fix: consistently use 1-based indexing for paths and 0 for indexes

Fixes #103

Author: danieledler

src/core/ClusterMap.cpp

@@ -95,15 +95,14 @@ void ClusterMap::readTree(const std::string& filename, bool includeFlow)
 
 		pathStream.clear();
 		pathStream.str(pathString);
-		unsigned int childIndex;
+		unsigned int childNumber;
 		Path path;
-		while (pathStream >> childIndex)
+		while (pathStream >> childNumber)
 		{
 			pathStream.get(); // Extract the delimiting character also
-			if (childIndex == 0)
+			if (childNumber == 0)
 				throw FileFormatError("There is a '0' in the tree path, lowest allowed integer is 1.");
-			--childIndex;
-			path.push_back(childIndex);
+			path.push_back(childNumber); // Keep 1-based indexing in path
 		}
 		m_nodePaths.add(nodeId, path);
 	}

src/core/ClusterMap.h

@@ -15,7 +15,7 @@
 
 namespace infomap {
 
-using Path = std::deque<unsigned int>;
+using Path = std::deque<unsigned int>; // 1-based indexing
 struct NodePath
 {
 	NodePath(unsigned int nodeId, const Path& path)
@@ -33,6 +33,7 @@ struct NodePaths
 	unsigned int size() { return nodePaths.size(); }
 	void clear() { nodePaths.clear(); }
 	void add(unsigned int nodeId, const Path& path) {
+		// path should use 1-based indexing
 		add(NodePath(nodeId, path));
 	}
 	void add(NodePath&& path) {

src/core/InfoNode.cpp

@@ -169,7 +169,7 @@ std::vector<unsigned int> InfoNode::calculatePath() const
 	const InfoNode* current = this;
 	std::vector<unsigned int> path;
 	while (current->parent != nullptr) {
-		path.push_back(current->childIndex());
+		path.push_back(current->childIndex() + 1);
 		current = current->parent;
 		if (current->owner != nullptr) {
 			current = current->owner;

src/core/InfoNode.h

@@ -356,6 +356,7 @@ class InfoNode
 
 	unsigned int childIndex() const;
 
+	// Generate 1-based tree path
 	std::vector<unsigned int> calculatePath() const;
 
 	unsigned int infomapChildDegree() const;

src/core/InfomapBase.cpp

@@ -534,10 +534,10 @@ InfomapBase& InfomapBase::initTree(const NodePaths& tree)
 		}
 		for (unsigned int i = 0; i < path.size(); ++i)
 		{
-			auto childIndex = path[i];
+			auto childNumber = path[i]; // 1-based indexing
 			// Create new node if path doesn't exist
 			// TODO: Check correct tree indexing?
-			if (node->childDegree() <= childIndex)
+			if (node->childDegree() < childNumber)
 			{
 				InfoNode* child = leafNode;
 				if (i + 1 < path.size()) {
@@ -2385,7 +2385,7 @@ void InfomapBase::writeTreeLinks(std::ostream& outStream, bool states)
 				if (sourceParentIt == targetParentIt) {
 					// Skip self-links
 					if (sourceChildIndex != targetChildIndex) {
-						auto parentId = io::stringify(sourceParentIt->calculatePath(), ":", 1);
+						auto parentId = io::stringify(sourceParentIt->calculatePath(), ":");
 						auto& linkMap = moduleLinks[parentId];
 						linkMap[std::make_pair(sourceChildIndex + 1, targetChildIndex + 1)] += flow;
 					}

src/core/InfomapIterator.h

@@ -133,7 +133,7 @@ struct InfomapIterator
 
 	unsigned int childIndex() const
 	{
-		return m_path.empty() ? 0 : m_path.back();
+		return m_path.empty() ? 0 : m_path.back() - 1;
 	}
 
 	unsigned int depth() const