int main (int argc, char* argv[])
{
/** We create a command line parser. */
OptionsParser parser ("GraphStats");
parser.push_back (new OptionOneParam (STR_URI_GRAPH, "graph input", true));
try
{
/** We parse the user options. */
IProperties* options = parser.parse (argc, argv);
// We load the graph
Graph graph = Graph::load (options->getStr(STR_URI_GRAPH));
// We create a graph marker.
GraphMarker marker (graph);
// We create an object for Breadth First Search for the de Bruijn graph.
BFS bfs (graph);
// We want to compute the distribution of connected components of the branching nodes.
// - key is a connected component class (for a given number of branching nodes for this component)
// - value is the number of times this component class occurs in the branching sub graph
map<size_t,size_t> distrib;
// We get an iterator for all nodes of the graph. We use a progress iterator to get some progress feedback
ProgressGraphIterator<BranchingNode,ProgressTimer> itBranching (graph.iteratorBranching(), "statistics");
// We want time duration of the iteration
TimeInfo ti;
ti.start ("compute");
// We need to keep each connected component.
list<set<BranchingNode> > components;
// We loop the branching nodes
for (itBranching.first(); !itBranching.isDone(); itBranching.next())
{
// We skip already visited nodes.
if (marker.isMarked (*itBranching)) { continue; }
// We launch the breadth first search; we get as a result the set of branching nodes in this component
const set<BranchingNode>& component = bfs.run (*itBranching);
// We memorize the component
components.push_back (component);
// We mark the nodes for this connected component
marker.mark (component);
// We update our distribution
distrib[component.size()] ++;
}
ti.stop ("compute");
// We compute the total number of branching nodes in all connected components.
size_t sum = 0; for (map<size_t,size_t>::iterator it = distrib.begin(); it != distrib.end(); it++) { sum += it->first*it->second; }
// Note: it must be equal to the number of branching nodes of the graph
assert (sum == itBranching.size());
size_t idx1=0;
size_t cc=0;
// We check that each component has no intersection with all other components.
// Note: this check may take a long time since we have N^2 intersections to compute.
for (list<set<BranchingNode> >::iterator it1 = components.begin(); it1 != components.end(); it1++, idx1++)
{
size_t idx2=0;
for (list<set<BranchingNode> >::iterator it2 = components.begin(); it2 != components.end(); it2++, idx2++)
{
if (it1 != it2)
{
set<BranchingNode> inter;
set_intersection (it1->begin(),it1->end(),it2->begin(),it2->end(), std::inserter(inter,inter.begin()));
if (inter.size()!=0) { printf ("ERROR, intersection should be empty...\n"); exit(EXIT_FAILURE); }
}
if (++cc % 50 == 0)
{
cc = 0;
printf ("[check] %.1f %.1f\r", 100.0*(float)idx1/(float)components.size(), 100.0*(float)idx2/(float)components.size());
fflush (stdout);
}
}
}
printf ("\n");
// We aggregate the computed information
Properties props ("connected_components");
props.add (1, "graph_name", "%s", graph.getName().c_str());
props.add (1, "nb_branching_nodes", "%d", sum);
props.add (1, "nb_connected_components", "%d", distrib.size());
for (map<size_t,size_t>::iterator it = distrib.begin(); it!=distrib.end(); it++)
{
props.add (2, "component");
props.add (3, "nb_nodes", "%d", it->first);
props.add (3, "nb_occurs", "%d", it->second);
props.add (3, "freq_nodes", "%f", 100.0*(float)(it->first*it->second) / (float)sum);
props.add (3, "freq_occurs", "%f", 100.0*(float)it->second / (float)sum);
}
props.add (1, ti.getProperties("time"));
// We dump the results in a XML file in the current directory
XmlDumpPropertiesVisitor v (graph.getName() + ".xml", false);
props.accept (&v);
}
catch (OptionFailure& e)
{
return e.displayErrors (std::cout);
}
catch (Exception& e)
{
std::cerr << "EXCEPTION: " << e.getMessage() << std::endl;
}
return EXIT_SUCCESS;
}
int main (int argc, char* argv[])
{
/** We create a command line parser. */
OptionsParser parser;
parser.push_back (new OptionOneParam (STR_URI_INPUT, "graph file", true));
IProperties* params = 0;
try {
/** We parse the user options. */
params = parser.parse (argc, argv);
}
catch (OptionFailure& e)
{
e.getParser().displayErrors (stdout);
e.getParser().displayHelp (stdout);
return EXIT_FAILURE;
}
// We create the graph with the bank and other options
Graph graph = Graph::load (params->getStr(STR_URI_INPUT));
// We create a graph marker.
