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transformator.cpp
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transformator.cpp
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/*
* Copyright (c) 2009-2019: G-CSC, Goethe University Frankfurt
*
* Author: Stephan Grein
* Creation date: 2013-11-06
*
* This file is part of NeuroBox, which is based on UG4.
*
* NeuroBox and UG4 are free software: You can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License version 3
* (as published by the Free Software Foundation) with the following additional
* attribution requirements (according to LGPL/GPL v3 §7):
*
* (1) The following notice must be displayed in the appropriate legal notices
* of covered and combined works: "Based on UG4 (www.ug4.org/license)".
*
* (2) The following notice must be displayed at a prominent place in the
* terminal output of covered works: "Based on UG4 (www.ug4.org/license)".
*
* (3) The following bibliography is recommended for citation and must be
* preserved in all covered files:
* "Reiter, S., Vogel, A., Heppner, I., Rupp, M., and Wittum, G. A massively
* parallel geometric multigrid solver on hierarchically distributed grids.
* Computing and visualization in science 16, 4 (2013), 151-164"
* "Vogel, A., Reiter, S., Rupp, M., Nägel, A., and Wittum, G. UG4 -- a novel
* flexible software system for simulating PDE based models on high performance
* computers. Computing and visualization in science 16, 4 (2013), 165-179"
* "Stepniewski, M., Breit, M., Hoffer, M. and Queisser, G.
* NeuroBox: computational mathematics in multiscale neuroscience.
* Computing and visualization in science (2019).
* "Breit, M. et al. Anatomically detailed and large-scale simulations studying
* synapse loss and synchrony using NeuroBox. Front. Neuroanat. 10 (2016), 8"
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*/
/// TODO: Use the ForAllSections(sec) construct to replace the cumbersome for loop constructs in the other methods if necessary!
/// NOTE: Section* sec = chk_access() and secname(sec) will give the currently
/// accessed session, this could be handy in future, e. g. for the clamp constructs
/// TODO: Find out why purge does not work as expected: exit() is called on quit() hoc command. This is not what we want in advance.
#include "transformator.h"
// define nil (how to circumvent that define?)
#define nil NULL
// necessary NEURON includes
#include "oc2iv.h"
#include "ocjump.cpp"
#include "ivocmain.cpp"
#include "section.h"
// #include "cabcode.c" -> depends on python probably and we do not need it
// extern void hoc_final_exit();
// extern void ivoc_final_exit();
// necessary stdlib includes
#include <string>
#include <vector>
#include <sstream>
#include <map>
#include <iostream>
// ug includes
#include <common/log.h>
#include <common/error.h>
#include <lib_disc/function_spaces/integrate.h>
// extern C functions (NEURON)
extern bool hoc_valid_stmt(const char* stmt, Object* ob);
#ifndef MPMNEURON_REVISION
extern int ivocmain(int, char**, char**);
#else
extern int ivocmain(int, const char**, const char**);
extern const char* secname(Section*);
extern Section* chk_access(void);
// extern Section* nrn_noerr_access(); -> depends on python probably
#endif
//void ivoc_cleanup() { return; } // TODO: UNDEF this afterwards (When fixing includes in ivoc.cpp it becomes available!)
