QGVScene::QGVScene(const QString &name, QObject *parent) : QGraphicsScene(parent),
_label (NULL)
{
_context = new QGVGvcPrivate(gvContext());
_graph = new QGVGraphPrivate(agopen(name.toLocal8Bit().data(), Agdirected, NULL));
//setGraphAttribute("fontname", QFont().family());
}
void GraphvizPlotter::plot() {
if(path.length() == 0) {
throw "Path is empty";
}
if(name.length() == 0) {
throw "Name is empty";
}
// nacte nastaveny format grafu
std::string format = getStringOutputFormat();
// vytvori konecne umisteni a nazev souboru
std::string filename = path + name + "." + format;
// vytvori potrebne struktury graphvizu
GVC_t *gvc;
Agraph_t *g;
gvc = gvContext();
// parsovani ze struktury DOT do interni reprezentace graphvizu
g = agmemread(getDot().c_str());
// pouziti defaultniho nastroje dot
gvLayout(gvc, g, "dot");
// vykresleni grafu do souboru
gvRenderFilename(gvc, g, format.c_str(), filename.c_str());
// uvolneni vsech struktur graphvizu z pameti
gvFreeLayout(gvc, g);
agclose(g);
}
/**
* Render a tree to tree graph image via graphviz (dot)
*/
int r3_tree_render_file(const node * tree, const char * format, char * filename)
{
Agraph_t *g;
/* set up a graphviz context - but only once even for multiple graphs */
static GVC_t *gvc;
if (!gvc) {
gvc = gvContext();
}
/* Create a simple digraph */
g = agopen("g", Agdirected, 0);
// create self node
Agnode_t *ag_root = agnode(g, "{root}", 1);
r3_tree_build_ag_nodes(g, ag_root, tree, 0);
gvLayout(gvc, g, "dot");
gvRenderFilename(gvc, g, format, filename);
gvFreeLayout(gvc, g);
agclose(g);
return 0;
}
void ImplemGraphviz::drawGraph()
{
GVC_t *gvc=gvContext();
G=agopen("G",AGRAPH); //Ici pour modifier afin que le graphe soit orienté : AGRAPH -> AGDIGRAPH
if(graphe->isColore())
{
GrapheColore* graph=(GrapheColore*) graphe->getGraph();
creerListeNodes(graph);
creerListeEdges(graph);
}
else
{
Graphe* graph=(Graphe*) graphe->getGraph();
creerListeNodes(graph);
creerListeEdges(graph);
}
gvLayout(gvc,G,"dot");
gvRenderFilename(gvc,G,"svg",lienSVG.toStdString().c_str());
load(lienSVG);
adjustSize();
parentWidget()->adjustSize();
}
GVSkeletonGraph::GVSkeletonGraph(QString name, QFont font) {
setlocale(LC_NUMERIC,"en_US.UTF-8"); // Débug séparateur de décimales en version française
_context = gvContext();
_graph = _agopen(name, AGDIGRAPHSTRICT);
setGraphAttributes();
setFont(font);
}
/*
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% %
% %
% R e g i s t e r D O T I m a g e %
% %
% %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% RegisterDOTImage() adds attributes for the Display Postscript image
% format to the list of supported formats. The attributes include the image
% format tag, a method to read and/or write the format, whether the format
% supports the saving of more than one frame to the same file or blob,
% whether the format supports native in-memory I/O, and a brief
% description of the format.
%
% The format of the RegisterDOTImage method is:
%
% size_t RegisterDOTImage(void)
%
*/
ModuleExport size_t RegisterDOTImage(void)
{
MagickInfo
*entry;
entry=SetMagickInfo("DOT");
#if defined(MAGICKCORE_GVC_DELEGATE)
entry->decoder=(DecodeImageHandler *) ReadDOTImage;
#endif
entry->blob_support=MagickFalse;
entry->description=ConstantString("Graphviz");
entry->module=ConstantString("DOT");
(void) RegisterMagickInfo(entry);
entry=SetMagickInfo("GV");
#if defined(MAGICKCORE_GVC_DELEGATE)
entry->decoder=(DecodeImageHandler *) ReadDOTImage;
#endif
entry->blob_support=MagickFalse;
entry->description=ConstantString("Graphviz");
entry->module=ConstantString("DOT");
(void) RegisterMagickInfo(entry);
#if defined(MAGICKCORE_GVC_DELEGATE)
graphic_context=gvContext();
#endif
return(MagickImageCoderSignature);
}
__attribute__((used)) char* vizRenderFromString(const char *string, const char *format, const char *engine) {
Agraph_t *graph;
char *result;
unsigned int length;
if (context == NULL) {
context = gvContext();
gvAddLibrary(context, &gvplugin_core_LTX_library);
gvAddLibrary(context, &gvplugin_dot_layout_LTX_library);
gvAddLibrary(context, &gvplugin_neato_layout_LTX_library);
}
graph = agmemread((char *) string);
gvLayout(context, graph, engine);
gvRenderData(context, graph, format, &result, &length);
gvFreeLayout(context, graph);
agclose(graph);
return result;
}
GVSkeletonGraph::GVSkeletonGraph(QString name, QFont font) {
setlocale(LC_NUMERIC,"en_US.UTF-8");
_context = gvContext();
_graph = _agopen(name, AGDIGRAPHSTRICT);
setGraphAttributes();
setFont(font);
}
void LoadAGraphThread::run()
{
kDebug() << m_dotFileName;
GVC_t *gvc;
FILE* fp;
gvc = gvContext();
fp = fopen(m_dotFileName.toUtf8().data(), "r");
m_g = agread(fp);
}
int main(int argc, char** argv)
{
Agraph_t *g;
Agnode_t *n,*m;
Agedge_t *e;
Agsym_t *a;
GVC_t *gvc;
/* set up renderer context */
gvc = gvContext();
/* Accept -T and -o options like dot.
