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jasleenksainijasleenksaini
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GraphManager Final Update
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14 files changed

+614
-608
lines changed

14 files changed

+614
-608
lines changed

‎Simulator/Connections/NG911/Connections911.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,7 +22,7 @@ void Connections911::setup()
2222
AllVertices &vertices = layout.getVertices();
2323

2424
// Get list of edges sorted by target in ascending order from GraphManager
25-
GraphManager &gm = GraphManager::getInstance();
25+
GraphManager<NG911VertexProperties> &gm = GraphManager<NG911VertexProperties>::getInstance();
2626
auto sorted_edge_list = gm.edgesSortByTarget();
2727

2828
// add sorted edges

‎Simulator/Core/Core.cpp‎

Lines changed: 16 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -147,11 +147,22 @@ int Core::runSimulation(string executableName, string cmdLineArguments)
147147

148148
// Ask all objects to register their Graph properties
149149
OperationManager::getInstance().executeOperation(Operations::registerGraphProperties);
150-
// Read graph from GraphML file. Uses ParameterManager to get the file name.
151-
// TODO: This method returns false if it fails to read the graph, we ignore it at the
152-
// moment since it currently fails for the Neural Network model because they don't
153-
// yet use GraphML.
154-
GraphManager::getInstance().readGraph();
150+
151+
// Retrieve class attribute from the 'LayoutParams' in the config file
152+
// This value indicate the simulation type (Neural or NG911) for graph manager configuration
153+
// Log fatal error if no simulation type is found and terminate
154+
string configData;
155+
ParameterManager::getInstance().getStringByXpath("//LayoutParams/@class", configData);
156+
157+
if (configData.find("Neur")) {
158+
GraphManager<NeuralVertexProperties>::getInstance().readGraph();
159+
}
160+
if (configData.find("91")) {
161+
GraphManager<NG911VertexProperties>::getInstance().readGraph();
162+
} else {
163+
LOG4CPLUS_FATAL(consoleLogger, "ERROR: Unknown simulation type'");
164+
return -1;
165+
}
155166

156167
// Invoke instantiated simulator objects to load parameters from the configuration file
157168
LOG4CPLUS_TRACE(consoleLogger, "Loading parameters from configuration file");

‎Simulator/Layouts/Layout.cpp‎

Lines changed: 172 additions & 170 deletions
Original file line numberDiff line numberDiff line change
@@ -6,173 +6,175 @@
66
* @brief The Layout class defines the layout of neurons in neural networks
77
*/
88

