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/*
© Copyright 2008 Randal A. Koene <randalk@netmorph.org>
With design assistance from J. van Pelt & A. van Ooyen, and support
from the Netherlands Organization for Scientific Research (NWO)
Program Computational Life Sciences grant CLS2003 (635.100.005) and
from the EC Marie Curie Research and Training Network (RTN)
NEURoVERS-it 019247.
This file is part of NETMORPH.
NETMORPH is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
NETMORPH 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 General Public License for more details.
You should have received a copy of the GNU General Public License
along with NETMORPH. If not, see <http://www.gnu.org/licenses/>.
*/
// prepost_structure.cc
// Randal A. Koene, 20041118
#include "global.hh"
#include "prepost_structure.hh"
#include "axon_direction_model.hh"
#include "neuron.hh"
#include "network.hh"
#include "Command_Line_Parameters.hh"
// [UPDATE 20080702:] The case in which we define INCLUDE_SCHEMA_PARENT_SET_PROTOCOL_DIRECTION_MODELS is now REQUIRED for compilation.
// [UPDATE AC 20110322:] Added _typeid to fibre_structure to enable distinction between Apical and Basal dendrites.
natural_schema_parent_set axons_most_specific_natural_set[UNTYPED_NEURON+1] = {
all_axons_sps,
all_interneuron_axons_sps,
all_multipolar_axons_sps,
all_bipolar_axons_sps,
all_pyramidal_axons_sps,
all_axons_sps
};
presynaptic_structure::presynaptic_structure(neuron & _n, Segment & initseg, spatial & acoords, int _typeid): fibre_structure(_n,initseg,acoords, _typeid) {
// If a general or specific parameter settings so indicate, the terminal
// segment created in this constructor can be associated with a direction
// model.
// [***INCOMPLETE] Only general parameter settings are recognized so far.
// See TL#200511060626.2, DIL#20051105072005.1 and TL#200603111137.1.
// Despite this incompleteness, the linking of contributing models is already
// done through arbor-specific detection in the CLP.
// PROTOCOL: As described in task log entries of DIL#20070612153815.1, protocol-compliant sets have
// model schema assigned to them. Therefore, components need only look for the schema of the most
// specific (narrow) set to which they belong.
// [***INCOMPLETE] This is a crude way to parse applicable subsets
// (see TL#200603120618.4)
// Beware: I assume elmodel==NULL during initialization!
// A hierarchy of natural subsets (see DIL#20060323042401.1)
network * net = general_neuron_parameters.Cached_Net();
if (!net) error("Error: Applicable model schema for the network must be determined before specifying models and parameters for each neuron.\n");
int regid = net->Regions().find(*N()) + 1; // Adding 1 automatically shifts regid to 0 (the "universal network") when the neuron is not found in a defined region.
terminal_segment * ts = terminalsegments.head();
neuron_type ntype = N()->TypeID();
natural_schema_parent_set nset = axons_most_specific_natural_set[ntype];
//cout << "PRESYN FIBER: NEURON " << N()->numerical_ID() << " belongs to region number " << regid << " with nset " << nset << '\n';
bmmodel = branching_model_region_subset_schemas[regid][nset]->clone(this);
ts->set_branch_angle_model(branch_angle_model_region_subset_schemas[regid][nset]->clone());
elmodel = arbor_elongation_model_region_subset_schemas[regid][nset]->clone();
ts->set_ERI_model(elongation_rate_initialization_model_region_subset_schemas[regid][nset]->clone()); // This must come before TSEM (see TL#200807020156.10).
