[med-svn] [cnrun] 11/25: ban 'using namespace' in header files; namespace s/CNRun/cnrun/
andrei zavada
hmmr-guest at moszumanska.debian.org
Thu Nov 6 22:08:30 UTC 2014
This is an automated email from the git hooks/post-receive script.
hmmr-guest pushed a commit to branch WIP
in repository cnrun.
commit 04e35dff066189a049a911c171e3b43f433fc134
Author: Andrei Zavada <johnhommer at gmail.com>
Date: Tue Apr 1 01:04:46 2014 +0300
ban 'using namespace' in header files; namespace s/CNRun/cnrun/
global variables? in C++??
---
upstream/src/libcn/base-neuron.hh | 3 +-
upstream/src/libcn/base-synapse.hh | 4 +-
upstream/src/libcn/base-unit.cc | 62 +++++++++----------
upstream/src/libcn/base-unit.hh | 4 +-
upstream/src/libcn/hosted-attr.hh | 2 +-
upstream/src/libcn/hosted-neurons.cc | 82 ++++++++++++-------------
upstream/src/libcn/hosted-neurons.hh | 2 +-
upstream/src/libcn/hosted-synapses.cc | 56 ++++++++---------
upstream/src/libcn/hosted-synapses.hh | 2 +-
upstream/src/libcn/integrate-base.hh | 2 +-
upstream/src/libcn/integrate-rk65.hh | 2 +-
upstream/src/libcn/model-cycle.cc | 18 +++---
upstream/src/libcn/model-nmlio.cc | 14 ++---
upstream/src/libcn/model-struct.cc | 98 ++++++++++++++----------------
upstream/src/libcn/model.hh | 2 +-
upstream/src/libcn/mx-attr.hh | 2 +-
upstream/src/libcn/sources.cc | 14 ++---
upstream/src/libcn/sources.hh | 2 +-
upstream/src/libcn/standalone-attr.hh | 2 +-
upstream/src/libcn/standalone-neurons.cc | 82 ++++++++++++-------------
upstream/src/libcn/standalone-neurons.hh | 2 +-
upstream/src/libcn/standalone-synapses.cc | 12 ++--
upstream/src/libcn/standalone-synapses.hh | 2 +-
upstream/src/libcn/types.cc | 12 ++--
upstream/src/libcn/types.hh | 2 +-
upstream/src/tools/hh-latency-estimator.cc | 2 +
26 files changed, 239 insertions(+), 248 deletions(-)
diff --git a/upstream/src/libcn/base-neuron.hh b/upstream/src/libcn/base-neuron.hh
index d35cdfe..47a6ee0 100644
--- a/upstream/src/libcn/base-neuron.hh
+++ b/upstream/src/libcn/base-neuron.hh
@@ -28,9 +28,8 @@
using namespace std;
-using namespace CNRun;
-namespace CNRun {
+namespace cnrun {
#define CN_MIN_DISTANCE .1
diff --git a/upstream/src/libcn/base-synapse.hh b/upstream/src/libcn/base-synapse.hh
index ae5ce71..286b5b1 100644
--- a/upstream/src/libcn/base-synapse.hh
+++ b/upstream/src/libcn/base-synapse.hh
@@ -27,11 +27,9 @@
using namespace std;
-using namespace CNRun;
-
-namespace CNRun {
+namespace cnrun {
class C_BaseSynapse;
class C_BaseNeuron;
diff --git a/upstream/src/libcn/base-unit.cc b/upstream/src/libcn/base-unit.cc
index 82c9394..56ec66d 100644
--- a/upstream/src/libcn/base-unit.cc
+++ b/upstream/src/libcn/base-unit.cc
@@ -29,17 +29,17 @@ using namespace std;
-double CNRun::__cn_dummy_double;
+double cnrun::__cn_dummy_double;
-unsigned short CNRun::__cn_default_unit_precision = 8;
+unsigned short cnrun::__cn_default_unit_precision = 8;
-int CNRun::__cn_verbosely = 2;
+int cnrun::__cn_verbosely = 2;
// mind that child
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
C_BaseUnit( TUnitType intype, const char *inlabel,
CModel* inM, int s_mask)
: _type (intype), _status (0 |/* CN_UENABLED |*/ s_mask),
@@ -64,7 +64,7 @@ C_BaseUnit( TUnitType intype, const char *inlabel,
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
reset_state()
{
if ( M && M->verbosely > 3 )
@@ -76,7 +76,7 @@ reset_state()
int
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
param_idx_by_sym( const char *sym) const
{
for ( int i = 0; i < p_no(); ++i )
@@ -86,7 +86,7 @@ param_idx_by_sym( const char *sym) const
}
int
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
var_idx_by_sym( const char *sym) const
{
for ( unsigned short i = 0; i < v_no(); ++i )
@@ -103,7 +103,7 @@ var_idx_by_sym( const char *sym) const
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
start_listening( int mask)
{
if ( !M ) {
@@ -159,7 +159,7 @@ start_listening( int mask)
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
stop_listening()
{
// do deferred write
@@ -210,7 +210,7 @@ stop_listening()
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
tell()
{
if ( _binwrite_handle != -1 && !(_status & CN_ULISTENING_DEFERWRITE) ) {
@@ -247,7 +247,7 @@ tell()
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
dump( bool with_params, FILE *strm) const
{
fprintf( strm, "[%lu] (%s) \"%s\"\n", _serial_id, species(), _label);
@@ -290,7 +290,7 @@ dump( bool with_params, FILE *strm) const
// source interface
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
detach_source( C_BaseSource *s, TSinkType sink_type, unsigned short idx)
{
list <SSourceInterface <C_BaseSource> >::iterator K;
@@ -302,7 +302,7 @@ detach_source( C_BaseSource *s, TSinkType sink_type, unsigned short idx)
void
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
apprise_from_sources()
{
for ( auto &S : sources )
@@ -318,7 +318,7 @@ apprise_from_sources()
}
}
-CNRun::C_BaseUnit::
+cnrun::C_BaseUnit::
~C_BaseUnit()
{
if ( M && M->verbosely > 5 )
@@ -345,7 +345,7 @@ CNRun::C_BaseUnit::
bool
-CNRun::C_BaseNeuron::
+cnrun::C_BaseNeuron::
connects_to( const C_BaseNeuron &to) const
{
for ( auto &A : _axonal_harbour )
@@ -354,8 +354,8 @@ connects_to( const C_BaseNeuron &to) const
return false;
}
-C_BaseSynapse*
-CNRun::C_BaseNeuron::
+cnrun::C_BaseSynapse*
+cnrun::C_BaseNeuron::
connects_via( C_BaseNeuron &to,
SCleft::mapped_type *g_ptr) const
{
@@ -374,7 +374,7 @@ connects_via( C_BaseNeuron &to,
void
-CNRun::C_BaseNeuron::
+cnrun::C_BaseNeuron::
dump( bool with_params, FILE *strm) const
{
C_BaseUnit::dump( with_params);
@@ -391,7 +391,7 @@ dump( bool with_params, FILE *strm) const
-CNRun::C_BaseNeuron::
+cnrun::C_BaseNeuron::
~C_BaseNeuron()
{
if ( M && M->verbosely > 4 )
@@ -422,7 +422,7 @@ CNRun::C_BaseNeuron::
// --- SSpikeloggerService
double
-CNRun::SSpikeloggerService::
+cnrun::SSpikeloggerService::
sdf( double at, double sample_width, double sigma, unsigned *nspikes) const
{
if ( nspikes )
@@ -446,7 +446,7 @@ sdf( double at, double sample_width, double sigma, unsigned *nspikes) const
double
-CNRun::SSpikeloggerService::
+cnrun::SSpikeloggerService::
shf( double at, double sample_width) const
{
double dt,
@@ -476,7 +476,7 @@ shf( double at, double sample_width) const
size_t
-CNRun::SSpikeloggerService::
+cnrun::SSpikeloggerService::
get_sxf_vector_custom( vector<double> *sdf_buffer, vector<double> *shf_buffer,
vector<unsigned> *nspikes_buffer,
double sample_period_custom, double sigma_custom,
@@ -507,7 +507,7 @@ get_sxf_vector_custom( vector<double> *sdf_buffer, vector<double> *shf_buffer,
void
-CNRun::SSpikeloggerService::
+cnrun::SSpikeloggerService::
sync_history()
{
if ( !_client->M || (_client->M && _client->M->_status & CN_MDL_DISKLESS) )
@@ -544,7 +544,7 @@ sync_history()
size_t
-CNRun::SSpikeloggerService::
+cnrun::SSpikeloggerService::
n_spikes_since( double since) const
{
size_t i = 0;
@@ -561,7 +561,7 @@ n_spikes_since( double since) const