extern double hoc_ac_;
// using namespace
using namespace ug::membrane_potential_mapping;
// initialize static members
int Transformator::ARGC = 0;
char* Transformator::ARGV[] = {0};
char* Transformator::ENV[] = {0};
/////////////////////////////////////////////////////////
// feedback
/////////////////////////////////////////////////////////
void Transformator::feedback(const char* uCmp, const char* subset, const char* subset_vol, double density) {
ug::GridSubsetHandler sh(*mGrid);
// size_t si = sh.get_subset_index(subset_vol);
mGrid->attach_to_vertices(ug::aPosition);
ug::Grid::VertexAttachmentAccessor<ug::APosition3> aaPos(*mGrid, ug::aPosition);
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// iterate over all triangles in subset 0
for(TetrahedronIterator iter = sh.begin<Tetrahedron>(0); iter != sh.end<Tetrahedron>(0); ++iter) {
Tetrahedron* h = *iter;
ug::vector3 neuron_point(x3d, y3d, z3d);
if (ContainsPoint(h, neuron_point, aaPos)) {
m_saved_neuron_point = neuron_point;
// double Ca_i = 0.;
// TODO: integrate on subset with "subset name" with integrate.h from Andreas Vogel
// IIntegrand<number, 3> integrand;
// number Ca_i = ug::Integrate<1,2, Tetrahedron>(sh.begin<Tetrahedron>(0), sh.end<Tetrahedron>(0), aaPos, integrand, 0, "");
// TODO: For this to work specify channel model first with NMDL language of NEURON
// stmt << "forsec current_section { Cai = " << Ca_i << "}";
break;
}
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
void Transformator::feedbacks(const char* uCmp, const char* subset, const char* subset_vol, double density) {
ug::GridSubsetHandler sh(*mGrid);
// size_t si = sh.get_subset_index(subset_vol);
mGrid->attach_to_vertices(ug::aPosition);
ug::Grid::VertexAttachmentAccessor<ug::APosition3> aaPos(*mGrid, ug::aPosition);
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// iterate over all triangles in subset 0
for(TetrahedronIterator iter = sh.begin<Tetrahedron>(0); iter != sh.end<Tetrahedron>(0); ++iter) {
Tetrahedron* h = *iter;
ug::vector3 neuron_point(x3d, y3d, z3d);
if (ContainsPoint(h, neuron_point, aaPos)) {
// m_saved_neuron_point = neuron_point;
mNeuronPoints.push_back(neuron_point);
// TODO: integrate on subset with "subset name" with integrate.h from Andreas Vogel
// IIntegrand<number, 3> integrand;
// number Ca_i = ug::Integrate<1,2, Tetrahedron>(sh.begin<Tetrahedron>(0), sh.end<Tetrahedron>(0), aaPos, integrand, 0, "");
// TODO: For this to work specify channel model first with NMDL language of NEURON
// stmt << "forsec current_section { Cai = " << Ca_i << "}";
break;
}
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
/// set feedback
void Transformator::set_feedback() {
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
ug::vector3 neuron_point(x3d, y3d, z3d);
double Ca_i = 0;
if (m_saved_neuron_point.x() == neuron_point.x() && m_saved_neuron_point.y() == neuron_point.y() && m_saved_neuron_point.z() == neuron_point.z()) {
Ca_i = m_saved_neuron_point_integral;
}
stmt << "forsec current_section { cai = " << Ca_i << "}"; // for this to work specify channel model with NMDL language of NEURON
break;
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
/// set feedbacks
void Transformator::set_feedbacks() {
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
ug::vector3 neuron_point(x3d, y3d, z3d);
double Ca_i = 0;
size_t index = 0;
for (std::vector<ug::vector3>::const_iterator cit = mNeuronPoints.begin(); cit != mNeuronPoints.end(); cit++) {
if (cit->x() == neuron_point.x() && cit->y() == neuron_point.y() && cit->z() == neuron_point.z()) {
Ca_i = mIntegrals[index];
stmt << "forsec current_section { cai = " << Ca_i << "}"; // for this to work specify channel model with NMDL language of NEURON
break;
}
index++;
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
/////////////////////////////////////////////////////////
// init feedback
/////////////////////////////////////////////////////////
void Transformator::init_feedback(const char* uCmp, const char* subset, const char* subset_vol, double density, const char* channel) {
ug::GridSubsetHandler sh(*mGrid);
// size_t si = sh.get_subset_index(subset_vol);
mGrid->attach_to_vertices(ug::aPosition);
ug::Grid::VertexAttachmentAccessor<ug::APosition3> aaPos(*mGrid, ug::aPosition);
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// iterate over all triangles in subset 0
for(TetrahedronIterator iter = sh.begin<Tetrahedron>(0); iter != sh.end<Tetrahedron>(0); ++iter) {
