Fix context and log issues in Grind

numass-main/build.gradle

@@ -11,8 +11,6 @@ dependencies {
     compile group: 'commons-cli', name: 'commons-cli', version: '1.+'
     compile group: 'commons-io', name: 'commons-io', version: '2.+'
     compile project(':dataforge-stat:dataforge-minuit')
-    compile project(':dataforge-fx')
-    compile project(':dataforge-plots:plots-jfc')
     compile project(':numass-storage')
     compile project(':dataforge-grind:grind-terminal')
 }

numass-main/src/main/groovy/inr/numass/LaunchGrindShell.groovy

@@ -3,6 +3,7 @@ package inr.numass
 import hep.dataforge.context.Global
 import hep.dataforge.grind.GrindWorkspaceBuilder
 import hep.dataforge.grind.terminal.GrindTerminal
+import inr.numass.workspace.*
 
 /**
  * Created by darksnake on 29-Aug-16.
@@ -19,19 +20,25 @@ println "Loading config file from $cfgPath"
 //Global.instance().pluginManager().loadPlugin("inr.numass:numass")
 println "Starting Grind shell"
 
-if(cfgPath) {
+if (cfgPath) {
     try {
         GrindTerminal.dumb().launch {
-            GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder()
+            GrindWorkspaceBuilder numass = new GrindWorkspaceBuilder(it.shell.context).read(new File(cfgPath)).startup {
-                    .withSpec(NumassWorkspaceSpec)
+                it.loadTask(NumassPrepareTask)
-                    .from(new File(cfgPath))
+                it.loadTask(NumassTableFilterTask)
-            shell.bind("numass", numass)
+                it.loadTask(NumassFitScanTask)
+                it.loadTask(NumassSubstractEmptySourceTask)
+                it.loadTask(NumassFitScanSummaryTask)
+                it.loadTask(NumassFitTask)
+                it.loadTask(NumassFitSummaryTask)
+            }
+            it.shell.bind("numass", numass)
         }
     } catch (Exception ex) {
         ex.printStackTrace();
     } finally {
         Global.terminate();
     }
-} else{
+} else {
     println "No configuration path. Provide path via --config option"
 }

numass-main/src/main/groovy/inr/numass/NumassWorkspaceSpec.groovy

@@ -1,41 +0,0 @@
-/*
- * Copyright 2015 Alexander Nozik.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package inr.numass
-
-import groovy.transform.CompileStatic
-import hep.dataforge.grind.WorkspaceSpec
-import inr.numass.workspace.*
-
-/**
- * Created by darksnake on 16-Aug-16.
- */
-@CompileStatic
-class NumassWorkspaceSpec extends WorkspaceSpec {
-
-    NumassWorkspaceSpec() {
-        //load tasks
-        super.task(NumassPrepareTask)
-        super.task(NumassTableFilterTask)
-        super.task(NumassFitScanTask)
-        super.task(NumassSubstractEmptySourceTask)
-        super.task(NumassFitScanSummaryTask)
-        super.task(NumassFitTask)
-        super.task(NumassFitSummaryTask)
-    }
-
-
-}

numass-main/src/main/groovy/inr/numass/scripts/workspace/TestWorkspace.groovy

@@ -7,7 +7,7 @@ import hep.dataforge.grind.GrindWorkspaceBuilder
  */
 
 
-new GrindWorkspaceBuilder().from {
+new GrindWorkspaceBuilder().read {
     new File("D:\\Work\\Numass\\sterile2016\\workspace.groovy")
 }.runTask("numass.prepare", "fill_2").computeAll()
 

numass-main/src/main/java/inr/numass/NumassPlugin.java

@@ -44,7 +44,7 @@ import org.apache.commons.math3.util.FastMath;
  * @author Alexander Nozik
  */
 @PluginDef(group = "inr.numass", name = "numass",
-        dependsOn = {"hep.dataforge:actions", "hep.dataforge:math", "hep.dataforge:MINUIT", "hep.dataforge:plots-jfc"},
+        dependsOn = {"hep.dataforge:actions", "hep.dataforge:math", "hep.dataforge:MINUIT"},
         description = "Numass data analysis tools")
 public class NumassPlugin extends BasicPlugin {
 

numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java

@@ -37,7 +37,7 @@ import java.util.List;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
-import static inr.numass.utils.TritiumUtils.evaluateExpression;
+import static inr.numass.utils.TritiumUtils.pointExpression;
 
