Merge remote-tracking branch 'origin/no_more_spikes' into codegen_imp…

…rovement

brian2/codegen/runtime/numpy_rt/templates/group_variable_set.py_

@@ -0,0 +1,6 @@
+# USES_VARIABLES { _group_idx }
+_idx = _group_idx
+_vectorisation_idx = _idx
+{% for line in code_lines %}
+{{line}}
+{% endfor %}

brian2/codegen/runtime/numpy_rt/templates/ratemonitor.py_

@@ -1,5 +1,5 @@
-# { USES_VARIABLES _rate, _t, _spikes, _num_source_neurons, t, dt }
-
+# { USES_VARIABLES _rate, _t, _spikespace, _num_source_neurons, t, dt }
+_spikes = _spikespace[:_spikespace[-1]]
 _new_len = len(_t) + 1
 _t.resize(_new_len)
 _rate.resize(_new_len)

brian2/codegen/runtime/numpy_rt/templates/reset.py_

@@ -1,5 +1,5 @@
-# USES_VARIABLES { _spikes }
-_idx = _spikes
+# USES_VARIABLES { _spikespace }
+_idx = _spikespace[:_spikespace[-1]]
 _vectorisation_idx = _idx
 {% for line in code_lines %}
 {{line}}

brian2/codegen/runtime/numpy_rt/templates/spikemonitor.py_

@@ -1,7 +1,7 @@
-# { USES_VARIABLES _i, _t, _spikes, _count, t, _source_start, _source_end}
+# { USES_VARIABLES _i, _t, _spikespace, _count, t, _source_start, _source_end}
 import numpy as np
+_spikes = _spikespace[:_spikespace[-1]]
 # Take subgroups into account
-_spikes = np.asarray(_spikes)
 _spikes = _spikes[(_spikes >= _source_start) & (_spikes < _source_end)]
 _spikes -= _source_start
 _n_spikes = len(_spikes)

brian2/codegen/runtime/weave_rt/templates/group_variable_set.cpp

@@ -0,0 +1,40 @@
+////////////////////////////////////////////////////////////////////////////
+//// MAIN CODE /////////////////////////////////////////////////////////////
+
+{% macro main() %}
+	// USES_VARIABLES { _group_idx }
+
+	////// HANDLE DENORMALS ///
+	{% for line in denormals_code_lines %}
+	{{line}}
+	{% endfor %}
+
+	////// HASH DEFINES ///////
+	{% for line in hashdefine_lines %}
+	{{line}}
+	{% endfor %}
+
+	///// POINTERS ////////////
+	{% for line in pointers_lines %}
+	{{line}}
+	{% endfor %}
+
+	//// MAIN CODE ////////////
+	for(int _idx_group_idx=0; _idx_group_idx<_num_group_idx; _idx_group_idx++)
+	{
+		const int _idx = _group_idx[_idx_group_idx];
+		const int _vectorisation_idx = _idx;
+		{% for line in code_lines %}
+		{{line}}
+		{% endfor %}
+	}
+{% endmacro %}
+
+////////////////////////////////////////////////////////////////////////////
+//// SUPPORT CODE //////////////////////////////////////////////////////////
+
+{% macro support_code() %}
+	{% for line in support_code_lines %}
+	{{line}}
+	{% endfor %}
+{% endmacro %}

brian2/codegen/runtime/weave_rt/templates/ratemonitor.cpp

@@ -1,6 +1,7 @@
 {% macro main() %}
 
-    // USES_VARIABLES { _t, _rate, t, dt, _spikes }
+    // USES_VARIABLES { _t, _rate, t, dt, _spikespace }
+	const int _num_spikes = _spikespace[_num_spikespace-1];
 
     // Calculate the new length for the arrays
     const npy_int _new_len = (npy_int)(_t.attr("shape")[0]) + 1;

brian2/codegen/runtime/weave_rt/templates/reset.cpp

@@ -2,7 +2,7 @@
 //// MAIN CODE /////////////////////////////////////////////////////////////
 
 {% macro main() %}
-	// USES_VARIABLES { _spikes }
+	// USES_VARIABLES { _spikespace }
 
 	////// HANDLE DENORMALS ///
 	{% for line in denormals_code_lines %}
@@ -20,9 +20,10 @@
 	{% endfor %}
 