9-
#include "Layout.h"
10-
#include "Factory.h"
11-
#include "GraphManager.h"
12-
#include "OperationManager.h"
13-
#include "ParameterManager.h"
14-
#include "ParseParamError.h"
15-
#include "RecordableBase.h"
16-
#include "Simulator.h"
17-
#include "Util.h"
18-
19-
/// Constructor
20-
Layout::Layout() : numEndogenouslyActiveNeurons_(0)
21-
{
22-
// Get a copy of the console logger to use in the case of errors
23-
log4cplus::Logger consoleLogger = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("console"));
24-
25-
// Create Vertices/Neurons class using type definition in configuration file
26-
string type;
27-
ParameterManager::getInstance().getStringByXpath("//VerticesParams/@class", type);
28-
vertices_ = Factory<AllVertices>::getInstance().createType(type);
29-
30-
// If the factory returns an error (nullptr), exit
31-
if (vertices_ == nullptr) {
32-
LOG4CPLUS_INFO(consoleLogger, "INVALID CLASS: " + type);
33-
exit(EXIT_FAILURE);
34-
}
35-
36-
// Register loadParameters function as a loadParameters operation in the Operation Manager
37-
function<void()> loadParametersFunc = std::bind(&Layout::loadParameters, this);
38-
OperationManager::getInstance().registerOperation(Operations::loadParameters,
39-
loadParametersFunc);
40-
41-
// Register printParameters function as a printParameters operation in the OperationManager
42-
function<void()> printParametersFunc = bind(&Layout::printParameters, this);
43-
OperationManager::getInstance().registerOperation(Operations::printParameters,
44-
printParametersFunc);
45-
46-
// Register registerGraphProperties method as registerGraphProperties operation
47-
// in the OperationManager
48-
function<void()> registerGraphPropertiesFunc = bind(&Layout::registerGraphProperties, this);
49-
OperationManager::getInstance().registerOperation((Operations::registerGraphProperties),
50-
registerGraphPropertiesFunc);
51-
52-
// Get a copy of the file logger to use log4cplus macros
53-
fileLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("file"));
54-
}
55-
56-
AllVertices &Layout::getVertices() const
57-
{
58-
return *vertices_;
59-
}
60-
61-
int Layout::getNumVertices() const
62-
{
63-
return numVertices_;
64-
}
65-
66-
/// Load member variables from configuration file. Registered to OperationManager as Operations::op::loadParameters
67-
void Layout::loadParameters()
68-
{
69-
numVertices_ = GraphManager::getInstance().numVertices();
70-
}
71-
72-
void Layout::registerGraphProperties()
73-
{
74-
GraphManager &gm = GraphManager::getInstance();
75-
gm.registerProperty("y", &VertexProperty::y);
76-
gm.registerProperty("x", &VertexProperty::x);
77-
gm.registerProperty("type", &VertexProperty::type);
78-
}
79-
80-
/// Setup the internal structure of the class.
81-
/// Allocate memories to store all layout state, no sequential dependency in this method
82-
void Layout::setup()
83-
{
84-
// Allocate memory
85-
xloc_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices_);
86-
yloc_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices_);
87-
dist2_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices_, numVertices_);
88-
dist_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices_, numVertices_);
89-
90-
// more allocation of internal memory
91-
starterMap_.assign(numVertices_, false);
92-
vertexTypeMap_.assign(numVertices_, vertexType::VTYPE_UNDEF);
93-
94-
// Loop over all vertices and set their x and y locations
95-
GraphManager::VertexIterator vi, vi_end;
96-
GraphManager &gm = GraphManager::getInstance();
97-
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
98-
assert(*vi < numVertices_);
99-
xloc_[*vi] = gm[*vi].x;
100-
yloc_[*vi] = gm[*vi].y;
101-
}
102-
103-
// Now we calculate the distance and distance^2
104-
// between each pair of vertices
105-
for (int n = 0; n < numVertices_ - 1; n++) {
106-
for (int n2 = n + 1; n2 < numVertices_; n2++) {
107-
// distance^2 between two points in point-slope form
108-
dist2_(n, n2) = (xloc_[n] - xloc_[n2]) * (xloc_[n] - xloc_[n2])
109-
+ (yloc_[n] - yloc_[n2]) * (yloc_[n] - yloc_[n2]);
110-
111-
// both points are equidistant from each other
112-
dist2_(n2, n) = dist2_(n, n2);
113-
}
114-
}
115-
116-
// Finally take the square root to get the distances
117-
dist_ = sqrt(dist2_);
118-
119-
// Register variable: vertex locations if need
