)

sources = np.atleast_1d(sources).astype(np.int32)
targets = np.atleast_1d(targets).astype(np.int32)

print("here", sources, targets)
# Check whether the values in sources/targets make sense
error_message = (
"The given {source_or_target} indices contain "
Expand Down Expand Up @@ -1920,6 +1921,18 @@ def _add_synapses_from_arrays(self, sources, targets, n, p, namespace=None):
f"'{self.target.name}', using pre-defined arrays)"
)

needed_variables.extend(
[
"N_incoming",
"N_outgoing",
"N",
"N_pre",
"N_post",
"_source_offset",
"_target_offset",
]
)

codeobj = create_runner_codeobj(
self,
abstract_code,
Expand Down