Fixes for numass-viewer
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@ -12,14 +12,16 @@ import hep.dataforge.storage.api.StateLoader;
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import hep.dataforge.storage.api.Storage;
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import hep.dataforge.storage.commons.JSONMetaWriter;
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import hep.dataforge.storage.servlet.Utils;
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import static inr.numass.server.HandlerUtils.renderStates;
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import java.io.StringWriter;
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import java.util.HashMap;
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import java.util.Map;
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import org.slf4j.LoggerFactory;
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import ratpack.handling.Context;
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import ratpack.handling.Handler;
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import java.io.StringWriter;
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import java.util.HashMap;
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import java.util.Map;
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import static inr.numass.server.HandlerUtils.renderStates;
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/**
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*
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* @author Alexander Nozik
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@ -98,7 +100,7 @@ public class NumassRootHandler implements Handler {
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}
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private void renderLoader(Context ctx, StringBuilder b, Loader loader) {
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String href = "/storage?path=" + loader.getFullPath();
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String href = "/storage?path=" + loader.getPath();
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b.append(String.format("<p><a href=\"%s\">%s</a> (%s)</p>", href, loader.getName(), loader.getType()));
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}
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}
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@ -311,7 +311,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
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public boolean isReversed() {
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//TODO replace by meta tag in later revisions
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return SetDirectionUtility.isReversed(getFullPath(), n -> {
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return SetDirectionUtility.isReversed(getPath(), n -> {
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List<Envelope> points = getPoints();
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if (getPoints().size() >= 2) {
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return readTime(points.get(0).meta()).isAfter(readTime(points.get(1).meta()));
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@ -20,8 +20,10 @@ import hep.dataforge.events.EventBuilder;
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import hep.dataforge.exceptions.StorageException;
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import hep.dataforge.meta.Meta;
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import hep.dataforge.meta.MetaBuilder;
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import hep.dataforge.storage.filestorage.FilePointLoader;
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import hep.dataforge.storage.filestorage.FileStorage;
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import hep.dataforge.storage.filestorage.VFSUtils;
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import org.apache.commons.io.FilenameUtils;
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import org.apache.commons.vfs2.FileObject;
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import org.apache.commons.vfs2.FileSystemException;
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import org.apache.commons.vfs2.FileType;
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@ -146,6 +148,13 @@ public class NumassStorage extends FileStorage {
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}
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} else if (file.getName().toString().endsWith(NUMASS_ZIP_EXTENSION)) {
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this.loaders.put(file.getName().getBaseName(), NumassDataLoader.fromZip(this, file));
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} else if (file.getName().toString().endsWith(".points")) {
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try {
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loaders.put(FilenameUtils.getBaseName(file.getName().getBaseName()),
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FilePointLoader.fromFile(this, file, true));
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} catch (Exception ex) {
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getContext().getLogger().error("Failed to build numass point loader from file {}", file.getName());
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}
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} else {
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//updating non-numass loader files
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updateFile(file);
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@ -5,7 +5,7 @@ if (!hasProperty('mainClass')) {
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}
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mainClassName = mainClass
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version = "0.3.4"
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version = "0.3.5"
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description = "The viewer for numass data"
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@ -23,7 +23,7 @@ package inr.numass.viewer;
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import hep.dataforge.computation.ProgressCallback;
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import hep.dataforge.context.Context;
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import hep.dataforge.exceptions.StorageException;
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import hep.dataforge.names.Name;
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import hep.dataforge.plots.PlotUtils;
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import hep.dataforge.plots.data.DynamicPlottable;
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import hep.dataforge.plots.data.DynamicPlottableSet;
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@ -31,6 +31,7 @@ import hep.dataforge.plots.fx.PlotContainer;
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import hep.dataforge.plots.jfreechart.JFreeChartFrame;
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import hep.dataforge.storage.api.PointLoader;
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import hep.dataforge.storage.api.Storage;
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import hep.dataforge.storage.commons.StorageUtils;
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import hep.dataforge.tables.DataPoint;
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import hep.dataforge.tables.MapPoint;
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import hep.dataforge.values.Value;
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@ -88,17 +89,23 @@ public class MspViewController {
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public void fillMspData(Storage rootStorage) {
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if (rootStorage != null) {
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context.taskManager().submit("viewer.msp.fill", (ProgressCallback callback) -> {
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try {
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// callback.updateTitle("Fill msp data (" + rootStorage.getName() + ")");
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// callback.updateTitle("Fill msp data (" + rootStorage.getName() + ")");