// ----- CSynapse
-CNRun::C_BaseSynapse::
+cnrun::C_BaseSynapse::
C_BaseSynapse( TUnitType intype,
C_BaseNeuron *insource, C_BaseNeuron *intarget,
double ing, CModel *inM, int s_mask)
@@ -582,8 +582,8 @@ C_BaseSynapse( TUnitType intype,
-CNRun::C_BaseSynapse*
-CNRun::C_BaseSynapse::
+cnrun::C_BaseSynapse*
+cnrun::C_BaseSynapse::
clone_to_target( C_BaseNeuron *tgt, double g)
{
// check if we have no existing connection already to tgt
@@ -604,8 +604,8 @@ clone_to_target( C_BaseNeuron *tgt, double g)
-CNRun::C_BaseSynapse*
-CNRun::C_BaseSynapse::
+cnrun::C_BaseSynapse*
+cnrun::C_BaseSynapse::
make_clone_independent( C_BaseNeuron *tgt)
{
double g = g_on_target( *tgt);
@@ -643,7 +643,7 @@ make_clone_independent( C_BaseNeuron *tgt)
void
-CNRun::C_BaseSynapse::
+cnrun::C_BaseSynapse::
dump( bool with_params, FILE *strm) const
{
C_BaseUnit::dump( with_params);
@@ -657,7 +657,7 @@ dump( bool with_params, FILE *strm) const
-CNRun::C_BaseSynapse::
+cnrun::C_BaseSynapse::
~C_BaseSynapse()
{
if ( M && M->verbosely > 4 )
diff --git a/upstream/src/libcn/base-unit.hh b/upstream/src/libcn/base-unit.hh
index 4a44aea..ef8fb72 100644
--- a/upstream/src/libcn/base-unit.hh
+++ b/upstream/src/libcn/base-unit.hh
@@ -26,8 +26,8 @@
using namespace std;
-using namespace CNRun;
-namespace CNRun {
+
+namespace cnrun {
// this gets referenced in case of out-of-bounds idx or misspelled sym
// in param accessors
diff --git a/upstream/src/libcn/hosted-attr.hh b/upstream/src/libcn/hosted-attr.hh
index fc8fc7a..d971578 100644
--- a/upstream/src/libcn/hosted-attr.hh
+++ b/upstream/src/libcn/hosted-attr.hh
@@ -21,7 +21,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
class C_HostedAttributes {
diff --git a/upstream/src/libcn/hosted-neurons.cc b/upstream/src/libcn/hosted-neurons.cc
index ac5445b..2a036e0 100644
--- a/upstream/src/libcn/hosted-neurons.cc
+++ b/upstream/src/libcn/hosted-neurons.cc
@@ -23,7 +23,7 @@
#endif
-CNRun::C_HostedNeuron::
+cnrun::C_HostedNeuron::
C_HostedNeuron( TUnitType intype, const char *inlabel,
double inx, double iny, double inz,
CModel* inM, int s_mask,
@@ -51,7 +51,7 @@ C_HostedNeuron( TUnitType intype, const char *inlabel,
void
-CNRun::C_HostedConductanceBasedNeuron::
+cnrun::C_HostedConductanceBasedNeuron::
do_detect_spike_or_whatever()
{
if ( unlikely (E() >= M->spike_threshold) ) {
@@ -79,7 +79,7 @@ do_detect_spike_or_whatever()
// ===== HH and variations
-const char* const CNRun::__CN_ParamNames_NeuronHH_d[] = {
+const char* const cnrun::__CN_ParamNames_NeuronHH_d[] = {
"Na conductance, " __CN_PU_CONDUCTANCE,
"Na equi potential, " __CN_PU_POTENTIAL,
"K conductance, " __CN_PU_CONDUCTANCE,
@@ -94,7 +94,7 @@ const char* const CNRun::__CN_ParamNames_NeuronHH_d[] = {
"Externally applied DC, " __CN_PU_CURRENT,
};
-const char* const CNRun::__CN_ParamSyms_NeuronHH_d[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronHH_d[] = {
"gNa",
"ENa",
"gK",
@@ -109,7 +109,7 @@ const char* const CNRun::__CN_ParamSyms_NeuronHH_d[] = {
"Idc",
};
-const double CNRun::__CN_Params_NeuronHH_d[] = {
+const double cnrun::__CN_Params_NeuronHH_d[] = {
7.15, // gNa: Na conductance in 1/(mOhms * cm^2)
50.0, // ENa: Na equi potential in mV
1.430, // gK: K conductance in 1/(mOhms * cm^2)
@@ -131,20 +131,20 @@ const double CNRun::__CN_Params_NeuronHH_d[] = {
-const double CNRun::__CN_Vars_NeuronHH_d[] = {
+const double cnrun::__CN_Vars_NeuronHH_d[] = {
-66.81, // 0 - membrane potential E
0.023, // 1 - prob. for Na channel activation m
0.800, // 2 - prob. for not Na channel blocking h
0.220, // 3 - prob. for K channel activation n
};
-const char* const CNRun::__CN_VarNames_NeuronHH_d[] = {
+const char* const cnrun::__CN_VarNames_NeuronHH_d[] = {
"Membrane potential, " __CN_PU_POTENTIAL,
"Prob. of Na channel activation",
"1-Prob. of Na channel blocking",
"Prob. of K channel activation",
};
-const char* const CNRun::__CN_VarSyms_NeuronHH_d[] = {
+const char* const cnrun::__CN_VarSyms_NeuronHH_d[] = {
"E",
".m",
".h",
@@ -155,7 +155,7 @@ const char* const CNRun::__CN_VarSyms_NeuronHH_d[] = {
void
__attribute__ ((hot))
-CNRun::CNeuronHH_d::
+cnrun::CNeuronHH_d::
derivative( vector<double>& x, vector<double>& dx)
{
// differential eqn for E, the membrane potential
@@ -235,7 +235,7 @@ derivative( vector<double>& x, vector<double>& dx)
-const char* const CNRun::__CN_ParamNames_NeuronHH2_d[] = {
+const char* const cnrun::__CN_ParamNames_NeuronHH2_d[] = {
"Na conductance, " __CN_PU_CONDUCTANCE,
"Na equi potential, " __CN_PU_POTENTIAL,
"K conductance, " __CN_PU_CONDUCTANCE,
@@ -254,7 +254,7 @@ const char* const CNRun::__CN_ParamNames_NeuronHH2_d[] = {
"Externally applied DC, " __CN_PU_CURRENT,
};
-const char* const CNRun::__CN_ParamSyms_NeuronHH2_d[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronHH2_d[] = {
"gNa",
"ENa",
"gK",
@@ -273,7 +273,7 @@ const char* const CNRun::__CN_ParamSyms_NeuronHH2_d[] = {
"Idc",
};
-const double CNRun::__CN_Params_NeuronHH2_d[] = {
+const double cnrun::__CN_Params_NeuronHH2_d[] = {
7.15, // gNa: Na conductance in 1/(mOhms * cm^2)
50.0, // ENa: Na equi potential in mV
1.43, // gK: K conductance in 1/(mOhms * cm^2)
@@ -297,7 +297,7 @@ const double CNRun::__CN_Params_NeuronHH2_d[] = {
};
-const double CNRun::__CN_Vars_NeuronHH2_d[] = {
+const double cnrun::__CN_Vars_NeuronHH2_d[] = {
// as in a single-neuron run
-66.56, // 0 - membrane potential E
0.0217, // 1 - prob. for Na channel activation m
@@ -316,7 +316,7 @@ const double CNRun::__CN_Vars_NeuronHH2_d[] = {
void
-CNRun::CNeuronHH2_d::
+cnrun::CNeuronHH2_d::
derivative( vector<double>& x, vector<double>& dx)
{
enum TParametersNeuronHH2 {
@@ -381,7 +381,7 @@ derivative( vector<double>& x, vector<double>& dx)
//#ifdef CN_WANT_MORE_NEURONS
-const char* const CNRun::__CN_ParamNames_NeuronEC_d[] = {
+const char* const cnrun::__CN_ParamNames_NeuronEC_d[] = {
"Na conductance, " __CN_PU_CONDUCTANCE,
"Na equi potential, " __CN_PU_POTENTIAL,
"K conductance, " __CN_PU_CONDUCTANCE,
@@ -397,7 +397,7 @@ const char* const CNRun::__CN_ParamNames_NeuronEC_d[] = {
"gh2",
"Vh, " __CN_PU_POTENTIAL
};
-const char* const CNRun::__CN_ParamSyms_NeuronEC_d[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronEC_d[] = {
"gNa",
"ENa",
"gK",
@@ -413,7 +413,7 @@ const char* const CNRun::__CN_ParamSyms_NeuronEC_d[] = {
"gh2",
"Vh"
};
-const double CNRun::__CN_Params_NeuronEC_d[] = {
+const double cnrun::__CN_Params_NeuronEC_d[] = {
7.15, // 0 - gNa: Na conductance in 1/(mOhms * cm^2)
50.0, // 1 - ENa: Na equi potential in mV
1.43, // 2 - gK: K conductance in 1/(mOhms * cm^2)
@@ -430,7 +430,7 @@ const double CNRun::__CN_Params_NeuronEC_d[] = {
-20.0, // 13 - Vh
};
-const char* const CNRun::__CN_VarNames_NeuronEC_d[] = {
+const char* const cnrun::__CN_VarNames_NeuronEC_d[] = {
"Membrane potential",
"Prob. of Na channel activation",
"Prob. of not Na channel blocking",
@@ -438,7 +438,7 @@ const char* const CNRun::__CN_VarNames_NeuronEC_d[] = {
