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 "nrn_ansi.h"
#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)
int	nrn_segment_node_index (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 502 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 233 of file neuronapi.cpp.

nrn_cas()

Section* nrn_cas

(

void

)

Definition at line 167 of file neuronapi.cpp.

nrn_class_name()

char const* nrn_class_name

(

const Object *

obj

)

Definition at line 448 of file neuronapi.cpp.

nrn_distance()

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

Definition at line 456 of file neuronapi.cpp.

nrn_double_pop()

double nrn_double_pop

(

void

)

Definition at line 288 of file neuronapi.cpp.

nrn_double_ptr_pop()

double* nrn_double_ptr_pop

(

void

)

Definition at line 296 of file neuronapi.cpp.

nrn_double_ptr_push()

void nrn_double_ptr_push

(

double *

addr

)

Definition at line 292 of file neuronapi.cpp.

nrn_double_push()

void nrn_double_push

(

double

val

)

Definition at line 284 of file neuronapi.cpp.

nrn_function_call()

void nrn_function_call	(	Symbol *	sym,
		int	narg
	)

Definition at line 382 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 416 of file neuronapi.cpp.

nrn_gargstr()

char* nrn_gargstr

(

int

arg

)

Definition at line 719 of file neuronapi.cpp.

nrn_get_plotshape_high()

float nrn_get_plotshape_high

(

ShapePlotInterface *

spi

)

Definition at line 487 of file neuronapi.cpp.

nrn_get_plotshape_interface()

ShapePlotInterface* nrn_get_plotshape_interface

(

Object *

ps

)

Definition at line 468 of file neuronapi.cpp.

nrn_get_plotshape_low()

float nrn_get_plotshape_low

(

ShapePlotInterface *

spi

)

Definition at line 483 of file neuronapi.cpp.

nrn_get_plotshape_section_list()

Object* nrn_get_plotshape_section_list

(

ShapePlotInterface *

spi

)

Definition at line 475 of file neuronapi.cpp.

nrn_get_plotshape_varname()

const char* nrn_get_plotshape_varname

(

ShapePlotInterface *

spi

)

Definition at line 479 of file neuronapi.cpp.

nrn_getarg()

double* nrn_getarg

(

int

arg

)

Definition at line 723 of file neuronapi.cpp.

nrn_global_symbol_table()

Symlist* nrn_global_symbol_table

(

void

)

Definition at line 687 of file neuronapi.cpp.

nrn_hoc_call()

int nrn_hoc_call

(

char const *const

command

)

Definition at line 494 of file neuronapi.cpp.

nrn_hoc_ret()

void nrn_hoc_ret

(

void

)

Definition at line 708 of file neuronapi.cpp.

nrn_ifarg()

bool nrn_ifarg

(

int

arg

)

Definition at line 731 of file neuronapi.cpp.

nrn_init()

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

Definition at line 58 of file neuronapi.cpp.

nrn_int_pop()

int nrn_int_pop

(

void

)

Definition at line 312 of file neuronapi.cpp.

nrn_int_push()

void nrn_int_push

(

int

i

)

Definition at line 308 of file neuronapi.cpp.

nrn_is_double_arg()

bool nrn_is_double_arg

(

int

arg

)

Definition at line 746 of file neuronapi.cpp.

nrn_is_object_arg()

bool nrn_is_object_arg

(

int

arg

)

Definition at line 736 of file neuronapi.cpp.

nrn_is_pdouble_arg()

bool nrn_is_pdouble_arg

(

int

arg

)

Definition at line 751 of file neuronapi.cpp.

nrn_is_str_arg()

bool nrn_is_str_arg

(

int

arg

)

Definition at line 741 of file neuronapi.cpp.

nrn_mechanism_insert()

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

Definition at line 147 of file neuronapi.cpp.

nrn_method_call()

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

Definition at line 378 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 388 of file neuronapi.cpp.

nrn_method_symbol()

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

Definition at line 374 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 176 of file neuronapi.cpp.

nrn_nseg_set()

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

Definition at line 181 of file neuronapi.cpp.

