Viewer redone

.hgignore

@@ -11,3 +11,5 @@ private/*
 .nb-gradle/*
 .idea/
 *.iml
+
+/numass-core/gen/

gradle/wrapper/gradle-wrapper.properties

@@ -0,0 +1,6 @@
+#Wed Apr 05 18:15:59 MSK 2017
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.4.1-all.zip

gradlew

@@ -0,0 +1,172 @@
+#!/usr/bin/env sh
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Escape application args
+save ( ) {
+    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+    echo " "
+}
+APP_ARGS=$(save "$@")
+
+# Collect all arguments for the java command, following the shell quoting and substitution rules
+eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+
+# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
+if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
+  cd "$(dirname "$0")"
+fi
+
+exec "$JAVACMD" "$@"

gradlew.bat

@@ -0,0 +1,84 @@
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega

numass-client/build.gradle

@@ -7,7 +7,7 @@ if (!hasProperty('mainClass')) {
 mainClassName = mainClass
 
 dependencies {
-    compile project(':numass-storage')
+    compile project(':numass-core')
     compile 'commons-cli:commons-cli:1.3.1'
     compile 'org.zeroturnaround:zt-zip:1.9'
 }

numass-control/build.gradle

@@ -6,7 +6,7 @@ configurations {
 }
 
 dependencies {
-    compile project(':numass-storage:numass-client')
+    compile project(':numass-client')
     compile "hep.dataforge:plots-jfc" //  project(':dataforge-plots:plots-jfc')
     compile "hep.dataforge:dataforge-control" //project(':dataforge-control')
     compile "hep.dataforge:dataforge-fx" //project(':dataforge-fx')

numass-core/build.gradle

@@ -9,6 +9,8 @@ buildscript {
 
 apply plugin: 'com.google.protobuf'
 
+description = "A bse package with minimal dependencies for numass"
+
 
 dependencies {
     compile "hep.dataforge:dataforge-storage" //project(':dataforge-storage')

numass-core/src/main/java/inr/numass/data/NMEvent.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 /**
  *

numass-core/src/main/java/inr/numass/data/NMFile.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.meta.Meta;
@@ -42,7 +42,7 @@ public class NMFile extends NamedMetaHolder implements NumassData {
         super(file.getName(), file.meta());
         points = new ArrayList<>();
         for (RawNMPoint point : file.getData()) {
-            points.add(new NMPoint(point));
+            points.add(PointBuilders.readRawPoint(point));
         }
     }
 

numass-core/src/main/java/inr/numass/data/NMPoint.java

@@ -13,14 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.MapPoint;
 
 import java.time.Instant;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 import java.util.stream.IntStream;
 
@@ -43,34 +42,6 @@ public class NMPoint implements NumassPoint {
         this.eventsCount = IntStream.of(spectrum).sum();
     }
 
-    public NMPoint(RawNMPoint point) {
-        if (point == null) {
-            throw new IllegalArgumentException();
-        }
-
-        this.pointLength = point.getLength();
-        this.u = point.getUset();
-//        this.uread = point.getUread();
-        this.startTime = point.getStartTime();
-        this.eventsCount = point.getEventsCount();
-        spectrum = calculateSpectrum(point);
-    }
-
-    private int[] calculateSpectrum(RawNMPoint point) {
-        assert point.getEventsCount() > 0;
-
-        int[] result = new int[RawNMPoint.MAX_CHANEL + 1];
-        Arrays.fill(result, 0);
-        point.getEvents().stream().forEach((event) -> {
-            if (event.getChanel() >= RawNMPoint.MAX_CHANEL) {
-                result[RawNMPoint.MAX_CHANEL]++;
-            } else {
-                result[event.getChanel()]++;
-            }
-        });
-        return result;
-    }
-
     /**
      * @return the absouteTime
      */
@@ -105,7 +76,6 @@ public class NMPoint implements NumassPoint {
         List<DataPoint> data = new ArrayList<>();
         for (int i = 0; i < RawNMPoint.MAX_CHANEL; i++) {
             data.add(new MapPoint(dataNames, i, spectrum[i]));
-
         }
         return data;
     }
@@ -121,13 +91,6 @@ public class NMPoint implements NumassPoint {
     }
 
 
-    /**
-     * @return the overflow
-     */
-    public int getOverflow() {
-        return spectrum[RawNMPoint.MAX_CHANEL];
-    }
-
     /**
      * @return the pointLength
      */

numass-core/src/main/java/inr/numass/data/NumassData.java

@@ -3,7 +3,7 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.meta.Annotated;
 import hep.dataforge.meta.Meta;

numass-core/src/main/java/inr/numass/data/NumassDataReader.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.data.FileDataFactory;
 import hep.dataforge.data.binary.Binary;

numass-core/src/main/java/inr/numass/data/NumassDataUtils.java

@@ -0,0 +1,134 @@
+package inr.numass.data;
+
+import hep.dataforge.tables.DataPoint;
+import hep.dataforge.tables.ListTable;
+import hep.dataforge.tables.Table;
+
+import java.time.Instant;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+/**
+ * Created by darksnake on 30-Jan-17.
+ */
+public class NumassDataUtils {
+
+    public static Collection<NumassPoint> joinSpectra(Stream<NumassData> spectra) {
+        Map<Double, NumassPoint> map = new LinkedHashMap<>();
+        spectra.forEach(datum -> {
+            datum.forEach(point -> {
+                double uset = point.getVoltage();
+                if (map.containsKey(uset)) {
+                    map.put(uset, join(point, map.get(uset)));
+                } else {
+                    map.put(uset, point);
+                }
+            });
+        });
+        return map.values();
+    }
+
+    /**
+     * Spectral sum of two points
+     *
+     * @param first
+     * @param second
+     * @return
+     */
+    public static NumassPoint join(NumassPoint first, NumassPoint second) {
+        if (first.getVoltage() != second.getVoltage()) {
+            throw new RuntimeException("Voltage mismatch");
+        }
+        int[] newArray = new int[first.getSpectrum().length];
+        Arrays.setAll(newArray, i -> first.getSpectrum()[i] + second.getSpectrum()[i]);
+        return new NMPoint(
+                first.getVoltage(),
+                Instant.EPOCH,
+                first.getLength() + second.getLength(),
+                newArray
+        );
+    }
+
+    public static NumassPoint substractPoint(NumassPoint point, NumassPoint reference) {
+        int[] array = new int[point.getSpectrum().length];
+        Arrays.setAll(array, i -> Math.max(0, point.getSpectrum()[i] - reference.getSpectrum()[i]));
+        return new NMPoint(
+                point.getVoltage(),
+                point.getStartTime(),
+                point.getLength(),
+                array
+        );
+    }
+
+    public static Collection<NumassPoint> substractReferencePoint(Collection<NumassPoint> points, double uset) {
+        NumassPoint reference = points.stream().filter(it -> it.getVoltage() == uset).findFirst()
+                .orElseThrow(() -> new RuntimeException("Reference point not found"));
+        return points.stream().map(it -> substractPoint(it, reference)).collect(Collectors.toList());
+    }
+
+
+    /**
+     * Поправка масштаба высокого.
+     *
+     * @param data
+     * @param beta
+     * @return
+     */
+    public static Table setHVScale(ListTable data, double beta) {
+        SpectrumDataAdapter reader = adapter();
+        ListTable.Builder res = new ListTable.Builder(data.getFormat());
+        for (DataPoint dp : data) {
+            double corrFactor = 1 + beta;
+            res.row(reader.buildSpectrumDataPoint(reader.getX(dp).doubleValue() * corrFactor, reader.getCount(dp), reader.getTime(dp)));
+        }
+        return res.build();
+    }
+
+    public static SpectrumDataAdapter adapter() {
+        return new SpectrumDataAdapter("Uset", "CR", "CRerr", "Time");
+    }
+
+    public static Table correctForDeadTime(ListTable data, double dtime) {
+        return correctForDeadTime(data, adapter(), dtime);
+    }
+
+    /**
+     * Коррекция на мертвое время в секундах
+     *
+     * @param data
+     * @param dtime
+     * @return
+     */
+    public static Table correctForDeadTime(ListTable data, SpectrumDataAdapter adapter, double dtime) {
+//        SpectrumDataAdapter adapter = adapter();
+        ListTable.Builder res = new ListTable.Builder(data.getFormat());
+        for (DataPoint dp : data) {
+            double corrFactor = 1 / (1 - dtime * adapter.getCount(dp) / adapter.getTime(dp));
+            res.row(adapter.buildSpectrumDataPoint(adapter.getX(dp).doubleValue(), (long) (adapter.getCount(dp) * corrFactor), adapter.getTime(dp)));
+        }
+        return res.build();
+    }
+
+    public static double countRateWithDeadTime(NumassPoint p, int from, int to, double deadTime) {
+        double wind = p.getCountInWindow(from, to) / p.getLength();
+        double res;
+        if (deadTime > 0) {
+            double total = p.getTotalCount();
+//            double time = p.getLength();
+//            res = wind / (1 - total * deadTime / time);
+            double timeRatio = deadTime / p.getLength();
+            res = wind / total * (1d - Math.sqrt(1d - 4d * total * timeRatio)) / 2d / timeRatio;
+        } else {
+            res = wind;
+        }
+        return res;
+    }
+
+    public static double countRateWithDeadTimeErr(NumassPoint p, int from, int to, double deadTime) {
+        return Math.sqrt(countRateWithDeadTime(p, from, to, deadTime) / p.getLength());
+    }
+}

