fix: Allow precomputed flow for state networks

danieledler · danieledler · commit ab7c5b55b294 · 2023-04-25T20:53:05.000+02:00
diff --git a/src/core/StateNetwork.h b/src/core/StateNetwork.h
@@ -105,6 +105,8 @@ class StateNetwork {
   double m_totalLinkWeightIgnored = 0.0;
   std::map<unsigned int, double> m_outWeights;
   bool m_haveNodeWeights = false;
+  bool m_haveStateNodeWeights = false;
+  bool m_haveFileInput = false;
   // Attributes
   std::map<unsigned int, std::string> m_names;
   std::map<unsigned int, PhysNode> m_physNodes;
@@ -177,6 +179,8 @@ class StateNetwork {
   std::map<unsigned int, std::string>& names() { return m_names; }
   const std::map<unsigned int, std::string>& names() const { return m_names; }
   bool haveNodeWeights() const { return m_haveNodeWeights; }
+  bool haveStateNodeWeights() const { return m_haveStateNodeWeights; }
+  bool haveFileInput() const { return m_haveFileInput; }
 
   virtual const std::map<unsigned int, std::vector<int>>& metaData() const = 0;
 
diff --git a/src/io/Config.cpp b/src/io/Config.cpp
@@ -190,7 +190,7 @@ Config::Config(const std::string& flags, bool isCLI) : isCLI(isCLI)
   } else if (flowModelArg == "precomputed") {
     setFlowModel(FlowModel::precomputed);
   } else if (!flowModelArg.empty()) {
-    throw std::runtime_error("Unrecognized flow model");
+    throw std::runtime_error(io::Str() << "Unrecognized flow model: '" << flowModelArg << "'");
   }
 
   if (regularized) {
diff --git a/src/io/Network.cpp b/src/io/Network.cpp
@@ -120,6 +120,7 @@ void Network::parseNetwork(const std::string& filename)
 
 void Network::parseNetwork(const std::string& filename, const InsensitiveStringSet& validHeadings, const InsensitiveStringSet& ignoreHeadings, const std::string& startHeading)
 {
+  m_haveFileInput = true;
   SafeInFile input(filename);
 
   // Parse standard links by default until possible heading is reached
@@ -450,7 +451,11 @@ void Network::parseStateNode(const std::string& line, StateNetwork::StateNode& s
     m_extractor.seekg(nameEnd + 1);
   }
   // Optional weight, default to 1.0
-  (m_extractor >> stateNode.weight) || (stateNode.weight = 1.0);
+  if ((m_extractor >> stateNode.weight)) {
+    m_haveStateNodeWeights = true;
+    if (stateNode.weight < 0)
+      throw std::runtime_error(io::Str() << "Negative state node weight (" << stateNode.weight << ") from line '" << line << "'");
+  }
 }
 
 void Network::parseLink(const std::string& line, unsigned int& n1, unsigned int& n2, double& weight)
diff --git a/src/utils/FlowCalculator.cpp b/src/utils/FlowCalculator.cpp
@@ -247,9 +247,15 @@ void FlowCalculator::usePrecomputedFlow(const StateNetwork& network, const Confi
   Log() << "\n  -> Using directed links with precomputed flow from input data.";
   Log() << "\n  -> Total link flow: " << sumLinkWeight << ".";
 
-  if (config.isCLI && !network.haveNodeWeights()) {
-    Log() << std::endl;
-    throw std::runtime_error("Missing node flow in input data. Should be passed as a third field under a *Vertices section.");
+  if (network.haveFileInput()) {
+    if (network.haveMemoryInput() && !network.haveStateNodeWeights()) {
+      Log() << std::endl;
+      throw std::runtime_error("Missing node flow in input data. Should be passed as a third field under a *States section.");
+    }
+    if (!network.haveMemoryInput() && !network.haveNodeWeights()) {
+      Log() << std::endl;
+      throw std::runtime_error("Missing node flow in input data. Should be passed as a third field under a *Vertices section.");
+    }
   }
 