nrn_obj_file_arg()

std::FILE* nrn_obj_file_arg

(

int

i

)

Definition at line 727 of file neuronapi.cpp.

nrn_object_new()

Object* nrn_object_new	(	Symbol *	sym,
		int	narg
	)

Definition at line 370 of file neuronapi.cpp.

nrn_object_pop()

Object* nrn_object_pop

(

void

)

Definition at line 320 of file neuronapi.cpp.

nrn_object_push()

void nrn_object_push

(

Object *

obj

)

Definition at line 316 of file neuronapi.cpp.

nrn_object_ref()

void nrn_object_ref

(

Object *

obj

)

Definition at line 440 of file neuronapi.cpp.

nrn_object_unref()

void nrn_object_unref

(

Object *

obj

)

Definition at line 444 of file neuronapi.cpp.

nrn_objgetarg()

Object** nrn_objgetarg

(

int

arg

)

Definition at line 715 of file neuronapi.cpp.

nrn_prop_exists()

bool nrn_prop_exists

(

const Object *

obj

)

Definition at line 452 of file neuronapi.cpp.

nrn_property_array_get()

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

Definition at line 613 of file neuronapi.cpp.

nrn_property_array_push()

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

Definition at line 664 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 639 of file neuronapi.cpp.

nrn_property_get()

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

Definition at line 600 of file neuronapi.cpp.

nrn_property_push()

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

Definition at line 652 of file neuronapi.cpp.

nrn_property_set()

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

Definition at line 626 of file neuronapi.cpp.

nrn_rangevar_get()

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

Definition at line 221 of file neuronapi.cpp.

nrn_rangevar_push()

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

Definition at line 229 of file neuronapi.cpp.

nrn_rangevar_set()

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

Definition at line 225 of file neuronapi.cpp.

nrn_register_function()

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

Definition at line 700 of file neuronapi.cpp.

nrn_secname()

char const* nrn_secname

(

Section *

sec

)

Definition at line 135 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 89 of file neuronapi.cpp.

nrn_section_is_active()

bool nrn_section_is_active

(

const Section *

sec

)

Definition at line 152 of file neuronapi.cpp.

nrn_section_length_get()

double nrn_section_length_get

(

Section *

sec

)

Definition at line 108 of file neuronapi.cpp.

nrn_section_length_set()

void nrn_section_length_set	(	Section *	sec,
		const double	length
	)

Definition at line 97 of file neuronapi.cpp.

nrn_section_new()

Section* nrn_section_new

(

char const *const

name

)

Definition at line 76 of file neuronapi.cpp.

nrn_section_pop()

void nrn_section_pop

(

void

)

Definition at line 143 of file neuronapi.cpp.

nrn_section_push()

void nrn_section_push

(

Section *

sec

)

Definition at line 139 of file neuronapi.cpp.

nrn_section_Ra_get()

double nrn_section_Ra_get

(

Section *

sec

)

Definition at line 112 of file neuronapi.cpp.

nrn_section_Ra_set()

void nrn_section_Ra_set	(	Section *	sec,
		double const	val
	)

Definition at line 116 of file neuronapi.cpp.

nrn_section_rallbranch_get()

double nrn_section_rallbranch_get

(

const Section *

sec

)

Definition at line 124 of file neuronapi.cpp.

nrn_section_rallbranch_set()

void nrn_section_rallbranch_set	(	Section *	sec,
		double const	val
	)

Definition at line 128 of file neuronapi.cpp.

nrn_section_ref()

void nrn_section_ref

(

Section *

sec

)

Definition at line 159 of file neuronapi.cpp.

nrn_section_unref()

void nrn_section_unref

(

Section *

sec

)

Definition at line 163 of file neuronapi.cpp.

nrn_sectionlist_data()

nrn_Item* nrn_sectionlist_data

(

const Object *

obj

)

Definition at line 237 of file neuronapi.cpp.

nrn_sectionlist_iterator_done()

int nrn_sectionlist_iterator_done

(

SectionListIterator *

sl

)

Definition at line 570 of file neuronapi.cpp.

nrn_sectionlist_iterator_free()

void nrn_sectionlist_iterator_free

(

SectionListIterator *

sl

)