"Ih1 activation",
"Ih2 activation"
};
-const char* const CNRun::__CN_VarSyms_NeuronEC_d[] = {
+const char* const cnrun::__CN_VarSyms_NeuronEC_d[] = {
"E",
".m",
".h",
@@ -446,7 +446,7 @@ const char* const CNRun::__CN_VarSyms_NeuronEC_d[] = {
".Ih1",
".Ih2"
};
-const double CNRun::__CN_Vars_NeuronEC_d[] = {
+const double cnrun::__CN_Vars_NeuronEC_d[] = {
-64.1251, // 0 - membrane potential E
0.0176331, // 1 - prob. for Na channel activation m
0.994931, // 2 - prob. for not Na channel blocking h
@@ -461,7 +461,7 @@ const double CNRun::__CN_Vars_NeuronEC_d[] = {
#define _xfunc(a,b,k,V) ((a) * (V) + (b)) / (1.0 - exp(((V)+(b)/(a))/(k)))
void
-CNRun::CNeuronEC_d::
+cnrun::CNeuronEC_d::
derivative( vector<double>& x, vector<double>& dx)
{
enum TParametersNeuronEC {
@@ -517,7 +517,7 @@ derivative( vector<double>& x, vector<double>& dx)
-const char* const CNRun::__CN_ParamNames_NeuronECA_d[] = {
+const char* const cnrun::__CN_ParamNames_NeuronECA_d[] = {
"Na conductance, " __CN_PU_CONDUCTANCE,
"Na equi potential, " __CN_PU_POTENTIAL,
"K conductance, " __CN_PU_CONDUCTANCE,
@@ -530,7 +530,7 @@ const char* const CNRun::__CN_ParamNames_NeuronECA_d[] = {
"gh",
"Vh",
};
-const char* const CNRun::__CN_ParamSyms_NeuronECA_d[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronECA_d[] = {
"gNa",
"ENa",
"gK",
@@ -543,7 +543,7 @@ const char* const CNRun::__CN_ParamSyms_NeuronECA_d[] = {
"gh",
"Vh",
};
-const double CNRun::__CN_Params_NeuronECA_d[] = {
+const double cnrun::__CN_Params_NeuronECA_d[] = {
52.0, // 0 - Na conductance in 1/(mOhms * cm^2)
55.0, // 1 - Na equi potential in mV
11.0, // 2 - K conductance in 1/(mOhms * cm^2)
@@ -557,7 +557,7 @@ const double CNRun::__CN_Params_NeuronECA_d[] = {
-20.0, // 10 - Vh
};
-const char* const CNRun::__CN_VarNames_NeuronECA_d[] = {
+const char* const cnrun::__CN_VarNames_NeuronECA_d[] = {
"Membrane potential",
"Prob. of Na channel activation",
"Prob. of Na channel blocking",
@@ -566,7 +566,7 @@ const char* const CNRun::__CN_VarNames_NeuronECA_d[] = {
"Ih1 activation",
"Ih2 activation"
};
-const char* const CNRun::__CN_VarSyms_NeuronECA_d[] = {
+const char* const cnrun::__CN_VarSyms_NeuronECA_d[] = {
"E",
".m",
".h",
@@ -575,7 +575,7 @@ const char* const CNRun::__CN_VarSyms_NeuronECA_d[] = {
".Ih1",
".Ih2"
};
-const double CNRun::__CN_Vars_NeuronECA_d[] = {
+const double cnrun::__CN_Vars_NeuronECA_d[] = {
-53.77902178, // E
0.0262406368, // prob. for Na channel activation m
0.9461831106, // prob. for not Na channel blocking h
@@ -588,7 +588,7 @@ const double CNRun::__CN_Vars_NeuronECA_d[] = {
void
-CNRun::CNeuronECA_d::
+cnrun::CNeuronECA_d::
derivative( vector<double>& x, vector<double>& dx)
{
enum TParametersNeuronECA { // lacks SParametersNeuronEC's gKl and EKl, so derives directly from HH
@@ -639,19 +639,19 @@ derivative( vector<double>& x, vector<double>& dx)
// =========== oscillators
-const char* const CNRun::__CN_ParamNames_OscillatorColpitts[] = {
+const char* const cnrun::__CN_ParamNames_OscillatorColpitts[] = {
"a",
"g",
"q",
"\316\267"
};
-const char* const CNRun::__CN_ParamSyms_OscillatorColpitts[] = {
+const char* const cnrun::__CN_ParamSyms_OscillatorColpitts[] = {
"a",
"g",
"q",
"eta"
};
-const double CNRun::__CN_Params_OscillatorColpitts[] = {
+const double cnrun::__CN_Params_OscillatorColpitts[] = {
1.0, // a
0.0797, // g
0.6898, // q
@@ -659,17 +659,17 @@ const double CNRun::__CN_Params_OscillatorColpitts[] = {
};
-const char* const CNRun::__CN_VarNames_OscillatorColpitts[] = {
+const char* const cnrun::__CN_VarNames_OscillatorColpitts[] = {
"x0",
"x1",
"x2"
};
-const char* const CNRun::__CN_VarSyms_OscillatorColpitts[] = {
+const char* const cnrun::__CN_VarSyms_OscillatorColpitts[] = {
"x0",
"x1",
"x2"
};
-const double CNRun::__CN_Vars_OscillatorColpitts[] = {
+const double cnrun::__CN_Vars_OscillatorColpitts[] = {
0.02,
0.69,
-0.53
@@ -677,7 +677,7 @@ const double CNRun::__CN_Vars_OscillatorColpitts[] = {
void
-CNRun::COscillatorColpitts::
+cnrun::COscillatorColpitts::
derivative( vector<double>& x, vector<double>& dx)
{
enum TParametersOscilColpitts {
@@ -733,31 +733,31 @@ const double __CN_Vars_OscillatorLV[] = {
-const char* const CNRun::__CN_ParamNames_OscillatorVdPol[] = {
+const char* const cnrun::__CN_ParamNames_OscillatorVdPol[] = {
"\316\267",
"\317\211\302\262",
// "\317\203"
};
-const char* const CNRun::__CN_ParamSyms_OscillatorVdPol[] = {
+const char* const cnrun::__CN_ParamSyms_OscillatorVdPol[] = {
"eta",
"omegasq", // omega^2
// "sigma"
};
-const double CNRun::__CN_Params_OscillatorVdPol[] = {
+const double cnrun::__CN_Params_OscillatorVdPol[] = {
1.0, // eta
0.1, // omega^2
// 0.0 // noise level
};
-const char* const CNRun::__CN_VarNames_OscillatorVdPol[] = {
+const char* const cnrun::__CN_VarNames_OscillatorVdPol[] = {
"Amplitude",
"v"
};
-const char* const CNRun::__CN_VarSyms_OscillatorVdPol[] = {
+const char* const cnrun::__CN_VarSyms_OscillatorVdPol[] = {
"A",
"v"
};
-const double CNRun::__CN_Vars_OscillatorVdPol[] = {
+const double cnrun::__CN_Vars_OscillatorVdPol[] = {
0.1, // amplitude
0.0 // internal var
};
diff --git a/upstream/src/libcn/hosted-neurons.hh b/upstream/src/libcn/hosted-neurons.hh
index 7ec0308..18c2398 100644
--- a/upstream/src/libcn/hosted-neurons.hh
+++ b/upstream/src/libcn/hosted-neurons.hh
@@ -22,7 +22,7 @@
# include "config.h"
#endif
-namespace CNRun {
+namespace cnrun {
class CModel;
diff --git a/upstream/src/libcn/hosted-synapses.cc b/upstream/src/libcn/hosted-synapses.cc
index 08a6dd6..cda2029 100644
--- a/upstream/src/libcn/hosted-synapses.cc
+++ b/upstream/src/libcn/hosted-synapses.cc
@@ -25,7 +25,7 @@ using namespace std;
// the base synapse here
-CNRun::C_HostedSynapse::
+cnrun::C_HostedSynapse::
C_HostedSynapse( TUnitType intype,
C_BaseNeuron *insource, C_BaseNeuron *intarget,
double ing, CModel *inM, int s_mask,
@@ -41,7 +41,7 @@ C_HostedSynapse( TUnitType intype,
-CNRun::C_HostedSynapse::
+cnrun::C_HostedSynapse::
~C_HostedSynapse()
{
if ( __cn_verbosely > 5 )
@@ -55,7 +55,7 @@ CNRun::C_HostedSynapse::
// -- parameters
-const char* const CNRun::__CN_ParamNames_SynapseAB_dd[] = {
+const char* const cnrun::__CN_ParamNames_SynapseAB_dd[] = {
// "Synaptic strength g, " __CN_PU_CONDUCTANCE,
"Reversal potential Esyn, " __CN_PU_POTENTIAL,
"Presyn threshold potential Epre, " __CN_PU_POTENTIAL,
@@ -64,7 +64,7 @@ const char* const CNRun::__CN_ParamNames_SynapseAB_dd[] = {
"Time of transmitter release, " __CN_PU_TIME,
// "Noise level \317\203",
};
-const char* const CNRun::__CN_ParamSyms_SynapseAB_dd[] = {
+const char* const cnrun::__CN_ParamSyms_SynapseAB_dd[] = {
// "gsyn",
"Esyn",
"Epre",
@@ -74,7 +74,7 @@ const char* const CNRun::__CN_ParamSyms_SynapseAB_dd[] = {
// "sigma",
};
-const double CNRun::__CN_Params_SynapseAB_dd[] = {
+const double cnrun::__CN_Params_SynapseAB_dd[] = {
// 0.12,
0,
-20,
@@ -84,7 +84,7 @@ const double CNRun::__CN_Params_SynapseAB_dd[] = {
// 0.