 /**
  * @author Darksnake
@@ -80,7 +80,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
         if (meta.hasValue("correction")) {
             final String correction = meta.getString("correction");
-            corrections.add((point) -> evaluateExpression(point, correction));
+            corrections.add((point) -> pointExpression(correction, point));
         }
 
         List<DataPoint> dataList = new ArrayList<>();
@@ -153,7 +153,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         return new Correction() {
             @Override
             public double corr(NMPoint point) {
-                return evaluateExpression(point, expr);
+                return pointExpression(expr, point);
             }
 
             @Override
@@ -161,7 +161,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
                 if (errExpr.isEmpty()) {
                     return 0;
                 } else {
-                    return evaluateExpression(point, errExpr);
+                    return pointExpression(errExpr, point);
                 }
             }
         };
@@ -202,7 +202,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         private final Function<NMPoint, Double> deadTimeFunction;
 
         public DeadTimeCorrection(String expr) {
-            deadTimeFunction = point -> evaluateExpression(point, expr);
+            deadTimeFunction = point -> pointExpression(expr, point);
         }
 
         @Override

numass-main/src/main/java/inr/numass/models/NamedSpectrumCaching.java

@@ -15,21 +15,23 @@
  */
 package inr.numass.models;
 
-import hep.dataforge.stat.parametric.AbstractParametricFunction;
-import static hep.dataforge.stat.parametric.FunctionUtils.getSpectrumDerivativeFunction;
-import static hep.dataforge.stat.parametric.FunctionUtils.getSpectrumFunction;
-import hep.dataforge.stat.parametric.ParametricFunction;
 import hep.dataforge.maths.MathUtils;
 import hep.dataforge.maths.NamedVector;
 import hep.dataforge.names.AbstractNamedSet;
+import hep.dataforge.stat.parametric.AbstractParametricFunction;
+import hep.dataforge.stat.parametric.ParametricFunction;
 import hep.dataforge.values.NamedValueSet;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Objects;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.analysis.interpolation.SplineInterpolator;
 import org.slf4j.LoggerFactory;
 
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Objects;
+
+import static hep.dataforge.stat.parametric.FunctionUtils.getSpectrumDerivativeFunction;
+import static hep.dataforge.stat.parametric.FunctionUtils.getSpectrumFunction;
+
 /**
  *
  * @author Darksnake
@@ -52,7 +54,7 @@ public class NamedSpectrumCaching extends AbstractParametricFunction {
         this.a = a;
         this.b = b;
         this.source = spectrum;
-        spectrumDerivCache = new HashMap<>(source.getDimension());
+        spectrumDerivCache = new HashMap<>(source.size());
 //        spectrumDerivCache = new CacheElement[source.getDimension()];
     }
 

numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java

@@ -41,7 +41,7 @@ public class NumassTransmission extends AbstractParametricBiFunction {
                     Map<String, Object> binding = new HashMap<>();
                     binding.put("Ei", Ei);
                     binding.put("Ef", Ef);
-                    return ExpressionUtils.evaluate(trapFuncStr, binding);
+                    return ExpressionUtils.function(trapFuncStr, binding);
                 };
             }
         } else {

numass-main/src/main/java/inr/numass/utils/ExpressionUtils.java

@@ -8,7 +8,7 @@ package inr.numass.utils;
 import groovy.lang.Binding;
 import groovy.lang.GroovyShell;
 import groovy.lang.Script;
-import hep.dataforge.utils.Utils;
+import hep.dataforge.utils.Misc;
 import org.codehaus.groovy.control.CompilerConfiguration;
 import org.codehaus.groovy.control.customizers.ImportCustomizer;
 
@@ -18,7 +18,7 @@ import java.util.Map;
  * @author Alexander Nozik
  */
 public class ExpressionUtils {
-    private static final Map<String, Script> cache = Utils.getLRUCache(100);
+    private static final Map<String, Script> cache = Misc.getLRUCache(100);
     private static final GroovyShell shell;
 
     static {
@@ -38,7 +38,7 @@ public class ExpressionUtils {
     }
 
 
-    public static double evaluate(String expression, Map<String, Object> binding) {
+    public static double function(String expression, Map<String, ? extends Object> binding) {
         synchronized (cache) {
             Binding b = new Binding(binding);
             Script script = getScript(expression);
@@ -46,4 +46,13 @@ public class ExpressionUtils {
             return ((Number) script.run()).doubleValue();
         }
     }
+
+    public static boolean condition(String expression, Map<String, ? extends Object> binding){
+        synchronized (cache) {
+            Binding b = new Binding(binding);
+            Script script = getScript(expression);
+            script.setBinding(b);
+            return (boolean) script.run();
+        }
+    }
 }

