Merge pull request #981 from brian-team/float32_support

Float32 support

.travis.yml

@@ -46,18 +46,24 @@ matrix:
     - python: "2.7"
       env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no CONDA_PY="27" DO_CONDA_BUILD='no' SPLIT_RUN=2 ARCHITECTURE="x86_64"
       os: osx
-#    - python: "2.7"
-#      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no  CONDA_PY="27" DO_CONDA_BUILD='no' SPLIT_RUN=1 ARCHITECTURE="x86"
-#      os: linux
-#    - python: "2.7"
-#      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no  CONDA_PY="27" DO_CONDA_BUILD='yes' SPLIT_RUN=2 ARCHITECTURE="x86"
-#      os: linux
+    - python: "2.7"
+      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no CONDA_PY="27" DO_CONDA_BUILD='yes' SPLIT_RUN=1 ARCHITECTURE="x86_64" FLOAT_DTYPE_32=yes
+      os: osx
+    - python: "2.7"
+      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no CONDA_PY="27" DO_CONDA_BUILD='no' SPLIT_RUN=2 ARCHITECTURE="x86_64" FLOAT_DTYPE_32=yes
+      os: osx
     - python: "2.7"
       env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes REPORT_COVERAGE=no  SPLIT_RUN=1 ARCHITECTURE="x86_64"
       os: linux
     - python: "2.7"
       env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes REPORT_COVERAGE=no  SPLIT_RUN=2 ARCHITECTURE="x86_64"
       os: linux
+    - python: "2.7"
+      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes REPORT_COVERAGE=no  SPLIT_RUN=1 ARCHITECTURE="x86_64" FLOAT_DTYPE_32=yes
+      os: linux
+    - python: "2.7"
+      env: PYTHON="2.7" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=yes REPORT_COVERAGE=no  SPLIT_RUN=2 ARCHITECTURE="x86_64" FLOAT_DTYPE_32=yes
+      os: linux
     - python: "3.5"
       env: PYTHON="3.5" STANDALONE=no CYTHON=yes MINIMAL_VERSIONS=no  REPORT_COVERAGE=no  CONDA_PY="35" DO_CONDA_BUILD='yes' ARCHITECTURE="x86_64"
       os: linux
@@ -77,9 +83,9 @@ matrix:
     - python: "2.7"
       env: PYTHON="2.7" STANDALONE=yes CYTHON=no MINIMAL_VERSIONS=no REPORT_COVERAGE=yes DO_CONDA_BUILD='no' ARCHITECTURE="x86_64"
       os: linux
-#    - python: "2.7"
-#      env: PYTHON="2.7" STANDALONE=yes CYTHON=no MINIMAL_VERSIONS=no REPORT_COVERAGE=no DO_CONDA_BUILD='no' ARCHITECTURE="x86"
-#      os: linux
+    - python: "2.7"
+      env: PYTHON="2.7" STANDALONE=yes CYTHON=no MINIMAL_VERSIONS=no REPORT_COVERAGE=yes DO_CONDA_BUILD='no' ARCHITECTURE="x86_64" FLOAT_DTYPE_32=yes
+      os: linux
     - python: "3.6"
       env: PYTHON="3.6" STANDALONE=yes CYTHON=no MINIMAL_VERSIONS=no REPORT_COVERAGE=no DO_CONDA_BUILD='no' ARCHITECTURE="x86_64"
       os: linux

appveyor.yml

@@ -84,11 +84,35 @@ environment:
       DO_CONDA_BUILD: "FALSE"
       SPLIT_RUN: "2"
 
+    - PYTHON: "C:\\Miniconda-x64"
+      PYTHON_VERSION: "2.7"
+      PYTHON_ARCH: "64"
+      platform: x64
+      STANDALONE: "FALSE"
+      CONDA_PY: "27"
+      DO_CONDA_BUILD: "FALSE"
+      FLOAT_DTYPE_32: "TRUE"
+      SPLIT_RUN: "1"
+
+    - PYTHON: "C:\\Miniconda-x64"
+      PYTHON_VERSION: "2.7"
+      PYTHON_ARCH: "64"
+      platform: x64
+      STANDALONE: "FALSE"
+      DO_CONDA_BUILD: "FALSE"
+      FLOAT_DTYPE_32: "TRUE"
+      SPLIT_RUN: "2"
+    - PYTHON: "C:\\Miniconda-x64"
+      PYTHON_VERSION: "2.7"
+      PYTHON_ARCH: "64"
+      platform: x64
+      STANDALONE: "TRUE"
     - PYTHON: "C:\\Miniconda-x64"
       PYTHON_VERSION: "2.7"
       PYTHON_ARCH: "64"
       platform: x64
       STANDALONE: "TRUE"
+      FLOAT_DTYPE_32: "TRUE"
 