};
-const double CNRun::__CN_Params_SynapseABMinus_dd[] = {
+const double cnrun::__CN_Params_SynapseABMinus_dd[] = {
// 0.12,
0,
-20,
@@ -94,7 +94,7 @@ const double CNRun::__CN_Params_SynapseABMinus_dd[] = {
// 0.
};
-const double CNRun::__CN_Params_SynapseMxAB_dd[] = {
+const double cnrun::__CN_Params_SynapseMxAB_dd[] = {
// 0.12,
0,
-20,
@@ -106,7 +106,7 @@ const double CNRun::__CN_Params_SynapseMxAB_dd[] = {
};
-const char* const CNRun::__CN_ParamNames_SynapseAB_dr[] = {
+const char* const cnrun::__CN_ParamNames_SynapseAB_dr[] = {
// "Synaptic strength g, " __CN_PU_CONDUCTANCE,
"Assumed (target->E - Esyn), " __CN_PU_POTENTIAL,
"Presyn threshold potential Epre, " __CN_PU_POTENTIAL,
@@ -115,7 +115,7 @@ const char* const CNRun::__CN_ParamNames_SynapseAB_dr[] = {
"Time of transmitter release, " __CN_PU_TIME,
// "Noise level \317\203",
};
-const char* const CNRun::__CN_ParamSyms_SynapseAB_dr[] = {
+const char* const cnrun::__CN_ParamSyms_SynapseAB_dr[] = {
// "gsyn",
"Ediff",
"Epre",
@@ -126,7 +126,7 @@ const char* const CNRun::__CN_ParamSyms_SynapseAB_dr[] = {
};
-const double CNRun::__CN_Params_SynapseMxAB_dr[] = {
+const double cnrun::__CN_Params_SynapseMxAB_dr[] = {
// 0.12,
-60 - 0, // Ediff: a reasonable Esyn - target->E, the latter being -60 mV at rest
-20,
@@ -142,7 +142,7 @@ const double CNRun::__CN_Params_SynapseMxAB_dr[] = {
-const char* const CNRun::__CN_ParamNames_SynapseAB_rr[] = {
+const char* const cnrun::__CN_ParamNames_SynapseAB_rr[] = {
// "Synaptic strength g, " __CN_PU_CONDUCTANCE,
"Assumed (target->E - Esyn), " __CN_PU_VOLTAGE,
"Rise rate \316\261, " __CN_PU_RATE,
@@ -150,7 +150,7 @@ const char* const CNRun::__CN_ParamNames_SynapseAB_rr[] = {
"Refractory period T, " __CN_PU_TIME,
// "Noise level \317\203",
};
-const char* const CNRun::__CN_ParamSyms_SynapseAB_rr[] = {
+const char* const cnrun::__CN_ParamSyms_SynapseAB_rr[] = {
// "gsyn",
"Ediff",
"alpha",
@@ -158,7 +158,7 @@ const char* const CNRun::__CN_ParamSyms_SynapseAB_rr[] = {
"T",
// "sigma",
};
-const double CNRun::__CN_Params_SynapseAB_rr[] = {
+const double cnrun::__CN_Params_SynapseAB_rr[] = {
// 0.12,
-60 - 0,
0.27785150819749,
@@ -169,21 +169,21 @@ const double CNRun::__CN_Params_SynapseAB_rr[] = {
-const char* const CNRun::__CN_ParamNames_SynapseRall_dd[] = {
+const char* const cnrun::__CN_ParamNames_SynapseRall_dd[] = {
// "Synaptic strength g, " __CN_PU_CONDUCTANCE,
"Reversal potential, " __CN_PU_POTENTIAL,
"Presynaptic threshold potential, " __CN_PU_POTENTIAL,
"\317\204, " __CN_PU_RATE,
// "Noise level \317\203",
};
-const char* const CNRun::__CN_ParamSyms_SynapseRall_dd[] = {
+const char* const cnrun::__CN_ParamSyms_SynapseRall_dd[] = {
// "gsyn",
"Esyn",
"Epre",
"tau",
// "sigma",
};
-const double CNRun::__CN_Params_SynapseRall_dd[] = {
+const double cnrun::__CN_Params_SynapseRall_dd[] = {
// 0.12,
0,
-20,
@@ -196,26 +196,26 @@ const double CNRun::__CN_Params_SynapseRall_dd[] = {
// -- variables
-const char* const CNRun::__CN_VarNames_SynapseAB[] = {
+const char* const cnrun::__CN_VarNames_SynapseAB[] = {
"Amount of neurotransmitter released S"
};
-const char* const CNRun::__CN_VarSyms_SynapseAB[] = {
+const char* const cnrun::__CN_VarSyms_SynapseAB[] = {
"S"
};
-const double CNRun::__CN_Vars_SynapseAB[] = {
+const double cnrun::__CN_Vars_SynapseAB[] = {
0.
};
-const char* const CNRun::__CN_VarNames_SynapseRall[] = {
+const char* const cnrun::__CN_VarNames_SynapseRall[] = {
"Amount of neurotransmitter released S",
"Amount of neurotransmitter absorbed R",
};
-const char* const CNRun::__CN_VarSyms_SynapseRall[] = {
+const char* const cnrun::__CN_VarSyms_SynapseRall[] = {
"S",
"R",
};
-const double CNRun::__CN_Vars_SynapseRall[] = {
+const double cnrun::__CN_Vars_SynapseRall[] = {
0.,
0.
