Merge pull request #230 from bowring/11april2024

Progress

TripoliCore/build.gradle.kts

@@ -72,6 +72,8 @@ dependencies {
     // https://mvnrepository.com/artifact/org.jblas/jblas
     implementation("org.jblas:jblas:1.2.5")
 
+    // https://mvnrepository.com/artifact/com.thoughtworks.xstream/xstream
+    implementation("com.thoughtworks.xstream:xstream:1.4.20")
 
 
     testImplementation("com.github.cirdles:commons:bc38781605")
@@ -84,15 +86,13 @@ tasks.test {
     useJUnitPlatform()
 }
 
-
 val timestamp = {
     SimpleDateFormat("dd MMMM yyyy").format(Date())
 }
 repositories {
     mavenCentral()
 }
 
-
 extraJavaModuleInfo {
     failOnMissingModuleInfo.set(false)
     automaticModule("commons-bc38781605.jar", "commons.bc38781605")
@@ -105,7 +105,7 @@ extraJavaModuleInfo {
 
     automaticModule("org.jblas:jblas", "jblas")
 
-    //automaticModule("javax.xml.bind:jaxb-api", "jaxb.api")//javax.xml.bind:jaxb-api:2.3.1
+    automaticModule("com.thoughtworks.xstream:xstream", "xstream")//javax.xml.bind:jaxb-api:2.3.1
 }
 
 

TripoliCore/src/main/java/module-info.java

@@ -26,6 +26,8 @@
     requires jakarta.xml.bind;
     requires java.xml.bind;
     requires jblas;
+    requires xstream;
+    requires java.logging;
 
 
     exports org.cirdles.tripoli;

TripoliCore/src/main/java/org/cirdles/tripoli/DataDictionary.java

@@ -0,0 +1,109 @@
+/****************************************************************************
+ * Copyright 2004-2024 James F. Bowring and www.Earth-Time.org
+ * Ported from OGTripoli
+ *
+ *  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 org.cirdles.tripoli;
+
+public enum DataDictionary {
+    ;
+    public static String[] EarthTimeBariumPhosphateICIsotopeNames = new String[]{
+            "pct130Ba_BaPO2",
+            "pct132Ba_BaPO2",
+            "pct134Ba_BaPO2",
+            "pct135Ba_BaPO2",
+            "pct136Ba_BaPO2",
+            "pct137Ba_BaPO2",
+            "pct138Ba_BaPO2",
+            "pct16O_BaPO2",
+            "pct17O_BaPO2",
+            "pct18O_BaPO2"
+    };
+
+    public static String[] EarthTimeThalliumICIsotopeNames = new String[]{
+            "pct203Tl_Tl",
+            "pct205Tl_Tl"
+    };
+
+    public static String[] EarthTimeTracerRatioNames = new String[]{
+            "206_204",
+            "207_206",
+            "206_208",
+            "206_205",
+            "207_205",
+            "208_205",
+            "202_205",
+            "238_235",
+            "233_235",
+            "233_236",
+            "235_205"};
+
+    public static String[] UPbReduxMeasuredRatioNames = new String[]{
+            "206_204",
+            "207_204",
+            "208_204",
+            "206_207",
+            "206_208",
+            "204_205",
+            "206_205",
+            "207_205",
+            "208_205",
+            "202_205",
+            "238_236",     //jan 2011
+            "233_236",
+            "238_235",
+            "233_235",
+            "238_233"};
+    public static String[] isotopeNames = new String[]
+            {"Pb205",
+                    "U235"};
+    public static String[] TracerTypes = new String[]
+            {"mixed 205-235",
+                    "mixed 205-233-235",
+                    "mixed 208-235",
+                    "mixed 205-233-236",
+                    "mixed 202-205-233-235",
+                    "mixed 202-205-233-236",
+                    "mixed 205-233-235-230Th"};
+
+    public static String getEarthTimeBariumPhosphateICIsotopeNames(int index) {
+        return EarthTimeBariumPhosphateICIsotopeNames[index];
+    }
+
+    public static String getEarthTimeThalliumICIsotopeNames(int index) {
+        return EarthTimeThalliumICIsotopeNames[index];
+    }
+
+    public static String getTracerRatioName(int index) {
+        return "r" + EarthTimeTracerRatioNames[index] + "t";
+    }
+
+    public static String getTracerIsotopeConcName(int index) {
+        return "conc" + isotopeNames[index] + "t";
+    }
+
+    public static String getMeasuredRatioName(int index) {
+        return "r" + UPbReduxMeasuredRatioNames[index] + "m";
+    }
+
+    public static String getElementNameOfRatio(String name) {
+        if (name.substring(1, 1).equals("0"))
+            return "Pb";
+        else
+            return "U";
+    }
+
+}
+

