neuronapi.cpp File Reference

#include "neuronapi.h"
#include "../../nrnconf.h"
#include "hocdec.h"
#include "cabcode.h"
#include "nrniv_mf.h"
#include "nrnmpi.h"
#include "nrnmpiuse.h"
#include "ocfunc.h"
#include "ocjump.h"
#include "parse.hpp"
#include "section.h"
#include "shapeplt.h"
#include <cstring>
#include <exception>

Go to the source code of this file.

Classes
struct	nrn_Item
	A public face of hoc_Item. More...
struct	SectionListIterator
struct	SymbolTableIterator

Functions
void	nrnpy_set_pr_etal (int(*cbpr_stdoe)(int, char *), int(*cbpass)())
int	ivocmain_session (int, const char **, const char **, int start_session)
	This used to be ivocmain, the main entrypoint to the HOC interpreter. More...
void	simpleconnectsection ()
Object *	hoc_newobj1 (Symbol *, int)
std::tuple< int, const char ** >	nrn_mpi_setup (int argc, const char **argv)
	A top-level initialization of MPI given argc and argv. More...
int	nrn_init (int argc, const char **argv)
void	nrn_stdout_redirect (int(*myprint)(int, char *))
Section *	nrn_section_new (char const *const name)
void	nrn_section_connect (Section *child_sec, double child_x, Section *parent_sec, double parent_x)
void	nrn_section_length_set (Section *sec, const double length)
double	nrn_section_length_get (Section *sec)
double	nrn_section_Ra_get (Section *sec)
void	nrn_section_Ra_set (Section *sec, double const val)
double	nrn_section_rallbranch_get (const Section *sec)
void	nrn_section_rallbranch_set (Section *sec, double const val)
char const *	nrn_secname (Section *sec)
void	nrn_section_push (Section *sec)
void	nrn_section_pop (void)
void	nrn_mechanism_insert (Section *sec, const Symbol *mechanism)
bool	nrn_section_is_active (const Section *sec)
void	nrn_section_ref (Section *sec)
void	nrn_section_unref (Section *sec)
Section *	nrn_cas (void)
int	nrn_nseg_get (const Section *sec)
void	nrn_nseg_set (Section *const sec, const int nseg)
void	nrn_segment_diam_set (Section *const sec, const double x, const double diam)
double	nrn_segment_diam_get (Section *const sec, const double x)
double	nrn_rangevar_get (Symbol *sym, Section *sec, double x)
void	nrn_rangevar_set (Symbol *sym, Section *sec, double x, double value)
void	nrn_rangevar_push (Symbol *sym, Section *sec, double x)
nrn_Item *	nrn_allsec (void)
nrn_Item *	nrn_sectionlist_data (const Object *obj)
Symbol *	nrn_symbol (char const *const name)
int	nrn_symbol_type (const Symbol *sym)
int	nrn_symbol_subtype (const Symbol *sym)
double *	nrn_symbol_dataptr (const Symbol *sym)
bool	nrn_symbol_is_array (const Symbol *sym)
void	nrn_symbol_push (Symbol *sym)
void	nrn_double_push (double val)
double	nrn_double_pop (void)
void	nrn_double_ptr_push (double *addr)
double *	nrn_double_ptr_pop (void)
void	nrn_str_push (char **str)
char **	nrn_str_pop (void)
void	nrn_int_push (int i)