 	//// MAIN CODE ////////////
+	const int _num_spikes = _spikespace[_num_spikespace-1];
 	for(int _index_spikes=0; _index_spikes<_num_spikes; _index_spikes++)
 	{
-		const int _idx = _spikes[_index_spikes];
+		const int _idx = _spikespace[_index_spikes];
 		const int _vectorisation_idx = _idx;
 		{% for line in code_lines %}
 		{{line}}

brian2/codegen/runtime/weave_rt/templates/spikemonitor.cpp

@@ -1,8 +1,8 @@
 {% macro main() %}
 
-    // USES_VARIABLES { _t, _i, t, _spikes, _count,
+    // USES_VARIABLES { _t, _i, t, _spikespace, _count,
     //                  _source_start, _source_end}
-
+	int _num_spikes = _spikespace[_num_spikespace-1];
     if (_num_spikes > 0)
     {
         // For subgroups, we do not want to record all spikes
@@ -12,15 +12,15 @@
         int _end_idx = - 1;
         for(int _i=0; _i<_num_spikes; _i++)
         {
-            const int _idx = _spikes[_i];
+            const int _idx = _spikespace[_i];
             if (_idx >= _source_start) {
                 _start_idx = _i;
                 break;
             }
         }
         for(int _i=_start_idx; _i<_num_spikes; _i++)
         {
-            const int _idx = _spikes[_i];
+            const int _idx = _spikespace[_i];
             if (_idx >= _source_end) {
                 _end_idx = _i;
                 break;
@@ -45,7 +45,7 @@
             // Copy the values across
             for(int _i=_start_idx; _i<_end_idx; _i++)
             {
-                const int _idx = _spikes[_i];
+                const int _idx = _spikespace[_i];
                 _t_data[_curlen + _i - _start_idx] = t;
                 _i_data[_curlen + _i - _start_idx] = _idx - _source_start;
                 _count[_idx - _source_start]++;

brian2/groups/group.py

@@ -203,15 +203,15 @@ def _set_with_code(self, variable, group_indices, code,
         # TODO: Find a name that makes sense for reset and variable setting
         # with code
         additional_variables = self.item_mapping.variables
-        additional_variables['_spikes'] = ArrayVariable('_spikes',
-                                                         Unit(1),
-                                                         value=group_indices.astype(np.int32),
-                                                         group_name=self.name)
+        additional_variables['_group_idx'] = ArrayVariable('_group_idx',
+                                                     Unit(1),
+                                                     value=group_indices.astype(np.int32),
+                                                     group_name=self.name)
         # TODO: Have an additional argument to avoid going through the index
         # array for situations where iterate_all could be used
         codeobj = create_runner_codeobj(self,
                                  abstract_code,
-                                 'reset',
+                                 'group_variable_set',
                                  additional_variables=additional_variables,
                                  additional_namespace=additional_namespace,
                                  check_units=check_units)

brian2/groups/neurongroup.py

@@ -390,8 +390,6 @@ def _create_variables(self):
         s.update({'_spikespace': ArrayVariable('_spikespace', Unit(1),
                                                self._spikespace,
                                                group_name=self.name)})
-        s.update({'_spikes': AttributeVariable(Unit(1), self,
-                                               'spikes', constant=False)})
 
         for eq in self.equations.itervalues():
             if eq.type in (DIFFERENTIAL_EQUATION, PARAMETER):

brian2/monitors/ratemonitor.py

@@ -53,8 +53,7 @@ def __init__(self, source, when=None, name='ratemonitor*',
         self.variables = {'t': AttributeVariable(second, self.clock, 't'),
                            'dt': AttributeVariable(second, self.clock,
                                                    'dt', constant=True),
-                           '_spikes': AttributeVariable(Unit(1),
-                                                        self.source, 'spikes'),
+                          '_spikespace': self.source.variables['_spikespace'],
                            # The template needs to have access to the
                            # DynamicArray here, having access to the underlying
                            # array is not enough since we want to do the resize

brian2/monitors/spikemonitor.py

@@ -58,8 +58,7 @@ def __init__(self, source, record=True, when=None, name='spikemonitor*',
         end = getattr(self.source, 'end', len(self.source))
 
         self.variables = {'t': AttributeVariable(second, self.clock, 't'),
-                           '_spikes': AttributeVariable(Unit(1), self.source,
-                                                        'spikes'),
+                          '_spikespace': self.source.variables['_spikespace'],
                            # The template needs to have access to the
                            # DynamicArray here, having access to the underlying
                            # array is not enough since we want to do the resize