GraphMarker<BranchingNode> marker (graph);
// We create an object for Breadth First Search for the de Bruijn graph.
BFS<BranchingNode> bfs (graph);
// We want to compute the distribution of connected components of the branching nodes.
// - key is a connected component class (for a given number of branching nodes for this component)
// - value is the number of times this component class occurs in the branching sub graph
map<size_t,Entry> distrib;
// We get an iterator for all nodes of the graph. We use a progress iterator to get some progress feedback
ProgressGraphIterator<BranchingNode,ProgressTimer> itBranching (graph.iterator<BranchingNode>(), "statistics");
// We want to know the number of connected components
size_t nbConnectedComponents = 0;
// We define some kind of unique identifier for a couple (indegree,outdegree)
map <InOut_t, size_t> topology;
size_t simplePathSizeMin = ~0;
size_t simplePathSizeMax = 0;
// We want time duration of the iteration
TimeInfo ti;
ti.start ("compute");
// We loop the branching nodes
for (itBranching.first(); !itBranching.isDone(); itBranching.next())
{
// We get branching nodes neighbors for the current branching node.
Graph::Vector<BranchingEdge> successors = graph.successors <BranchingEdge> (*itBranching);
Graph::Vector<BranchingEdge> predecessors = graph.predecessors<BranchingEdge> (*itBranching);
// We increase the occurrences number for the current couple (in/out) neighbors
topology [make_pair(predecessors.size(), successors.size())] ++;
// We loop the in/out neighbors and update min/max simple path size
for (size_t i=0; i<successors.size(); i++)
{
simplePathSizeMax = std::max (simplePathSizeMax, successors[i].distance);
simplePathSizeMin = std::min (simplePathSizeMin, successors[i].distance);
}
for (size_t i=0; i<predecessors.size(); i++)
{
simplePathSizeMax = std::max (simplePathSizeMax, predecessors[i].distance);
simplePathSizeMin = std::min (simplePathSizeMin, predecessors[i].distance);
}
// We skip already visited nodes.
if (marker.isMarked (*itBranching)) {
continue;
}
// We launch the breadth first search; we get as a result the set of branching nodes in this component
const set<BranchingNode>& component = bfs.run (*itBranching);
// We mark the nodes for this connected component
marker.mark (component);
// We update our distribution
distrib[component.size()].nbOccurs += 1;
// We update the number of connected components.
nbConnectedComponents++;
}
ti.stop ("compute");
// We compute the total number of branching nodes in all connected components.
size_t sumOccurs = 0;
size_t sumKmers = 0;
for (map<size_t,Entry>::iterator it = distrib.begin(); it != distrib.end(); it++)
{
sumOccurs += it->first*it->second.nbOccurs;
sumKmers += it->second.nbKmers;
}
// We sort the statistics by decreasing occurrence numbers. Since map have its own ordering, we need to put all
// the data into a vector and sort it with our own sorting criteria.
vector < pair<InOut_t,size_t> > stats;
for (map <InOut_t, size_t>::iterator it = topology.begin(); it != topology.end(); it++) {
stats.push_back (*it);
}
sort (stats.begin(), stats.end(), CompareFct);
// Note: it must be equal to the number of branching nodes of the graph
assert (sumOccurs == itBranching.size());
// We aggregate the computed information
Properties props ("topology");
props.add (1, "graph");
props.add (2, "name", "%s", graph.getName().c_str());
props.add (2, "db_input", "%s", graph.getInfo().getStr("input").c_str());
props.add (2, "db_nb_seq", "%d", graph.getInfo().getInt("sequences_number"));
props.add (2, "db_size", "%d", graph.getInfo().getInt("sequences_size"));
props.add (2, "kmer_size", "%d", graph.getInfo().getInt("kmer_size"));
props.add (2, "kmer_nks", "%d", graph.getInfo().getInt("nks"));
props.add (2, "nb_nodes", "%d", graph.getInfo().getInt("kmers_nb_solid"));
props.add (2, "nb_branching_nodes", "%d", graph.getInfo().getInt("nb_branching"));
props.add (2, "percent_branching_nodes", "%.1f",
graph.getInfo().getInt("kmers_nb_solid") > 0 ?
