void WikiMainPage::execute() {
bool createMainPage = wm -> checkCreateMainPages();
if( createMainPage == false ) {
logger.logInfo( "skip creating main page" );
return;
}
String wikiDir = wm -> getWikiPath();
String wikiPage = wm -> getMainPage();
// get sorted circuit list
MindService *ms = MindService::getService();
MindMap *mm = ms -> getMindMap();
ClassList<MindGlobalCircuitDef>& circuitList = mm -> getMindGlobalCircuits();
MapStringToClass<MindGlobalCircuitDef> circuitMap;
for( int k = 0; k < circuitList.count(); k++ ) {
MindGlobalCircuitDef *cd = circuitList.get( k );
circuitMap.add( cd -> getName() , cd );
}
// collect model circuit section lines
StringList lines;
for( int k = 0; k < circuitMap.count(); k++ ) {
MindGlobalCircuitDef *cd = circuitMap.getClassByIndex( k );
String name = cd -> getName();
String id = cd -> getId();
lines.add( " * [" + id + " " + name + "]" );
}
String sectionName = "Circuits";
wm -> updateFileSection( wikiDir , wikiPage , sectionName , lines );
}
void WikiAreaPages::createAreaPages_getExternalConnections( MindArea *area , MindLocalCircuitDef& circuit , MapStringToClass<MindLocalCircuitConnectionDef>& connections , bool isin ) {
ClassList<MindLocalCircuitConnectionDef> links;
circuit.getExternalConnections( links , isin );
MindService *ms = MindService::getService();
for( int k = 0; k < links.count(); k++ ) {
MindLocalCircuitConnectionDef *c = links.get( k );
// ignore secondary
if( !c -> isPrimary() )
continue;
String key;
if( isin == false ) {
MindRegion *region = ms -> getMindRegion( c -> getDstRegion() );
key = region -> getArea() -> getAreaId() + "#" + c -> getSrcRegion() + "#" + c -> getDstRegion() + "#1";
if( connections.get( key ) == NULL )
connections.add( key , c );
}
else {
MindRegion *region = ms -> getMindRegion( c -> getSrcRegion() );
key = region -> getArea() -> getAreaId() + "#" + c -> getDstRegion() + "#" + c -> getSrcRegion() + "#2";
if( connections.get( key ) == NULL )
connections.add( key , c );
}
}
}
void WikiAreaPages::createAreaPages_createAreaCircuitTable( MapStringToClass<MindLocalCircuitDef>& circuits , StringList& lines ) {
createAreaPages_createAreaCircuitTableLine( NULL , lines );
for( int k = 0; k < circuits.count(); k++ ) {
MindLocalCircuitDef *circuit = circuits.getClassByIndex( k );
createAreaPages_createAreaCircuitTableLine( circuit , lines );
}
}
void WikiTractsPages::createTracts_addTractTableLines( MapStringToClass<XmlBrainTractSet>& tractsets , StringList& lines ) {
lines.add( "*Tracts overview*:" );
lines.add( "|| *Tract* || *Name* || *Function* ||" );
for( int k = 0; k < tractsets.count(); k++ ) {
XmlBrainTractSet& one = tractsets.getClassRefByIndex( k );
createTracts_addTractSetTableLines( one , lines );
}
}
void WikiAreaPages::createDotFile( MindArea *area , MindLocalCircuitDef& circuit , MapStringToClass<MindLocalCircuitConnectionDef>& internals , MapStringToClass<MindLocalCircuitConnectionDef>& inputs , MapStringToClass<MindLocalCircuitConnectionDef>& outputs ) {
// create dot file
String fileName = wm -> getCircuitDotPath( circuit );
StringList text;
// header
text.add( "digraph \"" + area -> getAreaId() + "\" {" );
text.add( "\tcompound=true;" );
String defaultDotSetup = wm -> getDefaultDotSetup();
text.add( wm -> setSpecialCharacters( defaultDotSetup ) );
text.add( "" );
// list nodes
text.add( "\tsubgraph cluster_" + area -> getAreaId() + " {" );
text.add( "\tlabel=<<b>" + area -> getMindAreaDef() -> getAreaName() + "</b>>;" );
MapStringToClass<MindRegionDef>& regions = circuit.getRegions();
for( int k = 0; k < regions.count(); k++ ) {