int	nrn_int_pop (void)
void	nrn_object_push (Object *obj)
Object *	nrn_object_pop (void)
nrn_stack_types_t	nrn_stack_type (void)
char const *	nrn_stack_type_name (nrn_stack_types_t id)
Object *	nrn_object_new (Symbol *sym, int narg)
Symbol *	nrn_method_symbol (const Object *obj, char const *const name)
void	nrn_method_call (Object *obj, Symbol *method_sym, int narg)
void	nrn_function_call (Symbol *sym, int narg)
int	nrn_method_call_nothrow (Object *obj, Symbol *method_sym, int narg, char *error_msg, size_t error_msg_size)
int	nrn_function_call_nothrow (Symbol *sym, int narg, char *error_msg, size_t error_msg_size)
void	nrn_object_ref (Object *obj)
void	nrn_object_unref (Object *obj)
char const *	nrn_class_name (const Object *obj)
bool	nrn_prop_exists (const Object *obj)
double	nrn_distance (Section *sec0, double x0, Section *sec1, double x1)
ShapePlotInterface *	nrn_get_plotshape_interface (Object *ps)
Object *	nrn_get_plotshape_section_list (ShapePlotInterface *spi)
const char *	nrn_get_plotshape_varname (ShapePlotInterface *spi)
float	nrn_get_plotshape_low (ShapePlotInterface *spi)
float	nrn_get_plotshape_high (ShapePlotInterface *spi)
int	nrn_hoc_call (char const *const command)
SectionListIterator *	nrn_sectionlist_iterator_new (nrn_Item *my_sectionlist)
void	nrn_sectionlist_iterator_free (SectionListIterator *sl)
Section *	nrn_sectionlist_iterator_next (SectionListIterator *sl)
int	nrn_sectionlist_iterator_done (SectionListIterator *sl)
SymbolTableIterator *	nrn_symbol_table_iterator_new (Symlist *my_symbol_table)
void	nrn_symbol_table_iterator_free (SymbolTableIterator *st)
Symbol *	nrn_symbol_table_iterator_next (SymbolTableIterator *st)
int	nrn_symbol_table_iterator_done (SymbolTableIterator *st)
int	nrn_vector_capacity (const Object *vec)
double *	nrn_vector_data (Object *vec)
double	nrn_property_get (const Object *obj, const char *name)
double	nrn_property_array_get (const Object *obj, const char *name, int i)
void	nrn_property_set (Object *obj, const char *name, double value)
void	nrn_property_array_set (Object *obj, const char *name, int i, double value)
void	nrn_property_push (Object *obj, const char *name)
void	nrn_property_array_push (Object *obj, const char *name, int i)
char const *	nrn_symbol_name (const Symbol *sym)
Symlist *	nrn_symbol_table (const Symbol *sym)
Symlist *	nrn_global_symbol_table (void)
Symlist *	nrn_top_level_symbol_table (void)
int	nrn_symbol_array_length (const Symbol *sym)
void	nrn_register_function (void(*proc)(), const char *func_name, int type)
void	nrn_hoc_ret ()
Object **	nrn_objgetarg (int arg)
char *	nrn_gargstr (int arg)
double *	nrn_getarg (int arg)
std::FILE *	nrn_obj_file_arg (int i)
bool	nrn_ifarg (int arg)
bool	nrn_is_object_arg (int arg)
bool	nrn_is_str_arg (int arg)
bool	nrn_is_double_arg (int arg)
bool	nrn_is_pdouble_arg (int arg)