};
@@ -227,7 +227,7 @@ const double CNRun::__CN_Vars_SynapseRall[] = {
void
-CNRun::CSynapseAB_dd::
+cnrun::CSynapseAB_dd::
derivative( vector<double>& x, vector<double>& dx)
{
if ( x[0] - t_last_release_started <= P[_rtime_] ) {
@@ -248,7 +248,7 @@ derivative( vector<double>& x, vector<double>& dx)
void
-CNRun::CSynapseABMinus_dd::
+cnrun::CSynapseABMinus_dd::
derivative( vector<double>& x, vector<double>& dx)
{
if ( x[0] - t_last_release_started <= P[_rtime_] ) {
@@ -271,7 +271,7 @@ derivative( vector<double>& x, vector<double>& dx)
// -------- Multiplexing AB
void
-CNRun::CSynapseMxAB_dd::
+cnrun::CSynapseMxAB_dd::
derivative( vector<double>& x, vector<double>& dx)
{
// printf( "%s %lu %d %g\n", _source->label, _source->serial_id, _source->idx, _source->E(x));
@@ -299,7 +299,7 @@ derivative( vector<double>& x, vector<double>& dx)
void
-CNRun::CSynapseMxAB_dd::
+cnrun::CSynapseMxAB_dd::
update_queue()
{
unsigned k = _source -> n_spikes_in_last_dt();
@@ -328,7 +328,7 @@ update_queue()
void
-CNRun::CSynapseAB_rr::
+cnrun::CSynapseAB_rr::
derivative( vector<double>& x, vector<double>& dx)
{
// if ( source()->F(x) > 0 )
@@ -346,7 +346,7 @@ derivative( vector<double>& x, vector<double>& dx)
inline int Heaviside( double val) { return (val >= 0) ? 1 : 0; }
void
-CNRun::CSynapseRall_dd::
+cnrun::CSynapseRall_dd::
derivative( vector<double>& x, vector<double>& dx)
{
dR(dx) = 1 / P[_tau_] * (-R(x) + Heaviside( _source->E(x) - P[_Epre_]));
diff --git a/upstream/src/libcn/hosted-synapses.hh b/upstream/src/libcn/hosted-synapses.hh
index 56b0c7f..f709133 100644
--- a/upstream/src/libcn/hosted-synapses.hh
+++ b/upstream/src/libcn/hosted-synapses.hh
@@ -30,7 +30,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
class C_HostedSynapse
: public C_BaseSynapse, public C_HostedAttributes {
diff --git a/upstream/src/libcn/integrate-base.hh b/upstream/src/libcn/integrate-base.hh
index 928802c..558a180 100644
--- a/upstream/src/libcn/integrate-base.hh
+++ b/upstream/src/libcn/integrate-base.hh
@@ -18,7 +18,7 @@
#endif
-namespace CNRun {
+namespace cnrun {
class CModel;
diff --git a/upstream/src/libcn/integrate-rk65.hh b/upstream/src/libcn/integrate-rk65.hh
index 51c3360..ee37e74 100644
--- a/upstream/src/libcn/integrate-rk65.hh
+++ b/upstream/src/libcn/integrate-rk65.hh
@@ -20,7 +20,7 @@
# include "config.h"
#endif
-namespace CNRun {
+namespace cnrun {
class CIntegrateRK65
: public CIntegrate_base {
diff --git a/upstream/src/libcn/model-cycle.cc b/upstream/src/libcn/model-cycle.cc
index 083b27d..e5de3d9 100644
--- a/upstream/src/libcn/model-cycle.cc
+++ b/upstream/src/libcn/model-cycle.cc
@@ -66,7 +66,7 @@ double __Butchers_b[9] = {
void
-CNRun::CIntegrateRK65::
+cnrun::CIntegrateRK65::
prepare()
{
for ( unsigned short i = 0; i < 9; ++i )
@@ -84,7 +84,7 @@ prepare()
void
__attribute__ ((hot))
-CNRun::CIntegrateRK65::
+cnrun::CIntegrateRK65::
cycle()
{
// omp stuff found inapplicable due to considerable overhead in sys time
@@ -173,7 +173,7 @@ ctrl_c_handler( int signum)
unsigned int
-CNRun::CModel::
+cnrun::CModel::
advance( double dist, double *cpu_time_used_p)
{
chris_at_kbd = 0;
@@ -204,7 +204,7 @@ advance( double dist, double *cpu_time_used_p)
void
__attribute__ ((hot))
-CNRun::CModel::
+cnrun::CModel::
_setup_schedulers()
{
regular_periods.clear();
@@ -233,7 +233,7 @@ _setup_schedulers()
void
-CNRun::CModel::
+cnrun::CModel::
prepare_advance()
{
if ( _status & CN_MDL_LOGDT && !_dt_logger ) {
@@ -367,7 +367,7 @@ prepare_advance()
unsigned int
__attribute__ ((hot))
-CNRun::CModel::
+cnrun::CModel::
_do_advance_on_pure_hosted( double dist, double *cpu_time_used_p)
{
bool have_listeners = (lisn_unit_list.size() > 0),
@@ -406,7 +406,7 @@ _do_advance_on_pure_hosted( double dist, double *cpu_time_used_p)
unsigned int
__attribute__ ((hot))
-CNRun::CModel::
+cnrun::CModel::
_do_advance_on_pure_standalone( double dist, double *cpu_time_used_p)
{
bool have_listeners = (lisn_unit_list.size() > 0),
@@ -462,7 +462,7 @@ _do_advance_on_pure_standalone( double dist, double *cpu_time_used_p)
unsigned int
__attribute__ ((hot))
-CNRun::CModel::
+cnrun::CModel::
_do_advance_on_pure_ddtbound( double dist, double *cpu_time_used_p)
{
bool have_listeners = (lisn_unit_list.size() > 0),
@@ -514,7 +514,7 @@ _do_advance_on_pure_ddtbound( double dist, double *cpu_time_used_p)
unsigned int
__attribute__ ((hot))
-CNRun::CModel::
+cnrun::CModel::
_do_advance_on_mixed( double dist, double *cpu_time_used_p)
{
bool have_hosted_units = (hosted_unit_cnt() > 0),
diff --git a/upstream/src/libcn/model-nmlio.cc b/upstream/src/libcn/model-nmlio.cc
index 34cdda2..5006468 100644
--- a/upstream/src/libcn/model-nmlio.cc
+++ b/upstream/src/libcn/model-nmlio.cc
@@ -28,7 +28,7 @@ using namespace std;
int
-CNRun::CModel::
+cnrun::CModel::
import_NetworkML( const char *fname, bool appending)
{
LIBXML_TEST_VERSION;
@@ -76,7 +76,7 @@ find_named_root_child_elem( xmlNode *node, // node to start search from
}
int
-CNRun::CModel::
+cnrun::CModel::
import_NetworkML( xmlDoc *doc, const char *fname, bool appending)
{
int retval = 0;
@@ -158,7 +158,7 @@ out:
int
-CNRun::CModel::
+cnrun::CModel::
_process_populations( xmlNode *n)
{
xmlChar *group_id_s = nullptr,
@@ -228,7 +228,7 @@ _process_populations( xmlNode *n)
int
-CNRun::CModel::
+cnrun::CModel::
_process_projections( xmlNode *n)
{
// much the same code as in _process_populations
@@ -309,7 +309,7 @@ _process_projections( xmlNode *n)
int
-CNRun::CModel::
+cnrun::CModel::
_process_population_instances( xmlNode *n, const xmlChar *group_prefix, const xmlChar *type_s)
{
int retval = 0; // also keeps a count of added neurons
@@ -393,7 +393,7 @@ _process_population_instances( xmlNode *n, const xmlChar *group_prefix, const xm
int
-CNRun::CModel::
+cnrun::CModel::
_process_projection_connections( xmlNode *n,
const xmlChar *synapse_name, const xmlChar *type_s,
const xmlChar *src_grp_prefix, const xmlChar *tgt_grp_prefix)
@@ -461,7 +461,7 @@ _process_projection_connections( xmlNode *n,
int
-CNRun::CModel::
+cnrun::CModel::
export_NetworkML( const char *fname)
{
int retval = 0;
diff --git a/upstream/src/libcn/model-struct.cc b/upstream/src/libcn/model-struct.cc
index cecf467..d571672 100644
--- a/upstream/src/libcn/model-struct.cc
+++ b/upstream/src/libcn/model-struct.cc
@@ -29,7 +29,7 @@ using namespace std;
-CNRun::CModel::
+cnrun::CModel::
CModel( const char *inname, CIntegrate_base *inintegrator, int instatus)
: name (inname),
_status (instatus | CN_MDL_NOTREADY),
@@ -66,7 +66,7 @@ CModel( const char *inname, CIntegrate_base *inintegrator, int instatus)
}
-CNRun::CModel::
+cnrun::CModel::
~CModel()
{
if ( verbosely > 4 )
@@ -94,7 +94,7 @@ CNRun::CModel::
void
-CNRun::CModel::
+cnrun::CModel::
reset( bool also_reset_params)
{
_cycle = 0, V[0] = 0.;
@@ -130,8 +130,8 @@ reset( bool also_reset_params)
-CNRun::C_BaseUnit*