100.0 * (float)graph.getInfo().getInt("nb_branching") / (float) graph.getInfo().getInt("kmers_nb_solid") : 0
);
props.add (1, "branching_nodes");
props.add (2, "simple_path");
props.add (3, "size_min", "%d", simplePathSizeMin);
props.add (3, "size_max", "%d", simplePathSizeMax);
props.add (2, "neighborhoods");
for (size_t i=0; i<stats.size(); i++)
{
props.add (3, "neighborhood", "in=%d out=%d", stats[i].first.first, stats[i].first.second);
props.add (4, "nb_bnodes", "%d", stats[i].second);
props.add (4, "percentage", "%5.2f", itBranching.size() > 0 ?
100.0*(float)stats[i].second / (float)itBranching.size() : 0
);
}
props.add (2, "connected_components");
props.add (3, "nb_classes", "%d", distrib.size());
props.add (3, "nb_components", "%d", nbConnectedComponents);
for (map<size_t,Entry>::iterator it = distrib.begin(); it!=distrib.end(); it++)
{
props.add (3, "component_class");
props.add (4, "nb_occurs", "%d", it->second.nbOccurs);
props.add (4, "nb_bnodes", "%d", it->first);
props.add (4, "freq_bnodes", "%f", sumOccurs > 0 ?
100.0*(float)(it->first*it->second.nbOccurs) / (float)sumOccurs : 0
);
}
props.add (1, ti.getProperties("time"));
// We dump the results in a XML file in the current directory
XmlDumpPropertiesVisitor v (graph.getName() + ".xml", false);
props.accept (&v);
return EXIT_SUCCESS;
}
void BpDocument::composeFireCharacteristicsDiagram( void )
{
// Surface Module must be active and using fuel model inputs
PropertyDict *prop = m_eqTree->m_propDict;
if ( ! prop->boolean( "surfaceModuleActive" )
|| ! prop->boolean( "surfaceCalcFireCharacteristicsDiagram" ) )
{
return;
}
// Graph fonts.
QFont textFont( property()->string( "graphTextFontFamily" ),
property()->integer( "graphTextFontSize" ) );
QColor textColor( property()->color( "graphTextFontColor" ) );
QPen textPen( textColor );
QFont subTitleFont( property()->string( "graphSubtitleFontFamily" ),
property()->integer( "graphSubtitleFontSize" ) );
QColor subTitleColor( property()->color( "graphSubtitleFontColor" ) );
// Open the result file
QString resultFile = m_eqTree->m_resultFile;
FILE *fptr = 0;
if ( ! ( fptr = fopen( resultFile.latin1(), "r" ) ) )
// This code block should never be executed!
{
QString text("");
translate( text, "BpDocument:FireCharacteristicsDiagram:NoLogOpen",
resultFile );
error( text );
return;
}
// Allocate ros and hpua data arrays
int rows = tableRows();
int cols = tableCols();
int cells = rows * cols;
double *hpua = new double[ cells ];
checkmem( __FILE__, __LINE__, hpua, "double hpua", cells );
double *ros = new double[ cells ];
checkmem( __FILE__, __LINE__, ros, "double ros", cells );
// Set the variable names we're looking for
const char* hpuaName = "vSurfaceFireHeatPerUnitArea";
const char* rosName = "vSurfaceFireSpreadAtHead";
if ( prop->boolean( "surfaceConfSpreadDirInput" ) )
{
rosName = "vSurfaceFireSpreadAtVector";
}
// Read and store the ros and hpua values
char buffer[1024], varName[128], varUnits[128];
int row, col, cell;
double value;
double rosMax = 0.0;
double hpuaMax = 0.0;
while ( fgets( buffer, sizeof(buffer), fptr ) )
{
if ( strncmp( buffer, "CELL", 4 ) == 0 )
{
if ( strstr( buffer, hpuaName ) )
{
sscanf( buffer, "CELL %d %d %s cont %lf %s",
&row, &col, varName, &value, varUnits );
cell = ( col - 1 ) + ( cols * ( row - 1) );
if ( ( hpua[ cell ] = value ) > hpuaMax )
{
hpuaMax = value;
}
}
else if ( strstr( buffer, rosName ) )