Tetrahedron* h = *iter;
ug::vector3 neuron_point(x3d, y3d, z3d);
if (ContainsPoint(h, neuron_point, aaPos)) {
stmt.clear();
stmt << "forsec current_section { insert " << channel << "}";
hoc_valid_stmt(stmt.str().c_str(), 0);
break;
}
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
// init feedbacks
void Transformator::init_feedbacks(const char* uCmp, const char* subset, const char* subset_vol, double density, const char* channel) {
ug::GridSubsetHandler sh(*mGrid);
// size_t si = sh.get_subset_index(subset_vol);
mGrid->attach_to_vertices(ug::aPosition);
ug::Grid::VertexAttachmentAccessor<ug::APosition3> aaPos(*mGrid, ug::aPosition);
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// iterate over all triangles in subset 0
for(TetrahedronIterator iter = sh.begin<Tetrahedron>(0); iter != sh.end<Tetrahedron>(0); ++iter) {
// Tetrahedron* h = *iter;
ug::vector3 neuron_point(x3d, y3d, z3d);
for (std::vector<ug::vector3>::const_iterator cit = mNeuronPoints.begin(); cit != mNeuronPoints.end(); cit++) {
if (cit->x() == neuron_point.x() && cit->y() == neuron_point.y() && cit->z() == neuron_point.z()) {
stmt << "forsec current_section { insert " << channel << "}"; // for this to work specify channel model with NMDL language of NEURON
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.clear();
}
}
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
/////////////////////////////////////////////////////////
// adjust_resisitivity_obstacle
/////////////////////////////////////////////////////////
void Transformator::adjust_resistivity_obstacle(const char* uCmp, const char* subset, double Rai) {
ug::GridSubsetHandler sh(*mGrid);
//size_t si = sh.get_subset_index(subset);
mGrid->attach_to_vertices(ug::aPosition);
ug::Grid::VertexAttachmentAccessor<ug::APosition3> aaPos(*mGrid, ug::aPosition);
// get NEURON parameters
size_t no_sections = m_sections;
for (size_t k = 0; k <= no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// iterate over all triangles in subset 0
for(TetrahedronIterator iter = sh.begin<Tetrahedron>(0); iter != sh.end<Tetrahedron>(0); ++iter) {
Tetrahedron* h = *iter;
ug::vector3 neuron_point(x3d, y3d, z3d);
if (ContainsPoint(h, neuron_point, aaPos)) {
double Rai_new = Rai;
stmt << "forsec current_section { Ra = " << Rai_new << "}";
break;
}
}
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
}
Transformator::Transformator() : m_sections(0), m_totalPoints(0), m_finitialize(0.0), m_tstart(0), m_tstop(0), m_dt(0), m_t(0), m_limit(0){
init(ARGC, ARGV, ENV);
}
Transformator::Transformator(int argc, char* argv[], char* env[]) : m_sections(0), m_totalPoints(0), m_finitialize(0.0), m_tstart(0), m_tstop(0), m_dt(0), m_t(0), m_limit(0) {
init();
}
Transformator::Transformator(const char* modFiles) : m_sections(0), m_totalPoints(0), m_finitialize(0.0), m_tstart(0), m_tstop(0), m_dt(0), m_t(0), m_limit(0) {
init(modFiles);
}
bool Transformator::init(const char* modFiles) {
// init ivocmain (hoc) interpreter
#ifdef MPMNEURON_REVISION
const char* args[] = { modFiles };
const char* env[] = {0};
int init = ivocmain(1, args, env);
#else
std::stringstream ss;
ss << modFiles;
char* args[] = { const_cast<char*>(ss.str().c_str()) };
char* env[] = {0};
int init = ivocmain(1, ARGV, ENV);
#endif
// check for success
if (init != 0) {
UG_THROW("ivocmain (hoc interpreter) could not be initialized by Transformator::init." << std::endl);
}
return true;
}
Transformator::~Transformator() {
purge();
}
bool Transformator::init() {
// init ivocmain (hoc) interpreter
const char* a[] = {0};
const char* e[] = {0};
#ifdef MPMNEURON_REVISION
int init = ivocmain(0, a, e);
#else
int init = ivocmain(ARGC, ARGV, ENV);
#endif
// check for success
if (init != 0) {
UG_THROW("ivocmain (hoc interpreter) could not be initialized by Transformator::init." << std::endl);
}
return true;
}
bool Transformator::init(int argc, char* argv[], char* env[]) {
const char* a[] = {0};
const char* e[] = {0};
#ifdef MPMNEURON_REVISION
int init = ivocmain(0, a, e);
#else
int init = ivocmain(ARGC, ARGV, ENV);
#endif
// check for success
if (init != 0) {
UG_THROW("ivocmain (hoc interpreter) could not be initialized by Transformator::init." << std::endl);
}
// return status
return true;
}
void Transformator::prepare() {
// add initializing statements
m_stmts.clear();
m_stmts.push_back("objref current_section");
m_stmts.push_back("current_section_index = 0"); // Note: Was this correct here previously we excluded this?