   // Treat the link weights as flow
diff --git a/test/data/multilayer.net b/test/data/multilayer.net
@@ -0,0 +1,29 @@
+# A multilayer network using explicit format
+# Figure 3
+*Vertices 5
+# node_id name
+1 "i"
+2 "j"
+3 "k"
+4 "l"
+5 "m"
+*Multilayer
+# layer_id node_id layer_id node_id weight
+# intra
+1 1 1 4 0.8
+1 4 1 1 1
+1 1 1 5 0.8
+1 5 1 1 1
+1 4 1 5 1
+1 5 1 4 1
+2 1 2 2 0.8
+2 2 2 1 1
+2 1 2 3 0.8
+2 3 2 1 1
+2 2 2 3 1
+2 3 2 2 1
+# inter
+1 1 2 2 0.2
+1 1 2 3 0.2
+2 1 1 4 0.2
+2 1 1 5 0.2
diff --git a/test/data/states.net b/test/data/states.net
@@ -0,0 +1,35 @@
+# A network in state format
+# Figure 6
+*Vertices 5
+#node_id name
+1 "i"
+2 "j"
+3 "k"
+4 "l"
+5 "m"
+*States
+#state_id node_id name
+1 1 "α~_i"
+2 2 "β~_j"
+3 3 "γ~_k"
+4 1 "δ~_i"
+5 4 "ε~_l"
+6 5 "ζ~_m"
+*Links
+#source target weight
+1 2 0.8
+1 3 0.8
+1 5 0.2
+1 6 0.2
+2 1 1
+2 3 1
+3 1 1
+3 2 1
+4 5 0.8
+4 6 0.8
+4 2 0.2
+4 3 0.2
+5 4 1
+5 6 1
+6 4 1
+6 5 1
diff --git a/test/data/states_flow.net b/test/data/states_flow.net
@@ -0,0 +1,35 @@
+# A network in state format
+# Figure 6
+*Vertices 5
+#node_id name
+1 "i" 0.4
+2 "j" 0.15
+3 "k" 0.15
+4 "l" 0.15
+5 "m" 0.15
+*States
+#state_id node_id name
+1 1 "α~_i" 0.1
+2 2 "β~_j" 0.1
+3 3 "γ~_k" 0.3
+4 1 "δ~_i" 0.3
+5 4 "ε~_l" 0.1
+6 5 "ζ~_m" 0.1
+*Links
+#source target weight
+1 2 0.08
+1 3 0.08
+1 5 0.02
+1 6 0.02
+2 1 0.1
+2 3 0.1
+3 1 0.1
+3 2 0.1
+4 5 0.08
+4 6 0.08
+4 2 0.02
+4 3 0.02
+5 4 0.1
+5 6 0.1
+6 4 0.1
+6 5 0.1
diff --git a/test/data/states_flow_output.net b/test/data/states_flow_output.net
@@ -0,0 +1,29 @@
+# v2.7.0
+# ./Infomap  --silent --flow-model precomputed
+# State network as physical network
+*Vertices
+#id name flow
+1 "1" 0.1
+2 "2" 0.1
+3 "3" 0.3
+4 "4" 0.3
+5 "5" 0.1
+6 "6" 0.1
+*Arcs
+#source target flow
+1 2 0.08
+1 3 0.08
+1 5 0.02
+1 6 0.02
+2 1 0.1
+2 3 0.1
+3 1 0.1
+3 2 0.1
+4 2 0.02
+4 3 0.02
+4 5 0.08
+4 6 0.08
+5 4 0.1
+5 6 0.1
+6 4 0.1
+6 5 0.1
diff --git a/test/data/twotriangles_flow.net b/test/data/twotriangles_flow.net
@@ -0,0 +1,15 @@
+*Vertices
+1 "A" 0.1
+2 "B" 0.2
+3 "C" 0.3
+4 "D" 0.2
+5 "E" 0.1
+6 "F" 0.1
+*Edges
+1 2 0.1
+1 3 0.2
+2 3 0.3
+3 4 0.1
+4 5 0.1
+4 6 0.1
+5 6 0.1
diff --git a/test/data/twotriangles_flow_output.net b/test/data/twotriangles_flow_output.net
@@ -0,0 +1,19 @@
+# v2.7.0
+# ./Infomap  --silent --flow-model precomputed
+*Vertices
+#id name flow
+1 "A" 0.1
+2 "B" 0.2
+3 "C" 0.3
+4 "D" 0.2
+5 "E" 0.1
+6 "F" 0.1
+*Arcs
+#source target flow
+1 2 0.1
+1 3 0.2
+2 3 0.3
+3 4 0.1
+4 5 0.1
+4 6 0.1
+5 6 0.1
diff --git a/test/test_flow.py b/test/test_flow.py
@@ -0,0 +1,39 @@
+from infomap import Infomap
+import re
+from pathlib import Path
+import filecmp
+import pytest
+
+
+def test_precomputed_requirements():
+    im = Infomap(silent=True, flow_model="precomputed")
+    im.read_file("examples/networks/twotriangles.net")
+    with pytest.raises(RuntimeError, match=re.escape("Missing node flow in input data. Should be passed as a third field under a *Vertices section.")):
+        im.run()
+
+
+def test_precomputed_states_requirements():
+    im = Infomap(silent=True, flow_model="precomputed")
+    im.read_file("examples/networks/states.net")
+    with pytest.raises(RuntimeError, match=re.escape("Missing node flow in input data. Should be passed as a third field under a *States section.")):
+        im.run()
+
+
+def test_precomputed_from_file():
+    im = Infomap(silent=True, flow_model="precomputed")
+    im.read_file("test/data/twotriangles_flow.net")
+    im.run()
+    output_path = Path("test/data/output/twotriangles_flow_output.net")
+    output_path.parent.mkdir(exist_ok=True)
+    im.write_pajek(str(output_path), flow=True)
+    assert (filecmp.cmp(output_path, "test/data/twotriangles_flow_output.net"))
+
+
+def test_precomputed_states_from_file():
+    im = Infomap(silent=True, flow_model="precomputed")
+    im.read_file("test/data/states_flow.net")
+    im.run()
+    output_path = Path("test/data/output/states_flow_output.net")
+    output_path.parent.mkdir(exist_ok=True)
+    im.write_pajek(str(output_path), flow=True)
+    assert (filecmp.cmp(output_path, "test/data/states_flow_output.net"))
diff --git a/test/test_iterators.py b/test/test_iterators.py
@@ -1,5 +1,6 @@
 from infomap import Infomap
 from operator import itemgetter
+import pytest
 
