Merge branch 'SharedDevelopment' of https://github.com/UWB-Biocomputing/Graphitti into SharedDevelopment

Jasleen Kaur Saini · Jasleen Kaur Saini · commit 2c4c8faaf0e1 · 2025-01-16T11:19:55.000-08:00
diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml
@@ -10,9 +10,7 @@ on:
     paths:
       - '**.cpp'
       - '**.h'
-    branches:
-      - master
-      - development
+    types: [opened, synchronize, reopened]
 
 jobs:
   deploy:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -4,7 +4,7 @@ on:
   push:
     branches: [ master,development ]
   pull_request:
-    branches: [ master,development ]
+    types: [opened, synchronize, reopened]
 
 defaults: 
   run:
diff --git a/.gitignore b/.gitignore
@@ -45,6 +45,7 @@ tests
 serialFullTest
 serialFirstHalfTest
 serialSecondHalfTest
+serialFileAccessTest
 core 
 # core is generated by GDB during debugging 
 
diff --git a/Simulator/Edges/NG911/All911Edges.h b/Simulator/Edges/NG911/All911Edges.h
@@ -70,8 +70,8 @@ class All911Edges : public AllEdges {
                                       int maxEdgesPerVertex) {};
    virtual void deleteEdgeDeviceStruct(void *allEdgesDevice) {};
    virtual void copyEdgeHostToDevice(void *allEdgesDevice) {};
-   virtual void copyEdgeHostToDevice(void *allEdgesDevice, int numVertices,
-                                     int maxEdgesPerVertex) {};
+   virtual void copyEdgeHostToDevice(void *allEdgesDevice, int numVertices, int maxEdgesPerVertex) {
+   };
    virtual void copyEdgeDeviceToHost(void *allEdgesDevice) {};
    virtual void copyDeviceEdgeCountsToHost(void *allEdgesDevice) {};
    virtual void copyDeviceEdgeSumIdxToHost(void *allEdgesDevice) {};
diff --git a/Simulator/Edges/Neuro/AllDSSynapses_d.cpp b/Simulator/Edges/Neuro/AllDSSynapses_d.cpp
@@ -328,8 +328,7 @@ void AllDSSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const
       }
 
       for (int i = 0; i < countVertices_; i++) {
-         cout << "GPU edge_counts:"
-              << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
+         cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
       }
 
       cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;
diff --git a/Simulator/Edges/Neuro/AllDynamicSTDPSynapses_d.cpp b/Simulator/Edges/Neuro/AllDynamicSTDPSynapses_d.cpp
@@ -380,8 +380,7 @@ void AllDynamicSTDPSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const
       }
 
       for (int i = 0; i < countVertices_; i++) {
-         cout << "GPU edge_counts:"
-              << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
+         cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
       }
 
       cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;
diff --git a/Simulator/Edges/Neuro/AllNeuroEdges.cpp b/Simulator/Edges/Neuro/AllNeuroEdges.cpp
@@ -114,8 +114,7 @@ void AllNeuroEdges::printSynapsesProps() const
    }
 
    for (int i = 0; i < countVertices_; i++) {
-      cout << "edge_counts:"
-           << "vertex[" << i << "]" << edgeCounts_[i] << endl;
+      cout << "edge_counts:" << "vertex[" << i << "]" << edgeCounts_[i] << endl;
    }
 
    cout << "totalEdgeCount:" << totalEdgeCount_ << endl;
diff --git a/Simulator/Edges/Neuro/AllSTDPSynapses.cpp b/Simulator/Edges/Neuro/AllSTDPSynapses.cpp
@@ -118,33 +118,18 @@ void AllSTDPSynapses::printParameters() const
 {
    AllSpikingSynapses::printParameters();
 