 install:
   # Add the paths

brian2/codegen/generators/GSL_generator.py

@@ -764,7 +764,8 @@ def add_meta_variables(self, options):
             try:
                 N = int(self.variables['N'].get_value())
                 self.owner.variables.add_array('_last_timestep', size=N,
-                                               values=np.ones(N)*options['dt_start'])
+                                               values=np.ones(N)*options['dt_start'],
+                                               dtype=np.float64)
             except KeyError:
                 # has already been run
                 pass
@@ -855,7 +856,7 @@ def translate(self, code, dtype): # TODO: it's not so nice we have to copy the c
         self.function_names = self.find_function_names()
 
         scalar_code, vector_code, kwds = self.generator.translate_statement_sequence(scalar_statements,
-                                                 vector_statements)
+                                                                                     vector_statements)
 
         ############ translate code for GSL
 
@@ -864,7 +865,7 @@ def translate(self, code, dtype): # TODO: it's not so nice we have to copy the c
             for code in code_list:
                 m = re.search('\[(\w+)\]', code)
                 if m is not None:
-                    if m.group(1)!='0' and m.group(1)!='_idx':
+                    if m.group(1) != '0' and m.group(1) != '_idx':
                         from brian2.stateupdaters.base import UnsupportedEquationsException
                         raise UnsupportedEquationsException(("Equations result in state "
                                                              "updater code with indexing "
@@ -880,7 +881,7 @@ def translate(self, code, dtype): # TODO: it's not so nice we have to copy the c
 
         # analyze all needed variables; if not in self.variables: put in separate dic.
         # also keep track of variables needed for scalar statements and vector statements
-        other_variables = self.find_undefined_variables(scalar_statements[None]+\
+        other_variables = self.find_undefined_variables(scalar_statements[None] +
                                                         vector_statements[None])
         variables_in_scalar = self.find_used_variables(scalar_statements[None],
                                                        other_variables)
@@ -1006,7 +1007,7 @@ def __getattr__(self, item):
               'end_struct': '\n};',
               'open_cast': '(',
               'close_cast': ')',
-              'diff_var_declaration': 'const double '}
+              'diff_var_declaration': 'const scalar '}
 
     def c_data_type(self, dtype):
         return self.generator.c_data_type(dtype)
@@ -1016,16 +1017,19 @@ def initialize_array(self, varname, values):
         return 'double const %s[] = {%s};' % (varname, value_list)
 
     def var_replace_diff_var_lhs(self, var, ind):
+        scalar_dtype = self.c_data_type(prefs.core.default_float_dtype)
         f = 'f[{ind}]'.format(ind=ind)
         try:
             if 'unless refractory' in self.variable_flags[var]:
                 return {'_gsl_{var}_f{ind}'.format(var=var,ind=ind) : f,
-                        'double _gsl_{var}_f{ind};'.format(var=var,ind=ind): '',
-                        'double {f};'.format(f=f): ''} # in case the replacement
-                                    # of _gsl_var_find to f[ind] happens first
+                        '{scalar_dtype} _gsl_{var}_f{ind};'.format(var=var, ind=ind,
+                                                                   scalar_dtype=scalar_dtype): '',
+                        '{scalar_dtype} {f};'.format(f=f, scalar_dtype=scalar_dtype): ''} # in case the replacement
+                                                                                          # of _gsl_var_find to f[ind] happens first
         except KeyError:
             pass
-        return {'const double _gsl_{var}_f{ind}'.format(var=var, ind=ind) : f}
+        return {'const {scalar_dtype} _gsl_{var}_f{ind}'.format(scalar_dtype=scalar_dtype,
+                                                                var=var, ind=ind) : f}
 
     def var_init_lhs(self, var, type):
         return type + var

brian2/core/core_preferences.py

@@ -2,7 +2,7 @@
 Definitions, documentation, default values and validation functions for core
 Brian preferences.
 '''
-from numpy import float64, int32
+from numpy import float32, float64, int32
 
 from brian2.core.preferences import BrianPreference, prefs
 
@@ -14,16 +14,14 @@ def dtype_repr(dtype):
 
 
 def default_float_dtype_validator(dtype):
-    return dtype is float64
+    return dtype in [float32, float64]
 
 
 prefs.register_preferences('core', 'Core Brian preferences',
     default_float_dtype=BrianPreference(
         default=float64,
         docs='''
         Default dtype for all arrays of scalars (state variables, weights, etc.).
-
-        Currently, this is not supported (only float64 can be used).
         ''',
         representor=dtype_repr,
         validator=default_float_dtype_validator,