Variables
int	nrn_nobanner_
int	diam_changed
int	nrn_try_catch_nest_depth

Function Documentation

hoc_newobj1()

Object* hoc_newobj1	(	Symbol *	sym,
		int	narg
	)

Definition at line 497 of file hoc_oop.cpp.

ivocmain_session()

int ivocmain_session	(	int	argc,
		const char **	argv,
		const char **	env,
		int	start_session
	)

This used to be ivocmain, the main entrypoint to the HOC interpreter.

ivocmain_session parses command line argument, calls of initialization functions and drops into an interactive HOC session. This function is called for example by the "real main" in nrnmain.cpp , but can be also called from other external user applications that use NEURON. Additionally to the original implemenation a new parameter start_session was introduced to control whether an interactive HOC session shoudl be started or simply NEURON and all data structures be initialized and control returned to the caller.

Note

env argument should not be used as it might become invalid

Parameters

argc	argument count as found in C/C++ main functions
argv	argument vector as found in C/C++ main functions
env	environment variable array as optionally found in main functions.
start_session	set to 1 for default behavior (drop into interactive HOC session otherwise set to 0. If set to 1, but compiled with python support this function will still directly return (since in that mode we don't need an interactive HOC session either.

Returns

0 on success, otherwise error code.

Definition at line 361 of file ivocmain.cpp.

nrn_allsec()

nrn_Item* nrn_allsec

(

void

)

Definition at line 219 of file neuronapi.cpp.

nrn_cas()

Section* nrn_cas

(

void

)

Definition at line 166 of file neuronapi.cpp.

nrn_class_name()

char const* nrn_class_name

(

const Object *

obj

)

Definition at line 422 of file neuronapi.cpp.

nrn_distance()

double nrn_distance	(	Section *	sec0,
		double	x0,
		Section *	sec1,
		double	x1
	)

Definition at line 430 of file neuronapi.cpp.

nrn_double_pop()

double nrn_double_pop

(

void

)

Definition at line 262 of file neuronapi.cpp.

nrn_double_ptr_pop()

double* nrn_double_ptr_pop

(

void

)

Definition at line 270 of file neuronapi.cpp.

nrn_double_ptr_push()

void nrn_double_ptr_push

(

double *

addr

)

Definition at line 266 of file neuronapi.cpp.

nrn_double_push()

void nrn_double_push

(

double

val

)

Definition at line 258 of file neuronapi.cpp.

nrn_function_call()

void nrn_function_call	(	Symbol *	sym,
		int	narg
	)

Definition at line 356 of file neuronapi.cpp.

nrn_function_call_nothrow()

int nrn_function_call_nothrow	(	Symbol *	sym,
		int	narg,
		char *	error_msg,
		size_t	error_msg_size
	)

Definition at line 390 of file neuronapi.cpp.

nrn_gargstr()

char* nrn_gargstr

(

int

arg

)

Definition at line 693 of file neuronapi.cpp.

nrn_get_plotshape_high()

float nrn_get_plotshape_high

(

ShapePlotInterface *

spi

)

Definition at line 461 of file neuronapi.cpp.

nrn_get_plotshape_interface()

ShapePlotInterface* nrn_get_plotshape_interface

(

Object *

ps

)

Definition at line 442 of file neuronapi.cpp.

nrn_get_plotshape_low()

float nrn_get_plotshape_low

(

ShapePlotInterface *

spi

)

Definition at line 457 of file neuronapi.cpp.

nrn_get_plotshape_section_list()

Object* nrn_get_plotshape_section_list

(

ShapePlotInterface *

spi

)

Definition at line 449 of file neuronapi.cpp.

nrn_get_plotshape_varname()

const char* nrn_get_plotshape_varname

(

ShapePlotInterface *

spi

)

Definition at line 453 of file neuronapi.cpp.

nrn_getarg()

double* nrn_getarg

(

int

arg

)

Definition at line 697 of file neuronapi.cpp.

nrn_global_symbol_table()

Symlist* nrn_global_symbol_table

(

void

)

Definition at line 661 of file neuronapi.cpp.

nrn_hoc_call()

int nrn_hoc_call

(

char const *const

command

)

Definition at line 468 of file neuronapi.cpp.

nrn_hoc_ret()

void nrn_hoc_ret

(

void

)

Definition at line 682 of file neuronapi.cpp.

nrn_ifarg()

bool nrn_ifarg

(

int

arg

)

Definition at line 705 of file neuronapi.cpp.

nrn_init()

int nrn_init	(	int	argc,
		const char **	argv
	)

Definition at line 57 of file neuronapi.cpp.

nrn_int_pop()

int nrn_int_pop

(

void

)

Definition at line 286 of file neuronapi.cpp.

nrn_int_push()

void nrn_int_push

(

int

i

)

Definition at line 282 of file neuronapi.cpp.

nrn_is_double_arg()

bool nrn_is_double_arg

(

int

arg

)

Definition at line 720 of file neuronapi.cpp.

nrn_is_object_arg()

bool nrn_is_object_arg

(

int

arg

)