numass-core/src/main/java/inr/numass/data/NumassPoint.java

@@ -1,4 +1,4 @@
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.MapPoint;

numass-core/src/main/java/inr/numass/data/PointBuilders.java

@@ -0,0 +1,53 @@
+package inr.numass.data;
+
+import org.jetbrains.annotations.NotNull;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.function.Function;
+import java.util.stream.IntStream;
+
+/**
+ * Created by darksnake on 13-Apr-17.
+ */
+public class PointBuilders {
+    public static NumassPoint readProtoPoint(double u, Instant startTime, double pointLength, InputStream stream, Function<NumassProto.Point.Channel.Block.Event, Integer> peakFinder) throws IOException {
+        NumassProto.Point point = NumassProto.Point.parseFrom(stream);
+        NumassProto.Point.Channel ch = point.getChannels(0);
+        int[] spectrum = count(ch.getBlocksList().stream()
+                .flatMapToInt(block -> IntStream.concat(
+                        block.getPeaks().getAmplitudesList()
+                                .stream().mapToInt(it -> it.intValue()),
+                        block.getEventsList().stream()
+                                .mapToInt(event -> peakFinder.apply(event))
+                ))
+        );
+
+        return new NMPoint(u, startTime, pointLength, spectrum);
+    }
+
+    private static int[] calculateSpectrum(RawNMPoint point) {
+        assert point.getEventsCount() > 0;
+        return count(point.getEvents().stream().mapToInt(event -> event.getChanel()));
+    }
+
+    @NotNull
+    public static NumassPoint readRawPoint(@NotNull RawNMPoint point) {
+        return new NMPoint(point.getUset(), point.getStartTime(), point.getLength(), calculateSpectrum(point));
+    }
+
+    private static int[] count(IntStream stream) {
+        List<AtomicInteger> list = new ArrayList<>();
+        stream.forEach(i -> {
+            while (list.size() <= i) {
+                list.add(new AtomicInteger(0));
+            }
+            list.get(i).incrementAndGet();
+        });
+        return list.stream().mapToInt(i -> i.get()).toArray();
+    }
+}

numass-core/src/main/java/inr/numass/data/RawNMFile.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.meta.Meta;

numass-core/src/main/java/inr/numass/data/RawNMPoint.java

@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import java.time.Instant;
 import java.util.ArrayList;

numass-core/src/main/java/inr/numass/data/SetDirectionUtility.java

@@ -3,7 +3,7 @@
  * To change this template file, choose Tools | Templates
  * and open the template in the editor.
  */
-package inr.numass.storage;
+package inr.numass.data;
 
 import hep.dataforge.context.Context;
 import hep.dataforge.context.Global;

numass-core/src/main/java/inr/numass/storage/NumassDataFactory.java

@@ -6,6 +6,7 @@ import hep.dataforge.data.DataFilter;
 import hep.dataforge.data.DataTree;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.storage.commons.StorageUtils;
+import inr.numass.data.NumassData;
 
 /**
  * Created by darksnake on 03-Feb-17.

numass-core/src/main/java/inr/numass/storage/NumassDataLoader.java

@@ -26,6 +26,7 @@ import hep.dataforge.storage.api.Storage;
 import hep.dataforge.storage.filestorage.FileEnvelope;
 import hep.dataforge.storage.loaders.AbstractLoader;
 import hep.dataforge.tables.Table;
+import inr.numass.data.*;
 import org.apache.commons.vfs2.FileObject;
 import org.apache.commons.vfs2.VFS;
 import org.slf4j.LoggerFactory;
@@ -44,7 +45,6 @@ import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import static inr.numass.storage.RawNMPoint.MAX_EVENTS_PER_POINT;
 import static org.apache.commons.vfs2.FileType.FOLDER;
 
 /**
@@ -218,7 +218,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
         //Check if the point is composite
         boolean segmented = envelope.meta().getBoolean("split", false);
 
-        if (!segmented && events.size() > MAX_EVENTS_PER_POINT) {
+        if (!segmented && events.size() > RawNMPoint.MAX_EVENTS_PER_POINT) {
             pointTime = events.get(events.size() - 1).getTime() - events.get(0).getTime();
         }
 
@@ -235,7 +235,7 @@ public class NumassDataLoader extends AbstractLoader implements ObjectLoader<Env
      * @return
      */
     public NumassPoint readPoint(Envelope envelope) {
-        return readPoint(envelope, NMPoint::new);
+        return readPoint(envelope, PointBuilders::readRawPoint);
     }
 
     private Map<String, Supplier<Envelope>> getItems() {

numass-core/src/main/java/inr/numass/storage/NumassStorage.java

@@ -23,6 +23,8 @@ import hep.dataforge.meta.MetaBuilder;
 import hep.dataforge.storage.filestorage.FilePointLoader;
 import hep.dataforge.storage.filestorage.FileStorage;
 import hep.dataforge.storage.filestorage.VFSUtils;
+import inr.numass.data.NMFile;
+import inr.numass.data.NumassData;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.vfs2.FileObject;
 import org.apache.commons.vfs2.FileSystemException;

numass-core/src/main/proto/inr/numas/numass-proto.proto

@@ -1,6 +1,6 @@
 syntax = "proto3";
 
-package inr.numass.storage;
+package inr.numass.data;
 
 message Point {
     message Channel {

numass-main/build.gradle

@@ -11,7 +11,7 @@ description = "Main numass project"
 dependencies {
     compile group: 'commons-cli', name: 'commons-cli', version: '1.+'
     compile group: 'commons-io', name: 'commons-io', version: '2.+'
-    compile project(':numass-storage')
+    compile project(':numass-core')
     compile "hep.dataforge:dataforge-minuit" //project(':dataforge-stat:dataforge-minuit')
     compile "hep.dataforge:grind-terminal" //project(':dataforge-grind:grind-terminal')
 }

numass-main/src/main/groovy/inr/numass/scripts/DetectorSpectrumSubstraction.groovy

@@ -10,7 +10,7 @@ import hep.dataforge.io.ColumnedDataWriter
 import hep.dataforge.tables.ListTable
 import hep.dataforge.tables.MapPoint
 import hep.dataforge.tables.TableFormatBuilder
-import inr.numass.storage.NumassData
+import inr.numass.data.NumassData
 
 NumassData.metaClass.findPoint{double u ->
     delegate.getNMPoints().getWork { it.getVoltage() == u }.getMap(20, true)
@@ -56,7 +56,7 @@ NumassData data2 = NMFile.readFile(new File("D:\\Work\\Numass\\transmission 2013
 
 double[] points = [14500,15000,15500,16000,18100,18200,18300]
  
-ColumnedDataWriter.writeDataSet(System.out, buildSet(data1,data2,points), "Detector spectrum substraction");
+ColumnedDataWriter.writeTable(System.out, buildSet(data1,data2,points), "Detector spectrum substraction");
 
