Minor bugfixes and console printing

Minor bugfixes and console printing

Author: Adele Bai

.gitignore

@@ -3,3 +3,5 @@ marxan
 input
 input.dat
 output
+bin
+*.exe

heuristics.cpp

@@ -34,7 +34,7 @@ double GreedyScore(int ipu,int puno,int spno, vector<sspecies>& spec,vector<spu>
     double currpen, currcost, currscore;
 
     currpen = GreedyPen(ipu, puno, spno, spec, R, pu, SM, clumptype, thread);
-    currcost = pu[ipu].cost + ConnectionCost2(ipu, connections, R, 1, 1, cm);
+    currcost = pu[ipu].cost + ConnectionCost2(ipu, connections, R, 1, 1, cm, asymmetricconnectivity, fOptimiseConnectivityIn);
     if (currcost <= 0)
     {
         currscore = -1.0 / delta;
@@ -107,7 +107,7 @@ double RareScore(int isp,int ipu,int puno,vector<sspecies> &spec,vector<spu> &SM
         currpen = newamount - fold;
     } // Add new penalty if species isn't already in the system
 
-    currcost = pu[ipu].cost + ConnectionCost2(ipu, connections, R, 1, 1, cm);
+    currcost = pu[ipu].cost + ConnectionCost2(ipu, connections, R, 1, 1, cm, asymmetricconnectivity, fOptimiseConnectivityIn);
     if (currcost <= 0)
     {
         currscore = -1.0 / delta;

input.cpp

@@ -613,10 +613,11 @@ void readPenalties(vector<sspecies> &spec,int spno,sfname& fnames,map<int,int> &
 void readSparseMatrixSpOrder(int &iSMSize, vector<spusporder> &SM, int puno, int spno,
                              map<int,int> &PULookup,map<int,int> &SPLookup, vector<sspecies> &spec,
                              sfname &fnames) {
+    vector<map<int,spusporder>> SMTemp;
     FILE *fp;
     string readname;
-    char sLine[500],*sVarName,*sVarVal;
-    int i, _spid,spid, _puid, iInternalSMSize = 0, iBigMatrixSize, iLastSPID;
+    char sLine[500],*sVarVal;
+    int _spid, _puid, iInternalSMSize = 0, iBigMatrixSize, iLastSPID;
     double amount, rDensity, rInternalSMSize, rBigMatrixSize;
 
     readname = fnames.inputdir + fnames.matrixspordername;
@@ -627,54 +628,58 @@ void readSparseMatrixSpOrder(int &iSMSize, vector<spusporder> &SM, int puno, int
     if (fgets(sLine,500-1,fp) == NULL)
         displayErrorMessage("Error reading sparse matrix sporder.\n");
 
-    while (fgets(sLine,500-1,fp))
-        iInternalSMSize++;
-
-    rewind(fp);
-
-    iSMSize = iInternalSMSize;
-
     // create the sparse matrix
-    SM.resize(iInternalSMSize);
+    SMTemp.resize(spno);
 
-    iLastSPID = -1;
     // planning unit richness and offset are already set to zero
     // init with zero values
-    for (i=0;i<iInternalSMSize;i++)
+    while (fgets(sLine,500-1,fp))
     {
-        fgets(sLine,500-1,fp);
-
         sVarVal = strtok(sLine," ,;:^*\"/\t\'\\\n");
         sscanf(sVarVal,"%d",&_spid);
         sVarVal = strtok(NULL," ,;:^*\"/\t\'\\\n");
         sscanf(sVarVal,"%d",&_puid);
         sVarVal = strtok(NULL," ,;:^*\"/\t\'\\\n");
         sscanf(sVarVal,"%lf",&amount);
 
-        if (_spid < iLastSPID)
-        {
-            // error condition exists, file is not in ascending order for SPID
-            appendTraceFile("Error: PU v Species file %s is not in ascending order for SPID at record %i.\nAborting Program.",fnames.puvsprname,i+1);
-            displayErrorMessage("Error: PU v Species file %s is not in ascending order for SPID at record %i.\nAborting Program.",fnames.puvsprname,i+1);
+        int old_puid;
+        try {
+            old_puid = _puid;
+            _puid = PULookup.at(_puid);
+        }
+        catch (out_of_range ex) {
+            displayWarningMessage("Puid %d found in puvspr file but not found in pu file. Ignoring.\n", old_puid);
         }
 