Definition at line 562 of file neuronapi.cpp.

nrn_sectionlist_iterator_new()

SectionListIterator* nrn_sectionlist_iterator_new

(

nrn_Item *

my_sectionlist

)

Definition at line 558 of file neuronapi.cpp.

nrn_sectionlist_iterator_next()

Section* nrn_sectionlist_iterator_next

(

SectionListIterator *

sl

)

Definition at line 566 of file neuronapi.cpp.

nrn_segment_diam_get()

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

Definition at line 198 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 185 of file neuronapi.cpp.

nrn_segment_node_index()

int nrn_segment_node_index	(	Section *const	sec,
		const double	x
	)

Definition at line 214 of file neuronapi.cpp.

nrn_stack_type()

nrn_stack_types_t nrn_stack_type

(

void

)

Definition at line 329 of file neuronapi.cpp.

nrn_stack_type_name()

char const* nrn_stack_type_name

(

nrn_stack_types_t

id

)

Definition at line 349 of file neuronapi.cpp.

nrn_stdout_redirect()

void nrn_stdout_redirect

(

int(*)(int, char *)

myprint

)

Definition at line 65 of file neuronapi.cpp.

nrn_str_pop()

char** nrn_str_pop

(

void

)

Definition at line 304 of file neuronapi.cpp.

nrn_str_push()

void nrn_str_push

(

char **

str

)

Definition at line 300 of file neuronapi.cpp.

nrn_symbol()

Symbol* nrn_symbol

(

char const *const

name

)

Definition at line 246 of file neuronapi.cpp.

nrn_symbol_array_length()

int nrn_symbol_array_length

(

const Symbol *

sym

)

Definition at line 695 of file neuronapi.cpp.

nrn_symbol_dataptr()

double* nrn_symbol_dataptr

(

const Symbol *

sym

)

Definition at line 260 of file neuronapi.cpp.

nrn_symbol_is_array()

bool nrn_symbol_is_array

(

const Symbol *

sym

)

Definition at line 276 of file neuronapi.cpp.

nrn_symbol_name()

char const* nrn_symbol_name

(

const Symbol *

sym

)

Definition at line 677 of file neuronapi.cpp.

nrn_symbol_push()

void nrn_symbol_push

(

Symbol *

sym

)

Definition at line 280 of file neuronapi.cpp.

nrn_symbol_subtype()

int nrn_symbol_subtype

(

const Symbol *

sym

)

Definition at line 256 of file neuronapi.cpp.

nrn_symbol_table()

Symlist* nrn_symbol_table

(

const Symbol *

sym

)

Definition at line 681 of file neuronapi.cpp.

nrn_symbol_table_iterator_done()

int nrn_symbol_table_iterator_done

(

SymbolTableIterator *

st

)

Definition at line 586 of file neuronapi.cpp.

nrn_symbol_table_iterator_free()

void nrn_symbol_table_iterator_free

(

SymbolTableIterator *

st

)

Definition at line 578 of file neuronapi.cpp.

nrn_symbol_table_iterator_new()

SymbolTableIterator* nrn_symbol_table_iterator_new

(

Symlist *

my_symbol_table

)

Definition at line 574 of file neuronapi.cpp.

nrn_symbol_table_iterator_next()

Symbol* nrn_symbol_table_iterator_next

(

SymbolTableIterator *

st

)

Definition at line 582 of file neuronapi.cpp.

nrn_symbol_type()

int nrn_symbol_type

(

const Symbol *

sym

)

Definition at line 250 of file neuronapi.cpp.

nrn_top_level_symbol_table()

Symlist* nrn_top_level_symbol_table

(

void

)

Definition at line 691 of file neuronapi.cpp.

nrn_vector_capacity()

int nrn_vector_capacity

(

const Object *

vec

)

Definition at line 590 of file neuronapi.cpp.

nrn_vector_data()

double* nrn_vector_data

(

Object *

vec

)

Definition at line 595 of file neuronapi.cpp.

nrnpy_set_pr_etal()

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

Definition at line 816 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.