-   LOG4CPLUS_DEBUG(edgeLogger_, "\n\t---AllSTDPSynapses Parameters---"
-                                   << endl
-                                   << "\tEdges type: AllSTDPSynapses" << endl
-                                   << endl
-
-                                   << "\tSTDP gap" << defaultSTDPgap_ << endl
-                                   << "\n\tTauspost value: ["
-                                   << " I: " << tauspost_I_ << ", "
-                                   << " E: " << tauspost_E_ << "]" << endl
-                                   << "\n\tTauspre value: ["
-                                   << " I: " << tauspre_I_ << ", "
-                                   << " E: " << tauspre_E_ << "]" << endl
-                                   << "\n\tTaupos value: ["
-                                   << " I: " << taupos_I_ << ", "
-                                   << " E: " << taupos_E_ << "]" << endl
-                                   << "\n\tTau negvalue: ["
-                                   << " I: " << tauneg_I_ << ", "
-                                   << " E: " << tauneg_E_ << "]" << endl
-                                   << "\n\tWex value: ["
-                                   << " I: " << Wex_I_ << ", "
-                                   << " E: " << Wex_E_ << "]" << endl
-                                   << "\n\tAneg value: ["
-                                   << " I: " << Aneg_I_ << ", "
-                                   << " E: " << Aneg_E_ << "]" << endl
-                                   << "\n\tApos value: ["
-                                   << " I: " << Apos_I_ << ", "
-                                   << " E: " << Apos_E_ << "]" << endl);
+   LOG4CPLUS_DEBUG(
+      edgeLogger_,
+      "\n\t---AllSTDPSynapses Parameters---"
+         << "\n\tEdges type: AllSTDPSynapses \n\n"
+         << "\tSTDP gap" << defaultSTDPgap_ << "\n\n\tTauspost value: [" << " I: " << tauspost_I_
+         << ", " << " E: " << tauspost_E_ << "]" << "\n\n\tTauspre value: [" << " I: " << tauspre_I_
+         << ", " << " E: " << tauspre_E_ << "]" << "\n\n\tTaupos value: [" << " I: " << taupos_I_
+         << ", " << " E: " << taupos_E_ << "]" << "\n\n\tTau negvalue: [" << " I: " << tauneg_I_
+         << ", " << " E: " << tauneg_E_ << "]" << "\n\n\tWex value: [" << " I: " << Wex_I_ << ", "
+         << " E: " << Wex_E_ << "]" << "\n\n\tAneg value: [" << " I: " << Aneg_I_ << ", "
+         << " E: " << Aneg_E_ << "]" << "\n\n\tApos value: [" << " I: " << Apos_I_ << ", "
+         << " E: " << Apos_E_ << "]" << endl);
 }
 
 ///  Sets the data for Synapse to input's data.
diff --git a/Simulator/Edges/Neuro/AllSTDPSynapses_d.cpp b/Simulator/Edges/Neuro/AllSTDPSynapses_d.cpp
@@ -409,8 +409,7 @@ void AllSTDPSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const
          }
       }
       for (int i = 0; i < countVertices_; i++) {
-         cout << "GPU edge_counts:"
-              << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
+         cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
       }
       cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;
       cout << "GPU maxEdgesPerVertex:" << maxEdgesPerVertexPrint << endl;
diff --git a/Simulator/Edges/Neuro/AllSpikingSynapses.cpp b/Simulator/Edges/Neuro/AllSpikingSynapses.cpp
@@ -107,17 +107,14 @@ void AllSpikingSynapses::printParameters() const
                                    << endl
                                    << "\tEdges type: AllSpikingSynapses" << endl
                                    << endl);
-   LOG4CPLUS_DEBUG(edgeLogger_, "\n\tTau values: ["
-                                   << " II: " << tau_II_ << ", "
-                                   << " IE: " << tau_IE_ << ","
-                                   << "EI : " << tau_EI_ << ","
-                                   << " EE: " << tau_EE_ << "]" << endl);
+   LOG4CPLUS_DEBUG(edgeLogger_, "\n\tTau values: [" << " II: " << tau_II_ << "," << " IE: "
+                                                    << tau_IE_ << "," << " EI: " << tau_EI_ << ","
+                                                    << " EE: " << tau_EE_ << "]" << endl);
 