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callback.updateTitle("Load msp data (" + rootStorage.getName() + ")");
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List<DataPoint> mspData = new ArrayList<>();
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DataPoint last = null;
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for (String loaderName : rootStorage.loaders().keySet()) {
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if (loaderName.startsWith("msp")) {
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try (final PointLoader mspLoader = (PointLoader) rootStorage.getLoader(loaderName)) {
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callback.updateTitle("Load msp data (" + rootStorage.getName() + ")");
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List<DataPoint> mspData = new ArrayList<>();
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StorageUtils.loaderStream(rootStorage)
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.filter(pair -> pair.getValue() instanceof PointLoader)
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.filter(pair -> Name.of(pair.getKey()).getLast().toString().startsWith("msp"))
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.map(pair -> pair.getValue())
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.filter(loader -> PointLoader.POINT_LOADER_TYPE.equals(loader.getType()))
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.forEach(loader -> {
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try {
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PointLoader mspLoader = (PointLoader) loader;
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mspLoader.open();
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callback.updateMessage("Loading mass spectrometer data from " + mspLoader.getName());
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DataPoint last = null;
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for (DataPoint dp : mspLoader) {
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mspData.add(dp);
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last = dp;
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@ -109,30 +116,26 @@ public class MspViewController {
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} catch (Exception ex) {
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LoggerFactory.getLogger(getClass()).error("Can't read msp loader data", ex);
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}
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}
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}
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callback.updateMessage("Loading msp data finished");
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});
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callback.updateMessage("Loading msp data finished");
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// return mspData;
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// List<DataPoint> mspData = (List<DataPoint>) loadProcess.getTask().get();
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if (!mspData.isEmpty()) {
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DynamicPlottableSet plottables = new DynamicPlottableSet();
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if (!mspData.isEmpty()) {
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DynamicPlottableSet plottables = new DynamicPlottableSet();
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for (DataPoint point : mspData) {
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for (String name : point.names()) {
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if (!name.equals("timestamp")) {
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if (!plottables.hasPlottable(name)) {
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plottables.addPlottable(new DynamicPlottable(name, name));
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}
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for (DataPoint point : mspData) {
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for (String name : point.names()) {
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if (!name.equals("timestamp")) {
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if (!plottables.hasPlottable(name)) {
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plottables.addPlottable(new DynamicPlottable(name, name));
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}
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}
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plottables.put(point);
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}
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updateMspPane(plottables);
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plottables.put(point);
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}
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} catch (StorageException ex) {
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throw new RuntimeException(ex);
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updateMspPane(plottables);
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}
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});
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}
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@ -16,29 +16,13 @@ See the License for the specific language governing permissions and
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limitations under the License.
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-->
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<?import java.lang.*?>
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<?import javafx.geometry.*?>
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<?import javafx.geometry.Insets?>
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<?import javafx.scene.control.*?>
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<?import javafx.scene.layout.*?>
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<?import javafx.scene.text.*?>
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<?import org.controlsfx.control.*?>
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<?import javafx.geometry.Insets?>
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<?import javafx.scene.control.Button?>
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<?import javafx.scene.control.Label?>
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<?import javafx.scene.control.SplitPane?>
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<?import javafx.scene.control.Tab?>
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<?import javafx.scene.control.TabPane?>
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<?import javafx.scene.control.ToggleButton?>
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<?import javafx.scene.control.ToolBar?>
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<?import javafx.scene.control.TreeTableView?>
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<?import javafx.scene.layout.AnchorPane?>
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<?import javafx.scene.layout.BorderPane?>
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<?import javafx.scene.layout.HBox?>
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<?import javafx.scene.layout.Pane?>
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<?import javafx.scene.text.Font?>
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<?import org.controlsfx.control.StatusBar?>
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<AnchorPane id="AnchorPane" prefHeight="768.0" prefWidth="1024.0" xmlns="http://javafx.com/javafx/8.0.40" xmlns:fx="http://javafx.com/fxml/1" fx:controller="inr.numass.viewer.MainViewerController">
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<AnchorPane xmlns:fx="http://javafx.com/fxml/1" id="AnchorPane" prefHeight="768.0" prefWidth="1024.0"
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xmlns="http://javafx.com/javafx/8.0.60" fx:controller="inr.numass.viewer.MainViewerController">
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<children>
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<BorderPane prefHeight="200.0" prefWidth="200.0" AnchorPane.bottomAnchor="0.0" AnchorPane.leftAnchor="0.0" AnchorPane.rightAnchor="0.0" AnchorPane.topAnchor="0.0">
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<top>
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