Add graph logging with bonus command settings changes (#181)

* added example for settings

* added output example for graph

* spotless

* added graph serializer and output saver

* docstrings

* minor linter changes

* i should fix my autoformatter

* added getters for site edge variables

* some extra docstrings I missed

* Remove nutrients command

* cleaned up saveGraphComponents to just saveComponenets for layer saver in future

* abstract save method

* Update src/arcade/core/sim/output/OutputSaver.java

Co-authored-by: Jacob Evarts <[email protected]>

---------

Co-authored-by: Jacob Evarts <[email protected]>

Author: cainja

src/arcade/core/ARCADE.java

@@ -56,6 +56,9 @@ public abstract class ARCADE {
     /** Version number. */
     public static final String VERSION = loadVersion();
 
+    /** Command line settings for ARCADE simulation. */
+    protected MiniBox settings = new MiniBox();
+
     /**
      * Gets the resource relative to the location of the class.
      *
@@ -139,13 +142,13 @@ public static void main(String[] args) throws Exception {
         Box parameters = arcade.loadParameters(args[0]);
 
         // Parse arguments from command line.
-        MiniBox settings = arcade.parseArguments(args, commands);
+        arcade.settings = arcade.parseArguments(args, commands);
 
         // Build series
-        ArrayList<Series> series = arcade.buildSeries(parameters, settings);
+        ArrayList<Series> series = arcade.buildSeries(parameters);
 
         // Run series.
-        arcade.runSeries(series, settings);
+        arcade.runSeries(series);
     }
 
     /**
@@ -264,11 +267,9 @@ MiniBox parseArguments(String[] args, Box commands) {
      * Builds series based on setup file.
      *
      * @param parameters a container of default parameter values
-     * @param settings a container of parsed arguments
      * @return a list of {@link Series} instances
      */
-    ArrayList<Series> buildSeries(Box parameters, MiniBox settings)
-            throws IOException, SAXException {
+    ArrayList<Series> buildSeries(Box parameters) throws IOException, SAXException {
         String setupFile = settings.get("SETUP_FILE");
         String snapshotPath = settings.get("SNAPSHOT_PATH");
         boolean isVis = settings.contains("VIS");
@@ -288,9 +289,8 @@ ArrayList<Series> buildSeries(Box parameters, MiniBox settings)
      * valid series in the list are run.
      *
      * @param series the list of {@link Series} instances
-     * @param settings a container of parsed arguments
      */
-    void runSeries(ArrayList<Series> series, MiniBox settings) throws Exception {
+    void runSeries(ArrayList<Series> series) throws Exception {
         boolean isVis = settings.contains("VIS");
         String loadPath = settings.get("LOAD_PATH");
         boolean loadCells = settings.contains("LOAD_CELLS");

src/arcade/core/sim/output/OutputSaver.java

@@ -28,13 +28,13 @@
  */
 public abstract class OutputSaver implements Steppable {
     /** Logger for {@code OutputSaver}. */
-    private static final Logger LOGGER = Logger.getLogger(OutputSaver.class.getName());
+    protected static final Logger LOGGER = Logger.getLogger(OutputSaver.class.getName());
 
     /** Number of elements to format in output string. */
-    private static final int FORMAT_ELEMENTS = 6;
+    protected static final int FORMAT_ELEMENTS = 6;
 
     /** JSON representation. */
-    final Gson gson;
+    protected final Gson gson;
 
     /** {@link arcade.core.sim.Series} instance. */
     final Series series;
@@ -43,7 +43,7 @@ public abstract class OutputSaver implements Steppable {
     public String prefix;
 
     /** {@link arcade.core.sim.Simulation} instance. */
-    Simulation sim;
+    protected Simulation sim;
 
     /**
      * Creates an {@code OutputSaver} for the series.
@@ -109,6 +109,15 @@ public void saveLocations(int tick) {
     @Override
     public void step(SimState simstate) {
         int tick = (int) simstate.schedule.getTime();
+        save(tick);
+    }
+
+    /**
+     * Saves the relevant data.
+     *
+     * @param tick the simulation tick
+     */
+    public void save(int tick) {
         saveCells(tick);
         saveLocations(tick);
     }

src/arcade/patch/PatchARCADE.java

@@ -31,6 +31,8 @@ public OutputLoader getLoader(Series series) {
 
     @Override
     public OutputSaver getSaver(Series series) {
-        return new PatchOutputSaver(series);
+        PatchOutputSaver saver = new PatchOutputSaver(series);
+        saver.saveGraph = settings.contains("SAVE_GRAPH");
+        return saver;
     }
 }

src/arcade/patch/command.patch.xml

@@ -1,2 +1,3 @@
 <commands>
+    <switch id="SAVE_GRAPH" short="g" long="graph" help="Save the GRAPH output files" />
 </commands>

src/arcade/patch/env/component/PatchComponentSitesGraph.java

@@ -436,6 +436,15 @@ public boolean getRoot() {
         public double getPressure() {
             return pressure;
         }
+
+        /**
+         * Get the oxygen partial pressure of the node.
+         *
+         * @return the node oxygen partial pressure
+         */
+        public double getOxygen() {
+            return oxygen;
+        }
     }
 