    LOG4CPLUS_DEBUG(edgeLogger_, "\n\tDelay values: ["
-                                   << " II: " << delay_II_ << ", "
-                                   << " IE: " << delay_IE_ << ","
-                                   << "EI :" << delay_EI_ << ","
-                                   << " EE: " << delay_EE_ << "]" << endl);
+                                   << " II: " << delay_II_ << "," << " IE: " << delay_IE_ << ","
+                                   << " EI:" << delay_EI_ << "," << " EE: " << delay_EE_ << "]"
+                                   << endl);
 }
 
 ///  Sets the data for Synapse to input's data.
diff --git a/Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp b/Simulator/Edges/Neuro/AllSpikingSynapses_d.cpp
@@ -415,8 +415,7 @@ void AllSpikingSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const
          }
       }
       for (int i = 0; i < countVertices_; i++) {
-         cout << "GPU edge_counts:"
-              << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
+         cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;
       }
       cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;
       cout << "GPU maxEdgesPerVertex:" << maxEdgesPerVertexPrint << endl;
diff --git a/Simulator/Utils/Inputs/FSInput.cpp b/Simulator/Utils/Inputs/FSInput.cpp
@@ -22,25 +22,24 @@
 /// @return a pointer to a SInput object
 ISInput *FSInput::CreateInstance()
 {
-   if (Simulator::getInstance().getStimulusFileName().empty()) {
+   auto stimulusFileName = Simulator::getInstance().getStimulusFileName();
+   if (stimulusFileName.empty()) {
       return nullptr;
    }
 
    // load stimulus input file
-   TiXmlDocument siDoc(Simulator::getInstance().getStimulusFileName().c_str());
+   TiXmlDocument siDoc(stimulusFileName.c_str());
    if (!siDoc.LoadFile()) {
-      cerr << "Failed loading stimulus input file "
-           << Simulator::getInstance().getStimulusFileName() << ":"
-           << "\n\t" << siDoc.ErrorDesc() << endl;
+      cerr << "Failed loading stimulus input file " << stimulusFileName << ":" << "\n\t"
+           << siDoc.ErrorDesc() << endl;
       cerr << " error: " << siDoc.ErrorRow() << ", " << siDoc.ErrorCol() << endl;
       return nullptr;
    }
 
    // load input parameters
    TiXmlElement *parms = nullptr;
    if ((parms = siDoc.FirstChildElement("InputParams")) == nullptr) {
-      cerr << "Could not find <InputParms> in stimulus input file "
-           << Simulator::getInstance().getStimulusFileName() << endl;
+      cerr << "Could not find <InputParms> in stimulus input file " << stimulusFileName << endl;
       return nullptr;
    }
 