 
 

numass-main/src/main/groovy/inr/numass/scripts/FindBorder.groovy

@@ -6,12 +6,11 @@
 
 package inr.numass.scripts
 
-import inr.numass.storage.NMFile
+import hep.dataforge.grind.GrindMetaBuilder
-import inr.numass.storage.NumassData
-import inr.numass.storage.NumassDataLoader
 import hep.dataforge.meta.Meta
 import inr.numass.actions.FindBorderAction
-import hep.dataforge.grind.GrindMetaBuilder
+import inr.numass.data.NumassData
+import inr.numass.storage.NumassDataLoader
 
 File dataDir = new File("D:\\Work\\Numass\\data\\2016_04\\T2_data\\Fill_2_2\\set_6_e26d123e54010000")
 if(!dataDir.exists()){

numass-main/src/main/groovy/inr/numass/scripts/Loss2014.groovy

@@ -1,30 +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.scripts
-
-import hep.dataforge.context.Context
-import hep.dataforge.data.DataNode
-import hep.dataforge.stat.fit.FitTaskResult
-import inr.numass.Main
-import inr.numass.Numass
-
-
-//Main.main("-lc")
-Context context = Numass.buildContext();
-context.putValue("integralThreshold", 15d);
-DataNode resultPack = Main.run(context, "-c","D:\\sterile-new\\loss2014-11\\d2_19_1.xml")
-FitTaskResult result = resultPack.getData().get()
-result.print(new PrintWriter(System.out))

numass-main/src/main/groovy/inr/numass/scripts/ReadTextFile.groovy

@@ -12,4 +12,4 @@ import hep.dataforge.tables.Table
 
 File file = new File("D:\\Work\\Numass\\sterile2016\\empty.dat" )
 Table referenceTable = new ColumnedDataReader(file).toTable();
-ColumnedDataWriter.writeDataSet(System.out, referenceTable,"")
+ColumnedDataWriter.writeTable(System.out, referenceTable,"")

numass-main/src/main/groovy/inr/numass/scripts/Simulate.groovy

@@ -88,7 +88,7 @@ data = TritiumUtils.correctForDeadTime(data, new SpectrumDataAdapter(), 10e-9);
 //        allPars.setParValue("X", 0.4);
 
 
-ColumnedDataWriter.writeDataSet(System.out,data,"--- DATA ---");
+ColumnedDataWriter.writeTable(System.out,data,"--- DATA ---");
 FitState state = new FitState(data, model, allPars);
 //new PlotFitResultAction().eval(state);
         

numass-main/src/main/groovy/inr/numass/scripts/SimulatePileup.groovy

@@ -8,9 +8,9 @@ package inr.numass.scripts
 
 import hep.dataforge.grind.Grind
 import hep.dataforge.tables.DataPoint
-import inr.numass.storage.NMPoint
+import inr.numass.data.NMPoint
+import inr.numass.data.RawNMPoint
 import inr.numass.storage.NumassDataLoader
-import inr.numass.storage.RawNMPoint
 import inr.numass.utils.NMEventGeneratorWithPulser
 import inr.numass.utils.PileUpSimulator
 import inr.numass.utils.TritiumUtils

numass-main/src/main/groovy/inr/numass/scripts/Underflow.groovy

@@ -9,8 +9,8 @@ package inr.numass.scripts
 import hep.dataforge.io.ColumnedDataWriter
 import hep.dataforge.storage.commons.StorageUtils
 import hep.dataforge.tables.Table
-import inr.numass.storage.NMPoint
+import inr.numass.data.NMPoint
-import inr.numass.storage.NumassDataUtils
+import inr.numass.data.NumassDataUtils
 import inr.numass.storage.NumassStorage
 import inr.numass.utils.UnderflowCorrection
 
@@ -85,5 +85,5 @@ printPoint(data, [14000d, 14500d, 15000d, 15500d, 16500d])
 println()
 
 Table t = new UnderflowCorrection().fitAllPoints(data, 400, 600, 3100, 20);
-ColumnedDataWriter.writeDataSet(System.out, t, "underflow parameters")
+ColumnedDataWriter.writeTable(System.out, t, "underflow parameters")
 

numass-main/src/main/java/hep/dataforge/plotfit/PlotFitResultAction.java

@@ -29,7 +29,7 @@ import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.PlottableXYFunction;
 import hep.dataforge.stat.fit.FitState;
 import hep.dataforge.stat.models.XYModel;
-import hep.dataforge.tables.PointSource;
+import hep.dataforge.tables.NavigablePointSource;
 import hep.dataforge.tables.XYAdapter;
 
 import java.util.function.Function;
@@ -46,7 +46,7 @@ public class PlotFitResultAction extends OneToOneAction<FitState, FitState> {
     @Override
     protected FitState execute(Context context, String name, FitState input, Laminate metaData) {
 
-        PointSource data = input.getDataSet();
+        NavigablePointSource data = input.getDataSet();
         if (!(input.getModel() instanceof XYModel)) {
             getReport(context, name).reportError("The fit model should be instance of XYModel for this action. Action failed!");
             return input;

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

@@ -20,9 +20,9 @@ import hep.dataforge.data.binary.Binary;
 import hep.dataforge.io.BasicIOManager;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.names.Name;
+import inr.numass.data.NumassDataReader;
 import inr.numass.data.NumassPawReader;
-import inr.numass.storage.NumassDataReader;
+import inr.numass.data.RawNMFile;
-import inr.numass.storage.RawNMFile;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.output.TeeOutputStream;
 

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

@@ -80,7 +80,6 @@ public class NumassPlugin extends BasicPlugin {
         ActionManager actions = context.pluginManager().getOrLoad(ActionManager.class);
         actions.attach(context);
 
-        actions.register(SlicingAction.class);
         actions.register(PrepareDataAction.class);
         actions.register(ReadLegacyDataAction.class);
         actions.register(MergeDataAction.class);

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

@@ -21,10 +21,10 @@ import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.exceptions.ContentException;
 import hep.dataforge.meta.Laminate;
+import inr.numass.data.RawNMFile;
+import inr.numass.data.RawNMPoint;
 import inr.numass.debunch.DebunchReport;
 import inr.numass.debunch.FrameAnalizer;
-import inr.numass.storage.RawNMFile;
-import inr.numass.storage.RawNMPoint;
 
 import java.io.PrintWriter;
 

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

@@ -25,9 +25,9 @@ import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
 import hep.dataforge.values.Value;
-import inr.numass.storage.NMFile;
+import inr.numass.data.NMFile;
-import inr.numass.storage.NumassData;
+import inr.numass.data.NumassData;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.NumassPoint;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 
 import java.io.OutputStream;
@@ -69,7 +69,7 @@ public class FindBorderAction extends OneToOneAction<NumassData, Table> {
 
         OutputStream stream = buildActionOutput(context, name);
 
-        ColumnedDataWriter.writeDataSet(stream, bData, String.format("%s : lower = %d upper = %d", name, lowerBorder, upperBorder));
+        ColumnedDataWriter.writeTable(stream, bData, String.format("%s : lower = %d upper = %d", name, lowerBorder, upperBorder));
 
         report(context, name, "File {} completed", source.getName());
         return bData;

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

@@ -4,9 +4,9 @@ import hep.dataforge.actions.ManyToOneAction;
 import hep.dataforge.context.Context;
 import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.meta.Laminate;
-import inr.numass.storage.NMPoint;
+import inr.numass.data.NMPoint;
-import inr.numass.storage.NumassData;
+import inr.numass.data.NumassData;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.NumassPoint;
 
 import java.util.Collection;
 import java.util.Map;

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

@@ -61,7 +61,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
     @Override
     protected void afterGroup(Context context, String groupName, Meta outputMeta, Table output) {
         OutputStream stream = buildActionOutput(context, groupName);
-        ColumnedDataWriter.writeDataSet(stream, output, outputMeta.toString());
+        ColumnedDataWriter.writeTable(stream, output, outputMeta.toString());
     }
 