{
sscanf( buffer, "CELL %d %d %s cont %lf %s",
&row, &col, varName, &value, varUnits );
cell = ( col - 1 ) + ( cols * ( row - 1) );
if ( ( ros[ cell ] = value ) > rosMax )
{
rosMax = value;
}
}
}
}
fclose( fptr );
// Get variable pointers
EqVar *hpuaVar = m_eqTree->m_varDict->find( "vSurfaceFireHeatPerUnitArea" );
EqVar *rosVar = m_eqTree->m_varDict->find( "vSurfaceFireSpreadAtHead" );
EqVar *fliVar = m_eqTree->m_varDict->find( "vSurfaceFireLineIntAtHead" );
EqVar *flVar = m_eqTree->m_varDict->find( "vSurfaceFireFlameLengAtHead" );
// Conversion factor
double flFactor, fliFactor, rosFactor, hpuaFactor, offset;
appSiUnits()->conversionFactorOffset(
flVar->m_nativeUnits, flVar->m_displayUnits, &flFactor, &offset );
appSiUnits()->conversionFactorOffset(
fliVar->m_nativeUnits, fliVar->m_displayUnits, &fliFactor, &offset );
appSiUnits()->conversionFactorOffset(
hpuaVar->m_nativeUnits, hpuaVar->m_displayUnits, &hpuaFactor, &offset );
appSiUnits()->conversionFactorOffset(
rosVar->m_nativeUnits, rosVar->m_displayUnits, &rosFactor, &offset );
// Determine which of four different chart scales to use
static const int Scales = 4;
static double RosScale[Scales] = { 100., 200., 400., 800. }; // ft/min
static double HpuaScale[Scales] = { 2000., 4000., 8000., 16000. }; // Btu/ft2
double rosScale = 0.; // Max y-axis ros
double hpuaScale = 0.; // Max x-axis hpua
int scale;
for ( scale=0; scale<Scales; scale++ )
{
if ( rosMax < ( rosScale = RosScale[ scale ] ) )
{
break;
}
}
for ( scale=0; scale<Scales; scale++ )
{
if ( hpuaMax < ( hpuaScale = HpuaScale[scale] ) )
{
break;
}
}
// Set axis maximums to appropriate predefined scale in display units
rosMax = rosFactor * rosScale;
hpuaMax = hpuaFactor * hpuaScale;
double ratio = rosMax / hpuaMax;
// Create the graph
Graph graph;
GraphLine *graphLine;
GraphMarker *graphMarker;
static const int Points = 100;
double l_x[Points];
double l_y[Points];
// Draw the four standard hauling chart fli-fl levels
static const int Lines = 4;
static const double Fli[Lines] = { 100., 500., 1000., 2000. }; // Btu/ft/s
static const double Fl[Lines] = { 4., 8., 11., 15. }; // ft
// Create the hauling chart lines
// Put Fireline Int label 65% of the way along the HPUA axis (display units)
double xPosFli = 0.65 * hpuaMax;
// Put Flame Length label 85% of the way along the HPUA axis (display units)
double xPosFl = 0.85 * hpuaMax;
// Fireline Int and Flame Length label Y positions (display units)
double yPosFl[Lines], yPosFli[Lines];
// Icon locations (in display units)
double xIcon[Lines+1], yIcon[Lines+1];
double diff, minDiff;
QString label;
QPen redPen( "red", 1 );
QColor blackColor( "black" );
int alignCenter = Qt::AlignHCenter | Qt::AlignVCenter;
// Fireline intensity - flame length curves
int line, point;
for ( line = 0; line < Lines; line++ )
{
minDiff = 999999999.;
for ( point = 0; point < Points; point++ )
{
// Hpua value in native units (Btu/ft2)
l_x[point] = ( (point+1) * hpuaScale ) / (double) Points;
// Ros value in native units (ft/min)
l_y[point] = 60. * Fli[line] / l_x[point];
// Convert to display units
l_x[point] *= hpuaFactor;
l_y[point] *= rosFactor;
// Check for curve inflection point (for icon placement)
if ( ( diff = fabs( l_y[point]/l_x[point] - ratio ) ) < minDiff )
{
minDiff = diff;
xIcon[line+1] = l_x[point];
yIcon[line+1] = l_y[point];
}
}
// Create a graph line (with its own copy of the data).