     /**
@@ -534,6 +543,15 @@ public int getSign() {
             return type.category.sign;
         }
 
+        /**
+         * Gets the type of the edge.
+         *
+         * @return the edge type
+         */
+        public String getType() {
+            return type.toString();
+        }
+
         /**
          * Get the radius of the edge.
          *
@@ -543,6 +561,15 @@ public double getRadius() {
             return radius;
         }
 
+        /**
+         * Get the length of the edge.
+         *
+         * @return the edge length
+         */
+        public double getLength() {
+            return length;
+        }
+
         /**
          * Get the wall thickness of the edge.
          *
@@ -551,6 +578,33 @@ public double getRadius() {
         public double getWall() {
             return wall;
         }
+
+        /**
+         * Get the shear stress of the edge.
+         *
+         * @return the edge shear stress
+         */
+        public double getShear() {
+            return shear;
+        }
+
+        /**
+         * Get the circumferential stress of the edge.
+         *
+         * @return the edge circumferential stress
+         */
+        public double getCircum() {
+            return circum;
+        }
+
+        /**
+         * Get the volumetric flow rate of the edge.
+         *
+         * @return the edge volumetric flow rate
+         */
+        public double getFlow() {
+            return flow;
+        }
     }
 
     /**

src/arcade/patch/env/component/PatchComponentSitesGraphFactory.java

@@ -42,7 +42,7 @@ enum Border {
     }
 
     /** Edge types. */
-    enum EdgeType {
+    public enum EdgeType {
         /** Code for arteriole edge type. */
         ARTERIOLE(EdgeCategory.ARTERY),
 

src/arcade/patch/sim/PatchSimulation.java

@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Set;
 import sim.engine.Schedule;
 import sim.engine.SimState;
 import arcade.core.agent.action.Action;
@@ -147,6 +148,15 @@ public final Component getComponent(String key) {
         return components.get(key);
     }
 
+    /**
+     * Gets the set of keys for the component hash set.
+     *
+     * @return the set of component keys
+     */
+    public Set<String> getComponentKeys() {
+        return components.keySet();
+    }
+
     /**
      * Called at the start of the simulation to set up agents and environment and schedule actions
      * and components as needed.
@@ -354,8 +364,7 @@ public void doOutput(boolean isScheduled) {
             series.saver.schedule(schedule, series.getInterval());
         } else {
             int tick = (int) schedule.getTime() + 1;
-            series.saver.saveCells(tick);
-            series.saver.saveLocations(tick);
+            series.saver.save(tick);
         }
     }
 }

src/arcade/patch/sim/output/PatchOutputSaver.java

@@ -1,11 +1,19 @@
 package arcade.patch.sim.output;
 
 import com.google.gson.Gson;
+import sim.engine.SimState;
+import arcade.core.env.component.Component;
 import arcade.core.sim.Series;
 import arcade.core.sim.output.OutputSaver;
+import arcade.patch.env.component.PatchComponentSitesGraph;
+import arcade.patch.sim.PatchSimulation;
 
 /** Custom saver for patch-specific serialization. */
 public final class PatchOutputSaver extends OutputSaver {
+
+    /** {@code true} to save graph components, {@code false} otherwise. */
+    public boolean saveGraph;
+
     /**
      * Creates an {@code PatchOutputSaver} for the series.
      *
@@ -19,4 +27,38 @@ public PatchOutputSaver(Series series) {
     protected Gson makeGSON() {
         return PatchOutputSerializer.makeGSON();
     }
+
+    /**
+     * Save a list of {@link arcade.patch.env.component.PatchComponentSitesGraph} to a JSON.
+     *
+     * @param tick the simulation tick
+     */
+    public void saveComponents(int tick) {
+        for (String componentKey : ((PatchSimulation) sim).getComponentKeys()) {
+            Component component = sim.getComponent(componentKey);
+            if (component instanceof PatchComponentSitesGraph && saveGraph) {
+                String json =
+                        gson.toJson(
+                                (PatchComponentSitesGraph) component,
+                                PatchComponentSitesGraph.class);
+                String path = prefix + String.format("_%06d." + componentKey + ".GRAPH.json", tick);
+                write(path, format(json, FORMAT_ELEMENTS));
+            }
+        }
+    }
+
+    @Override
+    public void save(int tick) {
+        super.save(tick);
+        if (saveGraph) {
+            saveComponents(tick);
+        }
+    }
+
+    @Override
+    public void step(SimState simstate) {
+        super.step(simstate);
+        int tick = (int) simstate.schedule.getTime();
+        save(tick);
+    }
 }