MindRegionDef *region = regions.getClassByIndex( k );
String dotdef = wm -> hmindxml.getDotDef( region -> getId() );
String nodeline = "\t\"" + region -> getId() + "\"";
if( !dotdef.isEmpty() ) {
String s = wm -> setSpecialCharacters( dotdef );
s += ", label=<" + createDotFile_getRegionLabel( region ) + ">";
nodeline += " [" + s + "]";
}
nodeline += ";";
text.add( nodeline );
}
text.add( "\t}" );
// list connections
text.add( "" );
for( int k = 0; k < internals.count(); k++ ) {
MindLocalCircuitConnectionDef *c = internals.getClassByIndex( k );
MindConnectionLinkTypeDef *linkDef = c -> getPrimaryLinkType();
String props = wm -> getLinkProps( linkDef );
String linkline = "\t\"" + c -> getSrcRegion() + "\" -> \"" + c -> getDstRegion() + "\"" + props + ";";
text.add( linkline );
}
// add subgraph
String linkItem;
createDotFile_subgraph( area , circuit , true , inputs , text , linkItem );
createDotFile_subgraph( area , circuit , false , outputs , text , linkItem );
// footer
text.add( "}" );
// out to file
wm -> createFileContent( fileName , text );
}
void WikiAreaPages::createAreaPages_addInternalConnections( MindArea *area , MindLocalCircuitDef& circuit , StringList& lines , MapStringToClass<MindLocalCircuitConnectionDef>& connections ) {
if( connections.count() == 0 ) {
lines.add( " * no connections" );
return;
}
createAreaPages_addInternalConnectionTableLine( area , circuit , NULL , lines );
for( int k = 0; k < connections.count(); k++ ) {
MindLocalCircuitConnectionDef *c = connections.getClassByIndex( k );
createAreaPages_addInternalConnectionTableLine( area , circuit , c , lines );
}
}
void WikiAreaPages::createAreaPages_createCircuitsAndReferencesTableSection( String wikiDir , MindArea *area ) {
// skip circuits for target areas - will be in region pages
if( area -> isTargetArea() )
return;
// collect circuits which reference any of area regions
MindService *ms = MindService::getService();
StringList circuits;
wm -> circuitsxml.getCircuitList( circuits );
MapStringToString circuitKeys;
for( int k = 0; k < circuits.count(); k++ ) {
String circuitId = circuits.get( k );
XmlCircuitInfo& info = wm -> circuitsxml.getCircuitInfo( circuitId );
String key = createAreaPages_getCircuitKey( area , info );
if( key.isEmpty() )
continue;
circuitKeys.add( key , circuitId );
}
// add circuits section - sorted by relevance
StringList lines;
for( int k = circuitKeys.count() - 1; k >= 0; k-- ) {
String circuitId = circuitKeys.getClassByIndex( k );
XmlCircuitInfo& info = wm -> circuitsxml.getCircuitInfo( circuitId );
createAreaPages_getCircuitLines( info , lines );
}
String sectionName = "Thirdparty Circuits";
String wikiPage = wm -> getAreaPage( area -> getAreaId() );
wm -> updateFileSection( wikiDir , wikiPage , sectionName , lines );
lines.clear();
// add unique and sorted references - sorted by relevance
MapStringToClass<MindArea> refs;
for( int k = circuitKeys.count() - 1; k >= 0; k-- ) {
String circuitId = circuitKeys.getClassByIndex( k );
XmlCircuitInfo& info = wm -> circuitsxml.getCircuitInfo( circuitId );
if( !info.reference.equals( "UNKNOWN" ) )
if( refs.get( info.reference ) == NULL ) {
refs.add( info.reference , area );
lines.add( String( " * " ) + info.reference );
}
}
sectionName = "References";
wm -> updateFileSection( wikiDir , wikiPage , sectionName , lines );
}
void WikiAreaPages::createAreaPages_getInternalConnections( MindArea *area , MindLocalCircuitDef& circuit , MapStringToClass<MindLocalCircuitConnectionDef>& connections ) {
ClassList<MindLocalCircuitConnectionDef> links;