 //    @Override
@@ -135,7 +135,7 @@ public class MergeDataAction extends ManyToOneAction<Table, Table> {
     private Table mergeDataSets(String name, Collection<Table> ds) {
         //Сливаем все точки в один набор данных
         Map<Double, List<DataPoint>> points = new LinkedHashMap<>();
-        for (PointSource d : ds) {
+        for (Table d : ds) {
             if (!d.getFormat().names().contains(parnames)) {
                 throw new IllegalArgumentException();
             }

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

@@ -124,7 +124,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 //
 //        if (!dataList.isEmpty()) {
 //            //Генерируем автоматический формат по первой строчке
-//            format = DataFormat.of(dataList.getRow(0));
+//            format = DataFormat.of(dataList.getPoint(0));
 //        } else {
 //            format = DataFormat.of(parnames);
 //        }
@@ -132,7 +132,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
 
         OutputStream stream = buildActionOutput(context, name);
 
-        ColumnedDataWriter.writeDataSet(stream, data, head);
+        ColumnedDataWriter.writeTable(stream, data, head);
 
         return data;
     }
@@ -197,7 +197,7 @@ public class MonitorCorrectAction extends OneToOneAction<Table, Table> {
             String monitorFileName = meta.getString("monitorFile", "monitor");
             OutputStream stream = buildActionOutput(context, monitorFileName);
             ListTable data = new ListTable(monitorPoints);
-            ColumnedDataWriter.writeDataSet(stream, TableTransform.sort(data, "Timestamp", true), "Monitor points", monitorNames);
+            ColumnedDataWriter.writeTable(stream, TableTransform.sort(data, "Timestamp", true), "Monitor points", monitorNames);
         }
     }
 

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

@@ -26,9 +26,13 @@ import hep.dataforge.io.XMLMetaWriter;
 import hep.dataforge.meta.Laminate;
 import hep.dataforge.meta.Meta;
 import hep.dataforge.tables.*;
+import inr.numass.data.NumassData;
+import inr.numass.data.NumassPoint;
+import inr.numass.data.PointBuilders;
+import inr.numass.data.RawNMPoint;
 import inr.numass.debunch.DebunchReport;
 import inr.numass.debunch.FrameAnalizer;
-import inr.numass.storage.*;
+import inr.numass.storage.NumassDataLoader;
 import inr.numass.utils.ExpressionUtils;
 
 import java.io.OutputStream;
@@ -112,7 +116,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
             long total = point.getTotalCount();
             double uset = utransform.apply(point.getVoltage());
-            double uread = utransform.apply(point.getUread());
+            double uread = utransform.apply(point.getVoltage());
             double time = point.getLength();
             int a = getLowerBorder(meta, uset);
             int b = Math.min(upper, RawNMPoint.MAX_CHANEL);
@@ -163,7 +167,7 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
 
         OutputStream stream = buildActionOutput(context, name);
 
-        ColumnedDataWriter.writeDataSet(stream, data, head);
+        ColumnedDataWriter.writeTable(stream, data, head);
 //        log.logString("File %s completed", dataFile.getName());
         return data;
     }
@@ -201,9 +205,9 @@ public class PrepareDataAction extends OneToOneAction<NumassData, Table> {
         double cr = point.selectChanels(lower, upper).getCR();
         if (cr < maxCR) {
             DebunchReport report = new FrameAnalizer(rejectionprob, framelength, lower, upper).debunchPoint(point);
-            return new NMPoint(report.getPoint());
+            return PointBuilders.readRawPoint(report.getPoint());
         } else {
-            return new NMPoint(point);
+            return PointBuilders.readRawPoint(point);
         }
     }
 

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

@@ -23,8 +23,8 @@ import hep.dataforge.description.TypedActionDef;
 import hep.dataforge.description.ValueDef;
 import hep.dataforge.exceptions.ContentException;
 import hep.dataforge.meta.Laminate;
-import inr.numass.storage.NMFile;
+import inr.numass.data.NMFile;
-import inr.numass.storage.RawNMFile;
+import inr.numass.data.RawNMFile;
 
 import static inr.numass.NumassIO.getNumassData;
 

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

@@ -18,8 +18,8 @@ import hep.dataforge.plots.data.PlottableData;
 import hep.dataforge.plots.data.XYPlottable;
 import hep.dataforge.tables.*;
 import hep.dataforge.values.ValueType;
-import inr.numass.storage.NumassData;
+import inr.numass.data.NumassData;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.NumassPoint;
 
 import java.io.OutputStream;
 import java.util.*;
@@ -79,7 +79,7 @@ public class ShowEnergySpectrumAction extends OneToOneAction<NumassData, Table>
         OutputStream out = buildActionOutput(context, name);
         Table table = builder.build();
 
-        ColumnedDataWriter.writeDataSet(out, table, inputMeta.toString());
+        ColumnedDataWriter.writeTable(out, table, inputMeta.toString());
 
         if (inputMeta.hasMeta("plot") || inputMeta.getBoolean("plot", false)) {
             PlotFrame frame = PlotUtils.getPlotManager(context)