Definition at line 710 of file neuronapi.cpp.

nrn_is_pdouble_arg()

bool nrn_is_pdouble_arg

(

int

arg

)

Definition at line 725 of file neuronapi.cpp.

nrn_is_str_arg()

bool nrn_is_str_arg

(

int

arg

)

Definition at line 715 of file neuronapi.cpp.

nrn_mechanism_insert()

void nrn_mechanism_insert	(	Section *	sec,
		const Symbol *	mechanism
	)

Definition at line 146 of file neuronapi.cpp.

nrn_method_call()

void nrn_method_call	(	Object *	obj,
		Symbol *	method_sym,
		int	narg
	)

Definition at line 352 of file neuronapi.cpp.

nrn_method_call_nothrow()

int nrn_method_call_nothrow	(	Object *	obj,
		Symbol *	method_sym,
		int	narg,
		char *	error_msg,
		size_t	error_msg_size
	)

Definition at line 362 of file neuronapi.cpp.

nrn_method_symbol()

Symbol* nrn_method_symbol	(	const Object *	obj,
		char const *const	name
	)

Definition at line 348 of file neuronapi.cpp.

nrn_mpi_setup()

std::tuple<int, const char**> nrn_mpi_setup	(	int	argc,
		const char **	argv
	)

A top-level initialization of MPI given argc and argv.

Sets stubs, load dyn lib, and initializes

Definition at line 770 of file ivocmain.cpp.

nrn_nseg_get()

int nrn_nseg_get

(

const Section *

sec

)

Definition at line 175 of file neuronapi.cpp.

nrn_nseg_set()

void nrn_nseg_set	(	Section *const	sec,
		const int	nseg
	)

Definition at line 180 of file neuronapi.cpp.

nrn_obj_file_arg()

std::FILE* nrn_obj_file_arg

(

int

i

)

Definition at line 701 of file neuronapi.cpp.

nrn_object_new()

Object* nrn_object_new	(	Symbol *	sym,
		int	narg
	)

Definition at line 344 of file neuronapi.cpp.

nrn_object_pop()

Object* nrn_object_pop

(

void

)

Definition at line 294 of file neuronapi.cpp.

nrn_object_push()

void nrn_object_push

(

Object *

obj

)

Definition at line 290 of file neuronapi.cpp.

nrn_object_ref()

void nrn_object_ref

(

Object *

obj

)

Definition at line 414 of file neuronapi.cpp.

nrn_object_unref()

void nrn_object_unref

(

Object *

obj

)

Definition at line 418 of file neuronapi.cpp.

nrn_objgetarg()

Object** nrn_objgetarg

(

int

arg

)

Definition at line 689 of file neuronapi.cpp.

nrn_prop_exists()

bool nrn_prop_exists

(

const Object *

obj

)

Definition at line 426 of file neuronapi.cpp.

nrn_property_array_get()

double nrn_property_array_get	(	const Object *	obj,
		const char *	name,
		int	i
	)

Definition at line 587 of file neuronapi.cpp.

nrn_property_array_push()

void nrn_property_array_push	(	Object *	obj,
		const char *	name,
		int	i
	)

Definition at line 638 of file neuronapi.cpp.

nrn_property_array_set()

void nrn_property_array_set	(	Object *	obj,
		const char *	name,
		int	i,
		double	value
	)

Definition at line 613 of file neuronapi.cpp.

nrn_property_get()

double nrn_property_get	(	const Object *	obj,
		const char *	name
	)

Definition at line 574 of file neuronapi.cpp.

nrn_property_push()

void nrn_property_push	(	Object *	obj,
		const char *	name
	)

Definition at line 626 of file neuronapi.cpp.

nrn_property_set()

void nrn_property_set	(	Object *	obj,
		const char *	name,
		double	value
	)

Definition at line 600 of file neuronapi.cpp.

nrn_rangevar_get()

double nrn_rangevar_get	(	Symbol *	sym,
		Section *	sec,
		double	x
	)