brian2/core/variables.py

@@ -468,7 +468,8 @@ def get_len(self):
         return self.size
 
     def get_addressable_value(self, name, group):
-        return VariableView(name=name, variable=self, group=group, dimensions=None)
+        return VariableView(name=name, variable=self, group=group,
+                            dimensions=None)
 
     def get_addressable_value_with_unit(self, name, group):
         return VariableView(name=name, variable=self, group=group,
@@ -648,7 +649,7 @@ def __init__(self, name, owner, expr, device, dimensions=DIMENSIONLESS,
 
     def get_addressable_value(self, name, group):
         return VariableView(name=name, variable=self, group=group,
-                            dimensions=None)
+                            dimensions=DIMENSIONLESS)
 
     def get_addressable_value_with_unit(self, name, group):
         return VariableView(name=name, variable=self, group=group,
@@ -828,7 +829,7 @@ def get_item(self, item, level=0, namespace=None):
             else:
                 values = self.get_with_index_array(item)
 
-        if self.dim is None:
+        if self.dim is DIMENSIONLESS:
             return values
         else:
             return Quantity(values, self.dim)

brian2/devices/cpp_standalone/templates/objects.cpp

@@ -51,8 +51,7 @@ const int _num_{{name}} = {{N}};
 {% for S in synapses | sort(attribute='name') %}
 // {{S.name}}
 {% for path in S._pathways | sort(attribute='name') %}
-SynapticPathway<double> {{path.name}}(
-		{{dynamic_array_specs[path.variables['delay']]}},
+SynapticPathway {{path.name}}(
 		{{dynamic_array_specs[path.synapse_sources]}},
 		{{path.source.start}}, {{path.source.stop}});
 {% endfor %}
@@ -305,7 +304,7 @@ extern const int _num_{{name}};
 {% for S in synapses | sort(attribute='name') %}
 // {{S.name}}
 {% for path in S._pathways | sort(attribute='name') %}
-extern SynapticPathway<double> {{path.name}};
+extern SynapticPathway {{path.name}};
 {% endfor %}
 {% endfor %}
 

brian2/devices/cpp_standalone/templates/synapses_classes.cpp

@@ -12,25 +12,20 @@
 
 #include "brianlib/spikequeue.h"
 
-template<class scalar> class SynapticPathway;
-
-template <class scalar>
 class SynapticPathway
 {
 public:
 	int Nsource, Ntarget, _nb_threads;
-	std::vector<scalar> &delay;
 	std::vector<int> &sources;
 	std::vector<int> all_peek;
-	std::vector< CSpikeQueue<scalar> * > queue;
-	SynapticPathway(std::vector<scalar>& _delay, std::vector<int> &_sources,
-					int _spikes_start, int _spikes_stop)
-		: delay(_delay), sources(_sources)
+	std::vector< CSpikeQueue * > queue;
+	SynapticPathway(std::vector<int> &_sources, int _spikes_start, int _spikes_stop)
+		: sources(_sources)
 	{
 	   _nb_threads = {{ openmp_pragma('get_num_threads') }};
 
 	   for (int _idx=0; _idx < _nb_threads; _idx++)
-	       queue.push_back(new CSpikeQueue<scalar>(_spikes_start, _spikes_stop));
+	       queue.push_back(new CSpikeQueue(_spikes_start, _spikes_stop));
     };
 
 	~SynapticPathway()
@@ -65,7 +60,7 @@ class SynapticPathway
     	return &all_peek;
     }
 
-    void prepare(int n_source, int n_target, scalar *real_delays, int n_delays,
+    template <typename scalar> void prepare(int n_source, int n_target, scalar *real_delays, int n_delays,
                  int *sources, int n_synapses, double _dt)
     {
         Nsource = n_source;
@@ -86,7 +81,7 @@ class SynapticPathway
     		else if (n_delays == 1)
     		    queue[{{ openmp_pragma('get_thread_num') }}]->prepare(&real_delays[0], 1, &sources[padding], length, _dt);
     		else  // no synapses
-    		    queue[{{ openmp_pragma('get_thread_num') }}]->prepare(NULL, 0, &sources[padding], length, _dt);
+    		    queue[{{ openmp_pragma('get_thread_num') }}]->prepare((scalar *)NULL, 0, &sources[padding], length, _dt);
     	}
     }
 