numass-main/src/main/java/inr/numass/utils/TritiumUtils.java

@@ -129,16 +129,16 @@ public class TritiumUtils {
     /**
      * Evaluate groovy expression using numass point as parameter
      *
-     * @param point
      * @param expression
+     * @param point
      * @return
      */
-    public static double evaluateExpression(NMPoint point, String expression) {
+    public static double pointExpression(String expression, NMPoint point) {
         Map<String, Object> exprParams = new HashMap<>();
         exprParams.put("T", point.getLength());
         exprParams.put("U", point.getUread());
         exprParams.put("cr", ((double) point.getEventsCount()) / point.getLength());
         exprParams.put("point", point);
-        return ExpressionUtils.evaluate(expression, exprParams);
+        return ExpressionUtils.function(expression, exprParams);
     }
 }

numass-main/src/main/java/inr/numass/utils/UnderflowCorrection.java

@@ -30,7 +30,7 @@ public class UnderflowCorrection {
     public double get(Logable log, Meta meta, NMPoint point) {
         if (point.getUset() >= meta.getDouble("underflow.threshold", 17000)) {
             if (meta.hasValue("underflow.function")) {
-                return TritiumUtils.evaluateExpression(point, meta.getString("underflow.function"));
+                return TritiumUtils.pointExpression(meta.getString("underflow.function"), point);
             } else {
                 return 1;
             }

numass-main/src/main/java/inr/numass/workspace/NumassTableFilterTask.java

@@ -7,10 +7,14 @@ import hep.dataforge.data.DataNode;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.meta.Laminate;
 import hep.dataforge.meta.MetaBuilder;
+import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.tables.TableTransform;
 import hep.dataforge.workspace.SingleActionTask;
 import hep.dataforge.workspace.TaskModel;
+import inr.numass.utils.ExpressionUtils;
+
+import java.util.function.Predicate;
 
 /**
  * Created by darksnake on 13-Aug-16.
@@ -47,10 +51,17 @@ public class NumassTableFilterTask extends SingleActionTask<Table, Table> {
     private class FilterTableAction extends OneToOneAction<Table, Table> {
         @Override
         protected Table execute(Context context, String name, Table input, Laminate inputMeta) {
-            double uLo = inputMeta.getDouble("filter.from", 0);
+            if (inputMeta.hasValue("filter.from") || inputMeta.hasValue("filter.to")) {
-            double uHi = inputMeta.getDouble("filter.to", Double.POSITIVE_INFINITY);
+                double uLo = inputMeta.getDouble("filter.from", 0);
-            getLogger(inputMeta).debug("Filtering finished");
+                double uHi = inputMeta.getDouble("filter.to", Double.POSITIVE_INFINITY);
-            return TableTransform.filter(input, "Uset", uLo, uHi);
+                getLogger(inputMeta).debug("Filtering finished");
+                return TableTransform.filter(input, "Uset", uLo, uHi);
+            } else if (inputMeta.hasValue("filter.condition")) {
+                Predicate<DataPoint> predicate = (dp) -> ExpressionUtils.condition(inputMeta.getString("filter.condition"), dp.asMap());
+                return TableTransform.filter(input, predicate);
+            } else {
+                throw new RuntimeException("No filtering condition specified");
+            }
         }
     }
 }

numass-main/src/test/java/inr/numass/actions/PrepareDataActionTest.java

@@ -6,11 +6,11 @@
 package inr.numass.actions;
 
 import inr.numass.utils.ExpressionUtils;
+import org.junit.Assert;
+import org.junit.Test;
+
 import java.util.HashMap;
 import java.util.Map;
-import org.junit.Assert;
-
-import org.junit.Test;
 
 /**
  *
@@ -25,7 +25,7 @@ public class PrepareDataActionTest {
     public void testExpression() {
         Map<String, Object> exprParams = new HashMap<>();
         exprParams.put("U", 18000d);
-        double correctionFactor = ExpressionUtils.evaluate("1 + 13.265 * exp(- U / 2343.4)", exprParams);
+        double correctionFactor = ExpressionUtils.function("1 + 13.265 * exp(- U / 2343.4)", exprParams);
         Assert.assertEquals("Testing expression calculation", 1.006125, correctionFactor, 1e-5);
     }