Definition at line 207 of file neuronapi.cpp.

nrn_rangevar_push()

void nrn_rangevar_push	(	Symbol *	sym,
		Section *	sec,
		double	x
	)

Definition at line 215 of file neuronapi.cpp.

nrn_rangevar_set()

void nrn_rangevar_set	(	Symbol *	sym,
		Section *	sec,
		double	x,
		double	value
	)

Definition at line 211 of file neuronapi.cpp.

nrn_register_function()

void nrn_register_function	(	void(*)()	proc,
		const char *	func_name,
		int	type
	)

Definition at line 674 of file neuronapi.cpp.

nrn_secname()

char const* nrn_secname

(

Section *

sec

)

Definition at line 134 of file neuronapi.cpp.

nrn_section_connect()

void nrn_section_connect	(	Section *	child_sec,
		double	child_x,
		Section *	parent_sec,
		double	parent_x
	)

Definition at line 88 of file neuronapi.cpp.

nrn_section_is_active()

bool nrn_section_is_active

(

const Section *

sec

)

Definition at line 151 of file neuronapi.cpp.

nrn_section_length_get()

double nrn_section_length_get

(

Section *

sec

)

Definition at line 107 of file neuronapi.cpp.

nrn_section_length_set()

void nrn_section_length_set	(	Section *	sec,
		const double	length
	)

Definition at line 96 of file neuronapi.cpp.

nrn_section_new()

Section* nrn_section_new

(

char const *const

name

)

Definition at line 75 of file neuronapi.cpp.

nrn_section_pop()

void nrn_section_pop

(

void

)

Definition at line 142 of file neuronapi.cpp.

nrn_section_push()

void nrn_section_push

(

Section *

sec

)

Definition at line 138 of file neuronapi.cpp.

nrn_section_Ra_get()

double nrn_section_Ra_get

(

Section *

sec

)

Definition at line 111 of file neuronapi.cpp.

nrn_section_Ra_set()

void nrn_section_Ra_set	(	Section *	sec,
		double const	val
	)

Definition at line 115 of file neuronapi.cpp.

nrn_section_rallbranch_get()

double nrn_section_rallbranch_get

(

const Section *

sec

)

Definition at line 123 of file neuronapi.cpp.

nrn_section_rallbranch_set()

void nrn_section_rallbranch_set	(	Section *	sec,
		double const	val
	)

Definition at line 127 of file neuronapi.cpp.

nrn_section_ref()

void nrn_section_ref

(

Section *

sec

)

Definition at line 158 of file neuronapi.cpp.

nrn_section_unref()

void nrn_section_unref

(

Section *

sec

)

Definition at line 162 of file neuronapi.cpp.

nrn_sectionlist_data()

nrn_Item* nrn_sectionlist_data

(

const Object *

obj

)

Definition at line 223 of file neuronapi.cpp.

nrn_sectionlist_iterator_done()

int nrn_sectionlist_iterator_done

(

SectionListIterator *

sl

)

Definition at line 544 of file neuronapi.cpp.

nrn_sectionlist_iterator_free()

void nrn_sectionlist_iterator_free

(

SectionListIterator *

sl

)

Definition at line 536 of file neuronapi.cpp.

nrn_sectionlist_iterator_new()

SectionListIterator* nrn_sectionlist_iterator_new

(

nrn_Item *

my_sectionlist

)

Definition at line 532 of file neuronapi.cpp.

nrn_sectionlist_iterator_next()

Section* nrn_sectionlist_iterator_next

(

SectionListIterator *

sl

)

Definition at line 540 of file neuronapi.cpp.

nrn_segment_diam_get()

double nrn_segment_diam_get	(	Section *const	sec,
		const double	x
	)

Definition at line 197 of file neuronapi.cpp.

nrn_segment_diam_set()

void nrn_segment_diam_set	(	Section *const	sec,
		const double	x,
		const double	diam
	)

Definition at line 184 of file neuronapi.cpp.