diff --git a/Simulator/Utils/Inputs/SInputPoisson.cpp b/Simulator/Utils/Inputs/SInputPoisson.cpp
@@ -67,8 +67,7 @@ SInputPoisson::SInputPoisson(TiXmlElement *parms) :
                TiXmlDocument simDoc(maskNListFileName.c_str());
                if (!simDoc.LoadFile()) {
                   cerr << "Failed loading positions of stimulus input mask neurons list file "
-                       << maskNListFileName << ":"
-                       << "\n\t" << simDoc.ErrorDesc() << endl;
+                       << maskNListFileName << ":" << "\n\t" << simDoc.ErrorDesc() << endl;
                   cerr << " error: " << simDoc.ErrorRow() << ", " << simDoc.ErrorCol() << endl;
                   break;
                }
diff --git a/Simulator/Utils/ParameterManager.cpp b/Simulator/Utils/ParameterManager.cpp
@@ -55,8 +55,8 @@ bool ParameterManager::loadParameterFile(string path)
    // load the XML document
    xmlDocument_.reset(new TiXmlDocument(path.c_str()));
    if (!xmlDocument_->LoadFile()) {
-      cerr << "Failed loading simulation parameter file " << path << ":"
-           << "\n\t" << xmlDocument_->ErrorDesc() << endl;
+      cerr << "Failed loading simulation parameter file " << path << ":" << endl;
+      cerr << "\t" << xmlDocument_->ErrorDesc() << endl;
       cerr << " error row: " << xmlDocument_->ErrorRow()
            << ", error col: " << xmlDocument_->ErrorCol() << endl;
       return false;
@@ -123,8 +123,8 @@ bool ParameterManager::getIntByXpath(string xpath, int &referenceVar)
            << "Terminating integer cast. Value: " << tmp << endl;
       return false;
    } else if (regex_match(tmp, regex(".*[^\\def.]+.*"))) {
-      cerr << "Parsed parameter is likely a string. "
-           << "Terminating integer cast. Value: " << tmp << endl;
+      cerr << "Parsed parameter is likely a string. " << endl;
+      cerr << "Terminating integer cast. Value: " << tmp << endl;
       return false;
    }
    try {
@@ -278,8 +278,8 @@ bool ParameterManager::getIntVectorByXpath(const string &path, const string &ele
    // Open file using a local XmlDocument object
    TiXmlDocument xmlDocument(path.c_str());
    if (!xmlDocument.LoadFile()) {
-      cerr << "Failed to load " << path.c_str() << ":"
-           << "\n\t" << xmlDocument.ErrorDesc() << endl;
+      cerr << "Failed to load " << path.c_str() << ":" << endl;
+      cerr << "\t" << xmlDocument.ErrorDesc() << endl;
       return false;
    }
 
diff --git a/Testing/UnitTesting/SerializationFileAccessTest.cpp b/Testing/UnitTesting/SerializationFileAccessTest.cpp
@@ -0,0 +1,43 @@
+
+/**
+ * @file SerializationFileAccessTest.cpp
+ *
+ * @brief This file contains the unit test to check if serialization file can 
+ *        be accessed before the simulation starts, using GTest.
+ *
+ * @ingroup Testing/UnitTesting
+ */
+
+#include "Core.h"
+#include "gtest/gtest.h"
+#include <filesystem>
+#include <fstream>
+#include <iostream>
+#include <tinyxml.h>
+
+using namespace std;
+
+// Test case for isSerializedFileWritable function
+TEST(SerializationFileAccessTest, FileWritableTest)
+{
+   string executable = "./cgraphitti";
+   string configFile = "../configfiles/test-small-connected.xml";
+   string nonWritableFilePath = "/root/non_writable_file.txt";
+   string nonWritableArgument = "-c " + configFile + " -w " + nonWritableFilePath;
+
+   Core core;
+
+   // Test a non-writable file
+   ASSERT_EQ(-1, core.runSimulation(executable, nonWritableArgument));
+}
+
+// Optional: create a similar test file to test a a positive case
+// 1. Create a writable file
+// string writableFilePath = "writable_file.txt";
+// string writableArgument = "-c " + configFile + " -w " + writableFilePath;
+// std::ofstream writableFile(writableFilePath);
+// writableFile.close();
+// 2. Test
+// ASSERT_EQ(0, core.runSimulation(executable, writableArgument));
+// 3. Clean up the writable file
+// std::filesystem::remove(writableFilePath);
diff --git a/Testing/UnitTesting/XmlRecorderTests.cpp b/Testing/UnitTesting/XmlRecorderTests.cpp
@@ -175,9 +175,7 @@ TEST(XmlRecorderTest, ToXML)
    // Verify the expected XML output
    stringstream os;
    os << "<Matrix ";
-   os << "name=\""
-      << "TestVar"
-      << "\" ";
+   os << "name=\"" << "TestVar" << "\" ";
    os << "type=\"complete\" rows=\"" << 1 << "\" columns=\"" << variableHistory.size()
       << "\" multiplier=\"1.0\">" << endl;
    os << "   ";
diff --git a/Tools/InputGeneration/README.md b/Tools/InputGeneration/README.md
@@ -38,22 +38,23 @@ The stream of calls generated is saved to an XML file. This file contains a list
 ## Input file format
 