* Input files are ignored in this demo. */
dotneato_initialize(gvc, argc,argv);
/* Create a simple digraph */
g = agopen("g",AGDIGRAPH);
n = agnode(g,"n");
m = agnode(g,"m");
e = agedge(g,n,m);
/* Set an attribute - in this case one that affects the visible rendering */
if (!(a = agfindattr(g->proto->n, "color")))
a = agnodeattr(g, "color", "");
agxset(n, a->index, "red");
/* bind graph to GV context - currently must be done before layout */
gvBindContext(gvc,g);
/* Compute a layout */
neato_layout(g);
/* twopi_layout(g); */
/* dot_layout(g); */
/* Write the graph according to -T and -o options */
dotneato_write(gvc);
/* Clean out layout data */
/* neato_cleanup(g); */
/* twopi_cleanup(g); */
/* dot_cleanup(g); */
/* Free graph structures */
agclose(g);
/* Clean up output file and errors */
dotneato_terminate(gvc);
return 1;
}
/*----------------------------------------------------------------------------
* initialize the internal graphviz structure.
*/
static void
cls_inherit_graph_init (AnjutaClassInheritance *plugin, gchar* graph_label)
{
Agsym_t *sym;
gchar dpi_text[16];
snprintf (dpi_text, 16, "%d", INCH_TO_PIXELS_CONVERSION_FACTOR);
aginit ();
plugin->graph = agopen (graph_label, AGDIGRAPH);
plugin->gvc = gvContext();
if (!(sym = agfindattr(plugin->graph->proto->n, "dpi")))
sym = agraphattr(plugin->graph, "dpi", dpi_text);
agxset(plugin->graph, sym->index, dpi_text);
}
CFrmSettings::CFrmSettings()
{
this->gvc = gvContext();
Ui_Dialog tempDia;
tempDia.setupUi(this);
graph = NULL;
activeWindow = NULL;
QString path;
#ifndef WIN32
char *s = getenv("GVEDIT_PATH");
if (s)
path = s;
else
path = GVEDIT_DATADIR;
#endif
connect(WIDGET(QPushButton, pbAdd), SIGNAL(clicked()), this,
SLOT(addSlot()));
connect(WIDGET(QPushButton, pbNew), SIGNAL(clicked()), this,
SLOT(newSlot()));
connect(WIDGET(QPushButton, pbOpen), SIGNAL(clicked()), this,
SLOT(openSlot()));
connect(WIDGET(QPushButton, pbSave), SIGNAL(clicked()), this,
SLOT(saveSlot()));
connect(WIDGET(QPushButton, btnOK), SIGNAL(clicked()), this,
SLOT(okSlot()));
connect(WIDGET(QPushButton, btnCancel), SIGNAL(clicked()), this,
SLOT(cancelSlot()));
connect(WIDGET(QPushButton, pbOut), SIGNAL(clicked()), this,
SLOT(outputSlot()));
connect(WIDGET(QPushButton, pbHelp), SIGNAL(clicked()), this,
SLOT(helpSlot()));
connect(WIDGET(QComboBox, cbScope), SIGNAL(currentIndexChanged(int)),
this, SLOT(scopeChangedSlot(int)));
scopeChangedSlot(0);
#ifndef WIN32
loadAttrs(path + "/attrs.txt", WIDGET(QComboBox, cbNameG),
WIDGET(QComboBox, cbNameN), WIDGET(QComboBox, cbNameE));
#else
loadAttrs("../share/graphviz/gvedit/attributes.txt",
WIDGET(QComboBox, cbNameG), WIDGET(QComboBox, cbNameN),
WIDGET(QComboBox, cbNameE));
#endif
setWindowIcon(QIcon(":/images/icon.png"));
}
/* GVLayout */
GVLayout::GVLayout()
{
this->gvc = gvContext();
#ifdef USE_LIBGRAPH_NOT_LIBCGRAPH
this->gvgraph = agopen((char*)"g", AGDIGRAPH);
#else
this->gvgraph = agopen((char*)"g", Agdirected, NULL);
#endif
agsafeset(this->gvgraph, (char*)"splines", (char*)"true", (char*)"");
agsafeset(this->gvgraph, (char*)"overlap", (char*)"false", (char*)"");
agsafeset(this->gvgraph, (char*)"rankdir", (char*)"LR", (char*)"");
agsafeset(this->gvgraph, (char*)"nodesep", (char*)"2.0", (char*)"");
agsafeset(this->gvgraph, (char*)"labelloc", (char*)"t", (char*)"");
}
int main(int argc, char **argv)
{
graph_t *g, *prev = NULL;
GVC_t *gvc;
gvc = gvContext();
gvParseArgs(gvc, argc, argv);
while ((g = gvNextInputGraph(gvc))) {
if (prev) {
gvFreeLayout(gvc, prev);
agclose(prev);
}
gvLayoutJobs(gvc, g);
gvRenderJobs(gvc, g);
prev = g;
}
return (gvFreeContext(gvc));
}
int main(int argc, char **argv)
{
Agraph_t *g;
Agnode_t *n, *m;
Agedge_t *e;
Agsym_t *a;
#ifdef NO_LAYOUT_OR_RENDERING
aginit();
#else
/* set up a graphviz context - but only once even for multiple graphs */
static GVC_t *gvc;
if (!gvc)
gvc = gvContext();
#endif
/* Create a simple digraph */
g = agopen("g", AGDIGRAPH);
n = agnode(g, "n");
m = agnode(g, "m");
e = agedge(g, n, m);
/* Set an attribute - in this case one that affects the visible rendering */
agsafeset(n, "color", "red", "");
#ifdef NO_LAYOUT_OR_RENDERING