circuit.getInternalConnections( links );
for( int k = 0; k < links.count(); k++ ) {
MindLocalCircuitConnectionDef *c = links.get( k );
// ignore secondary
if( !c -> isPrimary() )
continue;
String key = c -> getSrcRegion() + "#" + c -> getDstRegion();
if( connections.get( key ) == NULL )
connections.add( key , c );
}
}
void MindMap::getMapRegions( MapStringToClass<MindRegionDef>& regionMap ) {
for( int k = 0; k < mindAreaMap.count(); k++ ) {
MindAreaDef *areaDef = mindAreaMap.getClassByIndex( k );
ClassList<MindRegionDef>& regionlist = areaDef -> getRegions();
for( int m = 0; m < regionlist.count(); m++ ) {
MindRegionDef *regionDef = regionlist.get( m );
regionMap.add( regionDef -> getId() , regionDef );
}
}
}
void WikiAreaPages::createAreaPages_addExternalConnections( MindArea *area , MindLocalCircuitDef& circuit , StringList& lines , MapStringToClass<MindLocalCircuitConnectionDef>& connections , bool p_inputs ) {
if( connections.count() == 0 ) {
lines.add( " * no connections" );
return;
}
createAreaPages_getExternalConnectionTableLine( area , circuit , NULL , lines , p_inputs , NULL );
// split connections by area types
MindService *ms = MindService::getService();
MapStringToClass<MapStringToClass<MindLocalCircuitConnectionDef>> groups;
for( int k = 0; k < connections.count(); k++ ) {
MindLocalCircuitConnectionDef *c = connections.getClassByIndex( k );
String regionId = ( p_inputs )? c -> getSrcRegion() : c -> getDstRegion();
MindRegion *region = ms -> getMindRegion( regionId );
String areaType = region -> getArea() -> getMindAreaDef() -> getAreaType();
MapStringToClass<MindLocalCircuitConnectionDef> *z = groups.get( areaType );
if( z == NULL ) {
z = new MapStringToClass<MindLocalCircuitConnectionDef>;
groups.add( areaType , z );
}
String key = connections.getKeyByIndex( k );
z -> add( key , c );
}
for( int k = 0; k < groups.count(); k++ ) {
String areaType = groups.getKeyByIndex( k );
MapStringToClass<MindLocalCircuitConnectionDef> *z = groups.getClassByIndex( k );
createAreaPages_getExternalConnectionTableLine( area , circuit , NULL , lines , p_inputs , areaType );
for( int m = 0; m < z -> count(); m++ ) {
MindLocalCircuitConnectionDef *c = z -> getClassByIndex( m );
createAreaPages_getExternalConnectionTableLine( area , circuit , c , lines , p_inputs , NULL );
}
}
}
void XmlSpinalCordLayout::loadLevel( Xml xmlLevel , MapStringToClass<StringList>& levelData ) {
for( Xml xmlChild = xmlLevel.getFirstChild( "lamina" ); xmlChild.exists(); xmlChild = xmlChild.getNextChild( "lamina" ) ) {
String id = xmlChild.getAttribute( "id" );
String elements = xmlChild.getAttribute( "elements" );
StringList& items = levelData.getRef( id );
StringList parts;
elements.split( parts , "," );
for( int k = 0; k < parts.count(); k++ ) {
String element = parts.get( k );
ASSERTMSG( hmind -> getIndexedElement( element ) != NULL , "unknown element index=" + element );
if( items.find( element ) < 0 )
items.add( element );
}
}
}
void WikiAreaPages::createDotFile_subgraph( MindArea *area , MindLocalCircuitDef& circuit , bool p_inputs , MapStringToClass<MindLocalCircuitConnectionDef>& connections , StringList& text , String& linkItem ) {
MindService *ms = MindService::getService();
String postfix = ( p_inputs )? "IN" : "OUT";
String postfixString = ( p_inputs )? "Inputs" : "Outputs";
// inter-area links
text.add( "" );
if( p_inputs ) {
text.add( "\tsubgraph cluster_ExtIn {" );
text.add( "\tlabel=<<b>Inputs</b>>;" );
text.add( "\t/* external inbound links */" );
}
else {
text.add( "\tsubgraph cluster_ExtOut {" );
text.add( "\tlabel=<<b>Outputs</b>>;" );
