From d9e5ff90ec6f23d46d932ad2af75a1cc7653997d Mon Sep 17 00:00:00 2001
From: darksnake <darksnake@LUNA.localdomain>
Date: Sat, 29 Oct 2016 03:10:11 +0300
Subject: [PATCH] Working on unified output. Minor fixes.

---
 .../inr/numass/scripts/Underflow.groovy       |  2 +-
 .../main/java/inr/numass/NumassPlugin.java    |  2 +-
 .../models/sterile/NumassTransmission.java    | 40 +++++++++++++------
 .../inr/numass/utils/ExpressionUtils.java     |  1 +
 4 files changed, 31 insertions(+), 14 deletions(-)

diff --git a/numass-main/src/main/groovy/inr/numass/scripts/Underflow.groovy b/numass-main/src/main/groovy/inr/numass/scripts/Underflow.groovy
index c1db7221..f31f3df1 100644
--- a/numass-main/src/main/groovy/inr/numass/scripts/Underflow.groovy
+++ b/numass-main/src/main/groovy/inr/numass/scripts/Underflow.groovy
@@ -14,7 +14,7 @@ import inr.numass.utils.UnderflowCorrection
 
 //File dataDir = new File("D:\\Work\\Numass\\data\\2016_04\\T2_data\\Fill_2_2\\set_7_b2a3433e54010000")
 //File dataDir = new File("D:\\Work\\Numass\\data\\2016_04\\T2_data\\Fill_2_2\\set_6_e26d123e54010000")
-File dataDir = new File("D:\\Work\\Numass\\data\\2016_10\\Fill_1\\set_10")
+File dataDir = new File("D:\\Work\\Numass\\data\\2016_10\\Fill_2_wide\\\\set_21")
 if(!dataDir.exists()){
     println "dataDir directory does not exist"
 }
diff --git a/numass-main/src/main/java/inr/numass/NumassPlugin.java b/numass-main/src/main/java/inr/numass/NumassPlugin.java
index f0d27f6f..91a2a49c 100644
--- a/numass-main/src/main/java/inr/numass/NumassPlugin.java
+++ b/numass-main/src/main/java/inr/numass/NumassPlugin.java
@@ -101,7 +101,7 @@ public class NumassPlugin extends BasicPlugin {
     }
 
     private void loadMath(MathPlugin math) {
-        math.registerBivariate("numass.trap2016", (Ei, Ef) -> {
+        math.registerBivariate("numass.trap.lowFields", (Ei, Ef) -> {
             return 3.92e-5 * FastMath.exp(-(Ei - Ef) / 300d) + 1.97e-4 - 6.818e-9 * Ei;
         });
 
diff --git a/numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java b/numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java
index f59543e5..8647a34d 100644
--- a/numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java
+++ b/numass-main/src/main/java/inr/numass/models/sterile/NumassTransmission.java
@@ -6,12 +6,17 @@
 package inr.numass.models.sterile;
 
 import hep.dataforge.context.Context;
-import hep.dataforge.stat.parametric.AbstractParametricBiFunction;
 import hep.dataforge.maths.MathPlugin;
 import hep.dataforge.meta.Meta;
+import hep.dataforge.stat.parametric.AbstractParametricBiFunction;
 import hep.dataforge.values.NamedValueSet;
 import inr.numass.models.LossCalculator;
+import inr.numass.utils.ExpressionUtils;
 import org.apache.commons.math3.analysis.BivariateFunction;
+import org.slf4j.LoggerFactory;
+
+import java.util.HashMap;
+import java.util.Map;
 
 /**
  *
@@ -28,12 +33,32 @@ public class NumassTransmission extends AbstractParametricBiFunction {
         super(list);
         this.calculator = LossCalculator.instance();
         if (meta.hasValue("trapping")) {
-            trapFunc = MathPlugin.buildFrom(context).buildBivariateFunction(meta.getString("trapping"));
+            String trapFuncStr = meta.getString("trapping");
+            if (trapFuncStr.startsWith("function::")) {
+                trapFunc = MathPlugin.buildFrom(context).buildBivariateFunction(trapFuncStr.substring(10));
+            } else {
+                trapFunc = (Ei, Ef) -> {
+                    Map<String, Object> binding = new HashMap<>();
+                    binding.put("Ei", Ei);
+                    binding.put("Ef", Ef);
+                    return ExpressionUtils.evaluate(trapFuncStr, binding);
+                };
+            }
         } else {
-            trapFunc = getTrapFunction(context, meta.getNodeOrEmpty("trapping"));
+            LoggerFactory.getLogger(getClass()).warn("Trapping function not defined. Using default");
+            trapFunc = MathPlugin.buildFrom(context).buildBivariateFunction("numass.trap.nominal");
         }
     }
 
+    public static double getX(double eIn, NamedValueSet set) {
+        //From our article
+        return set.getDouble("X") * Math.log(eIn / ION_POTENTIAL) * eIn * ION_POTENTIAL / 1.9580741410115568e6;
+    }
+
+    public static double p0(double eIn, NamedValueSet set) {
+        return LossCalculator.instance().getLossProbability(0, getX(eIn, set));
+    }
+
     private BivariateFunction getTrapFunction(Context context, Meta meta) {
         return MathPlugin.buildFrom(context).buildBivariateFunction(meta);
     }
@@ -55,15 +80,6 @@ public class NumassTransmission extends AbstractParametricBiFunction {
         return true;
     }
 
-    public static double getX(double eIn, NamedValueSet set) {
-        //From our article
-        return set.getDouble("X") * Math.log(eIn / ION_POTENTIAL) * eIn * ION_POTENTIAL / 1.9580741410115568e6;
-    }
-
-    public static double p0(double eIn, NamedValueSet set) {
-        return LossCalculator.instance().getLossProbability(0, getX(eIn, set));
-    }
-
     @Override
     public double value(double eIn, double eOut, NamedValueSet set) {
         //calculate X taking into account its energy dependence
diff --git a/numass-main/src/main/java/inr/numass/utils/ExpressionUtils.java b/numass-main/src/main/java/inr/numass/utils/ExpressionUtils.java
index c23e5c0c..424a7878 100644
--- a/numass-main/src/main/java/inr/numass/utils/ExpressionUtils.java
+++ b/numass-main/src/main/java/inr/numass/utils/ExpressionUtils.java
@@ -26,6 +26,7 @@ public class ExpressionUtils {
         ImportCustomizer importCustomizer = new ImportCustomizer();
         // import static com.mrhaki.blog.Type.*
         importCustomizer.addStaticStars("java.lang.Math");
+        importCustomizer.addStaticStars("org.apache.commons.math3.util.FastMath");
 
         CompilerConfiguration configuration = new CompilerConfiguration();
         configuration.addCompilationCustomizers(importCustomizer); // Create shell and execute script.