JNIEXPORT jobject JNICALL Java_neuron_Neuron_oGet
(JNIEnv *env, jclass, jstring js){
const char* s = env->GetStringUTFChars(js, 0);
Symbol* sym = hoc_table_lookup(s, hoc_top_level_symlist);
assert(sym && sym->type == OBJECTVAR);
Object** po = hoc_top_level_data[sym->u.oboff].pobj;
env->ReleaseStringUTFChars(js, s);
jobject jo = h2jObject(*po);
hoc_obj_unref(*po);
return jo;
}
HocCommand::~HocCommand() {
if (obj_) {
nrn_notify_pointer_disconnect(this);
}
if (s_) {
delete s_;
}
if (po_) {
hoc_obj_unref(po_);
}
}
JNIEXPORT jobject JNICALL Java_neuron_Neuron_hGetObjectField
(JNIEnv *env, jclass, jlong v, jstring js){
const char* s = env->GetStringUTFChars(js, 0);
Object* o = (Object*)v;
Symbol* sym = hoc_table_lookup(s, o->ctemplate->symtable);
assert(sym && sym->type == OBJECTVAR);
Object** po = o->u.dataspace[sym->u.oboff].pobj;
env->ReleaseStringUTFChars(js, s);
jobject jo = h2jObject(*po);
hoc_obj_unref(*po);
return jo;
}
static double extra_scatter_gather_remove(void* v) {
Object* o = *hoc_objgetarg(1);
for (int direction=0; direction < 2; ++direction) {
ExtraScatterList* esl = extra_scatterlist[direction];
if (esl) for (int i = esl->count()-1; i >= 0; --i) {
Object* o1 = esl->item(i);
// if esl exists then python exists
if ((*nrnpy_pysame)(o, o1)) {
esl->remove(i);
hoc_obj_unref(o1);
}
}
}
return 0.;
}
JNIEXPORT void JNICALL Java_neuron_Neuron_hSetObjectField__Ljava_lang_String_2Ljava_lang_Object_2I
(JNIEnv *env, jclass, jstring js, jobject joval, jint type){
jnisave
const char* s = env->GetStringUTFChars(js, 0);
Symbol* sym = hoc_table_lookup(s, hoc_top_level_symlist);
assert(sym && sym->type == OBJECTVAR);
Object** po = hoc_top_level_data[sym->u.oboff].pobj;
Object** poval = nj_j2hObject(joval, type);
Object* old = *po;
*po = *poval;
(*po)->refcount++;
hoc_obj_unref(old);
env->ReleaseStringUTFChars(js, s);
jnirestore
}
void LinearMechanism::lmfree() {
if (f_callable_) {
hoc_obj_unref(f_callable_);
f_callable_ = NULL;
}
if (model_) {
delete model_;
model_ = NULL;
}
if (nodes_) {
nrn_notify_pointer_disconnect(this);
nnode_ = 0;
delete [] nodes_;
nodes_ = NULL;
elayer_ = NULL;
}
}
JNIEXPORT void JNICALL Java_neuron_Neuron_hocObjectUnref
(JNIEnv *, jclass, jlong i) {
Object* o = (Object*)i;
//printf("hocObjectUnref %d %s\n", (long)i, hoc_object_name(o));
hoc_obj_unref(o);
}
void fit_praxis(void) {
extern Symbol* hoc_lookup();
extern char* gargstr();
char* after_quad;
int i;
double err, fmin;
double* px;
/* allow nested calls to fit_praxis. I.e. store all the needed
statics specific to this invocation with proper reference
counting and then unref/destoy on exit from this invocation.
Before the prax call save the statics from earlier invocation
without increasing the
ref count and on exit restore without decreasing the ref count.
*/
/* save before setting statics, restore after prax */
double minerrsav, *minargsav, maxstepsizesav, tolerancesav;
long int printmodesav, nvarsav;
Symbol* efun_sym_sav;
Object* efun_py_save, *efun_py_arg_save;
void* vec_py_save_save;
/* store statics specified by this invocation */
/* will be copied just before calling prax */
double minerr_, *minarg_;
long int nvar_;
Symbol* efun_sym_;
Object* efun_py_, *efun_py_arg_;
void* vec_py_save_;
minerr_ = 0.0;
nvar_ = 0;
minarg_ = NULL;
efun_sym_ = NULL;
efun_py_ = NULL;
efun_py_arg_ = NULL;
vec_py_save_ = NULL;
fmin = 0.;
if (hoc_is_object_arg(1)) {
assert(nrnpy_praxis_efun);
efun_py_ = *hoc_objgetarg(1);
hoc_obj_ref(efun_py_);
efun_py_arg_ = *vector_pobj(vector_arg(2));
hoc_obj_ref(efun_py_arg_);
vec_py_save_ = vector_new2(efun_py_arg_->u.this_pointer);
nvar_ = vector_capacity(vec_py_save_);
px = vector_vec(vec_py_save_);
}else{
nvar_ = (int)chkarg(1, 0., 1e6);
efun_sym_ = hoc_lookup(gargstr(2));
if (!efun_sym_
|| (efun_sym_->type != FUNCTION
&& efun_sym_->type != FUN_BLTIN)) {
hoc_execerror(gargstr(2), "not a function name");
}
if (!hoc_is_pdouble_arg(3)) {
void* vec = vector_arg(3);
if (vector_capacity(vec) != nvar_) {
hoc_execerror("first arg not equal to size of Vector",0);
}
px = vector_vec(vec);
}else{
px = hoc_pgetarg(3);
}
}
minarg_ = (double*)ecalloc(nvar_, sizeof(double));
if (maxstepsize == 0.) {
hoc_execerror("call attr_praxis first to set attributes", 0);
}
machep = 1e-15;
if (ifarg(4)) {
after_quad = gargstr(4);
}else{
after_quad = (char*)0;
}
/* save the values set by earlier invocation */
minerrsav = minerr;
minargsav = minarg;
tolerancesav = tolerance;
maxstepsizesav = maxstepsize;
printmodesav = printmode;
nvarsav = nvar;
efun_sym_sav = hoc_efun_sym;
efun_py_save = efun_py;
efun_py_arg_save = efun_py_arg;
vec_py_save_save = vec_py_save;
/* copy this invocation values to the statics */
minerr = minerr_;
minarg = minarg_;
nvar = nvar_;
hoc_efun_sym = efun_sym_;
efun_py = efun_py_;
efun_py_arg = efun_py_arg_;
vec_py_save = vec_py_save_;
minerr=1e9;
err = praxis(&tolerance, &machep, &maxstepsize, nvar, &printmode,
px, efun, &fmin, after_quad);
err = minerr;
if (minerr < 1e9) {
for (i=0; i<nvar; ++i) { px[i] = minarg[i]; }
}
/* restore the values set by earlier invocation */
minerr = minerrsav;
minarg = minargsav;
tolerance = tolerancesav;
maxstepsize = maxstepsizesav;
printmode = printmodesav;
nvar = nvar_; /* in case one calls prax_pval */
hoc_efun_sym = efun_sym_sav;
efun_py = efun_py_save;
efun_py_arg = efun_py_arg_save;
vec_py_save = vec_py_save_save;
if (efun_py_) {
double* px = vector_vec(efun_py_arg_->u.this_pointer);
for (i=0; i < nvar_; ++i) {
px[i] = minarg_[i];
}
hoc_obj_unref(efun_py_);
hoc_obj_unref(efun_py_arg_);
vector_delete(vec_py_save_);
}
if (minarg_) {
free(minarg_);
}
hoc_retpushx(err);
}