/* Just write the graph without layout */
agwrite(g, stdout);
#else
/* Use the directed graph layout engine */
gvLayout(gvc, g, "dot");
/* Output in .dot format */
gvRender(gvc, g, "dot", stdout);
gvFreeLayout(gvc, g);
#endif
agclose(g);
return 0;
}
static bool GenDrawFormatFile(Digraph& dg, VNG_Param& param, const string& fmt, char** result, unsigned int* length)
{
GVC_t* gvc = gvContext();
//创建图
Agraph_t* g = CreateGraph(dg, param);
gvLayout(gvc,g,"dot");
//写入到缓存数组中
gvRenderData(gvc,g,fmt.c_str(), result, length);
//gvFreeRenderData(result);
gvFreeLayout(gvc,g);
agclose(g);
// gvfreecontext函数返回错误个数
// 错误数为0表示没有问题
return (gvFreeContext(gvc) == 0);
}
GraphVizUtils::VerticesCoordinates GraphVizUtils::getVerticesCoordinates(
GraphIF * graph, GraphVizEngine layoutEngine,
GraphDimmention graphMaxWidth, GraphDimmention graphMaxHeight) {
GVC_t *gvc { };
Agraph_t *g { };
std::string dotFormatedGraph { };
char * graphRenderedData { };
unsigned int length { };
VerticesCoordinates verticesCoordinates { };
std::stringstream ss { };
gvc = gvContext();
dotFormatedGraph = OutputUtils::impl::DOT::exportGraph(graph);
g = agmemread(dotFormatedGraph.c_str());
gvLayout(gvc, g, EnumUtils::getGraphVizEngineString(layoutEngine));
gvRenderData(gvc, g, "plain", &graphRenderedData, &length);
ss << graphRenderedData;
switch (layoutEngine) {
case GraphVizEngine::DOT:
break;
case GraphVizEngine::NEATO:
verticesCoordinates =
GraphVizUtils::impl::getVerticesCoordinatesAsNeato(ss,
graph->getNumberOfVertices(), graphMaxWidth,
graphMaxHeight);
break;
default:
break;
}
gvFreeRenderData(graphRenderedData);
gvFreeLayout(gvc, g);
agclose(g);
gvFreeContext(gvc);
return verticesCoordinates;
}
void EuclideanNetwork::show(std::string filename, const char* filetype) {
GVC_t *gvc;
Agraph_t *g;
std::stringstream sStream;
std::vector<Agnode_t *> vNodes;
std::vector<Agedge_t *> vEdges;
int i = 0;
if (v < 1) return;
gvc = gvContext();
g = agopen("g", Agundirected, 0);
while (i < v) {
sStream.str("");
sStream << i;
vNodes.push_back(agnode(g, sStream.str().c_str(), 1));
sStream.str("");
sStream << x[i]*7 << "," << y[i]*7 << "!";
agsafeset(vNodes[vNodes.size()-1], "height", "0.4", "");
agsafeset(vNodes[vNodes.size()-1], "width", "0.4", "");
agsafeset(vNodes[vNodes.size()-1], "fixedsize", "true", "");
agsafeset(vNodes[vNodes.size()-1], "pos", sStream.str().c_str(), "");
i++;
}
for (std::set<Edge>::iterator x = e.begin(); x != e.end(); ++x) {
sStream.str("");
sStream << ((*x).wage * scale);
vEdges.push_back(agedge(g, vNodes[(*x).v1], vNodes[(*x).v2], sStream.str().c_str(), 1));
}
gvLayout(gvc, g, "fdp");
gvRenderFilename(gvc, g, filetype, filename.c_str());
gvFreeLayout(gvc, g);
agclose(g);
gvFreeContext(gvc);
return;
}
__attribute__((used)) char* vizRenderFromString(char *string, char *format) {
GVC_t *context = gvContext();
gvAddLibrary(context, &gvplugin_core_LTX_library);
gvAddLibrary(context, &gvplugin_dot_layout_LTX_library);
Agraph_t *graph = agmemread(string);
gvLayout(context, graph, "dot");
char *result;
unsigned int length;
gvRenderData(context, graph, format, &result, &length);
gvFreeLayout(context, graph);
agclose(graph);
gvFinalize(context);
gvFreeContext(context);
return result;
}
xme_status_t
xme_hal_graphviz_init(void)
{
if (0 == xme_hal_graphviz_initializationCount)
{
//Init graphviz;
xme_hal_graphviz_gvc = gvContext();
xme_hal_graphviz_mutex = xme_hal_sync_createCriticalSection();
xme_hal_graphviz_initializationCount++;
return XME_STATUS_SUCCESS;
}
else
{
xme_hal_graphviz_initializationCount++;
return XME_STATUS_SUCCESS;
}
}
/*
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% %
% %
% R e g i s t e r D O T I m a g e %
% %
% %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% RegisterDOTImage() adds attributes for the Display Postscript image
% format to the list of supported formats. The attributes include the image
% format tag, a method to read and/or write the format, whether the format
% supports the saving of more than one frame to the same file or blob,
% whether the format supports native in-memory I/O, and a brief
% description of the format.