 The developer's documentation contains more information about the [simulation input file
-format and the class that loads and manages the event inputs]
-(https://uwb-biocomputing.github.io/Graphitti/Developer/GraphAndEventInputs.html).
+format and the class that loads and manages the event inputs](https://uwb-biocomputing.github.io/Graphitti/Developer/GraphAndEventInputs.html).
 
 Below is an example of a simulation input file:
 
 
 ```XML
-?xml version='1.0' encoding='UTF-8'?>
+<?xml version='1.0' encoding='UTF-8'?>
 <simulator_inputs>
-  <data description="SPD Calls - Cluster Point Process" clock_tick_size="1" clock_tick_unit="sec">
-    <vertex id="194" name="SEATTLE PD Caller region">
-      <event time="12" duration="568" x="-122.43656117361931" y="47.604800151342786" type="Law" vertex_id="194"/>
-      <event time="99" duration="36" x="-122.43611438152655" y="47.5321990385178" type="EMS" vertex_id="194"/>
-      <event time="336" duration="100" x="-122.34868883298704" y="47.56973909330686" type="Law" vertex_id="194"/>
-      <event time="601" duration="367" x="-122.44122311134316" y="47.70298531339788" type="Law" vertex_id="194"/>
-      <event time="766" duration="96" x="-122.28084792007573" y="47.70594997190379" type="Fire" vertex_id="194"/>
+  <data description="SYNTH_OUTPUT2 Calls - Cluster Point Process" clock_tick_size="1" clock_tick_unit="sec">
+    <vertex id="4" name="UNKNOWN">
+      <event time="26" duration="38" x="13.111984735748287" y="62.57456126541278" type="Law" patience="54" on_site_time="33" vertex_id="4"/>
+      <event time="35" duration="30" x="13.101924628231098" y="62.5788162451589" type="Fire" patience="2" on_site_time="12" vertex_id="4"/>
+      <event time="60" duration="48" x="13.103238844738144" y="62.57852864894537" type="Fire" patience="26" on_site_time="71" vertex_id="4"/>
+      <event time="61" duration="33" x="13.103729766137114" y="62.57884701874643" type="Fire" patience="27" on_site_time="2" vertex_id="4"/>
+      <event time="74" duration="32" x="13.104050198095443" y="62.578851926237746" type="Fire" patience="23" on_site_time="38" vertex_id="4"/>
+      <event time="77" duration="41" x="13.125015368211848" y="62.547956222166015" type="EMS" patience="2" on_site_time="239" vertex_id="4"/>
+      <event time="111" duration="45" x="13.12497529802989" y="62.54820796343649" type="EMS" patience="46" on_site_time="77" vertex_id="4"/>
       ...
     </vertex>
   </data>
diff --git a/docs/Developer/GraphAndEventInputs.md b/docs/Developer/GraphAndEventInputs.md
@@ -45,13 +45,16 @@ The list of events is provided to Graphitti as an XML input file. We couldn't fi
 ```xml
 <?xml version='1.0' encoding='UTF-8'?>
 <simulator_inputs>
-  <data description="SPD_calls_sept2020" clock_tick_size="1" clock_tick_unit="sec">
-    <vertex id="194" name="SEATTLE PD Caller region">
-      <event time="0" duration="0" x="-122.38496236371942" y="47.570236838209546" type="EMS"/>
-      <event time="34" duration="230" x="-122.37482094435583" y="47.64839548276973" type="EMS"/>
-      <event time="37" duration="169" x="-122.4036487601129" y="47.55833788618255" type="Fire"/>
-      <event time="42" duration="327" x="-122.38534886929502" y="47.515324716436346" type="Fire"/>
-...
+  <data description="SYNTH_OUTPUT2 Calls - Cluster Point Process" clock_tick_size="1" clock_tick_unit="sec">
+    <vertex id="4" name="UNKNOWN">
+      <event time="26" duration="38" x="13.111984735748287" y="62.57456126541278" type="Law" patience="54" on_site_time="33" vertex_id="4"/>
+      <event time="35" duration="30" x="13.101924628231098" y="62.5788162451589" type="Fire" patience="2" on_site_time="12" vertex_id="4"/>
+      <event time="60" duration="48" x="13.103238844738144" y="62.57852864894537" type="Fire" patience="26" on_site_time="71" vertex_id="4"/>
+      <event time="61" duration="33" x="13.103729766137114" y="62.57884701874643" type="Fire" patience="27" on_site_time="2" vertex_id="4"/>
+      <event time="74" duration="32" x="13.104050198095443" y="62.578851926237746" type="Fire" patience="23" on_site_time="38" vertex_id="4"/>
+      <event time="77" duration="41" x="13.125015368211848" y="62.547956222166015" type="EMS" patience="2" on_site_time="239" vertex_id="4"/>
+      <event time="111" duration="45" x="13.12497529802989" y="62.54820796343649" type="EMS" patience="46" on_site_time="77" vertex_id="4"/>
+      ...
     <vertex/>
 ...
   <data/>

