Added regression tests for all surrogate models provided by `surrogate.simple`...

Added regression tests for all surrogate models provided by `surrogate.simple` and `surrogate.smile`. Fixed minor bugs that prevented regression tests to work.

Closes #84
Resolve "Create regression tests for surrogate functions"

src/evoal/core/de.evoal.core.main/src/main/scripts/evoal-evaluate-search.sh

@@ -16,7 +16,7 @@ fi
 cd "$1" || exit 1
 
 POSITIONAL_ARGUMENTS=( "$@" )
-POSITIONAL_ARGUMENTS=("${POSITIONAL_ARGUMENTS[@]:4}")
+ADDITIONAL_ARGUMENTS=("${POSITIONAL_ARGUMENTS[@]:4}")
 
 declare -a LOCAL_JVM_ARGUMENTS=()
 
@@ -29,14 +29,14 @@ if [ ${EVOAL_DEBUG+x} ]; then
 fi
 
 if [ ${EVOAL_LOGGING+x} ]; then
-  POSITIONAL_ARGUMENTS+=( "-Bcore:logging=$EVOAL_LOGGING" )
+  ADDITIONAL_ARGUMENTS+=( "-Bcore:logging=$EVOAL_LOGGING" )
 fi
 
 set -x
 java ${LOCAL_JVM_ARGUMENTS[@]} \
      ${EVOAL_JVM_ARGUMENTS[@]} \
-     ${POSITIONAL_ARGUMENTS[@]} \
-     -Bcore:main=heuristic-search-evaluation \
+     "-Bcore:main=heuristic-search-evaluation" \
      "-Bcore:optimisation-configuration-file=$2" \
      "-Bcore:evaluation-output-folder=$3" \
-     "-Bcore:evaluation-iterations=$4"
+     "-Bcore:evaluation-iterations=$4" \
+     ${ADDITIONAL_ARGUMENTS[@]}

src/evoal/core/de.evoal.core.main/src/main/scripts/evoal-search.sh

@@ -14,7 +14,7 @@ fi
 cd "$1" || exit 1
 
 POSITIONAL_ARGUMENTS=( "$@" )
-POSITIONAL_ARGUMENTS=("${POSITIONAL_ARGUMENTS[@]:3}")
+ADDITIONAL_ARGUMENTS=("${POSITIONAL_ARGUMENTS[@]:3}")
 
 declare -a LOCAL_JVM_ARGUMENTS=()
 
@@ -27,13 +27,13 @@ if [ ${EVOAL_DEBUG+x} ]; then
 fi
 
 if [ ${EVOAL_LOGGING+x} ]; then
-  POSITIONAL_ARGUMENTS+=( "-Bcore:logging=$EVOAL_LOGGING" )
+  ADDITIONAL_ARGUMENTS+=( "-Bcore:logging=$EVOAL_LOGGING" )
 fi
 
 set -x
 java ${LOCAL_JVM_ARGUMENTS[@]} \
      ${EVOAL_JVM_ARGUMENTS[@]} \
-     ${POSITIONAL_ARGUMENTS[@]} \
-     -Bcore:main=heuristic-search \
+     "-Bcore:main=heuristic-search" \
      "-Bcore:optimisation-configuration-file=$2" \
-     "-Bcore:evaluation-output-folder=$3"
+     "-Bcore:evaluation-output-folder=$3" \
+     ${ADDITIONAL_ARGUMENTS[@]}

src/evoal/plugins/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/cdi/MachineLearningModuleProducer.java

@@ -42,6 +42,11 @@ public class MachineLearningModuleProducer {
 
         final File file = new File(configurationFile);
 
+        if(!file.exists()) {
+            log.info("Specified configuration file '{}' does not exist.", file);
+            throw  new IllegalArgumentException("Please specify an existing mll file.");
+        }
+
         if(!file.isFile()) {
             log.info("Configured surrogate configuration is a folder.");
             throw  new IllegalArgumentException("Please specify a surrogate file.");

src/evoal/plugins/de.evoal.surrogate.api/src/main/java/de/evoal/surrogate/main/ea/SurrogateFitnessFunction.java