nrn_stack_type()

nrn_stack_types_t nrn_stack_type

(

void

)

Definition at line 303 of file neuronapi.cpp.

nrn_stack_type_name()

char const* nrn_stack_type_name

(

nrn_stack_types_t

id

)

Definition at line 323 of file neuronapi.cpp.

nrn_stdout_redirect()

void nrn_stdout_redirect

(

int(*)(int, char *)

myprint

)

Definition at line 64 of file neuronapi.cpp.

nrn_str_pop()

char** nrn_str_pop

(

void

)

Definition at line 278 of file neuronapi.cpp.

nrn_str_push()

void nrn_str_push

(

char **

str

)

Definition at line 274 of file neuronapi.cpp.

nrn_symbol()

Symbol* nrn_symbol

(

char const *const

name

)

Definition at line 232 of file neuronapi.cpp.

nrn_symbol_array_length()

int nrn_symbol_array_length

(

const Symbol *

sym

)

Definition at line 669 of file neuronapi.cpp.

nrn_symbol_dataptr()

double* nrn_symbol_dataptr

(

const Symbol *

sym

)

Definition at line 246 of file neuronapi.cpp.

nrn_symbol_is_array()

bool nrn_symbol_is_array

(

const Symbol *

sym

)

Definition at line 250 of file neuronapi.cpp.

nrn_symbol_name()

char const* nrn_symbol_name

(

const Symbol *

sym

)

Definition at line 651 of file neuronapi.cpp.

nrn_symbol_push()

void nrn_symbol_push

(

Symbol *

sym

)

Definition at line 254 of file neuronapi.cpp.

nrn_symbol_subtype()

int nrn_symbol_subtype

(

const Symbol *

sym

)

Definition at line 242 of file neuronapi.cpp.

nrn_symbol_table()

Symlist* nrn_symbol_table

(

const Symbol *

sym

)

Definition at line 655 of file neuronapi.cpp.

nrn_symbol_table_iterator_done()

int nrn_symbol_table_iterator_done

(

SymbolTableIterator *

st

)

Definition at line 560 of file neuronapi.cpp.

nrn_symbol_table_iterator_free()

void nrn_symbol_table_iterator_free

(

SymbolTableIterator *

st

)

Definition at line 552 of file neuronapi.cpp.

nrn_symbol_table_iterator_new()

SymbolTableIterator* nrn_symbol_table_iterator_new

(

Symlist *

my_symbol_table

)

Definition at line 548 of file neuronapi.cpp.

nrn_symbol_table_iterator_next()

Symbol* nrn_symbol_table_iterator_next

(

SymbolTableIterator *

st

)

Definition at line 556 of file neuronapi.cpp.

nrn_symbol_type()

int nrn_symbol_type

(

const Symbol *

sym

)

Definition at line 236 of file neuronapi.cpp.

nrn_top_level_symbol_table()

Symlist* nrn_top_level_symbol_table

(

void

)

Definition at line 665 of file neuronapi.cpp.

nrn_vector_capacity()

int nrn_vector_capacity

(

const Object *

vec

)

Definition at line 564 of file neuronapi.cpp.

nrn_vector_data()

double* nrn_vector_data

(

Object *

vec

)

Definition at line 569 of file neuronapi.cpp.

nrnpy_set_pr_etal()

void nrnpy_set_pr_etal	(	int(*)(int, char *)	cbpr_stdoe,
		int(*)()	cbpass
	)

Definition at line 814 of file fileio.cpp.

simpleconnectsection()

void simpleconnectsection

(

)

Definition at line 664 of file cabcode.cpp.

Variable Documentation

diam_changed

int diam_changed

extern

Definition at line 55 of file cabcode.cpp.

nrn_nobanner_

int nrn_nobanner_

extern

Definition at line 119 of file hoc.cpp.

nrn_try_catch_nest_depth

int nrn_try_catch_nest_depth

extern

Definition at line 608 of file hoc.cpp.