Original file line number	Diff line number	Diff line change
`@@ -328,8 +328,7 @@ void AllDSSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const`
`328`	`328`	`}`
`329`	`329`
`330`	`330`	`for (int i = 0; i < countVertices_; i++) {`
`331`		`- cout << "GPU edge_counts:"`
`332`		`- << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
	`331`	`+ cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
`333`	`332`	`}`
`334`	`333`
`335`	`334`	`cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;`
Original file line number	Diff line number	Diff line change
`@@ -380,8 +380,7 @@ void AllDynamicSTDPSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const`
`380`	`380`	`}`
`381`	`381`
`382`	`382`	`for (int i = 0; i < countVertices_; i++) {`
`383`		`- cout << "GPU edge_counts:"`
`384`		`- << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
	`383`	`+ cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
`385`	`384`	`}`
`386`	`385`
`387`	`386`	`cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;`
Original file line number	Diff line number	Diff line change
`@@ -114,8 +114,7 @@ void AllNeuroEdges::printSynapsesProps() const`
`114`	`114`	`}`
`115`	`115`
`116`	`116`	`for (int i = 0; i < countVertices_; i++) {`
`117`		`- cout << "edge_counts:"`
`118`		`- << "vertex[" << i << "]" << edgeCounts_[i] << endl;`
	`117`	`+ cout << "edge_counts:" << "vertex[" << i << "]" << edgeCounts_[i] << endl;`
`119`	`118`	`}`
`120`	`119`
`121`	`120`	`cout << "totalEdgeCount:" << totalEdgeCount_ << endl;`
Original file line number	Diff line number	Diff line change
`@@ -409,8 +409,7 @@ void AllSTDPSynapses::printGPUEdgesProps(void *allEdgesDeviceProps) const`
`409`	`409`	`}`
`410`	`410`	`}`
`411`	`411`	`for (int i = 0; i < countVertices_; i++) {`
`412`		`- cout << "GPU edge_counts:"`
`413`		`- << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
	`412`	`+ cout << "GPU edge_counts:" << "neuron[" << i << "]" << synapseCountsPrint[i] << endl;`
`414`	`413`	`}`
`415`	`414`	`cout << "GPU totalSynapseCount:" << totalSynapseCountPrint << endl;`
`416`	`415`	`cout << "GPU maxEdgesPerVertex:" << maxEdgesPerVertexPrint << endl;`