%
% The format of the RegisterDOTImage method is:
%
% size_t RegisterDOTImage(void)
%
*/
ModuleExport size_t RegisterDOTImage(void)
{
MagickInfo
*entry;
entry=AcquireMagickInfo("DOT","DOT","Graphviz");
#if defined(MAGICKCORE_GVC_DELEGATE)
entry->decoder=(DecodeImageHandler *) ReadDOTImage;
#endif
entry->flags^=CoderBlobSupportFlag;
(void) RegisterMagickInfo(entry);
entry=AcquireMagickInfo("DOT","GV","Graphviz");
#if defined(MAGICKCORE_GVC_DELEGATE)
entry->decoder=(DecodeImageHandler *) ReadDOTImage;
#endif
entry->flags^=CoderBlobSupportFlag;
(void) RegisterMagickInfo(entry);
#if defined(MAGICKCORE_GVC_DELEGATE)
graphic_context=gvContext();
#endif
return(MagickImageCoderSignature);
}
int main (int argc, char* argv[])
{
graph_t *g;
graph_t *sg;
FILE *fp;
graph_t** cc;
int i, ncc;
GVC_t *gvc;
gvc = gvContext();
if (argc > 1)
fp = fopen(argv[1], "r");
else
fp = stdin;
g = agread(fp, 0);
cc = ccomps(g, &ncc, (char*)0);
for (i = 0; i < ncc; i++) {
sg = cc[i];
nodeInduce (sg);
gvLayout(gvc, sg, "neato");
}
pack_graph (ncc, cc, g, 0);
gvRender(gvc, g, "ps", stdout);
for (i = 0; i < ncc; i++) {
sg = cc[i];
gvFreeLayout(gvc, sg);
agdelete(g, sg);
}
agclose(g);
return (gvFreeContext(gvc));
}
void graph2png(const agent *a, const agent *n, const contr c, const contr r, const contr d, const char* filename) {
const agent *p = n + N + 1;
agent m = n[N];
GVC_t *gvc = gvContext();
Agraph_t* g = agopen("test", Agstrictundirected, 0);
agsafeset(g, "overlap", "false", "");
Agnode_t* nodes[N];
do { nodes[*p] = agnode(g, names[*p], 1); p++; }
while (--m);
for (agent i = 1; i < E + 1; i++) if (!ISSET(c, i) && !ISSET(d, i)) {
Agedge_t *e = agedge(g, nodes[X(a, i)], nodes[Y(a, i)], "", 1);
if (ISSET(r, i)) agsafeset(e, "color", "red", "");
}
gvLayout(gvc, g, "neato");
gvRenderFilename(gvc, g, "png", filename);
gvFreeLayout(gvc, g);
agclose(g);
gvFreeContext(gvc);
}
int main(int argc, char **argv)
{
Agraph_t *g;
Agnode_t *n, *m;
Agedge_t *e;
GVC_t *gvc;
/* set up a graphviz context */
gvc = gvContext();
/* parse command line args - minimally argv[0] sets layout engine */
gvParseArgs(gvc, argc, argv);
/* Create a simple digraph */
g = agopen("g", AGDIGRAPH);
n = agnode(g, "n");
m = agnode(g, "m");
e = agedge(g, n, m);
/* Set an attribute - in this case one that affects the visible rendering */
agsafeset(n, "color", "red", "");
/* Compute a layout using layout engine from command line args */
gvLayoutJobs(gvc, g);
/* Write the graph according to -T and -o options */
gvRenderJobs(gvc, g);
/* Free layout data */
gvFreeLayout(gvc, g);
/* Free graph structures */
agclose(g);
/* close output file, free context, and return number of errors */
return (gvFreeContext(gvc));
}
/** Constructor. */
SkillGuiGraphDrawingArea::SkillGuiGraphDrawingArea()
{
add_events(Gdk::SCROLL_MASK | Gdk::BUTTON_MOTION_MASK);
__gvc = gvContext();
__graph = NULL;
__graph_fsm = "";
__graph_dot = "";
__bbw = __bbh = __pad_x = __pad_y = 0.0;
__translation_x = __translation_y = 0.0;
__scale = 1.0;
__speed = 0.0;
__speed_max = 200.0;
__speed_ramp_distance = 40.0;
__translation_x_setpoint = __translation_y_setpoint = 0.0;
__scale_override = false;
__update_graph = true;
__recording = false;
timeval now;
gettimeofday(&now, NULL);
__last_update_time = (float)now.tv_sec + now.tv_usec/1000000.;
__mouse_motion = false;
gvplugin_skillgui_cairo_setup(__gvc, this);
__fcd_save = new Gtk::FileChooserDialog("Save Graph",
Gtk::FILE_CHOOSER_ACTION_SAVE);
__fcd_open = new Gtk::FileChooserDialog("Load Graph",
Gtk::FILE_CHOOSER_ACTION_OPEN);
__fcd_recording = new Gtk::FileChooserDialog("Recording Directory",
Gtk::FILE_CHOOSER_ACTION_CREATE_FOLDER);
