void LinearMechanism::create()
{
int i;
lmfree();
i = 0;
Object* o = *hoc_objgetarg(++i);
if (strcmp(o->ctemplate->sym->name, "PythonObject") == 0) {
f_callable_ = o;
hoc_obj_ref(o);
c_ = matrix_arg(++i);
} else {
f_callable_ = NULL;
c_ = matrix_arg(1);
}
g_ = matrix_arg(++i);
y_ = vector_arg(++i);
if (ifarg(i + 2) && hoc_is_object_arg(i + 2) && is_vector_arg(i + 2)) {
y0_ = vector_arg(++i);
}
b_ = vector_arg(++i);
if (ifarg(++i)) {
#if HAVE_IV
Oc oc;
#endif
if (hoc_is_double_arg(i)) {
nnode_ = 1;
nodes_ = new Node*[1];
double x = chkarg(i, 0., 1.);
Section* sec = chk_access();
nodes_[0] = node_exact(sec, x);
nrn_notify_when_double_freed(&NODEV(nodes_[0]), this);
}else{
Object* o = *hoc_objgetarg(i);
check_obj_type(o, "SectionList");
SectionList* sl = new SectionList(o);
sl->ref();
Vect* x = vector_arg(i+1);
Section* sec;
nnode_ = 0;
nodes_ = new Node*[x->capacity()];
for (sec = sl->begin(); sec; sec = sl->next()) {
nodes_[nnode_] = node_exact(sec, x->elem(nnode_));
nrn_notify_when_double_freed(&NODEV(nodes_[nnode_]), this);
++nnode_;
}
if (ifarg(i+2)) {
elayer_ = vector_arg(i+2);
}
sl->unref();
}
}
model_ = new LinearModelAddition(c_, g_, y_, y0_, b_,
nnode_, nodes_, elayer_, f_callable_);
}
JNIEXPORT jlong JNICALL Java_neuron_Neuron_vectorNew
(JNIEnv *env, jclass, jint size){
jnisave
Vect* v = vector_new1(size);
Object* ho = hoc_new_object(nrn_vec_sym, v);
hoc_obj_ref(ho);
jlong jc = (jlong)ho;
jnirestore
return jc;
}
HocCommand::HocCommand(Object* pobj) {
// must wrap a PyObject method or tuple of (method, arg1, ...)
// hold a reference to the wrapped PyObject
if (strcmp(pobj->ctemplate->sym->name, "PythonObject") != 0) {
hoc_execerror(hoc_object_name(pobj), "not a PythonObject");
}
po_ = pobj;
hoc_obj_ref(po_);
s_ = NULL;
obj_ = NULL;
}
static double extra_scatter_gather(void* v) {
int direction = int(chkarg(1, 0, 1));
Object* o = *hoc_objgetarg(2);
check_obj_type(o, "PythonObject");
ExtraScatterList* esl = extra_scatterlist[direction];
if (!esl) {
esl = new ExtraScatterList(2);
extra_scatterlist[direction] = esl;
}
esl->append(o);
hoc_obj_ref(o);
return 0.;
}
JNIEXPORT jlong JNICALL Java_neuron_Neuron_getNewHObject
(JNIEnv *env, jclass, jstring name, jint narg){
jnisave
const char* cn = env->GetStringUTFChars(name, 0);
// Symbol* s = hoc_table_lookup(cn, hoc_top_level_symlist);
Symbol* s = hoc_lookup(cn);
if (!s || s->type != TEMPLATE) {
printf("getNewHObject could not lookup %s or it is not a template.\n", cn);
return 0;
}
env->ReleaseStringUTFChars(name, cn);
Object* o = hoc_newobj1(s, narg);
hoc_obj_ref(o);
jnirestore
return (jlong)o;
}
static jobject h2jObject(Object* o) {
jobject jo;
if (o == 0) {
return 0;
}
hoc_obj_ref(o);
// one of several possibilities here
if (o->ctemplate->id < 0) { // a Java object
jo = (jobject)o->u.this_pointer;
}else if (o->ctemplate->sym == nrn_jobj_sym) {
// an unregistered java object
jo = (jobject)o->u.this_pointer;
}else{ //encapsulate in HocObject, HocVector, etc.
jo = nj_encapsulate(o);
}
return jo;
}
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);
}