m_stmts.push_back("current_section = new SectionList()");
m_stmts.push_back("forall { current_section_index = current_section_index + 1 }");
m_stmts.push_back("hoc_ac_ = current_section_index");
// error indicator
bool ret = true;
// execute all statements in accumulator
for (std::vector<std::string>::const_iterator it = m_stmts.begin(); it != m_stmts.end(); it++) {
ret = (ret && hoc_valid_stmt((*it).c_str(), 0));
}
// clear accumulator
m_stmts.clear();
// assign number of retrieved sections to member
m_sections = static_cast<size_t>(hoc_ac_);
// total points
size_t total_points = 0;
for (size_t k = 0; k < m_sections+1; k++) { // was +1
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
ret = (ret && hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0));
total_points += static_cast<size_t>(hoc_ac_);
}
m_totalPoints = total_points;
// check for succcess of all prepare statements
if (!ret) {
UG_LOG("At least one of the statements in Transformator::prepare did not succeed." << std::endl);
}
}
void Transformator::load_geom(const std::string& file) {
if (m_geometry.compare(file) == 0) {
UG_WARNING("NEURON/hoc interpreter does not allow reloading the same geometry file. You may encounter undefined behaviour!")
}
// create hoc command
std::stringstream ss;
ss << "{load_file(1, \"" << file << "\")}";
// check for success
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (!ret) {
UG_LOG("Could not load hoc file: " << file << " with Transformator::load_hoc." << std::endl);
}
// cleanup stringstream
ss.str("");
ss.flush();
// set defining geometry file
m_geometry = file;
// set number of sections
prepare();
}
void Transformator::load_stim(const std::string& file) {
if (m_stimulation.compare(file) == 0) {
UG_WARNING("NEURON/hoc interpreter does not allow reloading the same stimulation file. You may encounter undefined behaviour!")