120-
//Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
121-
//string baseName = "Location";
122-
//string xLocation = "x_" + baseName;
123-
//string yLocation = "y_" + baseName;
124-
//recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
125-
//recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
126-
127-
// test purpose
128-
// cout << "xloc_: " << &xloc_ << endl;
129-
// RecordableBase& location = xloc_;
130-
// cout << "location: " << &location << endl;
131-
}
132-
133-
134-
/// Prints out all parameters to logging file. Registered to OperationManager as Operation::printParameters
135-
void Layout::printParameters() const
136-
{
137-
GraphManager::VertexIterator vi, vi_end;
138-
GraphManager &gm = GraphManager::getInstance();
139-
stringstream output;
140-
output << "\nLAYOUT PARAMETERS" << endl;
141-
output << "\tEndogenously active neuron positions: ";
142-
143-
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
144-
assert(*vi < numVertices_);
145-
if (gm[*vi].active) {
146-
output << *vi << " ";
147-
}
148-
}
149-
output << endl;
150-
151-
output << "\tInhibitory neuron positions: ";
152-
153-
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
154-
assert(*vi < numVertices_);
155-
if (gm[*vi].type == "INH") {
156-
output << *vi << " ";
157-
}
158-
}
159-
output << endl;
160-
161-
LOG4CPLUS_DEBUG(fileLogger_, output.str());
162-
}
163-
164-
/// Creates a vertex type map.
165-
/// @param numVertices number of the vertices to have in the type map.
166-
void Layout::generateVertexTypeMap()
167-
{
168-
DEBUG(cout << "\nInitializing vertex type map: VTYPE_UNDEF" << endl;);
169-
vertexTypeMap_.assign(numVertices_, vertexType::VTYPE_UNDEF);
170-
}
171-
172-
/// Populates the starter map.
173-
/// Selects num_endogenously_active_neurons excitory neurons and converts them into starter neurons.
174-
/// @param numVertices number of vertices to have in the map.
175-
void Layout::initStarterMap()
176-
{
177-
starterMap_.assign(numVertices_, false);
178-
}
9+
#include "Layout.h"
10+
#include "Factory.h"
11+
#include "GraphManager.h"
12+
#include "OperationManager.h"
13+
#include "ParameterManager.h"
14+
#include "ParseParamError.h"
15+
#include "RecordableBase.h"
16+
#include "Simulator.h"
17+
#include "Util.h"
18+
19+
/// Constructor
20+
Layout::Layout() : numEndogenouslyActiveNeurons_(0)
21+
{
22+
// Get a copy of the console logger to use in the case of errors
23+
log4cplus::Logger consoleLogger = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("console"));
24+
25+
// Create Vertices/Neurons class using type definition in configuration file
26+
string type;
27+
ParameterManager::getInstance().getStringByXpath("//VerticesParams/@class", type);
28+
vertices_ = Factory<AllVertices>::getInstance().createType(type);
29+
30+
// If the factory returns an error (nullptr), exit
31+
if (vertices_ == nullptr) {
32+
LOG4CPLUS_INFO(consoleLogger, "INVALID CLASS: " + type);
33+
exit(EXIT_FAILURE);
34+
}
35+
36+
// Register loadParameters function as a loadParameters operation in the Operation Manager
37+
function<void()> loadParametersFunc = std::bind(&Layout::loadParameters, this);
38+
OperationManager::getInstance().registerOperation(Operations::loadParameters,
39+
loadParametersFunc);
40+
41+
// Register printParameters function as a printParameters operation in the OperationManager
42+
function<void()> printParametersFunc = bind(&Layout::printParameters, this);
43+
OperationManager::getInstance().registerOperation(Operations::printParameters,
44+
printParametersFunc);
45+
46+
// Register registerGraphProperties method as registerGraphProperties operation
47+
// in the OperationManager
48+
function<void()> registerGraphPropertiesFunc = bind(&Layout::registerGraphProperties, this);
49+
OperationManager::getInstance().registerOperation((Operations::registerGraphProperties),
50+
registerGraphPropertiesFunc);
51+
52+
// Get a copy of the file logger to use log4cplus macros
53+
fileLogger_ = log4cplus::Logger::getInstance(LOG4CPLUS_TEXT("file"));
54+
}
55+
56+
AllVertices &Layout::getVertices() const
57+
{
58+
return *vertices_;
59+
}
60+
61+
int Layout::getNumVertices() const
62+
{
63+
return numVertices_;
64+
}
65+
66+
/// Load member variables from configuration file. Registered to OperationManager as Operations::op::loadParameters