//Add response buttons the the dialog:
__fcd_save->add_button(Gtk::Stock::CANCEL, Gtk::RESPONSE_CANCEL);
__fcd_save->add_button(Gtk::Stock::SAVE, Gtk::RESPONSE_OK);
__fcd_open->add_button(Gtk::Stock::CANCEL, Gtk::RESPONSE_CANCEL);
__fcd_open->add_button(Gtk::Stock::SAVE, Gtk::RESPONSE_OK);
__fcd_recording->add_button(Gtk::Stock::CANCEL, Gtk::RESPONSE_CANCEL);
__fcd_recording->add_button(Gtk::Stock::OK, Gtk::RESPONSE_OK);
__filter_pdf = new Gtk::FileFilter();
__filter_pdf->set_name("Portable Document Format (PDF)");
__filter_pdf->add_pattern("*.pdf");
__filter_svg = new Gtk::FileFilter();
__filter_svg->set_name("Scalable Vector Graphic (SVG)");
__filter_svg->add_pattern("*.svg");
__filter_png = new Gtk::FileFilter();
__filter_png->set_name("Portable Network Graphic (PNG)");
__filter_png->add_pattern("*.png");
__filter_dot = new Gtk::FileFilter();
__filter_dot->set_name("DOT Graph");
__filter_dot->add_pattern("*.dot");
__fcd_save->add_filter(*__filter_pdf);
__fcd_save->add_filter(*__filter_svg);
__fcd_save->add_filter(*__filter_png);
__fcd_save->add_filter(*__filter_dot);
__fcd_save->set_filter(*__filter_pdf);
__fcd_open->add_filter(*__filter_dot);
__fcd_open->set_filter(*__filter_dot);
add_events(Gdk::SCROLL_MASK | Gdk::BUTTON_MOTION_MASK |
Gdk::BUTTON_PRESS_MASK | Gdk::BUTTON_RELEASE_MASK );
#ifndef GLIBMM_DEFAULT_SIGNAL_HANDLERS_ENABLED
signal_expose_event().connect(sigc::mem_fun(*this, &SkillGuiGraphDrawingArea::on_expose_event));
signal_button_press_event().connect(sigc::mem_fun(*this, &SkillGuiGraphDrawingArea::on_button_press_event));
signal_button_release_event().connect(sigc::mem_fun(*this, &SkillGuiGraphDrawingArea::on_button_release_event));
signal_motion_notify_event().connect(sigc::mem_fun(*this, &SkillGuiGraphDrawingArea::on_motion_notify_event));
#endif
}
void GraphvizAdapterImpl::init_context_() {
gvc_ = gvContext();
}
SBML_ODESOLVER_API int drawJacoby(cvodeData_t *data, char *file, char *format) {
#if !USE_GRAPHVIZ
SolverError_error(
WARNING_ERROR_TYPE,
SOLVER_ERROR_NO_GRAPHVIZ,
"odeSolver has been compiled without GRAPHIZ functionality. ",
"Graphs are printed to stdout in the graphviz' .dot format.");
drawJacobyTxt(data, file);
#else
int i, j;
GVC_t *gvc;
Agraph_t *g;
Agnode_t *r;
Agnode_t *s;
Agedge_t *e;
Agsym_t *a;
char name[WORDSIZE];
char label[WORDSIZE];
char *output[3];
char *command = "dot";
char *formatopt;
char *outfile;
/* setting name of outfile */
ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
sprintf(outfile, "-o%s_jm.%s", file, format);
/* setting output format */
ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
sprintf(formatopt, "-T%s", format);
/* construct command-line */
output[0] = command;
output[1] = formatopt;
output[2] = outfile;
output[3] = NULL;
/* set up renderer context */
gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvParseArgs(gvc, 3, output);
#endif
g = agopen("G", AGDIGRAPH);
/* avoid overlapping nodes, for graph embedding by neato */
a = agraphattr(g, "overlap", "");
agxset(g, a->index, "scale");
/* set graph label */
if ( Model_isSetName(data->model->m) )
sprintf(label, "%s at time %g", Model_getName(data->model->m),
data->currenttime);
else if ( Model_isSetId(data->model->m) )
sprintf(label, "%s at time %g", Model_getId(data->model->m),
data->currenttime);
else
sprintf(label, "label=\"at time %g\";\n", data->currenttime);
a = agraphattr(g, "label", "");
agxset(g, a->index, label);
/*
Set edges from species A to species B if the
corresponding entry in the jacobian ((d[B]/dt)/d[A])
is not '0'. Set edge color 'red' and arrowhead 'tee'
if negative.