}
// create hoc command
std::stringstream ss;
ss << "{load_file(1, \"" << file << "\")}";
// check for success
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (!ret) {
UG_LOG("Could not load hoc file: " << file << " with Transformator::load_hoc." << std::endl);
}
// cleanup stringstream
ss.str("");
ss.flush();
// set defining stimulation file
m_stimulation = file;
}
void Transformator::setup_hoc(number tstart, number tstop, number dt, number finitialize) {
// command string
std::stringstream ss;
// return value
bool ret = true;
// tstart
ss << "{tstart = " << tstart << "}";
ret = (ret && hoc_valid_stmt(ss.str().c_str(), 0));
ss.str("");
// tstop
ss << "{tstop = " << tstop << "}";
ret = (ret && hoc_valid_stmt(ss.str().c_str(), 0));
ss.str("");
// dt
ss << "{dt = " << dt << "}";
ret = (ret && hoc_valid_stmt(ss.str().c_str(), 0));
ss.str("");
// finitialize
ss << "{finitialize(" << finitialize << ")}";
ret = (ret && hoc_valid_stmt(ss.str().c_str(), 0));
ss.str("");
m_finitialize = finitialize;
// setup initial values (i. e. -75.0 mV)
m_vms.clear();
size_t no_sections = m_sections;
std::vector<std::pair<std::vector<number>, number> > local_vms;
for (size_t k = 0; k < no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = hoc_ac_;
if (ret) {
for (size_t j=0; j < no_points; j++) {
// stmt string
std::stringstream stmt;
// VM
stmt << "forsec current_section { hoc_ac_ = v(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
number vm = hoc_ac_;
stmt.str("");
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// create vector with membrane potential
std::vector<number> coords;
coords.push_back(x3d);
coords.push_back(y3d);
coords.push_back(z3d);
std::pair<std::vector<number>, number> pair = std::pair<std::vector<number>, number>(coords, vm);
local_vms.push_back(pair);
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
m_vms.push_back(local_vms);
local_vms.clear();
}
bool Transformator::set_hoc_variable(const std::string& var, number value) {
std::stringstream ss;
ss.precision(std::numeric_limits<number>::digits10);
ss << var << " = " << value;
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not execute hoc stmt: " << "var = " << value << " in Transformator::set_hoc_variable" << std::endl);
}
return ret;
}
bool Transformator::set_hoc_variable_sec(const std::string& var, number value, const std::string& section) {
std::stringstream ss;
ss << "access" << " " << section;
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not execute hoc stmt: " << "access " << section << " in Transformator::set_hoc_variable_sec (Probably section does not exist)" << std::endl);
return ret;
}
return set_hoc_variable(var, value);
}
number Transformator::get_hoc_variable(const std::string& var) {
std::stringstream ss;
ss << "hoc_ac_" << " = " << var;
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not execute hoc stmt: " << "hoc_ac_ = " << var << " in Transformator::get_hoc_variable" << std::endl);
}
return static_cast<number>(hoc_ac_);
}
number Transformator::get_hoc_variable_sec(const std::string& var, const std::string& section) {
std::stringstream ss;
ss << "access" << " " << section;
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not execute hoc stmt: " << "access " << section << " in Transformator::set_hoc_variable_sec (Probably section does not exist)" << std::endl);
return ret;
}
return get_hoc_variable(var);
}
number Transformator::execute_hoc_stmt(const std::string& stmt) const {
bool ret = hoc_valid_stmt(stmt.c_str(), 0);
number val = 0.;
if (ret != 1) {
UG_LOG("Could not execute hoc stmt: " << stmt << " in Transformator::execute_hoc_stmt." << std::endl);
}
val = static_cast<number>(hoc_ac_);
return val;
}
std::vector<number> Transformator::execute_hoc_stmts(const std::vector<std::string>& stmts) const {
bool ret = true;
std::vector<number> val;
for (std::vector<std::string>::const_iterator it = stmts.begin(); it != stmts.end(); it++) {
ret = (ret && hoc_valid_stmt(it->c_str(), 0));
val.push_back(static_cast<number>(hoc_ac_));
}
if (ret != 1) {
UG_LOG("Could not execute at least one of the hoc stmts in Transformator::execute_hoc_stmts." << std::endl);
}
return val;
}
bool Transformator::fadvance() {
bool ret = hoc_valid_stmt("fadvance()", 0);
