From accff41291459d7ea695681a32868d08c6440619 Mon Sep 17 00:00:00 2001
From: Alexander Nozik <altavir@gmail.com>
Date: Wed, 23 Nov 2016 14:52:21 +0300
Subject: [PATCH] Plugin system fixes

---
 .../inr/numass/actions/PrepareDataAction.java | 26 -------------------
 .../workbench/NumassWorkbenchController.java  |  2 +-
 .../numass/workspace/NumassPrepareTask.java   | 26 -------------------
 3 files changed, 1 insertion(+), 53 deletions(-)

diff --git a/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java b/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java
index b0d3b0a1..b8f3fbb7 100644
--- a/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java
+++ b/numass-main/src/main/java/inr/numass/actions/PrepareDataAction.java
@@ -104,13 +104,6 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
                             .reduce((d1, d2) -> d1 * d1 + d2 * d2).getAsDouble()
             );
 
-//            // count rate after all corrections
-//            double cr = TritiumUtils.countRateWithDeadTime(point, a, b, deadTimeFunction.apply(point));
-//            // count rate error after all corrections
-//            double crErr = TritiumUtils.countRateWithDeadTimeErr(point, a, b, deadTimeFunction.apply(point));
-//
-//            double correctionFactor = correction(getReport(name), point, meta);
-
             double cr = wind / point.getLength() * correctionFactor;
             double crErr;
             if (relativeCorrectionError == 0) {
@@ -151,25 +144,6 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
     }
 
 
-//    /**
-//     * The factor to correct for count below detector threshold
-//     *
-//     * @param log
-//     * @param point
-//     * @param meta
-//     * @return
-//     */
-//    private double correction(Logable log, NMPoint point, Laminate meta) {
-//        if (meta.hasValue("correction")) {
-////            log.report("Using correction from formula: {}", meta.getString("correction"));
-//            return evaluateExpression(point, meta.getString("correction"));
-//        } else if (meta.hasMeta("underflow")) {
-//            return new UnderflowCorrection().get(log, meta.getMeta("underflow"), point);
-//        } else {
-//            return 1;
-//        }
-//    }
-
     @ValueDef(name = "value", type = "[NUMBER, STRING]", info = "Value or function to multiply count rate")
     @ValueDef(name = "err", type = "[NUMBER, STRING]", info = "error of the value")
     private Correction makeCorrection(Meta corrMeta) {
diff --git a/numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java b/numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java
index 50079f8b..e4ee2606 100644
--- a/numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java
+++ b/numass-main/src/main/java/inr/numass/workbench/NumassWorkbenchController.java
@@ -170,7 +170,7 @@ public class NumassWorkbenchController implements Initializable, StagePaneHolder
         context.getLog().addListener(new FXReportListener(logPane));
 
         // display plots iside workbench
-        PlotsPlugin.buildFrom(context).setPlotHolderDelegate(this);
+        PlotsPlugin.buildFrom(context).setPlotHolder(this);
     }
 
     private Tab findTabWithName(TabPane pane, String name) {
diff --git a/numass-main/src/main/java/inr/numass/workspace/NumassPrepareTask.java b/numass-main/src/main/java/inr/numass/workspace/NumassPrepareTask.java
index 69120daf..311d2fe7 100644
--- a/numass-main/src/main/java/inr/numass/workspace/NumassPrepareTask.java
+++ b/numass-main/src/main/java/inr/numass/workspace/NumassPrepareTask.java
@@ -35,21 +35,6 @@ import java.net.URI;
  */
 public class NumassPrepareTask extends AbstractTask<Table> {
 
-    /*
-        <action type="readStorage" uri="file://D:\Work\Numass\data\2016_04\T2_data\">
-		<include pattern="Fill_2*"/>
-		<exclude pattern="Fill_2_4_Empty*"/>
-		<exclude pattern="Fill_2_1.set_1*"/>
-		<exclude pattern="Fill_2_1.set_2*"/>
-		<exclude pattern="Fill_2_1.set_3*"/>
-		<exclude pattern="Fill_2_1.set_4*"/>
-	</action>
-	<action type="prepareData" lowerWindow="500" upperWindow="1700" deadTime="4.9534e-6 + 1.51139e-10*U">
-		<underflow function = "1.0 + 15.216 * Math.exp( - U / 2477.46 )" threshold = "14000"/>
-	</action>
-	<action type="monitor" monitorPoint="${numass.monitorPoint}" monitorFile="${numass.setName}_monitor"/>
-	<action type="merge" mergeName="${numass.setName}"/>
-     */
     @Override
     protected DataNode<Table> run(TaskModel model, ProgressCallback callback, DataNode<?> input) {
         Meta config = model.meta();
@@ -59,10 +44,6 @@ public class NumassPrepareTask extends AbstractTask<Table> {
         Meta dataMeta = config.getMeta("data");
         URI storageUri = input.getCheckedData("dataRoot", URI.class).get();
         DataSet.Builder<NumassData> dataBuilder = readData(callback, context, storageUri, dataMeta);
-//        if (config.hasMeta("empty")) {
-//            dataBuilder.putNode("empty", readData(callback, context, storageUri, config.getMeta("empty")).build());
-//        }
-
         DataNode<NumassData> data = dataBuilder.build();
 
         //preparing table data
@@ -79,13 +60,6 @@ public class NumassPrepareTask extends AbstractTask<Table> {
             DataTree.Builder<Table> resultBuilder = DataTree.builder(Table.class);
             DataTree.Builder<Table> tablesForMerge = new DataTree.Builder<>(tables);
 
-//            //extracting empty data
-//            if (config.hasMeta("empty")) {
-//                DataNode<Table> emptySourceNode = tables.getCheckedNode("empty", Table.class);
-//                Meta emptyMergeMeta = new MetaBuilder("emptySource").setValue("mergeName", "emptySource");
-//                resultBuilder.putData("merge.empty", runAction(new MergeDataAction(), callback, context, emptySourceNode, emptyMergeMeta).getData());
-//                tablesForMerge.removeNode("empty");
-//            }
 
             config.getMetaList("merge").forEach(mergeNode -> {
                 Meta mergeMeta = Template.compileTemplate(mergeNode, config);