-CNRun::CModel::
+cnrun::C_BaseUnit*
+cnrun::CModel::
unit_by_label( const char *inlabel) const
{
for_all_units_const (U)
@@ -140,8 +140,8 @@ unit_by_label( const char *inlabel) const
return nullptr;
}
-CNRun::C_BaseNeuron*
-CNRun::CModel::
+cnrun::C_BaseNeuron*
+cnrun::CModel::
neuron_by_label( const char *inlabel) const
{
for_all_units_const (U)
@@ -150,8 +150,8 @@ neuron_by_label( const char *inlabel) const
return nullptr;
}
-CNRun::C_BaseSynapse*
-CNRun::CModel::
+cnrun::C_BaseSynapse*
+cnrun::CModel::
synapse_by_label( const char *inlabel) const
{
for_all_units_const (U)
@@ -168,7 +168,7 @@ synapse_by_label( const char *inlabel) const
// ----- registering units with core lists
void
-CNRun::CModel::
+cnrun::CModel::
_include_base_unit( C_BaseUnit* u)
{
for_all_units (U)
@@ -204,7 +204,7 @@ skip_lisn_reg:
int
-CNRun::CModel::
+cnrun::CModel::
include_unit( C_HostedNeuron *u, bool is_last)
{
_include_base_unit( u);
@@ -227,7 +227,7 @@ include_unit( C_HostedNeuron *u, bool is_last)
}
int
-CNRun::CModel::
+cnrun::CModel::
include_unit( C_HostedSynapse *u, bool is_last)
{
_include_base_unit( u);
@@ -249,7 +249,7 @@ include_unit( C_HostedSynapse *u, bool is_last)
int
-CNRun::CModel::
+cnrun::CModel::
include_unit( C_StandaloneNeuron *u)
{
_include_base_unit( u);
@@ -270,7 +270,7 @@ include_unit( C_StandaloneNeuron *u)
int
-CNRun::CModel::
+cnrun::CModel::
include_unit( C_StandaloneSynapse *u)
{
/*
@@ -296,8 +296,8 @@ include_unit( C_StandaloneSynapse *u)
// preserve the unit if !do_delete, so it can be re-included again
-CNRun::C_BaseUnit*
-CNRun::CModel::
+cnrun::C_BaseUnit*
+cnrun::CModel::
exclude_unit( C_BaseUnit *u, bool do_delete)
{
if ( __cn_verbosely > 5 )
@@ -372,7 +372,7 @@ exclude_unit( C_BaseUnit *u, bool do_delete)
// listeners & spikeloggers
void
-CNRun::CModel::
+cnrun::CModel::
register_listener( C_BaseUnit *u)
{
if ( find( lisn_unit_list.begin(), lisn_unit_list.end(), u) == lisn_unit_list.end() )
@@ -380,7 +380,7 @@ register_listener( C_BaseUnit *u)
}
void
-CNRun::CModel::
+cnrun::CModel::
unregister_listener( C_BaseUnit *u)
{
const auto& U = find( lisn_unit_list.begin(), lisn_unit_list.end(), u);
@@ -395,7 +395,7 @@ unregister_listener( C_BaseUnit *u)
void
-CNRun::CModel::
+cnrun::CModel::
register_spikelogger( C_BaseNeuron *n)
{
spikelogging_neu_list.push_back( n);
@@ -404,7 +404,7 @@ register_spikelogger( C_BaseNeuron *n)
}
void
-CNRun::CModel::
+cnrun::CModel::
unregister_spikelogger( C_BaseNeuron *n)
{
for_all_spikelogging_neurons (N)
@@ -426,7 +426,7 @@ unregister_spikelogger( C_BaseNeuron *n)
// units with sources
void
-CNRun::CModel::
+cnrun::CModel::
register_unit_with_sources( C_BaseUnit *u)
{
for ( auto& I : u->sources )
@@ -439,7 +439,7 @@ register_unit_with_sources( C_BaseUnit *u)
}
void
-CNRun::CModel::
+cnrun::CModel::
unregister_unit_with_sources( C_BaseUnit *u)
{
start_over_1:
@@ -467,16 +467,8 @@ start_over_2:
-
-
-
-
-
-
-
-
-CNRun::C_BaseNeuron*
-CNRun::CModel::
+cnrun::C_BaseNeuron*
+cnrun::CModel::
add_neuron_species( const char *type_s, const char *label, bool finalize,
double x, double y, double z)
{
@@ -488,8 +480,8 @@ add_neuron_species( const char *type_s, const char *label, bool finalize,
return add_neuron_species( t, label, finalize, x, y, z);
}
-CNRun::C_BaseNeuron*
-CNRun::CModel::
+cnrun::C_BaseNeuron*
+cnrun::CModel::
add_neuron_species( TUnitType type, const char *label, bool finalize,
double x, double y, double z)
{
@@ -559,8 +551,8 @@ add_neuron_species( TUnitType type, const char *label, bool finalize,
-CNRun::C_BaseSynapse*
-CNRun::CModel::
+cnrun::C_BaseSynapse*
+cnrun::CModel::
add_synapse_species( const char *type_s, const char *src_l, const char *tgt_l,
double g, bool allow_clone, bool finalize)
{
@@ -657,8 +649,8 @@ add_synapse_species( const char *type_s, const char *src_l, const char *tgt_l,
-CNRun::C_BaseSynapse*
-CNRun::CModel::
+cnrun::C_BaseSynapse*
+cnrun::CModel::
add_synapse_species( TUnitType ytype, C_BaseNeuron *src, C_BaseNeuron *tgt,
double g, bool allow_clone, bool finalize)
{
@@ -801,7 +793,7 @@ add_synapse_species( TUnitType ytype, C_BaseNeuron *src, C_BaseNeuron *tgt,
void
-CNRun::CModel::
+cnrun::CModel::
finalize_additions()
{
V.resize( _var_cnt), W.resize( _var_cnt);
@@ -831,7 +823,7 @@ finalize_additions()
void
-CNRun::CModel::
+cnrun::CModel::
cull_deaf_synapses()
{
// needs fixing
@@ -886,7 +878,7 @@ grand_restart:
// needs to be called after a neuron is put out
void
-CNRun::CModel::
+cnrun::CModel::
cull_blind_synapses()
{
for_all_hosted_synapses_reversed (Y)
@@ -906,7 +898,7 @@ cull_blind_synapses()
void
-CNRun::CModel::
+cnrun::CModel::
reset_state_all_units()
{
for_all_units (U)
@@ -922,7 +914,7 @@ reset_state_all_units()
// tags
int
-CNRun::CModel::
+cnrun::CModel::
process_listener_tags( const list<STagGroupListener> &Listeners)
{
regex_t RE;
@@ -952,7 +944,7 @@ process_listener_tags( const list<STagGroupListener> &Listeners)
int
-CNRun::CModel::
+cnrun::CModel::
process_spikelogger_tags( const list<STagGroupSpikelogger> &Spikeloggers)
{
regex_t RE;
@@ -1006,7 +998,7 @@ process_spikelogger_tags( const list<STagGroupSpikelogger> &Spikeloggers)
int
-CNRun::CModel::
+cnrun::CModel::
process_putout_tags( const list<STagGroup> &ToRemove)
{
// execute some
@@ -1037,7 +1029,7 @@ process_putout_tags( const list<STagGroup> &ToRemove)
int
-CNRun::CModel::
+cnrun::CModel::
process_decimate_tags( const list<STagGroupDecimate> &ToDecimate)
{
// decimate others
@@ -1076,7 +1068,7 @@ process_decimate_tags( const list<STagGroupDecimate> &ToDecimate)
int
-CNRun::CModel::
+cnrun::CModel::
process_paramset_static_tags( const list<STagGroupNeuronParmSet> &tags)
{
regex_t RE;
@@ -1140,7 +1132,7 @@ process_paramset_static_tags( const list<STagGroupNeuronParmSet> &tags)
int
-CNRun::CModel::
+cnrun::CModel::
process_paramset_static_tags( const list<STagGroupSynapseParmSet> &tags)
{
for ( auto& P : tags ) {
@@ -1228,7 +1220,7 @@ process_paramset_static_tags( const list<STagGroupSynapseParmSet> &tags)
void
-CNRun::CModel::
+cnrun::CModel::
coalesce_synapses()
{
startover:
@@ -1263,7 +1255,7 @@ startover:
int
-CNRun::CModel::
+cnrun::CModel::
process_paramset_source_tags( const list<STagGroupSource> &tags)
{
regex_t RE;
@@ -1317,7 +1309,7 @@ pl_ending( size_t cnt)
}
void
-CNRun::CModel::
+cnrun::CModel::
dump_metrics( FILE *strm)
{
fprintf( strm,
@@ -1352,7 +1344,7 @@ dump_metrics( FILE *strm)
}
void
-CNRun::CModel::
+cnrun::CModel::
dump_state( FILE *strm)
{
fprintf( strm,
@@ -1367,7 +1359,7 @@ dump_state( FILE *strm)
void
-CNRun::CModel::
+cnrun::CModel::
dump_units( FILE *strm)
{
fprintf( strm, "\nUnit types in the model:\n");
diff --git a/upstream/src/libcn/model.hh b/upstream/src/libcn/model.hh
index 017209e..2dd17a8 100644
--- a/upstream/src/libcn/model.hh
+++ b/upstream/src/libcn/model.hh
@@ -47,7 +47,7 @@ parameters.
