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commit 04e35dff066189a049a911c171e3b43f433fc134 Author: Andrei Zavada <[email protected]> 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 }; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cnrun.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