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

@@ -1,275 +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.actions;
-
-import hep.dataforge.actions.OneToOneAction;
-import hep.dataforge.context.Context;
-import hep.dataforge.description.TypedActionDef;
-import hep.dataforge.io.ColumnedDataWriter;
-import hep.dataforge.io.PrintFunction;
-import hep.dataforge.maths.GridCalculator;
-import hep.dataforge.maths.NamedMatrix;
-import hep.dataforge.maths.integration.UnivariateIntegrator;
-import hep.dataforge.meta.Laminate;
-import hep.dataforge.meta.MetaBuilder;
-import hep.dataforge.plots.PlotFrame;
-import hep.dataforge.plots.PlotUtils;
-import hep.dataforge.plots.data.PlottableXYFunction;
-import hep.dataforge.stat.fit.FitState;
-import hep.dataforge.stat.fit.FitTaskResult;
-import hep.dataforge.stat.fit.Param;
-import hep.dataforge.stat.fit.ParamSet;
-import hep.dataforge.stat.simulation.GaussianParameterGenerator;
-import hep.dataforge.tables.ListTable;
-import hep.dataforge.tables.MapPoint;
-import hep.dataforge.tables.Table;
-import hep.dataforge.values.NamedValueSet;
-import inr.numass.models.ExperimentalVariableLossSpectrum;
-import inr.numass.models.LossCalculator;
-import inr.numass.utils.NumassIntegrator;
-import org.apache.commons.math3.analysis.UnivariateFunction;
-import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
-import org.apache.commons.math3.analysis.interpolation.UnivariateInterpolator;
-import org.apache.commons.math3.stat.StatUtils;
-import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
-import org.slf4j.LoggerFactory;
-
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.nio.charset.Charset;
-import java.util.Arrays;
-
-/**
- * @author darksnake
- */
-@TypedActionDef(name = "showLoss", inputType = FitState.class, outputType = FitState.class,
-        info = "Show loss spectrum for fit with loss model. Calculate excitation to ionisation ratio.")
-@Deprecated
-public class ShowLossSpectrumAction extends OneToOneAction<FitState, FitState> {
-
-    private static final String[] names = {"X", "exPos", "ionPos", "exW", "ionW", "exIonRatio"};
-
-    public static double calcultateIonRatio(NamedValueSet set, double threshold) {
-        UnivariateIntegrator integrator = NumassIntegrator.getHighDensityIntegrator();
-        UnivariateFunction integrand = LossCalculator.getSingleScatterFunction(set);
-        return 1d - integrator.integrate(integrand, 5d, threshold);
-    }
-
-    public static Table generateSpread(PrintWriter writer, String name, NamedValueSet parameters, NamedMatrix covariance) {
-        int numCalls = 1000;
-        int gridPoints = 200;
-        double a = 8;
-        double b = 32;
-
-        double[] grid = GridCalculator.getUniformUnivariateGrid(a, b, gridPoints);
-
-        double[] upper = new double[gridPoints];
-        double[] lower = new double[gridPoints];
-        double[] dispersion = new double[gridPoints];
-
-        double[] central = new double[gridPoints];
-
-        UnivariateFunction func = LossCalculator.getSingleScatterFunction(parameters);
-        for (int j = 0; j < gridPoints; j++) {
-            central[j] = func.value(grid[j]);
-        }
-
-        Arrays.fill(upper, Double.NEGATIVE_INFINITY);
-        Arrays.fill(lower, Double.POSITIVE_INFINITY);
-        Arrays.fill(dispersion, 0);
-
-        GaussianParameterGenerator generator = new GaussianParameterGenerator(parameters, covariance);
-
-        for (int i = 0; i < numCalls; i++) {
-            func = LossCalculator.getSingleScatterFunction(generator.generate());
-            for (int j = 0; j < gridPoints; j++) {
-                double val = func.value(grid[j]);
-                upper[j] = Math.max(upper[j], val);
-                lower[j] = Math.min(lower[j], val);
-                dispersion[j] += (val - central[j]) * (val - central[j]) / numCalls;
-            }
-        }
-        String[] pointNames = {"e", "central", "lower", "upper", "dispersion"};
-        ListTable.Builder res = new ListTable.Builder(pointNames);
-        for (int i = 0; i < gridPoints; i++) {
-            res.row(new MapPoint(pointNames, grid[i], central[i], lower[i], upper[i], dispersion[i]));
-
-        }
-        return res.build();
-    }
-
-    @Override
-    protected FitState execute(Context context, String name, FitState input, Laminate meta) {
-        ParamSet pars = input.getParameters();
-        if (!pars.names().contains(names)) {
-            LoggerFactory.getLogger(getClass()).error("Wrong input FitState. Must be loss spectrum fit.");
-            throw new RuntimeException("Wrong input FitState");
-        }
-
-        UnivariateFunction scatterFunction;
-        boolean calculateRatio = false;
-        PlotFrame frame = PlotUtils.getPlotManager(context)
-                .buildPlotFrame(getName(), name + ".loss",
-                        new MetaBuilder("plot")
-                                .setValue("plotTitle", "Differential scattering crossection for " + name)
-                );
-        switch (input.getModel().meta().getString("name", "")) {
-            case "scatter-variable":
-                scatterFunction = LossCalculator.getSingleScatterFunction(pars);
-                calculateRatio = true;
-
-                LossCalculator.plotScatter(frame, pars);
-                break;
-            case "scatter-empiric-experimental":
-                scatterFunction = new ExperimentalVariableLossSpectrum.Loss(0.3).total(pars);
-
-                frame.add(PlottableXYFunction.plotFunction("Cross-section", (x) -> scatterFunction.value(x), 0, 100, 1000));
-                break;
-            default:
-                throw new RuntimeException("Can work only with variable loss spectra");
-        }
-
-        double threshold = 0;
-        double ionRatio = -1;
-        double ionRatioError = -1;
-        if (calculateRatio) {
-            threshold = meta.getDouble("ionThreshold", 17);
-            ionRatio = calcultateIonRatio(pars, threshold);
-            report(context, name, "The ionization ratio (using threshold {}) is {}", threshold, ionRatio);
-            ionRatioError = calultateIonRatioError(context, name, input, threshold);
-            report(context, name, "the ionization ration standard deviation (using threshold {}) is {}", threshold, ionRatioError);
-        }
-
-        if (meta.getBoolean("printResult", false)) {
-            PrintWriter writer = new PrintWriter(new OutputStreamWriter(buildActionOutput(context, name), Charset.forName("UTF-8")));
-//            writer.println("*** FIT PARAMETERS ***");
-            input.print(writer);
-//            for (Param param : pars.getSubSet(names).getParams()) {
-//                writer.println(param.toString());
-//            }
-//            writer.println();
-//            onComplete.printf("Chi squared over degrees of freedom: %g/%d = %g", input.getChi2(), input.ndf(), chi2 / this.ndf());
-
-            writer.println();
-
-            writer.println("*** LOSS SPECTRUM INFORMATION ***");
-            writer.println();
-
-            if (calculateRatio) {
-                writer.printf("The ionization ratio (using threshold %f) is %f%n", threshold, ionRatio);
-                writer.printf("The ionization ratio standard deviation (using threshold %f) is %f%n", threshold, ionRatioError);
-                writer.println();
-            }
-
-//            double integralThreshold = reader.getDouble("numass.eGun", 19005d) - reader.getDouble("integralThreshold", 14.82);
-//            double integralRatio = calculateIntegralExIonRatio(input.getDataSet(), input.getParameters().getDouble("X"), integralThreshold);
-//            writer.printf("The excitation to ionization ratio from integral spectrum (using threshold %f) is %f%n", integralThreshold, integralRatio);
-            writer.println();
-
-            writer.println("*** SUMMARY ***");
-
-            writer.printf("%s\t", "name");
-
-            for (String parName : names) {
-                writer.printf("%s\t%s\t", parName, parName + "_err");
-            }
-            if (calculateRatio) {
-                writer.printf("%s\t", "ionRatio");
-                writer.printf("%s\t", "ionRatioErr");
-            }
-            writer.printf("%s%n", "chi2");
-
-            writer.printf("%s\t", name);
-
-            for (Param param : pars.getSubSet(names).getParams()) {
-                writer.printf("%f\t%f\t", param.value(), param.getErr());
-            }
-
-            if (calculateRatio) {
-                writer.printf("%f\t", ionRatio);
-                writer.printf("%f\t", ionRatioError);
-            }
-
-            writer.printf("%f%n", input.getChi2() / ((FitTaskResult) input).ndf());
-            writer.println();
-
-            writer.println("***LOSS SPECTRUM***");
-            writer.println();
-            PrintFunction.printFunctionSimple(writer, scatterFunction, 0, 100, 500);
-
-            if (meta.getBoolean("showSpread", false)) {
-                writer.println("***SPECTRUM SPREAD***");
-                writer.println();
-
-                ParamSet parameters = input.getParameters().getSubSet("exPos", "ionPos", "exW", "ionW", "exIonRatio");
-                NamedMatrix covariance = input.getCovariance();
-                Table spreadData = generateSpread(writer, name, parameters, covariance);
-                ColumnedDataWriter.writeDataSet(System.out, spreadData, "", spreadData.getFormat().namesAsArray());
-            }
-        }
-
-        return input;
-    }
-
-    private double calculateIntegralExIonRatio(Table data, double X, double integralThreshold) {
-        double scatterProb = 1 - Math.exp(-X);
-
-        double[] x = data.getColumn("Uset").asList().stream().mapToDouble((val) -> val.doubleValue()).toArray();
-        double[] y = data.getColumn("CR").asList().stream().mapToDouble((val) -> val.doubleValue()).toArray();
-
-        double yMax = StatUtils.max(y);
-
-        UnivariateInterpolator interpolator = new LinearInterpolator();
-        UnivariateFunction interpolated = interpolator.interpolate(x, y);
-
-        double thresholdValue = interpolated.value(integralThreshold);
-
-        double one = 1 - X * Math.exp(-X);
-
-        double ionProb = (one - thresholdValue / yMax);
-        double exProb = (thresholdValue / yMax - one + scatterProb);
-        return exProb / ionProb;
-    }
-
-    public double calultateIonRatioError(Context context, String dataNeme, FitState state, double threshold) {
-        ParamSet parameters = state.getParameters().getSubSet("exPos", "ionPos", "exW", "ionW", "exIonRatio");
-        NamedMatrix covariance = state.getCovariance();
-        return calultateIonRatioError(context, dataNeme, parameters, covariance, threshold);
-    }
-
-    @SuppressWarnings("Unchecked")
-    public double calultateIonRatioError(Context context, String name, NamedValueSet parameters, NamedMatrix covariance, double threshold) {
-        int number = 10000;
-
-        double[] res = new GaussianParameterGenerator(parameters, covariance)
-                .generate(number)
-                .stream()
-                .mapToDouble((vector) -> calcultateIonRatio(vector, threshold))
-                .filter(d -> !Double.isNaN(d))
-                .toArray();
-
-//        Histogram hist = new Histogram(0.3, 0.5, 0.002);
-//        hist.fill(res);
-//        PlotFrame frame = PlotUtils.getPlotManager(context)
-//                .buildPlotFrame(getName(), name + ".ionRatio",
-//                        new MetaBuilder("plot").setValue("plotTitle", "Ion ratio Distribution for " + name)
-//                );
-//        frame.add(PlottableData.plot("ionRatio", new XYAdapter("binCenter", "count"), hist));
-
-        return new DescriptiveStatistics(res).getStandardDeviation();
-    }
-
-}