using namespace std;
-namespace CNRun {
+namespace cnrun {
// CModel _status bits
#define CN_MDL_LOGDT (1 << 0)
diff --git a/upstream/src/libcn/mx-attr.hh b/upstream/src/libcn/mx-attr.hh
index c3b0b3d..3ecb3e0 100644
--- a/upstream/src/libcn/mx-attr.hh
+++ b/upstream/src/libcn/mx-attr.hh
@@ -20,7 +20,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
class C_MultiplexingAttributes {
protected:
diff --git a/upstream/src/libcn/sources.cc b/upstream/src/libcn/sources.cc
index 805cf15..78ad7b2 100644
--- a/upstream/src/libcn/sources.cc
+++ b/upstream/src/libcn/sources.cc
@@ -23,7 +23,7 @@
using namespace std;
-const char * const CNRun::__SourceTypes[] = {
+const char * const cnrun::__SourceTypes[] = {
"Null",
"Tape",
"Periodic",
@@ -32,7 +32,7 @@ const char * const CNRun::__SourceTypes[] = {
};
-CNRun::CSourceTape::
+cnrun::CSourceTape::
CSourceTape( const char *id, const char *infname, bool inis_looping)
: C_BaseSource (id, SRC_TAPE), is_looping (inis_looping)
{
@@ -61,7 +61,7 @@ CSourceTape( const char *id, const char *infname, bool inis_looping)
}
double
-CNRun::CSourceTape::
+cnrun::CSourceTape::
operator() ( double t)
{
// position I such that *I < t < *(I+1)
@@ -79,7 +79,7 @@ operator() ( double t)
-CNRun::CSourcePeriodic::
+cnrun::CSourcePeriodic::
CSourcePeriodic( const char *id, const char *infname, bool inis_looping, double inperiod)
: C_BaseSource (id, SRC_PERIODIC), is_looping (inis_looping)
{
@@ -124,9 +124,9 @@ CSourcePeriodic( const char *id, const char *infname, bool inis_looping, double
-const char * const CNRun::distribution_names[] = { "uniform", "gaussian" };
+const char * const cnrun::distribution_names[] = { "uniform", "gaussian" };
-CNRun::CSourceNoise::
+cnrun::CSourceNoise::
CSourceNoise( const char *id,
double in_min, double in_max,
TDistribution indist_type,
@@ -145,7 +145,7 @@ CSourceNoise( const char *id,
}
-CNRun::CSourceNoise::
+cnrun::CSourceNoise::
~CSourceNoise()
{
gsl_rng_free( rng);
diff --git a/upstream/src/libcn/sources.hh b/upstream/src/libcn/sources.hh
index fbc99bc..6b8ec1b 100644
--- a/upstream/src/libcn/sources.hh
+++ b/upstream/src/libcn/sources.hh
@@ -24,7 +24,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
typedef enum { SRC_NULL, SRC_TAPE, SRC_PERIODIC, SRC_FUNCTION, SRC_NOISE } TSourceType;
diff --git a/upstream/src/libcn/standalone-attr.hh b/upstream/src/libcn/standalone-attr.hh
index 4b6e086..832ae7a 100644
--- a/upstream/src/libcn/standalone-attr.hh
+++ b/upstream/src/libcn/standalone-attr.hh
@@ -21,7 +21,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
class C_StandaloneAttributes {
diff --git a/upstream/src/libcn/standalone-neurons.cc b/upstream/src/libcn/standalone-neurons.cc
index 1b00391..ba8c751 100644
--- a/upstream/src/libcn/standalone-neurons.cc
+++ b/upstream/src/libcn/standalone-neurons.cc
@@ -22,7 +22,7 @@
-CNRun::C_StandaloneNeuron::
+cnrun::C_StandaloneNeuron::
C_StandaloneNeuron( TUnitType intype, const char *inlabel,
double x, double y, double z,
CModel *inM, int s_mask)
@@ -35,7 +35,7 @@ C_StandaloneNeuron( TUnitType intype, const char *inlabel,
}
-CNRun::C_StandaloneNeuron::
+cnrun::C_StandaloneNeuron::
~C_StandaloneNeuron()
{
if ( M && M->verbosely > 5 )
@@ -49,19 +49,19 @@ CNRun::C_StandaloneNeuron::
// --------- Rhythm'n'Blues
-const char* const CNRun::__CN_ParamNames_NeuronHH_r[] = {
+const char* const cnrun::__CN_ParamNames_NeuronHH_r[] = {
"a, " __CN_PU_FREQUENCY,
"I\342\202\200, " __CN_PU_CURRENT,
"r in F(I) = a (I-I\342\202\200)^r",
"Externally applied DC, " __CN_PU_CURRENT,
};
-const char* const CNRun::__CN_ParamSyms_NeuronHH_r[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronHH_r[] = {
"a",
"I0",
"r",
"Idc",
};
-const double CNRun::__CN_Params_NeuronHH_r[] = {
+const double cnrun::__CN_Params_NeuronHH_r[] = {
0.185, // a,
0.0439, // I0,
0.564, // r in F(I) = a * (I-I0)^r
@@ -69,19 +69,19 @@ const double CNRun::__CN_Params_NeuronHH_r[] = {
};
-const char* const CNRun::__CN_VarNames_NeuronHH_r[] = {
+const char* const cnrun::__CN_VarNames_NeuronHH_r[] = {
"Spiking rate, " __CN_PU_FREQUENCY,
};
-const char* const CNRun::__CN_VarSyms_NeuronHH_r[] = {
+const char* const cnrun::__CN_VarSyms_NeuronHH_r[] = {
"F",
};
-const double CNRun::__CN_Vars_NeuronHH_r[] = {
+const double cnrun::__CN_Vars_NeuronHH_r[] = {
0. // frequency F
};
double
-CNRun::CNeuronHH_r::
+cnrun::CNeuronHH_r::
F( vector<double>& x) const
{
double subsq = Isyn(x) - P[_I0_] + P[_Idc_];
@@ -93,7 +93,7 @@ F( vector<double>& x) const
}
void
-CNRun::CNeuronHH_r::
+cnrun::CNeuronHH_r::
preadvance()
{
double subsq = Isyn() - P[_I0_] + P[_Idc_];
@@ -113,33 +113,33 @@ preadvance()
-const char* const CNRun::__CN_ParamNames_OscillatorPoissonDot[] = {
+const char* const cnrun::__CN_ParamNames_OscillatorPoissonDot[] = {
"Rate \316\273, " __CN_PU_RATE,
"Resting potential, " __CN_PU_POTENTIAL,
"Potential when firing, " __CN_PU_POTENTIAL,
};
-const char* const CNRun::__CN_ParamSyms_OscillatorPoissonDot[] = {
+const char* const cnrun::__CN_ParamSyms_OscillatorPoissonDot[] = {
"lambda",
"Vrst",
"Vfir",
};
-const double CNRun::__CN_Params_OscillatorPoissonDot[] = {
+const double cnrun::__CN_Params_OscillatorPoissonDot[] = {
0.02, // firing rate Lambda [1/ms]=[10^3 Hz]
-60.0, // input neuron resting potential
20.0, // input neuron potential when firing
};
-const char* const CNRun::__CN_VarNames_OscillatorPoissonDot[] = {
+const char* const cnrun::__CN_VarNames_OscillatorPoissonDot[] = {
"Membrane potential, " __CN_PU_POTENTIAL,
"Spikes recently fired",
// "Time"
};
-const char* const CNRun::__CN_VarSyms_OscillatorPoissonDot[] = {
+const char* const cnrun::__CN_VarSyms_OscillatorPoissonDot[] = {
"E",
"nspk",
// "t"
};
-const double CNRun::__CN_Vars_OscillatorPoissonDot[] = {
+const double cnrun::__CN_Vars_OscillatorPoissonDot[] = {
-60., // = Vrst, per initialization code found in ctor
0,
// 0.
@@ -170,7 +170,7 @@ factorial( unsigned n)
}
void
-CNRun::COscillatorDotPoisson::
+cnrun::COscillatorDotPoisson::
possibly_fire()
{
double lt = P[_lambda_] * M->dt(),
@@ -198,7 +198,7 @@ possibly_fire()
void
-CNRun::COscillatorDotPoisson::
+cnrun::COscillatorDotPoisson::
do_detect_spike_or_whatever()
{
unsigned n = n_spikes_in_last_dt();
@@ -221,21 +221,21 @@ do_detect_spike_or_whatever()
-const char* const CNRun::__CN_ParamNames_OscillatorPoisson[] = {
+const char* const cnrun::__CN_ParamNames_OscillatorPoisson[] = {
"Rate \316\273, " __CN_PU_RATE,
"Input neuron resting potential, " __CN_PU_POTENTIAL,
"Input neuron potential when firing, " __CN_PU_POTENTIAL,
"Spike time, " __CN_PU_TIME,
"Spike time + refractory period, " __CN_PU_TIME,
};
-const char* const CNRun::__CN_ParamSyms_OscillatorPoisson[] = {
+const char* const cnrun::__CN_ParamSyms_OscillatorPoisson[] = {
"lambda",
"trel",
"trel+trfr",
"Vrst",
"Vfir",
};
-const double CNRun::__CN_Params_OscillatorPoisson[] = {
+const double cnrun::__CN_Params_OscillatorPoisson[] = {
0.02, // firing rate Lambda [1/ms]=[10^3 Hz]
0.0, // spike time
0.0, // refractory period + spike time
@@ -243,20 +243,20 @@ const double CNRun::__CN_Params_OscillatorPoisson[] = {
20.0, // input neuron potential when firing
};
-const char* const CNRun::__CN_VarNames_OscillatorPoisson[] = {