@@ -10,7 +10,7 @@ import javax.inject.Inject;
 import javax.inject.Named;
 
 @Dependent
-@Named("surrogate")
+@Named("de.evoal.surrogate.optimisation.surrogate")
 public class SurrogateFitnessFunction implements OptimisationFunction {
 
     @Inject

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/surrogate.simple/01-run-search.sh

+#!/bin/sh
+
+export EVOAL_HOME=$( cd -- "$(dirname $0)/../../" >/dev/null 2>&1 ; pwd -P )
+
+$SHELL $EVOAL_HOME/bin/evoal-search.sh . search.ol output -Bsurrogate:configuration-file=training.mll -Bsurrogate:pre-trained=simple.pson

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/surrogate.simple/search.ol

+import "definitions" from de.evoal.core.math;
+
+import "definitions" from de.evoal.core.optimisation;
+import "definitions" from de.evoal.core.ea.optimisation;
+import "definitions" from de.evoal.surrogate.optimisation;
+
+import "data" from surrogate;
+
+module search {
+	specify problem 'example-search' {
+		description := "Simple search";
+		'search-space' := [data 'x:0'];
+		'optimisation-space' := [data 'y:0', data 'y:1', data 'y:2'];
+		'maximise' := true;
+		'optimisation-function' := 'unknown-function' {};
+	}
+		
+		
+	configure 'evolutionary-algorithm' for 'example-search' {
+		'number-of-generations' := 10;
+		'size-of-population' := 50;
+		'maximum-age' := 10;
+	    'offspring-fraction' := 0.6;
+
+		'initialisation' := 'random-population' {};
+		
+		'comparator' := 'weighted-sum' {
+			'weights' := [1.0, 1.0, 1.0];
+		};
+	
+	    genotype := 'vector-genotype' {
+	        chromosomes := [
+				'double-chromosome' {
+                    genes:= [
+                            gene {content:= data 'x:0';}
+                    ];
+	            }
+			];
+	    };
+	
+	    handlers := [];
+	
+	    selectors := selectors {
+	        offspring := 'elite-selector' {
+	                'size-factor' := 0.3;
+	                'non-elite-selector' := 'tournament-selector' {
+	                        'size-factor' := 0.1;
+	                };
+	        };
+	        survivor := 'elite-selector' {
+	                'size-factor' := 0.3;
+	                'non-elite-selector' := 'tournament-selector' {
+	                        'size-factor' := 0.1;
+	                };
+	        };
+	    };
+	    
+		alterers := alterers {
+	        crossover := [
+	                'single-point-crossover' {
+	                        probability := 0.5;
+	
+	                }
+	        ];
+	        mutator := [
+	                'mean-alterer' {
+	                        probability := 0.5;
+	                        }
+	        ];
+	    };
+	
+		'optimisation-function' := 'surrogate' {};
+	}
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/surrogate.simple/simple.pson