*/
for ( i=0; i<data->model->neq; i++ ) {
for ( j=0; j<data->model->neq; j++ ) {
if ( evaluateAST(data->model->jacob[i][j], data) != 0 ) {
sprintf(name, "%s", data->model->names[j]);
r = agnode(g,name);
agset(r, "label", data->model->names[j]);
sprintf(label, "%s.htm", data->model->names[j]);
a = agnodeattr(g, "URL", "");
agxset(r, a->index, label);
sprintf(name,"%s", data->model->names[i]);
s = agnode(g,name);
agset(s, "label", data->model->names[i]);
sprintf(label, "%s.htm", data->model->names[i]);
a = agnodeattr(g, "URL", "");
agxset(s, a->index, label);
e = agedge(g,r,s);
a = agedgeattr(g, "label", "");
sprintf(name, "%g", evaluateAST(data->model->jacob[i][j], data));
agxset (e, a->index, name);
if ( evaluateAST(data->model->jacob[i][j], data) < 0 ) {
a = agedgeattr(g, "arrowhead", "");
agxset(e, a->index, "tee");
a = agedgeattr(g, "color", "");
agxset(e, a->index, "red");
}
}
}
}
/* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvBindContext(gvc, g);
dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvLayoutJobs(gvc, g);
#endif
/* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvRenderJobs(gvc, g);
#endif
/* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeLayout(gvc, g);
#endif
/* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
dot_cleanup(g);
#endif
agclose(g);
/* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
gvFREEcontext(gvc);
dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
dotneato_terminate(gvc);
#elif (GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6) || GRAPHVIZ_MAJOR_VERSION >= 3
gvFreeContext(gvc);
#endif
xfree(formatopt);
xfree(outfile);
#endif
return 1;
}
int render_graph(rendering_ctx_t *rctx,
const char* filename,
const char* format)
{
Agraph_t *g;
Agnode_t *n;
Agnode_t *d;
Agedge_t *e;
GVC_t *gvc;
rnsGraph_t *rnsGraph;
char w[32];
FILE *fp;
fp = fopen(filename, "w+");
gvc = gvContext();
rnsGraph = rctx->graph;
if (rctx->directed){
g = agopen("g", Agstrictdirected, 0);
}else{
g = agopen("g", Agstrictundirected, 0);
}
size_t i, j;
for (i=0; i<rnsGraph->size; i++){
if ( !rnsGraph->repos[i]) {
continue;
}
n = agnode(g, rnsGraph->repos[i]->id, 1);
for (j=0; j<rnsGraph->repos[i]->maxLinks; j++){
if (!rnsGraph->repos[i]->links[j]){
continue;
}
d = agnode(g, rnsGraph->repos[i]->links[j]->repo->id, 1);
e = agedge(g, n, d, 0, 1);
snprintf(w, sizeof(w), "%1.3g", (double) cost(rnsGraph->repos[i],
rnsGraph->repos[i]->links[j]));
agsafeset(e, "label", w, "");
if (rnsGraph->repos[i]->links[j]->is_path){
agsafeset(e, "color", "red", "");
}
}
}
// char *args[] = {
// "sfdp",
// "-x",
// "-Tpng",
// "-Goverlap=scale",
// "-GK=5.0",
// "-ooutput/random.png"
// };
// gvParseArgs (gvc, sizeof(args)/sizeof(char*), args);
// gvLayoutJobs(gvc, g);
// gvRenderJobs(gvc, g);
gvLayout(gvc, g, "dot");
gvRender(gvc, g, format, fp);
gvFreeLayout(gvc, g);
agclose(g);
fclose(fp);
return (gvFreeContext(gvc));
}
if (Ty *p = pq_cast<Ty>(X)) return p; \
throw PlException("null ptr " #Ty); \
}
ptrcast(GVC_t, gvc)
ptrcast(Agraph_t, graph)
ptrcast(Agnode_t, node)
ptrcast(Agedge_t, edge)
ptrcast(Agsym_t, sym)
ptrcast(Agrec_t, rec)
/** GVC_t *gvContext()
* minimal interface to Graphviz context: create context for graph construction setup and rendering
*/
PREDICATE(gvContext, 1) {
if (GVC_t *C = gvContext())
return PL_A1 = C;
throw PlException("gvContext failed");
}
/** int gvFreeContext(GVC_t *gvc)
*
* minimal interface to Graphviz context: call after rendering done
* Beware! naked pointers. Need to introduce guarded allocation.
*/
PREDICATE(gvFreeContext, 1) {
gvFreeContext(gvc(PL_A1));
return TRUE;
}
/** Agraph_t* G = agopen(name, type, &disc);
void*
AI_alert_correlation_thread ( void *arg )
{
int i;
struct stat st;
char corr_dot_file[4096] = { 0 };
#ifdef HAVE_LIBGVC
char corr_ps_file [4096] = { 0 };
#endif
double avg_correlation = 0.0,
std_deviation = 0.0,
corr_threshold = 0.0,
kb_correlation = 0.0,
bayesian_correlation = 0.0,
neural_correlation = 0.0;
size_t n_correlations = 0,
n_corr_functions = 0,
n_corr_weights = 0;
FILE *fp = NULL;
AI_alert_correlation_key corr_key;
AI_alert_correlation *corr = NULL;
AI_alert_type_pair_key pair_key;
AI_alert_type_pair *pair = NULL,
*unpair = NULL;
AI_snort_alert *alert_iterator = NULL,
*alert_iterator2 = NULL;
pthread_t manual_corr_thread;
#ifdef HAVE_LIBGVC
char corr_png_file[4096] = { 0 };
GVC_t *gvc = NULL;
graph_t *g = NULL;
#endif
double (**corr_functions)( const AI_snort_alert*, const AI_snort_alert* ) = NULL;
double (**corr_weights)() = NULL;
#ifdef HAVE_LIBPYTHON2_6
PyObject *pyA = NULL,
*pyB = NULL;
PyObject *pArgs = NULL,
*pRet = NULL;
PyObject **py_corr_functions = NULL;
PyObject **py_weight_functions = NULL;
size_t n_py_corr_functions = 0;
size_t n_py_weight_functions = 0;