ts->set_elongation_model(terminal_segment_elongation_model_region_subset_schemas[regid][nset]->clone(ts));
ts->set_TSBM_model(TSBM_region_subset_schemas[regid][nset]->clone(ts));
ts->set_TSTM_model(TSTM_region_subset_schemas[regid][nset]->clone());
ts->set_direction_model(direction_model_region_subset_schemas[regid][nset]->clone());
structure_initialization_region_subset_schemas[regid][nset].initialize(this);
}
terminal_segment_ptr * presynaptic_structure::array_of_terminal_segments() {
// an array with pointers to all terminal segments in all axonal trees
terminalarraylength = terminalsegments.length();
PLL_LOOP_FORWARD(fibre_structure,Next(),1) terminalarraylength += e->TerminalSegments()->length();
if (terminalarraylength==0) return NULL;
terminal_segment_ptr * tsarray = new terminal_segment_ptr[terminalarraylength];
int i = 0;
PLL_LOOP_FORWARD_NESTED(fibre_structure,this,1,ps) {
PLL_LOOP_FORWARD(terminal_segment,ps->TerminalSegments()->head(),1) tsarray[i++] = e;
}
return tsarray;
}
#ifdef SAMPLES_INCLUDE_NETWORK_STATISTICS_BASE
void presynaptic_structure::Collect_Data(network_statistics_base & nsb) {
if (nsb.netstats[axons_termsegs_n].Collect()) nsb.netstats[axons_termsegs_n].Collect_Data((double) terminalsegments.length());
fibre_collected_data fcd(nsb,true);
PLL_LOOP_FORWARD(terminal_segment,terminalsegments.head(),1) e->Collect_Data(fcd); // this must be done first (includes update_segment_vector())
fibre_segment::Collect_Data(fcd);
nsb.netstats[axons_arbor_len].Collect_Data(fcd.arborlength);
}
#endif
natural_schema_parent_set dendrites_most_specific_natural_set[UNTYPED_NEURON+1] = {
all_dendrites_sps,
all_interneuron_dendrites_sps,
all_multipolar_dendrites_sps,
all_bipolar_dendrites_sps,
all_pyramidal_dendrites_sps,
all_dendrites_sps
};
postsynaptic_structure::postsynaptic_structure(neuron & _n, Segment & initseg, spatial & acoords, int _typeid): fibre_structure(_n,initseg,acoords, _typeid) {
// If a general or specific parameter settings so indicate, the terminal
// segment created in this constructor can be associated with a direction
// model.
// [***INCOMPLETE] Only general parameter settings are recognized so far.
// See TL#200511060626.2.
// PROTOCOL: As described in task log entries of DIL#20070612153815.1, protocol-compliant sets have
// model schema assigned to them. Therefore, components need only look for the schema of the most
// specific (narrow) set to which they belong.
// [***INCOMPLETE] This is a crude way to parse applicable subsets
// (see TL#200603120618.4)
// A hierarchy of natural subsets (see DIL#20060323042401.1)
network * net = general_neuron_parameters.Cached_Net();
if (!net) error("Error: Applicable model schema for the network must be determined before specifying models and parameters for each neuron.\n");
int regid = net->Regions().find(*N()) + 1; // Adding 1 automatically shifts regid to 0 (the "universal network") when the neuron is not found in a defined region.
terminal_segment * ts = terminalsegments.head();
neuron_type ntype = N()->TypeID();
natural_schema_parent_set nset = dendrites_most_specific_natural_set[ntype];
if ((ntype==PYRAMIDAL) && (_typeid==ALL_APICAL_PYRAMIDAL_DENDRITES_AEM)) nset = all_apical_pyramidal_dendrites_sps;
bmmodel = branching_model_region_subset_schemas[regid][nset]->clone(this);
ts->set_branch_angle_model(branch_angle_model_region_subset_schemas[regid][nset]->clone());
elmodel = arbor_elongation_model_region_subset_schemas[regid][nset]->clone();
ts->set_ERI_model(elongation_rate_initialization_model_region_subset_schemas[regid][nset]->clone()); // This must come before TSEM (see TL#200807020156.10).
ts->set_elongation_model(terminal_segment_elongation_model_region_subset_schemas[regid][nset]->clone(ts));
ts->set_TSBM_model(TSBM_region_subset_schemas[regid][nset]->clone(ts));
ts->set_TSTM_model(TSTM_region_subset_schemas[regid][nset]->clone());
ts->set_direction_model(direction_model_region_subset_schemas[regid][nset]->clone());
structure_initialization_region_subset_schemas[regid][nset].initialize(this);
}
terminal_segment_ptr * postsynaptic_structure::array_of_terminal_segments() {
// an array with pointers to all terminal segments in all dendritic trees
terminalarraylength = terminalsegments.length();
PLL_LOOP_FORWARD(fibre_structure,Next(),1) terminalarraylength += e->TerminalSegments()->length();
if (terminalarraylength==0) return NULL;
terminal_segment_ptr * tsarray = new terminal_segment_ptr[terminalarraylength];
int i = 0;
PLL_LOOP_FORWARD_NESTED(fibre_structure,this,1,ps) {
PLL_LOOP_FORWARD(terminal_segment,ps->TerminalSegments()->head(),1) tsarray[i++] = e;
}
return tsarray;
}
#ifdef SAMPLES_INCLUDE_NETWORK_STATISTICS_BASE
void postsynaptic_structure::Collect_Data(network_statistics_base & nsb) {
if (nsb.netstats[dendrites_termsegs_n].Collect()) nsb.netstats[dendrites_termsegs_n].Collect_Data((double) terminalsegments.length());
fibre_collected_data fcd(nsb,false);
PLL_LOOP_FORWARD(terminal_segment,terminalsegments.head(),1) e->Collect_Data(fcd); // this must be done first
fibre_segment::Collect_Data(fcd);
nsb.netstats[dendrites_arbor_len].Collect_Data(fcd.arborlength);
}
#endif
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