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

@@ -1,90 +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.actions;
-
-import hep.dataforge.tables.MapPoint;
-import hep.dataforge.tables.SimplePointSource;
-import hep.dataforge.tables.TableFormat;
-import hep.dataforge.values.Value;
-import inr.numass.storage.NMFile;
-import inr.numass.storage.NumassPoint;
-import org.apache.commons.math3.util.Pair;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- *
- * @author Darksnake
- */
-public class SlicedData extends SimplePointSource {
-    private static final String TNAME = "Time"; 
-    //format = {U,username1,username2, ...}
-    private static final String UNAME = "U";
-
-
-    public SlicedData(NMFile file, Map<String, Pair<Integer, Integer>> intervals, boolean normalize) {
-        super(prepateFormat(intervals));
-        fill(file, intervals, normalize);
-    }
-
-    private static TableFormat prepateFormat(Map<String,Pair<Integer,Integer>> intervals){
-        ArrayList<String> names = new ArrayList<>(intervals.keySet());
-        names.add(0, TNAME);
-        names.add(0, UNAME);
-        return TableFormat.forNames(names);
-    }
-    
-    private void fill(NMFile file, Map<String,Pair<Integer,Integer>> intervals, boolean normalize){
-        for (NumassPoint point : file) {
-            
-            //создаем основу для будущей точки
-            HashMap<String,Value> map = new HashMap<>();
-            
-            //Кладем напряжение
-            map.put(UNAME, Value.of(point.getVoltage()));
-            double t = point.getLength();
-            map.put(TNAME,  Value.of(t));
-            
-            for (Map.Entry<String, Pair<Integer, Integer>> entry : intervals.entrySet()) {
-                String name = entry.getKey();
-                Pair<Integer, Integer> pair = entry.getValue();
-                int a = pair.getFirst();
-                int b = pair.getSecond();
-                
-                int count;
-                // проверяем порядок границ и переворачиваем если нужно
-                if(b>a){
-                    count = point.getCountInWindow(a, b);
-                } else if(b<a) {
-                    count = point.getCountInWindow(b, a);
-                } else{
-                    count = point.getCount(a);
-                }
-                //пихаем все в map
-                if(normalize){
-                    map.put(name,  Value.of(count/t));
-                } else {
-                    map.put(name,  Value.of(count));
-                }
-            }
-            this.addRow(new MapPoint(map));
-        }
-        
-    }
-    
-}

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

@@ -1,81 +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.actions;
-
-import hep.dataforge.actions.OneToOneAction;
-import hep.dataforge.context.Context;
-import hep.dataforge.description.TypedActionDef;
-import hep.dataforge.exceptions.ContentException;
-import hep.dataforge.io.ColumnedDataWriter;
-import hep.dataforge.meta.Laminate;
-import hep.dataforge.meta.Meta;
-import inr.numass.storage.NMFile;
-import inr.numass.storage.RawNMPoint;
-import org.apache.commons.math3.util.Pair;
-
-import java.io.OutputStream;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- * @author Darksnake
- */
-@TypedActionDef(name = "slicing", inputType = NMFile.class, outputType = NMFile.class)
-public class SlicingAction extends OneToOneAction<NMFile, NMFile> {
-
-    public static final String name = "slicing";
-
-    @Override
-    public String getName() {
-        return name;
-    }
-
-    @Override
-    protected NMFile execute(Context context, String name, NMFile source, Laminate meta) throws ContentException {
-        boolean normalize;
-        Map<String, Pair<Integer, Integer>> slicingConfig;
-
-        LinkedHashMap<String, Pair<Integer, Integer>> res = new LinkedHashMap<>();
-        List<? extends Meta> list = meta.getMeta("sliceconfig").getMetaList("slicepoint");
-
-        for (Meta slice : list) {
-            String title = slice.getString("title", slice.getName());
-            int from = slice.getInt("from", 0);
-            int to = slice.getInt("to", RawNMPoint.MAX_CHANEL);
-            res.put(title, new Pair<>(from, to));
-        }
-        slicingConfig = res;
-
-        normalize = meta.getBoolean("normalize", false);
-
-        if (slicingConfig == null) {
-            throw new RuntimeException("Slice configuration not defined");
-        }
-        report(context, name, "File {} started", source.getName());
-
-        SlicedData sData = new SlicedData(source, slicingConfig, normalize);
-
-        OutputStream stream = buildActionOutput(context, name);
-
-        ColumnedDataWriter.writeDataSet(stream, sData, null);
-
-        report(context, name, "File {} completed", source.getName());
-
-        return source;
-    }
-
-}

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

@@ -49,7 +49,7 @@ public class SubstractSpectrumAction extends OneToOneAction<Table, Table> {
 
             Table res = builder.build();
             OutputStream stream = buildActionOutput(context, name);
-            ColumnedDataWriter.writeDataSet(stream, res, inputMeta.toString());
+            ColumnedDataWriter.writeTable(stream, res, inputMeta.toString());
             return res;
         } catch (IOException ex) {
             throw new RuntimeException("Could not read reference file", ex);

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

@@ -113,7 +113,7 @@ public class SummaryAction extends ManyToOneAction<FitState, Table> {
     @Override
     protected void afterGroup(Context context, String groupName, Meta outputMeta, Table output) {
         OutputStream stream = buildActionOutput(context, groupName);
-        ColumnedDataWriter.writeDataSet(stream, output, groupName);
+        ColumnedDataWriter.writeTable(stream, output, groupName);
 
         super.afterGroup(context, groupName, outputMeta, output);
     }

numass-main/src/main/java/inr/numass/data/ESpectrum.java

@@ -1,84 +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.data;
-
-import hep.dataforge.io.ColumnedDataWriter;
-import hep.dataforge.tables.MapPoint;
-import hep.dataforge.tables.SimplePointSource;
-import hep.dataforge.tables.TableFormat;
-import hep.dataforge.tables.TableFormatBuilder;
-import hep.dataforge.values.Value;
-import hep.dataforge.values.ValueType;
-import inr.numass.storage.NumassPoint;
-
-import java.io.OutputStream;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-/**
- *
- * @author Darksnake
- */
-public class ESpectrum extends SimplePointSource {
-
-    private final static String binCenter = "chanel";
-    int binning = 1;
-
-    public ESpectrum(List<NumassPoint> points, int binning, boolean normalize) {
-        super(prepareFormat(points));
-        this.binning = binning;
-        fill(points, normalize);
-    }
-
-    private static TableFormat prepareFormat(List<NumassPoint> points) {
-        TableFormatBuilder builder = new TableFormatBuilder();
-
-        builder.addString(binCenter);
-        points.stream().forEach((point) -> {
-            builder.addColumn(format("%.3f", point.getUread()), 10, ValueType.NUMBER);
-        });
-
-        return builder.build();
-    }
-
-    private void fill(List<NumassPoint> points, boolean normalize) {
-        assert !points.isEmpty();
-
-        List<Map<Double, Double>> spectra = new ArrayList<>();
-
-        for (NumassPoint numassPoint : points) {
-            spectra.add(numassPoint.getMap(binning, normalize));
-        }
-
-        for (Double x : spectra.get(0).keySet()) {
-            Map<String, Value> res = new HashMap<>();
-            res.put(binCenter, Value.of(x));
-            for (int j = 0; j < points.size(); j++) {
-                res.put(format("%.3f", points.get(j).getUread()), Value.of(spectra.get(j).get(x)));
-            }
-            this.addRow(new MapPoint(res));
-
-        }
-    }
-
-    public void printToFile(OutputStream stream) {
-        ColumnedDataWriter.writeDataSet(stream, this, null);
-//        new ColumnedDataWriter(stream, this.getFormat().asArray()).writeDataSet(this, null);
-    }
-
-}

numass-main/src/main/java/inr/numass/data/ESpectrumUtils.java

@@ -1,42 +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.data;
-
-import static java.lang.Math.max;
-
-/**
- * инструменты для работы с энергитическим спектром (который в каналах)
- * @author Darksnake
- */
-public class ESpectrumUtils {
-    public static int[] substract(int[] sp1, int[] sp2) {
-        return substract(sp1, sp2, 0, sp1.length);
-    }    
-    
-    public static int[] substract(int[] sp1, int[] sp2, int from, int to) {
-        assert sp1.length == sp2.length;
-        assert to >= from;
-        assert to <= sp1.length;
-        
-        int[] res = new int[sp1.length];
-        for (int i = from; i < to; i++) {
-            res[i] = max(0, sp1[i]-sp2[i]);
-        }
-        return res;
-    }        
-    
-   
-}

numass-main/src/main/java/inr/numass/data/NumassPawReader.java

@@ -15,8 +15,8 @@
  */
 package inr.numass.data;
 