brian2/devices/cpp_standalone/templates/synapses_initialise_queue.cpp

@@ -4,15 +4,16 @@
 {% set pathobj = owner.name %}
 void _run_{{codeobj_name}}() {
 	using namespace brian;
-	{{pointers_lines|autoindent}}
-
-    double* real_delays = {{pathobj}}.delay.empty() ? 0 : &({{pathobj}}.delay[0]);
+    {{pointers_lines|autoindent}}
+    {% set scalar = c_data_type(owner.variables['delay'].dtype) %}
+    std::vector<{{scalar}}> &real_delays = {{get_array_name(owner.variables['delay'], access_data=False)}};
+    {{scalar}}* real_delays_data = real_delays.empty() ? 0 : &(real_delays[0]);
     int32_t* sources = {{pathobj}}.sources.empty() ? 0 : &({{pathobj}}.sources[0]);
-    const unsigned int n_delays = {{pathobj}}.delay.size();
+    const unsigned int n_delays = real_delays.size();
     const unsigned int n_synapses = {{pathobj}}.sources.size();
     {{pathobj}}.prepare({{constant_or_scalar('_n_sources', variables['_n_sources'])}},
                         {{constant_or_scalar('_n_targets', variables['_n_targets'])}},
-                        real_delays, n_delays, sources,
+                        real_delays_data, n_delays, sources,
                         n_synapses,
                         {{_source_dt}});
 }
@@ -22,6 +23,8 @@ void _run_{{codeobj_name}}() {
 #ifndef _INCLUDED_{{codeobj_name}}
 #define _INCLUDED_{{codeobj_name}}
 
+#include "objects.h"
+
 void _run_{{codeobj_name}}();
 
 #endif

brian2/groups/neurongroup.py

@@ -1,6 +1,7 @@
 '''
 This model defines the `NeuronGroup`, the core of most simulations.
 '''
+import collections
 import string
 
 import numpy as np
@@ -399,6 +400,10 @@ def __init__(self, N, model,
                  codeobj_class=None):
         Group.__init__(self, dt=dt, clock=clock, when='start', order=order,
                        name=name)
+        if dtype is None:
+            dtype = {}
+        if isinstance(dtype, collections.MutableMapping):
+            dtype['lastspike'] = self._clock.variables['t'].dtype
 
         self.codeobj_class = codeobj_class
 

brian2/input/spikegeneratorgroup.py

@@ -99,7 +99,8 @@ def __init__(self, N, indices, times, dt=None, clock=None,
         # standard variables
         self.variables.add_constant('N', value=N)
         self.variables.add_array('period', dimensions=second.dim, size=1,
-                                 constant=True, read_only=True, scalar=True)
+                                 constant=True, read_only=True, scalar=True,
+                                 dtype=self._clock.variables['t'].dtype)
         self.variables.add_arange('i', N)
         self.variables.add_dynamic_array('spike_number',
                                          values=np.arange(len(indices)),
@@ -113,7 +114,8 @@ def __init__(self, N, indices, times, dt=None, clock=None,
                                          read_only=True, constant=True)
         self.variables.add_dynamic_array('spike_time', values=times, size=len(times),
                                          dimensions=second.dim, index='spike_number',
-                                         read_only=True, constant=True)
+                                         read_only=True, constant=True,
+                                         dtype=self._clock.variables['t'].dtype)
         self.variables.add_array('_spikespace', size=N+1, dtype=np.int32)
         self.variables.add_array('_lastindex', size=1, values=0, dtype=np.int32,
                                  read_only=True, scalar=True)

brian2/monitors/ratemonitor.py

@@ -26,7 +26,9 @@ class PopulationRateMonitor(Group, CodeRunner):
         ``source.name+'_ratemonitor_0'``, etc.
     codeobj_class : class, optional
         The `CodeObject` class to run code with.
-
+    dtype : dtype, optional
+        The dtype to use to store the ``rate`` variable. Defaults to
+        `~numpy.float64`, i.e. double precision.
     Notes
     -----
     Currently, this monitor can only monitor the instantaneous firing rates at
@@ -35,8 +37,8 @@ class PopulationRateMonitor(Group, CodeRunner):
     '''
     invalidates_magic_network = False
     add_to_magic_network = True
-    def __init__(self, source, name='ratemonitor*',
-                 codeobj_class=None):
+    def __init__(self, source, name='ratemonitor*', codeobj_class=None,
+                 dtype=np.float64):
 
         #: The group we are recording from
         self.source = source
@@ -55,9 +57,10 @@ def __init__(self, source, name='ratemonitor*',
         self.variables.add_constant('_source_stop', stop)
         self.variables.add_reference('_spikespace', source)
         self.variables.add_dynamic_array('rate', size=0, dimensions=hertz.dim,
-                                         read_only=True)
+                                         read_only=True, dtype=dtype)
         self.variables.add_dynamic_array('t', size=0, dimensions=second.dim,
-                                         read_only=True)
+                                         read_only=True,
+                                         dtype=self._clock.variables['t'].dtype)
         self.variables.add_reference('_num_source_neurons', source, 'N')
         self.variables.add_array('N', dtype=np.int32, size=1,
                                  scalar=True, read_only=True)