67+
void Layout::loadParameters()
68+
{
69+
numVertices_ = GraphManager<NeuralVertexProperties>::getInstance().numVertices();
70+
}
71+
72+
void Layout::registerGraphProperties()
73+
{
74+
GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
75+
gm.registerProperty("y", &VertexProperties::y);
76+
gm.registerProperty("x", &VertexProperties::x);
77+
gm.registerProperty("type", &VertexProperties::type);
78+
}
79+
80+
81+
/// Setup the internal structure of the class.
82+
/// Allocate memories to store all layout state, no sequential dependency in this method
83+
void Layout::setup()
84+
{
85+
// Allocate memory
86+
xloc_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices_);
87+
yloc_ = VectorMatrix(MATRIX_TYPE, MATRIX_INIT, 1, numVertices_);
88+
dist2_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices_, numVertices_);
89+
dist_ = CompleteMatrix(MATRIX_TYPE, MATRIX_INIT, numVertices_, numVertices_);
90+
91+
// more allocation of internal memory
92+
starterMap_.assign(numVertices_, false);
93+
vertexTypeMap_.assign(numVertices_, vertexType::VTYPE_UNDEF);
94+
95+
// Loop over all vertices and set their x and y locations
96+
GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
97+
GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
98+
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
99+
assert(*vi < numVertices_);
100+
xloc_[*vi] = gm[*vi].x;
101+
yloc_[*vi] = gm[*vi].y;
102+
}
103+
104+
// Now we calculate the distance and distance^2
105+
// between each pair of vertices
106+
for (int n = 0; n < numVertices_ - 1; n++) {
107+
for (int n2 = n + 1; n2 < numVertices_; n2++) {
108+
// distance^2 between two points in point-slope form
109+
dist2_(n, n2) = (xloc_[n] - xloc_[n2]) * (xloc_[n] - xloc_[n2])
110+
+ (yloc_[n] - yloc_[n2]) * (yloc_[n] - yloc_[n2]);
111+
112+
// both points are equidistant from each other
113+
dist2_(n2, n) = dist2_(n, n2);
114+
}
115+
}
116+
117+
// Finally take the square root to get the distances
118+
dist_ = sqrt(dist2_);
119+
120+
// Register variable: vertex locations if need
121+
//Recorder &recorder = Simulator::getInstance().getModel().getRecorder();
122+
//string baseName = "Location";
123+
//string xLocation = "x_" + baseName;
124+
//string yLocation = "y_" + baseName;
125+
//recorder.registerVariable(xLocation, xloc_, Recorder::UpdatedType::CONSTANT);
126+
//recorder.registerVariable(yLocation, yloc_, Recorder::UpdatedType::CONSTANT);
127+
128+
// test purpose
129+
// cout << "xloc_: " << &xloc_ << endl;
130+
// RecordableBase& location = xloc_;
131+
// cout << "location: " << &location << endl;
132+
}
133+
134+
135+
/// Prints out all parameters to logging file. Registered to OperationManager as Operation::printParameters
136+
void Layout::printParameters() const
137+
{
138+
GraphManager<NeuralVertexProperties>::VertexIterator vi, vi_end;
139+
GraphManager<NeuralVertexProperties> &gm = GraphManager<NeuralVertexProperties>::getInstance();
140+
stringstream output;
141+
output << "\nLAYOUT PARAMETERS" << endl;
142+
output << "\tEndogenously active neuron positions: ";
143+
144+
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
145+
assert(*vi < numVertices_);
146+
if (gm[*vi].active) {
147+
output << *vi << " ";
148+
}
149+
}
150+
output << endl;
151+
152+
output << "\tInhibitory neuron positions: ";
153+
154+
for (boost::tie(vi, vi_end) = gm.vertices(); vi != vi_end; ++vi) {
155+
assert(*vi < numVertices_);
156+
if (gm[*vi].type == "INH") {
157+
output << *vi << " ";
158+
}
159+
}
160+
output << endl;
161+
162+
LOG4CPLUS_DEBUG(fileLogger_, output.str());
163+
}
164+
165+
/// Creates a vertex type map.
166+
/// @param numVertices number of the vertices to have in the type map.
167+
void Layout::generateVertexTypeMap()
168+
{
169+
DEBUG(cout << "\nInitializing vertex type map: VTYPE_UNDEF" << endl;);
170+
vertexTypeMap_.assign(numVertices_, vertexType::VTYPE_UNDEF);
171+
}
172+
173+
/// Populates the starter map.
174+
/// Selects num_endogenously_active_neurons excitory neurons and converts them into starter neurons.
175+
/// @param numVertices number of vertices to have in the map.
176+
void Layout::initStarterMap()
177+
{
178+
starterMap_.assign(numVertices_, false);
179+
}
180+

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