+{
+  "mappings" : [ {
+    "functions" : [ {
+      "inputDimensions" : [ "x:0" ],
+      "name" : "identity",
+      "outputDimensions" : [ "y:0" ],
+      "parameters" : [ ],
+      "state" : [ ],
+      "outputParameters" : { }
+    }, {
+      "inputDimensions" : [ "x:0" ],
+      "name" : "linear-regression",
+      "outputDimensions" : [ "y:1" ],
+      "parameters" : [ {
+        "name" : "intercept",
+        "value" : {
+          "type" : "double",
+          "value" : 0.0
+        }
+      }, {
+        "name" : "slope",
+        "value" : {
+          "type" : "double",
+          "value" : 1.0
+        }
+      } ],
+      "state" : [ {
+        "name" : "intercept",
+        "value" : {
+          "type" : "double",
+          "value" : 11.712570037202154
+        }
+      }, {
+        "name" : "slope",
+        "value" : {
+          "type" : "double",
+          "value" : -0.15365798063682554
+        }
+      }, {
+        "name" : "r²",
+        "value" : {
+          "type" : "double",
+          "value" : 0.025909832934437375
+        }
+      } ],
+      "outputParameters" : { }
+    }, {
+      "inputDimensions" : [ "x:0" ],
+      "name" : "simple-quadratic-regression",
+      "outputDimensions" : [ "y:2" ],
+      "parameters" : [ {
+        "name" : "intercept",
+        "value" : {
+          "type" : "double",
+          "value" : 0.0
+        }
+      }, {
+        "name" : "slope",
+        "value" : {
+          "type" : "double",
+          "value" : 1.0
+        }
+      } ],
+      "state" : [ {
+        "name" : "intercept",
+        "value" : {
+          "type" : "double",
+          "value" : 8.826315970399465
+        }
+      }, {
+        "name" : "slope",
+        "value" : {
+          "type" : "double",
+          "value" : 0.09933588719842316
+        }
+      }, {
+        "name" : "r²",
+        "value" : {
+          "type" : "double",
+          "value" : 0.5440278766948579
+        }
+      } ],
+      "outputParameters" : { }
+    } ],
+    "inputDimensions" : [ "x:0" ],
+    "name" : "transfer",
+    "outputDimensions" : [ "y:0", "y:1", "y:2" ]
+  } ],
+  "outputParameters" : {
+    "y:2" : [ {
+      "name" : "r²",
+      "value" : {
+        "type" : "double",
+        "value" : 0.5485875979279088
+      }
+    } ],
+    "y:1" : [ {
+      "name" : "r²",
+      "value" : {
+        "type" : "double",
+        "value" : 0.03565073460509294
+      }
+    } ],
+    "y:0" : [ {
+      "name" : "r²",
+      "value" : {
+        "type" : "double",
+        "value" : -7.063682935513912
+      }
+    } ]
+  }
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/surrogate.simple/surrogate.ddl

+module surrogate {
+	data:
+		/**
+		 * Source dimension of the training data.
+		 */
+		quotient real data 'x:0';
+		
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:0';
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:1';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:2';
+
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/surrogate.simple/training.mll

+import "definitions" from de.evoal.surrogate.ml;
+import "definitions" from de.evoal.surrogate.simple.ml;
+
+import "data" from surrogate;
+
+module training {
+	prediction svr
+		maps 'x:0'
+	    to 'y:0', 'y:1', 'y:2'
+	    using
+	    	layer transfer
+				with 
+				  function 'identity'
+					mapping 'x:0'
+					to 'y:0'
+
+				  function 'linear-regression'
+					mapping 'x:0'
+					to 'y:1'
+					with parameters
+						intercept := 0.0;
+						slope := 1.0;
+
+				  function 'simple-quadratic-regression'
+					mapping 'x:0'
+					to 'y:2'
+					with parameters
+						intercept := 0.0;
+						slope := 1.0;
+						
+
+        predict svr from "data.json"
+        and measure
+            'R²'();
+        end
+        and store to "simple.pson"
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/training.simple/01-run-training.sh

+#!/bin/sh
+
+export EVOAL_HOME=$( cd -- "$(dirname $0)/../../" >/dev/null 2>&1 ; pwd -P )
+
+$SHELL $EVOAL_HOME/bin/evoal-training.sh . training.mll

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/training.simple/surrogate.ddl

+module surrogate {
+	data:
+		/**
+		 * Source dimension of the training data.
+		 */
+		quotient real data 'x:0';
+		
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:0';
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:1';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:2';
+
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/examples/training.simple/training.mll

+import "definitions" from de.evoal.surrogate.ml;
+import "definitions" from de.evoal.surrogate.simple.ml;
+
+import "data" from surrogate;
+
+module training {
+	prediction svr
+		maps 'x:0'
+	    to 'y:0', 'y:1', 'y:2'
+	    using
+	    	layer transfer
+				with 
+				  function 'identity'
+					mapping 'x:0'
+					to 'y:0'
+
+				  function 'linear-regression'
+					mapping 'x:0'
+					to 'y:1'
+					with parameters
+						intercept := 0.0;
+						slope := 1.0;
+
+				  function 'simple-quadratic-regression'
+					mapping 'x:0'
+					to 'y:2'
+					with parameters
+						intercept := 0.0;
+						slope := 1.0;
+						
+
+        predict svr from "data.json"
+        and measure
+            'R²'();
+        end
+        and store to "simple.pson"
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.simple/src/main/java/module-info.java