text.add( "\t/* external outbound links */" );
}
MapStringToClass<MindRegion> areaTypes;
MapStringToString areas;
MapStringToClass<MapStringToClass<MindRegion>> areaTypeRegionMap;
MapStringToClass<ClassList<MindLocalCircuitConnectionDef>> areaTypeConnectivityMap;
for( int k = 0; k < connections.count(); k++ ) {
MindLocalCircuitConnectionDef *c = connections.getClassByIndex( k );
String regionId = ( p_inputs )? c -> getSrcRegion() : c -> getDstRegion();
String regionLocalId = ( p_inputs )? c -> getDstRegion() : c -> getSrcRegion();
MindRegion *region = ms -> getMindRegion( regionId );
MindRegion *regionLocal = ms -> getMindRegion( regionLocalId );
String areaId = region -> getArea() -> getAreaId();
String areaType = region -> getArea() -> getMindAreaDef() -> getAreaType();
String key = areaType;
MapStringToClass<MindRegion> *typeRegions = areaTypeRegionMap.get( key );
ClassList<MindLocalCircuitConnectionDef> *typeConnectivity = areaTypeConnectivityMap.get( key );
if( typeRegions == NULL ) {
typeRegions = new MapStringToClass<MindRegion>;
typeConnectivity = new ClassList<MindLocalCircuitConnectionDef>;
areaTypeRegionMap.add( key , typeRegions );
areaTypeConnectivityMap.add( key , typeConnectivity );
}
if( typeRegions -> get( regionId ) == NULL )
typeRegions -> add( regionId , region );
areas.addnew( areaId , areaType );
areaTypes.addnew( areaType , regionLocal );
typeConnectivity -> add( c );
}
// add named lines
String s;
String localArea = area -> getAreaId();
// header
text.add( "" );
for( int k = 0; k < areaTypes.count(); k++ ) {
String areaType = areaTypes.getKeyByIndex( k );
text.add( "\tsubgraph cluster_" + areaType + "_" + postfix + " {" );
text.add( "\tlabel=\"" + areaType + " " + postfixString + "\";" );
text.add( "\t\"" + areaType + "." + postfix + "\" [ shape=box, style=dotted , label = <" );
text.add( "\t\t<TABLE BORDER=\"0\" CELLBORDER=\"1\" CELLSPACING=\"4\" CELLPADDING=\"2\"><TR>" );
// regions
MapStringToClass<MindRegion> *typeRegions = areaTypeRegionMap.get( areaType );
for( int a = 0; a < typeRegions -> count(); a++ ) {
String regionId = typeRegions -> getKeyByIndex( a );
MindRegion *region = typeRegions -> getClassByIndex( a );
String color = getRegionColor( regionId );
String label = createDotFile_getRegionLabel( region -> getRegionInfo() );
text.add( "\t\t<TD PORT=\"" + regionId + "\" BGCOLOR=\"" + color + "\">" + label + "</TD>" );
}
text.add( "\t\t</TR></TABLE>> ];" );
text.add( "\t}" );
text.add( "" );
// links
ClassList<MindLocalCircuitConnectionDef> *typeConnectivity = areaTypeConnectivityMap.get( areaType );
for( int a = 0; a < typeConnectivity -> count(); a++ ) {
MindLocalCircuitConnectionDef *c = typeConnectivity -> get( a );
MindConnectionLinkTypeDef *linkDef = c -> getPrimaryLinkType();
String props = wm -> getLinkProps( linkDef );
String srcId;
String dstId;
if( p_inputs ) {
srcId = "\"" + areaType + "." + postfix + "\":\"" + c -> getSrcRegion() + "\"";
dstId = "\"" + c -> getDstRegion() + "\"";
}
else {
srcId = "\"" + c -> getSrcRegion() + "\"";
dstId = "\"" + areaType + "." + postfix + "\":\"" + c -> getDstRegion() + "\"";
}
text.add( "\t" + srcId + " -> " + dstId + props + ";" );
}
text.add( "" );
}
text.add( "\t}" );
areaTypeRegionMap.destroy();
areaTypeConnectivityMap.destroy();
}
void WikiTractsPages::createNeurons_addFibers( int level , MapStringToClass<XmlBrainFiber>& fibers , StringList& lines ) {
for( int k = 0; k < fibers.count(); k++ ) {
XmlBrainFiber& fiber = fibers.getClassRefByIndex( k );
createNeurons_addFiberInfo( level , fiber , lines );
}
}