+const char* const cnrun::__CN_VarNames_OscillatorPoisson[] = {
"Membrane potential E, " __CN_PU_POTENTIAL,
};
-const char* const CNRun::__CN_VarSyms_OscillatorPoisson[] = {
+const char* const cnrun::__CN_VarSyms_OscillatorPoisson[] = {
"E",
};
-const double CNRun::__CN_Vars_OscillatorPoisson[] = {
+const double cnrun::__CN_Vars_OscillatorPoisson[] = {
-60.,
};
void
-CNRun::COscillatorPoisson::
+cnrun::COscillatorPoisson::
possibly_fire()
{
if ( _status & CN_NFIRING )
@@ -284,7 +284,7 @@ possibly_fire()
void
-CNRun::COscillatorPoisson::
+cnrun::COscillatorPoisson::
do_detect_spike_or_whatever()
{
unsigned n = n_spikes_in_last_dt();
@@ -309,7 +309,7 @@ do_detect_spike_or_whatever()
// Map neurons require descrete time
-const double CNRun::__CN_Params_NeuronMap[] = {
+const double cnrun::__CN_Params_NeuronMap[] = {
60.0, // 0 - Vspike: spike Amplitude factor
3.0002440, // 1 - alpha: "steepness / size" parameter
-2.4663490, // 3 - gamma: "shift / excitation" parameter
@@ -317,14 +317,14 @@ const double CNRun::__CN_Params_NeuronMap[] = {
0.,
// Old comment by TN: beta chosen such that Isyn= 10 "nA" is the threshold for spiking
};
-const char* const CNRun::__CN_ParamNames_NeuronMap[] = {
+const char* const cnrun::__CN_ParamNames_NeuronMap[] = {
"Spike amplitude factor, " __CN_PU_POTENTIAL,
"\"Steepness / size\" parameter \316\261",
"\"Shift / excitation\" parameter \316\263",
"Input sensitivity \316\262, " __CN_PU_RESISTANCE,
"External DC, " __CN_PU_CURRENT,
};
-const char* const CNRun::__CN_ParamSyms_NeuronMap[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronMap[] = {
"Vspike",
"alpha",
"gamma",
@@ -332,20 +332,20 @@ const char* const CNRun::__CN_ParamSyms_NeuronMap[] = {
"Idc"
};
-const double CNRun::__CN_Vars_NeuronMap[] = {
+const double cnrun::__CN_Vars_NeuronMap[] = {
-50, // E
};
-const char* const CNRun::__CN_VarNames_NeuronMap[] = {
+const char* const cnrun::__CN_VarNames_NeuronMap[] = {
"Membrane potential E, " __CN_PU_POTENTIAL
};
-const char* const CNRun::__CN_VarSyms_NeuronMap[] = {
+const char* const cnrun::__CN_VarSyms_NeuronMap[] = {
"E",
};
void
-CNRun::CNeuronMap::
+cnrun::CNeuronMap::
preadvance()
{
double Vspxaxb = P[_Vspike_] * (P[_alpha_] + P[_gamma_]);
@@ -376,38 +376,38 @@ preadvance()
// ----- Pulse
-const char* const CNRun::__CN_ParamNames_NeuronDotPulse[] = {
+const char* const cnrun::__CN_ParamNames_NeuronDotPulse[] = {
"Frequency f, " __CN_PU_FREQUENCY,
"Resting potential Vrst, " __CN_PU_VOLTAGE,
"Firing potential Vfir, " __CN_PU_VOLTAGE,
};
-const char* const CNRun::__CN_ParamSyms_NeuronDotPulse[] = {
+const char* const cnrun::__CN_ParamSyms_NeuronDotPulse[] = {
"f",
"Vrst",
"Vfir",
};
-const double CNRun::__CN_Params_NeuronDotPulse[] = {
+const double cnrun::__CN_Params_NeuronDotPulse[] = {
10,
-60,
20
};
-const char* const CNRun::__CN_VarNames_NeuronDotPulse[] = {
+const char* const cnrun::__CN_VarNames_NeuronDotPulse[] = {
"Membrane potential E, " __CN_PU_VOLTAGE,
"Spikes recently fired",
};
-const char* const CNRun::__CN_VarSyms_NeuronDotPulse[] = {
+const char* const cnrun::__CN_VarSyms_NeuronDotPulse[] = {
"E",
"nspk",
};
-const double CNRun::__CN_Vars_NeuronDotPulse[] = {
+const double cnrun::__CN_Vars_NeuronDotPulse[] = {
-60., // E
0
};
void
-CNRun::CNeuronDotPulse::
+cnrun::CNeuronDotPulse::
possibly_fire()
{
enum TParametersNeuronDotPulse { _f_, _Vrst_, _Vfir_ };
@@ -426,7 +426,7 @@ possibly_fire()
}
void
-CNRun::CNeuronDotPulse::
+cnrun::CNeuronDotPulse::
param_changed_hook()
{
if ( P[_f_] < 0 ) {
diff --git a/upstream/src/libcn/standalone-neurons.hh b/upstream/src/libcn/standalone-neurons.hh
index 70168f0..0465dfb 100644
--- a/upstream/src/libcn/standalone-neurons.hh
+++ b/upstream/src/libcn/standalone-neurons.hh
@@ -21,7 +21,7 @@
#endif
-namespace CNRun {
+namespace cnrun {
class C_StandaloneNeuron
: public C_BaseNeuron, public C_StandaloneAttributes {
diff --git a/upstream/src/libcn/standalone-synapses.cc b/upstream/src/libcn/standalone-synapses.cc
index 79eed22..f29caf2 100644
--- a/upstream/src/libcn/standalone-synapses.cc
+++ b/upstream/src/libcn/standalone-synapses.cc
@@ -23,7 +23,7 @@
-CNRun::C_StandaloneSynapse::
+cnrun::C_StandaloneSynapse::
C_StandaloneSynapse( TUnitType intype,
C_BaseNeuron* insource, C_BaseNeuron* intarget,
double ing, CModel* inM, int s_mask)
@@ -38,7 +38,7 @@ C_StandaloneSynapse( TUnitType intype,
}
-CNRun::C_StandaloneSynapse::
+cnrun::C_StandaloneSynapse::
~C_StandaloneSynapse()
{
if ( __cn_verbosely > 5 )
@@ -58,20 +58,20 @@ CNRun::C_StandaloneSynapse::
-const double CNRun::__CN_Params_SynapseMap[] = {
+const double cnrun::__CN_Params_SynapseMap[] = {
// 0.075,
18.94463, // Decay rate time constant
0.25,
0
};
-const char* const CNRun::__CN_ParamNames_SynapseMap[] = {
+const char* const cnrun::__CN_ParamNames_SynapseMap[] = {
// "Synaptic strength g, " __CN_PU_CONDUCTANCE,
"Decay rate time constant \317\204, " __CN_PU_RATE,
"Release quantile \316\264",
"Reversal potential Vrev, " __CN_PU_POTENTIAL
};
-const char* const CNRun::__CN_ParamSyms_SynapseMap[] = {
+const char* const cnrun::__CN_ParamSyms_SynapseMap[] = {
// "gsyn",
"tau",
"delta",
@@ -85,7 +85,7 @@ const char* const CNRun::__CN_ParamSyms_SynapseMap[] = {
void
-CNRun::CSynapseMxMap::
+cnrun::CSynapseMxMap::
update_queue()
{
unsigned k = _source -> n_spikes_in_last_dt();
diff --git a/upstream/src/libcn/standalone-synapses.hh b/upstream/src/libcn/standalone-synapses.hh
index e4b08c2..6da3d3d 100644
--- a/upstream/src/libcn/standalone-synapses.hh
+++ b/upstream/src/libcn/standalone-synapses.hh
@@ -25,7 +25,7 @@
#endif
-namespace CNRun {
+namespace cnrun {
class CModel;
diff --git a/upstream/src/libcn/types.cc b/upstream/src/libcn/types.cc
index 76c2694..e6fcfbc 100644
--- a/upstream/src/libcn/types.cc
+++ b/upstream/src/libcn/types.cc
@@ -26,7 +26,7 @@
using namespace std;
-CNRun::SCNDescriptor CNRun::__CNUDT[] = {
+cnrun::SCNDescriptor cnrun::__CNUDT[] = {
// ---------------- Neuron types
@@ -442,8 +442,8 @@ CNRun::SCNDescriptor CNRun::__CNUDT[] = {
-CNRun::TUnitType
-CNRun::
+cnrun::TUnitType
+cnrun::
unit_family_by_string( const char *id)
{
for ( int i = NT_FIRST; i <= YT_LAST; i++ )
@@ -452,8 +452,8 @@ unit_family_by_string( const char *id)
return NT_VOID;
}
-CNRun::TUnitType
-CNRun::
+cnrun::TUnitType
+cnrun::
unit_species_by_string( const char *id)
{
for ( int i = NT_FIRST; i <= YT_LAST; i++ )
@@ -466,7 +466,7 @@ unit_species_by_string( const char *id)
void
-CNRun::
+cnrun::
cnmodel_dump_available_units()
{
size_t u, p;
diff --git a/upstream/src/libcn/types.hh b/upstream/src/libcn/types.hh
index 7d2a328..dcbab3e 100644
--- a/upstream/src/libcn/types.hh
+++ b/upstream/src/libcn/types.hh
@@ -21,7 +21,7 @@
using namespace std;
-namespace CNRun {
+namespace cnrun {
enum TUnitType {
// neuron types
diff --git a/upstream/src/tools/hh-latency-estimator.cc b/upstream/src/tools/hh-latency-estimator.cc
index a90cea9..deaea57 100644
--- a/upstream/src/tools/hh-latency-estimator.cc
+++ b/upstream/src/tools/hh-latency-estimator.cc
@@ -18,6 +18,8 @@
# include "config.h"
#endif
+using namespace cnrun;
+
CModel *Model;
enum TOscillatorType { S_POISSON = 0, S_PULSE = 1 };
--
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