double py_value = 0.0,
py_weight = 0.0;
py_corr_functions = AI_get_py_functions ( &n_py_corr_functions );
py_weight_functions = AI_get_py_weights ( &n_py_weight_functions );
#endif
corr_functions = AI_get_corr_functions ( &n_corr_functions );
corr_weights = AI_get_corr_weights ( &n_corr_weights );
pthread_mutex_init ( &mutex, NULL );
/* Start the thread for parsing manual correlations from XML */
if ( pthread_create ( &manual_corr_thread, NULL, AI_manual_correlations_parsing_thread, NULL ) != 0 )
{
AI_fatal_err ( "Failed to create the manual correlations parsing thread", __FILE__, __LINE__ );
}
while ( 1 )
{
sleep ( config->correlationGraphInterval );
if ( stat ( config->corr_rules_dir, &st ) < 0 )
{
_dpd.errMsg ( "AIPreproc: Correlation rules directory '%s' not found, the correlation thread won't be active\n",
config->corr_rules_dir );
pthread_exit (( void* ) 0 );
return ( void* ) 0;
}
/* Set the lock flag to true, and keep it this way until I've done with correlating alerts */
pthread_mutex_lock ( &mutex );
if ( alerts )
{
AI_free_alerts ( alerts );
alerts = NULL;
}
if ( !( alerts = AI_get_clustered_alerts() ))
{
pthread_mutex_unlock ( &mutex );
continue;
}
if ( config->use_knowledge_base_correlation_index != 0 )
{
AI_kb_index_init ( alerts );
}
__AI_correlation_table_cleanup();
correlation_table = NULL;
/* Fill the table of correlated alerts */
for ( alert_iterator = alerts; alert_iterator; alert_iterator = alert_iterator->next )
{
for ( alert_iterator2 = alerts; alert_iterator2; alert_iterator2 = alert_iterator2->next )
{
if ( alert_iterator != alert_iterator2 && ! (
alert_iterator->gid == alert_iterator2->gid &&
alert_iterator->sid == alert_iterator2->sid &&
alert_iterator->rev == alert_iterator2->rev ))
{
if ( !( corr = ( AI_alert_correlation* ) malloc ( sizeof ( AI_alert_correlation ))))
AI_fatal_err ( "Fatal dynamic memory allocation error", __FILE__, __LINE__ );
corr_key.a = alert_iterator;
corr_key.b = alert_iterator2;
corr->key = corr_key;
corr->correlation = 0.0;
n_correlations = 0;
kb_correlation = AI_kb_correlation_coefficient ( corr_key.a, corr_key.b );
bayesian_correlation = AI_alert_bayesian_correlation ( corr_key.a, corr_key.b );
neural_correlation = AI_alert_neural_som_correlation ( corr_key.a, corr_key.b );
/* Use the correlation indexes for which we have a value */
if ( bayesian_correlation != 0.0 && config->bayesianCorrelationInterval != 0 )
{
corr->correlation += AI_bayesian_correlation_weight() * bayesian_correlation;
n_correlations++;
}
if ( kb_correlation != 0.0 && config->use_knowledge_base_correlation_index )
{
corr->correlation += kb_correlation;
n_correlations++;
}
if ( neural_correlation != 0.0 && config->neuralNetworkTrainingInterval != 0 )
{
corr->correlation += AI_neural_correlation_weight() * neural_correlation;
n_correlations++;
}
/* Get the correlation indexes from extra correlation modules */
if (( corr_functions ))
{
for ( i=0; i < n_corr_functions; i++ )
{
if ( corr_weights[i]() != 0.0 )
{
corr->correlation += corr_weights[i]() * corr_functions[i] ( corr_key.a, corr_key.b );
n_correlations++;
}
}
}
#ifdef HAVE_LIBPYTHON2_6
if (( py_corr_functions ))
{
pyA = AI_alert_to_pyalert ( corr_key.a );
pyB = AI_alert_to_pyalert ( corr_key.b );
if ( pyA && pyB )
{
for ( i=0; i < n_py_corr_functions; i++ )
{
if ( !( pArgs = Py_BuildValue ( "(OO)", pyA, pyB )))
{
PyErr_Print();
AI_fatal_err ( "Could not initialize the Python arguments for the call", __FILE__, __LINE__ );
}
if ( !( pRet = PyEval_CallObject ( py_corr_functions[i], pArgs )))
{
PyErr_Print();
AI_fatal_err ( "Could not call the correlation function from the Python module", __FILE__, __LINE__ );
}
if ( !( PyArg_Parse ( pRet, "d", &py_value )))
{
PyErr_Print();
AI_fatal_err ( "Could not parse the correlation value out of the Python correlation function", __FILE__, __LINE__ );
}
Py_DECREF ( pRet );
Py_DECREF ( pArgs );
if ( !( pRet = PyEval_CallObject ( py_weight_functions[i], (PyObject*) NULL )))
{
PyErr_Print();
AI_fatal_err ( "Could not call the correlation function from the Python module", __FILE__, __LINE__ );
}
if ( !( PyArg_Parse ( pRet, "d", &py_weight )))
{
PyErr_Print();
AI_fatal_err ( "Could not parse the correlation weight out of the Python correlation function", __FILE__, __LINE__ );
}
Py_DECREF ( pRet );
if ( py_weight != 0.0 )
{
corr->correlation += py_weight * py_value;
n_correlations++;
}
}
Py_DECREF ( pyA ); Py_DECREF ( pyB );
/* free ( pyA ); free ( pyB ); */
pyA = NULL; pyB = NULL;
}
}
#endif
if ( n_correlations != 0 )
{
corr->correlation /= (double) n_correlations;
}
HASH_ADD ( hh, correlation_table, key, sizeof ( AI_alert_correlation_key ), corr );
}
}
}
if ( HASH_COUNT ( correlation_table ) > 0 )
{
avg_correlation = 0.0;