-import inr.numass.storage.RawNMFile;
 import hep.dataforge.data.binary.Binary;
+
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;

numass-main/src/main/java/inr/numass/data/SpectrumInformation.java

@@ -15,17 +15,17 @@
  */
 package inr.numass.data;
 
-import hep.dataforge.stat.parametric.ParametricFunction;
-import static hep.dataforge.maths.MatrixOperations.inverse;
 import hep.dataforge.maths.NamedMatrix;
+import hep.dataforge.stat.parametric.ParametricFunction;
 import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.values.NamedValueSet;
-import inr.numass.utils.TritiumUtils;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.linear.Array2DRowRealMatrix;
 import org.apache.commons.math3.linear.RealMatrix;
 
+import static hep.dataforge.maths.MatrixOperations.inverse;
+
 /**
  *
  * @author Darksnake
@@ -57,7 +57,7 @@ public class SpectrumInformation {
      * @return
      */
     public NamedMatrix getInformationMatrix(NamedValueSet set, ListTable data, String... parNames) {
-        SpectrumDataAdapter reader = TritiumUtils.adapter();
+        SpectrumDataAdapter reader = NumassDataUtils.adapter();
 
         String[] names = parNames;
         if (names.length == 0) {

numass-main/src/main/java/inr/numass/debunch/DebunchData.java

@@ -15,8 +15,9 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;

numass-main/src/main/java/inr/numass/debunch/DebunchEvent.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
 
 /**
  *

numass-main/src/main/java/inr/numass/debunch/DebunchReport.java

@@ -15,8 +15,9 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
+
 import java.util.List;
 
 /**

numass-main/src/main/java/inr/numass/debunch/DebunchReportImpl.java

@@ -15,8 +15,9 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
+
 import java.util.ArrayList;
 import java.util.List;
 

numass-main/src/main/java/inr/numass/debunch/Debuncher.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
 
 /**
  *

numass-main/src/main/java/inr/numass/debunch/Frame.java

@@ -15,10 +15,11 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
+import org.apache.commons.math3.distribution.PoissonDistribution;
+
 import java.util.ArrayList;
 import java.util.List;
-import org.apache.commons.math3.distribution.PoissonDistribution;
 
 /**
  *

numass-main/src/main/java/inr/numass/debunch/FrameAnalizer.java

@@ -15,7 +15,7 @@
  */
 package inr.numass.debunch;
 
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 import org.apache.commons.math3.analysis.interpolation.LinearInterpolator;
 import org.apache.commons.math3.util.FastMath;

numass-main/src/main/java/inr/numass/tasks/NumassFitScanSummaryTask.java

@@ -85,7 +85,7 @@ public class NumassFitScanSummaryTask extends AbstractTask<Table> {
 
             try (OutputStream stream = buildActionOutput(context, nodeName)) {
                 String head = "Sterile neutrino mass scan summary\n" + meta.toString();
-                ColumnedDataWriter.writeDataSet(stream, res, head);
+                ColumnedDataWriter.writeTable(stream, res, head);
             } catch (IOException e) {
                 getLogger(meta).error("Failed to close output stream", e);
             }

numass-main/src/main/java/inr/numass/tasks/NumassPrepareTask.java

@@ -19,7 +19,7 @@ import hep.dataforge.workspace.TaskModel;
 import inr.numass.actions.MergeDataAction;
 import inr.numass.actions.MonitorCorrectAction;
 import inr.numass.actions.PrepareDataAction;
-import inr.numass.storage.NumassData;
+import inr.numass.data.NumassData;
 
 /**
  * Prepare data task

numass-main/src/main/java/inr/numass/tasks/NumassSubstractEmptySourceTask.java

@@ -53,7 +53,7 @@ public class NumassSubstractEmptySourceTask extends AbstractTask<Table> {
             res.getGoal().onComplete((r, err) -> {
                 if (r != null) {
                     OutputStream out = model.getContext().io().out("merge", input.getName() + ".subtract");
-                    ColumnedDataWriter.writeDataSet(out, r,
+                    ColumnedDataWriter.writeTable(out, r,
                             input.meta().getBuilder().setNode("empty", emptySource.meta()).toString());
                 }
             });

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

@@ -15,13 +15,14 @@
  */
 package inr.numass.utils;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
-import java.util.ArrayList;
 import org.apache.commons.math3.random.MersenneTwister;
 import org.apache.commons.math3.random.RandomGenerator;
 import org.apache.commons.math3.random.SynchronizedRandomGenerator;
 
+import java.util.ArrayList;
+
 /**
  *
  * @author Darksnake

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

@@ -16,9 +16,9 @@
 package inr.numass.utils;
 
 import hep.dataforge.meta.Meta;
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.NumassPoint;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
 import org.apache.commons.math3.distribution.EnumeratedRealDistribution;
 import org.apache.commons.math3.distribution.RealDistribution;
 import org.apache.commons.math3.random.EmpiricalDistribution;

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

@@ -1,7 +1,7 @@
 package inr.numass.utils;
 
 import hep.dataforge.meta.Meta;
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
 import org.apache.commons.math3.distribution.NormalDistribution;
 import org.apache.commons.math3.distribution.RealDistribution;
 import org.apache.commons.math3.random.RandomGenerator;

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

@@ -5,10 +5,10 @@
  */
 package inr.numass.utils;
 
-import inr.numass.storage.NMEvent;
+import inr.numass.data.NMEvent;
-import inr.numass.storage.NMPoint;
+import inr.numass.data.NumassPoint;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.PointBuilders;
-import inr.numass.storage.RawNMPoint;
+import inr.numass.data.RawNMPoint;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.ArrayList;
@@ -55,15 +55,15 @@ public class PileUpSimulator {
     }
 
     public NumassPoint generated() {
-        return new NMPoint(new RawNMPoint(uSet, generated, pointLength));
+        return PointBuilders.readRawPoint(new RawNMPoint(uSet, generated, pointLength));
     }
 
     public NumassPoint registered() {
-        return new NMPoint(new RawNMPoint(uSet, registered, pointLength));
+        return PointBuilders.readRawPoint(new RawNMPoint(uSet, registered, pointLength));
     }
 
     public NumassPoint pileup() {
-        return new NMPoint(new RawNMPoint(uSet, pileup, pointLength));
+        return PointBuilders.readRawPoint(new RawNMPoint(uSet, pileup, pointLength));
     }
 
     /**

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

@@ -15,11 +15,7 @@
  */
 package inr.numass.utils;
 
-import hep.dataforge.tables.DataPoint;
+import inr.numass.data.NumassPoint;
-import hep.dataforge.tables.ListTable;
-import hep.dataforge.tables.Table;
-import inr.numass.data.SpectrumDataAdapter;
-import inr.numass.storage.NumassPoint;
 import org.apache.commons.math3.analysis.UnivariateFunction;
 
 import java.util.HashMap;
@@ -32,48 +28,6 @@ import static java.lang.Math.*;
  */
 public class TritiumUtils {
 