 
 def test_iter_physical_on_physical():
@@ -10,6 +11,7 @@ def test_iter_physical_on_physical():
     modules = sorted([(node.node_id, node.module_id) for node in im.physical_nodes], key=itemgetter(0))
     assert modules == [(1, 1), (2, 1), (3, 1), (4, 2), (5, 2), (6, 2)]
 
+
 def test_iter_physical_on_states():
     im = Infomap(num_trials=10, silent=True)
     im.read_file("examples/networks/states.net")
@@ -20,30 +22,31 @@ def test_iter_physical_on_states():
 
 
 def test_iter_physical_reliability():
-    
+
     for _ in range(100):
         im = Infomap(num_trials=10, silent=True)
         im.read_file("examples/networks/states.net")
         im.run()
-        
+
         modules = [(node.node_id, node.module_id) for node in im.physical_nodes]
         assert modules == [(1, 1), (2, 1), (3, 1), (1, 2), (4, 2), (5, 2)]
 
+
 def test_multilevel_modules_on_states():
     im = Infomap(silent=True)
     im.read_file("examples/networks/states.net")
     im.run()
     modules = [(node, modules) for node, modules in im.get_multilevel_modules(states=True).items()]
     assert modules == [(1, (1,)), (2, (1,)), (3, (1,)), (4, (2,)), (5, (2,)), (6, (2,))]
 
+
 def test_multilevel_modules_on_physical():
     im = Infomap(silent=True)
     im.read_file("examples/networks/states.net")
     im.run()
-    # todo: Use unit test function to assert exception is raised
     # RuntimeError: Cannot get multilevel modules on higher-order network without states.
-    modules = im.get_multilevel_modules(states=False)
-
+    with pytest.raises(RuntimeError):
+        im.get_multilevel_modules(states=False)
 
 
 if __name__ == "__main__":
diff --git a/test/test_multilevel_modules.py b/test/test_multilevel_modules.py

Original file line number	Diff line number	Diff line change
`@@ -190,7 +190,7 @@ Config::Config(const std::string& flags, bool isCLI) : isCLI(isCLI)`
`190`	`190`	`} else if (flowModelArg == "precomputed") {`
`191`	`191`	`setFlowModel(FlowModel::precomputed);`
`192`	`192`	`} else if (!flowModelArg.empty()) {`
`193`		`- throw std::runtime_error("Unrecognized flow model");`
	`193`	`+ throw std::runtime_error(io::Str() << "Unrecognized flow model: '" << flowModelArg << "'");`
`194`	`194`	`}`
`195`	`195`
`196`	`196`	`if (regularized) {`
Original file line number	Diff line number	Diff line change
`@@ -120,6 +120,7 @@ void Network::parseNetwork(const std::string& filename)`
`120`	`120`
`121`	`121`	`void Network::parseNetwork(const std::string& filename, const InsensitiveStringSet& validHeadings, const InsensitiveStringSet& ignoreHeadings, const std::string& startHeading)`
`122`	`122`	`{`
	`123`	`+ m_haveFileInput = true;`
`123`	`124`	`SafeInFile input(filename);`
`124`	`125`
`125`	`126`	`// Parse standard links by default until possible heading is reached`
`@@ -450,7 +451,11 @@ void Network::parseStateNode(const std::string& line, StateNetwork::StateNode& s`
`450`	`451`	`m_extractor.seekg(nameEnd + 1);`
`451`	`452`	`}`
`452`	`453`	`// Optional weight, default to 1.0`
`453`		`- (m_extractor >> stateNode.weight) \|\| (stateNode.weight = 1.0);`
	`454`	`+ if ((m_extractor >> stateNode.weight)) {`
	`455`	`+ m_haveStateNodeWeights = true;`
	`456`	`+ if (stateNode.weight < 0)`
	`457`	`+ throw std::runtime_error(io::Str() << "Negative state node weight (" << stateNode.weight << ") from line '" << line << "'");`
	`458`	`+ }`
`454`	`459`	`}`
`455`	`460`
`456`	`461`	`void Network::parseLink(const std::string& line, unsigned int& n1, unsigned int& n2, double& weight)`