-        iLastSPID = _spid;
-
-        _puid = PULookup[_puid];
-        spid = SPLookup[_spid];
+        int old_spid;
+        try {
+            old_spid = _spid;
+            _spid = SPLookup.at(_spid);
+        }
+        catch (out_of_range ex) {
+            displayWarningMessage("Spid %d found in puvspr file but not found in spec file. Ignoring.\n", old_spid);
+        }
 
         // increment richness for planning unit containing this feature
-        spec[spid].richness += 1;
-        // if planning units richness is one, set its offset
-        if (spec[spid].richness == 1)
-            spec[spid].offset = i;
-
-        SM[i].amount = amount;
-        SM[i].puindex = _puid;
+        spec[_spid].richness += 1;
+        SMTemp[_spid][_puid].amount = amount;
     }
 
     fclose(fp);
 
+    // Fill the SM vector
+    int j = 0;
+    for (int i = 0; i < spno; i++) {
+        spec[i].offset = j;
+        for (auto& [puindex, value]: SMTemp[i]) {
+            spusporder temp;
+            temp.amount = value.amount;
+            temp.puindex = puindex;
+            SM.push_back(temp);
+            j++;
+        }
+    }
+
     iBigMatrixSize = puno * spno;
     rInternalSMSize = iInternalSMSize;
     rBigMatrixSize = iBigMatrixSize;

marxan.cpp

@@ -121,6 +121,7 @@ void executeRunLoop(int iSparseMatrixFileLength, long int repeats,int puno,int s
     int maxThreads = omp_get_max_threads();
 
     printf("Running multithreaded over number of threads: %d\n", maxThreads);
+    displayProgress1("Running multithreaded over number of threads: " + to_string(maxThreads) + "\n");
     #pragma omp parallel for
     for (int i = 1; i <= repeats; i++)
     {
@@ -331,6 +332,7 @@ void executeRunLoop(int iSparseMatrixFileLength, long int repeats,int puno,int s
             // On exceptions, append exception to log file in addition to existing buffer. 
             displayProgress1(runConsoleOutput.str());
             appendLogBuffer << "Exception occurred on run " << i << ": " << e.what() << endl;
+            displayProgress1(appendLogBuffer.str());
             appendTraceFile(appendLogBuffer.str());
 
             throw(e);
@@ -354,7 +356,11 @@ void executeRunLoop(int iSparseMatrixFileLength, long int repeats,int puno,int s
         string tempname2 = savename + "_sum" + getFileNameSuffix(fnames.savesum);
         writeSummary(tempname2, summaries, fnames.saverun);
     }
-    cout << "\nBest run: " << bestRun << " Best score: " << bestScore << "\n" << bestRunString;
+
+    stringstream bestOut;
+    bestOut << "\nBest run: " << bestRun << " Best score: " << bestScore << "\n" << bestRunString;
+    cout << bestOut.str();
+    displayProgress1(bestOut.str());
 } // executeRunLoop
 
 int executeMarxan(string sInputFileName)
@@ -1628,7 +1634,7 @@ void computeQuantumChangeScore(int spno,int puno, vector<spustuff>& pu, vector<s
 #endif
 
         change.cost += pu[j].cost * imode; /* Cost of this PU on it's own */
-        change.connection += ConnectionCost2(j, connections, R, imode, 1, cm);
+        change.connection += ConnectionCost2(j, connections, R, imode, 1, cm, asymmetricconnectivity, fOptimiseConnectivityIn);
         if (threshtype == 1)
         {
             tchangeconnection = change.connection;

utils.hpp

@@ -48,7 +48,7 @@ void trim(std::string &s) {
     rtrim(s);
 }
 
-// Adds '/' or '\' to end of dir string if not existent
+// Adds '/' to end of dir string if not existent
 inline
 std::string cleanDirectoryString(std::string dirName) {
     if (dirName.back() != '\\' && dirName.back() != '/') {

validation/validate_solution.py

@@ -1,6 +1,9 @@
 """
 This script checks the given marxan solution's cost and shortfall.
 Use this to independently validate whether a marxan solution 
+
+Example run
+python validate_solution.py "../bin/data/Base_30_costadd100/output/output_best.txt" "../bin/data/Base_30_costadd100/input/pu.dat" "../bin/data/Base_30_costadd100/input/spec.dat" "../bin/data/Base_30_costadd100/input/puvspr.dat"
 """
 import argparse
 import csv
@@ -91,7 +94,10 @@ def calculate_shortfall(contributions, targets):
     shortfall = 0.0
 
     for spec in targets:
-        shortfall += max(0, targets[spec] - contributions[spec])
+        if spec in contributions:
+            shortfall += max(0, targets[spec] - contributions[spec])
+        else:
+            shortfall += max(0, targets[spec])
 
     return shortfall