graphLine = graph.addGraphLine( Points, l_x, l_y, redPen );
// Fireline intensity label
label = QString( "%1" ).arg( ( Fli[line] * fliFactor ), 0, 'f', 0 );
yPosFli[line] = rosFactor * ( 60. * Fli[line] / ( xPosFli / hpuaFactor ) );
graph.addGraphMarker( xPosFli, yPosFli[line], label, textFont,
blackColor, alignCenter );
// Flame length label
label = QString( "%1" ).arg( ( Fl[line] * flFactor ), 0, 'f', 0 );
yPosFl[line] = rosFactor * ( 60. * Fli[line] / ( xPosFl / hpuaFactor ) );
graph.addGraphMarker( xPosFl, yPosFl[line], label, textFont,
blackColor, alignCenter );
} // Next line
// Fireline intensity label and units
translate( label, "BpDocument:FireCharacteristicsDiagram:FLI" );
graph.addGraphMarker( xPosFli, ( yPosFli[Lines-1] + 0.10 * rosMax ),
label, textFont, blackColor, alignCenter );
graph.addGraphMarker( xPosFli, ( yPosFli[Lines-1] + 0.05 * rosMax ),
fliVar->m_displayUnits, textFont, blackColor, alignCenter );
// Flame length label and units
translate( label, "BpDocument:FireCharacteristicsDiagram:FL" );
graph.addGraphMarker( xPosFl, ( yPosFl[Lines-1] + 0.10 * rosMax ),
label, textFont, blackColor, alignCenter );
graph.addGraphMarker( xPosFl, ( yPosFl[Lines-1] + 0.05 * rosMax ),
flVar->m_displayUnits, textFont, blackColor, alignCenter );
// Add icons
QPixmap pixmap[Lines];
pixmap[0] = QPixmap( fireman_xpm );
pixmap[1] = QPixmap( dozer_xpm );
pixmap[2] = QPixmap( torchtree_xpm );
pixmap[3] = QPixmap( mtnfire_xpm );
xIcon[0] = yIcon[0] = 0.0;
for ( line=0; line<Lines; line++ )
{
graphMarker = graph.addGraphMarker(
xIcon[line] + ( 0.5 * ( xIcon[line+1] - xIcon[line] ) ),
yIcon[line] + ( 0.5 * ( yIcon[line+1] - yIcon[line] ) ),
"", textFont, blackColor, alignCenter );
graphMarker->setGraphMarkerPixmap( pixmap[line] );
}
// Finally, add a marker for each output result
QColor bluePen( "blue" );
for ( cell=0; cell<cells; cell++ )
{
//fprintf( stderr, "%02d: %3.2f %3.2f\n", i, hpua[i], ros[i] );
graph.addGraphMarker( hpua[cell], ros[cell],
QString( "%1" ).arg( cell + 1 ), textFont, bluePen, alignCenter );
}
// Compose the graph
EqVar *zVar = 0;
GraphAxleParms xParms( 0.0, hpuaMax, 11 );
GraphAxleParms yParms( 0.0, rosMax, 11 );
composeGraphBasics( &graph, true, hpuaVar, rosVar, zVar, Lines,
&xParms, &yParms );
// Create a separate page for this graph.
translate( label, "BpDocument:FireCharacteristicsDiagram:Caption" );
graph.setSubTitle( label, subTitleFont, subTitleColor );
startNewPage( label, TocHaulChart );
// This is how we save the graph and its composer.
m_composer->graph( graph,
m_pageSize->m_marginLeft
+ m_pageSize->m_bodyWd * property()->real( "graphXOffset" ),
m_pageSize->m_marginTop
+ m_pageSize->m_bodyHt * property()->real( "graphYOffset" ),
m_pageSize->m_bodyWd * property()->real( "graphScaleWidth" ),
m_pageSize->m_bodyHt * property()->real( "graphScaleHeight" )
);
// Be polite and stop the composer.
m_composer->end();
delete[] ros; ros = 0;
delete[] hpua; hpua = 0;
return;
}