-    public static Table correctForDeadTime(ListTable data, double dtime) {
-        return correctForDeadTime(data, adapter(), dtime);
-    }
-
-    /**
-     * Коррекция на мертвое время в секундах
-     *
-     * @param data
-     * @param dtime
-     * @return
-     */
-    public static Table correctForDeadTime(ListTable data, SpectrumDataAdapter adapter, double dtime) {
-//        SpectrumDataAdapter adapter = adapter();
-        ListTable.Builder res = new ListTable.Builder(data.getFormat());
-        for (DataPoint dp : data) {
-            double corrFactor = 1 / (1 - dtime * adapter.getCount(dp) / adapter.getTime(dp));
-            res.row(adapter.buildSpectrumDataPoint(adapter.getX(dp).doubleValue(), (long) (adapter.getCount(dp) * corrFactor), adapter.getTime(dp)));
-        }
-        return res.build();
-    }
-
-    /**
-     * Поправка масштаба высокого.
-     *
-     * @param data
-     * @param beta
-     * @return
-     */
-    public static Table setHVScale(ListTable data, double beta) {
-        SpectrumDataAdapter reader = adapter();
-        ListTable.Builder res = new ListTable.Builder(data.getFormat());
-        for (DataPoint dp : data) {
-            double corrFactor = 1 + beta;
-            res.row(reader.buildSpectrumDataPoint(reader.getX(dp).doubleValue() * corrFactor, reader.getCount(dp), reader.getTime(dp)));
-        }
-        return res.build();
-    }
-
-    public static SpectrumDataAdapter adapter() {
-        return new SpectrumDataAdapter("Uset", "CR", "CRerr", "Time");
-    }
-
     /**
      * Integral beta spectrum background with given amplitude (total count rate
      * from)
@@ -107,24 +61,6 @@ public class TritiumUtils {
         return res * 1E-23;
     }
 
-    public static double countRateWithDeadTime(NumassPoint p, int from, int to, double deadTime) {
-        double wind = p.getCountInWindow(from, to) / p.getLength();
-        double res;
-        if (deadTime > 0) {
-            double total = p.getTotalCount();
-//            double time = p.getLength();
-//            res = wind / (1 - total * deadTime / time);
-            double timeRatio = deadTime / p.getLength();
-            res = wind / total * (1d - Math.sqrt(1d - 4d * total * timeRatio)) / 2d / timeRatio;
-        } else {
-            res = wind;
-        }
-        return res;
-    }
-
-    public static double countRateWithDeadTimeErr(NumassPoint p, int from, int to, double deadTime) {
-        return Math.sqrt(countRateWithDeadTime(p, from, to, deadTime) / p.getLength());
-    }
 
     /**
      * Evaluate groovy expression using numass point as parameter
@@ -136,7 +72,7 @@ public class TritiumUtils {
     public static double pointExpression(String expression, NumassPoint point) {
         Map<String, Object> exprParams = new HashMap<>();
         exprParams.put("T", point.getLength());
-        exprParams.put("U", point.getUread());
+        exprParams.put("U", point.getVoltage());
         exprParams.put("cr", ((double) point.getTotalCount()) / point.getLength());
         exprParams.put("point", point);
         return ExpressionUtils.function(expression, exprParams);

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

@@ -9,7 +9,7 @@ import hep.dataforge.tables.DataPoint;
 import hep.dataforge.tables.ListTable;
 import hep.dataforge.tables.MapPoint;
 import hep.dataforge.tables.Table;
-import inr.numass.storage.NumassPoint;
+import inr.numass.data.NumassPoint;
 import org.apache.commons.math3.analysis.ParametricUnivariateFunction;
 import org.apache.commons.math3.exception.DimensionMismatchException;
 import org.apache.commons.math3.fitting.SimpleCurveFitter;

numass-server/build.gradle

@@ -17,7 +17,7 @@ apply plugin: 'com.github.johnrengelman.shadow'
 mainClassName = "inr.numass.server.ServerRunner"
 
 dependencies {
-    compile project(':numass-storage')
+    compile project(':numass-core')
     compile "hep.dataforge:storage-servlet" // project(':dataforge-storage:storage-servlet')
     compile 'commons-daemon:commons-daemon:1.+'
 }

numass-server/src/main/java/inr/numass/server/NumassStorageHandler.java

@@ -12,7 +12,7 @@ import hep.dataforge.storage.api.PointLoader;
 import hep.dataforge.storage.api.Storage;
 import hep.dataforge.storage.servlet.ServletUtils;
 import hep.dataforge.storage.servlet.StorageRatpackHandler;
-import inr.numass.storage.NumassData;
+import inr.numass.data.NumassData;
 import org.slf4j.LoggerFactory;
 import ratpack.handling.Context;
 

numass-storage/src/main/java/inr/numass/storage/NumassDataUtils.java

@@ -1,69 +0,0 @@
-package inr.numass.storage;
-
-import java.time.Instant;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-/**
- * Created by darksnake on 30-Jan-17.
- */
-public class NumassDataUtils {
-
-    public static Collection<NumassPoint> joinSpectra(Stream<NumassData> spectra) {
-        Map<Double, NumassPoint> map = new LinkedHashMap<>();
-        spectra.forEach(datum -> {
-            datum.forEach(point -> {
-                double uset = point.getVoltage();
-                if (map.containsKey(uset)) {
-                    map.put(uset, join(point, map.get(uset)));
-                } else {
-                    map.put(uset, point);
-                }
-            });
-        });
-        return map.values();
-    }
-
-    /**
-     * Spectral sum of two points
-     *
-     * @param first
-     * @param second
-     * @return
-     */
-    public static NumassPoint join(NumassPoint first, NumassPoint second) {
-        if (first.getVoltage() != second.getVoltage()) {
-            throw new RuntimeException("Voltage mismatch");
-        }
-        int[] newArray = new int[first.getSpectrum().length];
-        Arrays.setAll(newArray, i -> first.getSpectrum()[i] + second.getSpectrum()[i]);
-        return new NMPoint(
-                first.getVoltage(),
-                Instant.EPOCH,
-                first.getLength() + second.getLength(),
-                newArray
-        );
-    }
-
-    public static NumassPoint substractPoint(NumassPoint point, NumassPoint reference) {
-        int[] array = new int[point.getSpectrum().length];
-        Arrays.setAll(array, i -> Math.max(0, point.getSpectrum()[i] - reference.getSpectrum()[i]));
-        return new NMPoint(
-                point.getVoltage(),
-                point.getStartTime(),
-                point.getLength(),
-                array
-        );
-    }
-
-    public static Collection<NumassPoint> substractReferencePoint(Collection<NumassPoint> points, double uset) {
-        NumassPoint reference = points.stream().filter(it -> it.getVoltage() == uset).findFirst()
-                .orElseThrow(() -> new RuntimeException("Reference point not found"));
-        return points.stream().map(it -> substractPoint(it, reference)).collect(Collectors.toList());
-    }
-
-}

numass-storage/src/main/java/inr/numass/storage/ProtoUtils.java

@@ -1,22 +0,0 @@
-package inr.numass.storage;
-
-/**
- * Created by darksnake on 13-Apr-17.
- */
-public class ProtoUtils {
-//    public static NumassPoint readProtoPoint(InputStream stream, Function<Channel.Block.Event, Long> peakFinder) throws IOException {
-//        Point point = NumassProto.Point.parseFrom(stream);
-//        Channel ch = point.getChannels(0);
-//        ch.getBlocksList().stream()
-//                .flatMapToLong(block -> {
-//                    return LongStream.concat(
-//                            block.getPeaks().getAmplitudesList()
-//                                    .stream().mapToLong(it -> it.longValue()),
-//                            block.getEventsList().stream()
-//                            .mapToLong(it->)
-//                            )
-//                });
-//
-//        return new NMPoint();
-}
-}

numass-test/build.gradle

@@ -1,5 +1,8 @@
+apply plugin: 'groovy'
+
 description = "Test module for numass client and server"
 
+
 task runServer(type: JavaExec) {
     description 'Start numass server locally'
 
@@ -23,7 +26,7 @@ task runClient(type: JavaExec) {
 }
 
 dependencies {
-    compile project(':numass-storage:numass-client')
+    compile project(':numass-client')
-    compile project(':numass-storage:numass-server')
+    compile project(':numass-server')
     compile "hep.dataforge:dataforge-grind" //project(':dataforge-grind')
 }