@@ -12,6 +12,8 @@ module de.evoal.surrogate.simple {
     requires de.evoal.core.main;
     requires de.evoal.surrogate.api;
 
+    opens de.evoal.surrogate.simple;
+
     exports de.evoal.surrogate.simple.identity to weld.core.impl;
     exports de.evoal.surrogate.simple.linear to weld.core.impl;
     exports de.evoal.surrogate.simple.quadratic to weld.core.impl;

src/evoal/plugins/de.evoal.surrogate.smile/src/main/examples/surrogate.svr/01-run-search.sh

+#!/bin/sh
+
+export EVOAL_HOME=$( cd -- "$(dirname $0)/../../" >/dev/null 2>&1 ; pwd -P )
+
+$SHELL $EVOAL_HOME/bin/evoal-search.sh . search.ol output -Bsurrogate:configuration-file=training.mll -Bsurrogate:pre-trained=svr.pson

src/evoal/plugins/de.evoal.surrogate.smile/src/main/examples/surrogate.svr/search.ol

+import "definitions" from de.evoal.core.math;
+
+import "definitions" from de.evoal.core.optimisation;
+import "definitions" from de.evoal.core.ea.optimisation;
+import "definitions" from de.evoal.surrogate.optimisation;
+
+import "data" from surrogate;
+
+module search {
+	specify problem 'example-search' {
+		description := "Simple search";
+		'search-space' := [data 'x:0'];
+		'optimisation-space' := [data 'y:0', data 'y:1', data 'y:2', data 'y:3', data 'y:4', data 'y:5', data 'y:6', data 'y:7'];
+		'maximise' := true;
+		'optimisation-function' := 'unknown-function' {};
+	}
+		
+		
+	configure 'evolutionary-algorithm' for 'example-search' {
+		'number-of-generations' := 10;
+		'size-of-population' := 50;
+		'maximum-age' := 10;
+	    'offspring-fraction' := 0.6;
+
+		'initialisation' := 'random-population' {};
+		
+		'comparator' := 'weighted-sum' {
+			'weights' := [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0];
+		};
+	
+	    genotype := 'vector-genotype' {
+	        chromosomes := [
+				'double-chromosome' {
+                    genes:= [
+                            gene {content:= data 'x:0';}
+                    ];
+	            }
+			];
+	    };
+	
+	    handlers := [];
+	
+	    selectors := selectors {
+	        offspring := 'elite-selector' {
+	                'size-factor' := 0.3;
+	                'non-elite-selector' := 'tournament-selector' {
+	                        'size-factor' := 0.1;
+	                };
+	        };
+	        survivor := 'elite-selector' {
+	                'size-factor' := 0.3;
+	                'non-elite-selector' := 'tournament-selector' {
+	                        'size-factor' := 0.1;
+	                };
+	        };
+	    };
+	    
+		alterers := alterers {
+	        crossover := [
+	                'single-point-crossover' {
+	                        probability := 0.5;
+	
+	                }
+	        ];
+	        mutator := [
+	                'mean-alterer' {
+	                        probability := 0.5;
+	                        }
+	        ];
+	    };
+	
+		'optimisation-function' := 'surrogate' {};
+	}
+}
\ No newline at end of file

src/evoal/plugins/de.evoal.surrogate.smile/src/main/examples/surrogate.svr/surrogate.ddl

+module surrogate {
+	data:
+		/**
+		 * Source dimension of the training data.
+		 */
+		quotient real data 'x:0';
+		
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:0';
+		
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:1';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:2';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:3';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:4';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:5';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:6';
+
+		/**
+		 * Target dimension of the training data.
+		 */
+		quotient real data 'y:7';
+
+}
\ No newline at end of file