if (!ret) {
UG_LOG("Could not execute the fadvance() command in Transformator::fadvance()." << std::endl);
}
return ret;
}
size_t Transformator::get_limit() const {
return m_limit;
}
size_t Transformator::get_sections() const {
return m_sections;
}
size_t Transformator::get_total_points() const {
return m_totalPoints;
}
number Transformator::get_tstart() {
// command string
std::stringstream ss;
ss << "hoc_ac_ = tstart";
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not acquire value of tstart by Transformator::get_tstart." << std::endl);
}
number tstart = static_cast<number>(hoc_ac_);
m_tstart = tstart;
return tstart;
}
number Transformator::get_tstop() {
// command string
std::stringstream ss;
ss << "hoc_ac_ = tstop";
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not acquire value of tstop by Transformator::get_tstop." << std::endl);
}
number tstop = static_cast<number>(hoc_ac_);
m_tstop = tstop;
return tstop;
}
number Transformator::get_dt() {
// command string
std::stringstream ss;
ss << "hoc_ac_ = dt";
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not acquire value of dt by Transformator::get_dt." << std::endl);
}
number dt = static_cast<number>(hoc_ac_);
m_dt = dt;
return dt;
}
number Transformator::get_finitialize() const {
return m_finitialize;
}
number Transformator::get_t() {
// command string
std::stringstream ss;
ss << "hoc_ac_ = t";
bool ret = hoc_valid_stmt(ss.str().c_str(), 0);
if (ret != 1) {
UG_LOG("Could not acquire value of t by Transformator::get_t." << std::endl);
}
number t = static_cast<number>(hoc_ac_);
m_t = t;
return t;
}
void Transformator::extract_vms(size_t limit, size_t steps) {
m_limit += limit;
m_vms.clear();
size_t no_sections = m_sections;
size_t no_steps = steps;
for (size_t i=1; i <= limit; i++) {
std::vector<std::pair<std::vector<number>, number> > local_vms;
// fadvance multiple times
bool ret_outer = true;
for (size_t l=1; l <= no_steps; l++) {
ret_outer = (ret_outer && hoc_valid_stmt("{fadvance()}", 0));
}
if (ret_outer) {
for (size_t k = 0; k < no_sections; k++) {
hoc_valid_stmt("j = 0", 0);
hoc_valid_stmt("current_section = new SectionList()", 0);
std::stringstream cmd;
cmd << "forall{ if (j == " << k << ") { {current_section.append() } } { j = j + 1} }";
hoc_valid_stmt(cmd.str().c_str(), 0);
cmd.str("");
bool ret = hoc_valid_stmt("forsec current_section { hoc_ac_ = n3d() - 1}", 0);
size_t no_points = static_cast<size_t>(hoc_ac_);
if (ret) {
for (size_t j=0; j <= no_points; j++) {
// stmt string
std::stringstream stmt;
// VM
stmt << "forsec current_section { hoc_ac_ = v(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
number vm = hoc_ac_;
stmt.str("");
// X
stmt << "forsec current_section { hoc_ac_ = x3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number x3d = hoc_ac_;
// Y
stmt << "forsec current_section { hoc_ac_ = y3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number y3d = hoc_ac_;
// Z
stmt << "forsec current_section { hoc_ac_ = z3d(" << j << ")}";
hoc_valid_stmt(stmt.str().c_str(), 0);
stmt.str("");
number z3d = hoc_ac_;
// create vector with membrane potential
std::vector<number> coords;
coords.push_back(x3d);
coords.push_back(y3d);
coords.push_back(z3d);
std::pair<std::vector<number>, number> pair = std::pair<std::vector<number>, number>(coords, vm);
local_vms.push_back(pair);
} // for points
} // ret no_points
// remove every covered section of current_section SectionList ...
hoc_valid_stmt("{current_section.remove(current_section)}", 0);
} // for no_sections
} // if ret_outer
m_vms.push_back(local_vms);
local_vms.clear();
} // for limit
}
std::vector<std::vector<std::pair<std::vector<number>, number> > > Transformator::get_vms(size_t limit) const {
std::vector<std::vector<std::pair<std::vector<number>, number> > >::const_iterator begin = m_vms.begin();
std::vector<std::vector<std::pair<std::vector<number>, number> > >::const_iterator end = m_vms.begin() + limit;
if (limit > m_vms.size()) {
return m_vms;
} else {
return std::vector<std::vector<std::pair<std::vector<number>, number> > >(begin, end);
}
}
void Transformator::purge() {
m_vms.clear();
hoc_valid_stmt("forall pt3dclear()", 0);
hoc_valid_stmt("forall delete_section()", 0);