std_deviation = 0.0;
/* Compute the average correlation coefficient */
for ( corr = correlation_table; corr; corr = ( AI_alert_correlation* ) corr->hh.next )
{
avg_correlation += corr->correlation;
}
avg_correlation /= (double) HASH_COUNT ( correlation_table );
/* Compute the standard deviation */
for ( corr = correlation_table; corr; corr = ( AI_alert_correlation* ) corr->hh.next )
{
std_deviation += ( corr->correlation - avg_correlation ) * ( corr->correlation - avg_correlation );
}
std_deviation = sqrt ( std_deviation / (double) HASH_COUNT ( correlation_table ));
corr_threshold = avg_correlation + ( config->correlationThresholdCoefficient * std_deviation );
snprintf ( corr_dot_file, sizeof ( corr_dot_file ), "%s/correlated_alerts.dot", config->corr_alerts_dir );
if ( stat ( config->corr_alerts_dir, &st ) < 0 )
{
if ( mkdir ( config->corr_alerts_dir, 0755 ) < 0 )
{
AI_fatal_err ( "Unable to create directory the correlated alerts directory", __FILE__, __LINE__ );
}
} else if ( !S_ISDIR ( st.st_mode )) {
AI_fatal_err ( "The specified directory for correlated alerts is not a directory", __FILE__, __LINE__ );
}
if ( !( fp = fopen ( corr_dot_file, "w" )))
AI_fatal_err ( "Could not write on the correlated alerts .dot file", __FILE__, __LINE__ );
fprintf ( fp, "digraph G {\n" );
/* Find correlated alerts */
for ( corr = correlation_table; corr; corr = ( AI_alert_correlation* ) corr->hh.next )
{
pair_key.from_sid = corr->key.a->sid;
pair_key.from_gid = corr->key.a->gid;
pair_key.from_rev = corr->key.a->rev;
pair_key.to_sid = corr->key.b->sid;
pair_key.to_gid = corr->key.b->gid;
pair_key.to_rev = corr->key.b->rev;
HASH_FIND ( hh, manual_correlations, &pair_key, sizeof ( pair_key ), pair );
HASH_FIND ( hh, manual_uncorrelations, &pair_key, sizeof ( pair_key ), unpair );
/* Yes, BlackLight wrote this line of code in a pair of minutes and immediately
* compiled it without a single error */
if ( !unpair && ( pair || (
corr->correlation >= corr_threshold &&
corr_threshold != 0.0 &&
corr->key.a->timestamp <= corr->key.b->timestamp && ! (
corr->key.a->gid == corr->key.b->gid &&
corr->key.a->sid == corr->key.b->sid &&
corr->key.a->rev == corr->key.b->rev ) && (
corr->key.a->ip_src_addr == corr->key.b->ip_src_addr || (
(corr->key.a->h_node[src_addr] && corr->key.b->h_node[src_addr]) ?
( corr->key.a->h_node[src_addr]->max_val == corr->key.b->h_node[src_addr]->max_val &&
corr->key.a->h_node[src_addr]->min_val == corr->key.b->h_node[src_addr]->min_val ) : 0
)) && (
corr->key.a->ip_dst_addr == corr->key.b->ip_dst_addr || (
(corr->key.a->h_node[dst_addr] && corr->key.b->h_node[dst_addr]) ?
( corr->key.a->h_node[dst_addr]->max_val == corr->key.b->h_node[dst_addr]->max_val &&
corr->key.a->h_node[dst_addr]->min_val == corr->key.b->h_node[dst_addr]->min_val ) : 0
))
)
)
) {
if ( !( corr->key.a->derived_alerts = ( AI_snort_alert** ) realloc ( corr->key.a->derived_alerts,
(++corr->key.a->n_derived_alerts) * sizeof ( AI_snort_alert* ))))
AI_fatal_err ( "Fatal dynamic memory allocation error", __FILE__, __LINE__ );
if ( !( corr->key.b->parent_alerts = ( AI_snort_alert** ) realloc ( corr->key.b->parent_alerts,
(++corr->key.b->n_parent_alerts) * sizeof ( AI_snort_alert* ))))
AI_fatal_err ( "Fatal dynamic memory allocation error", __FILE__, __LINE__ );
corr->key.a->derived_alerts[ corr->key.a->n_derived_alerts - 1 ] = corr->key.b;
corr->key.b->parent_alerts [ corr->key.b->n_parent_alerts - 1 ] = corr->key.a;
__AI_correlated_alerts_to_dot ( corr, fp );
if ( config->outdbtype != outdb_none )
{
AI_store_correlation_to_db ( corr );
}
}
}
fprintf ( fp, "}\n" );
fclose ( fp );
#ifdef HAVE_LIBGVC
snprintf ( corr_png_file, sizeof ( corr_png_file ), "%s/correlated_alerts.png", config->corr_alerts_dir );
snprintf ( corr_ps_file , sizeof ( corr_ps_file ), "%s/correlated_alerts.ps" , config->corr_alerts_dir );
if ( !( gvc = gvContext() ))
{
pthread_mutex_unlock ( &mutex );
continue;
}
if ( !( fp = fopen ( corr_dot_file, "r" )))
{
pthread_mutex_unlock ( &mutex );
continue;
}
if ( !( g = agread ( fp )))
{
pthread_mutex_unlock ( &mutex );
continue;
}
gvLayout ( gvc, g, "dot" );
gvRenderFilename ( gvc, g, "png", corr_png_file );
gvRenderFilename ( gvc, g, "ps" , corr_ps_file );
gvFreeLayout ( gvc, g );
agclose ( g );
fclose ( fp );
#endif
/* If no database output is defined, then the alerts have no alert_id, so we cannot use the
* web interface for correlating them, as they have no unique identifier */
if ( config->outdbtype != outdb_none )
{
if ( strlen ( config->webserv_dir ) != 0 )
{
__AI_correlated_alerts_to_json ();
}
}
}
pthread_mutex_unlock ( &mutex );
}
pthread_exit (( void* ) 0 );
return (void*) 0;
} /* ----- end of function AI_alert_correlation_thread ----- */