TripoliCore/src/main/java/org/cirdles/tripoli/constants/TripoliConstants.java

@@ -52,6 +52,7 @@ public enum TripoliConstants {
 
 
     public static final String SPACES_100 = CharBuffer.allocate(100).toString().replace('\0', ' ');
+    public static final String SPACES_150 = CharBuffer.allocate(150).toString().replace('\0', ' ');
 
     public static final String MISSING_STRING_FIELD = "MISSING";
 

TripoliCore/src/main/java/org/cirdles/tripoli/expressions/userFunctions/UserFunction.java

@@ -26,13 +26,19 @@ public class UserFunction implements Serializable {
     @Serial
     private static final long serialVersionUID = -5408855769497340457L;
     private String name;
+    private String etReduxName;
     private int columnIndex;
     private boolean treatAsIsotopicRatio;
     private boolean displayed;
     private boolean inverted;
 
+    public UserFunction(String name, int columnIndex) {
+        this(name, columnIndex, false, true);
+    }
+
     public UserFunction(String name, int columnIndex, boolean treatAsIsotopicRatio, boolean displayed) {
         this.name = name;
+        this.etReduxName = "";
         this.columnIndex = columnIndex;
         this.treatAsIsotopicRatio = treatAsIsotopicRatio;
         this.displayed = displayed;
@@ -43,6 +49,14 @@ public String getName() {
         return name;
     }
 
+    public String getEtReduxName() {
+        return etReduxName;
+    }
+
+    public void setEtReduxName(String etReduxName) {
+        this.etReduxName = etReduxName;
+    }
+
     public String showInvertedRatioName() {
         String retVal = name;
         if (treatAsIsotopicRatio) {
@@ -60,6 +74,10 @@ public boolean isTreatAsIsotopicRatio() {
         return treatAsIsotopicRatio;
     }
 
+    public void setTreatAsIsotopicRatio(boolean treatAsIsotopicRatio) {
+        this.treatAsIsotopicRatio = treatAsIsotopicRatio;
+    }
+
     public boolean isDisplayed() {
         return displayed;
     }

TripoliCore/src/main/java/org/cirdles/tripoli/sessions/analysis/Analysis.java

@@ -249,9 +249,11 @@ public void extractMassSpecDataFromPath(Path dataFilePath)
             }
         } else {
             // case1
+            analysisName = dataFilePath.toFile().getName().substring(0, dataFilePath.toFile().getName().length() - 4);
             analysisMethod = AnalysisMethod.createAnalysisMethodFromCase1(massSpecExtractedData);
             initializeBlockProcessing();
         }
+
     }
 
     public void initializeBlockProcessing() {
@@ -394,7 +396,7 @@ public AllBlockInitForMCMC.PlottingData assemblePostProcessPlottingData() {
 
     public final String prettyPrintAnalysisSummary() {
         return analysisName +
-                SPACES_100.substring(0, 40 - analysisName.length()) +
+                SPACES_150.substring(0, 100 - analysisName.length()) +
                 (null == analysisMethod ? "NO Method" : analysisMethod.prettyPrintMethodSummary(false));
     }
 
@@ -421,18 +423,20 @@ public final String prettyPrintAnalysisDataSummary() {
         StringBuilder sb = new StringBuilder();
         if (getAnalysisCaseNumber() == 1) {
             sb.append(String.format("%30s", "Column headers: "));
-            for (String header : massSpecExtractedData.getColumnHeaders()) {
+            for (String header : massSpecExtractedData.getUsedColumnHeaders()) {
                 sb.append(header + ", ");
             }
             sb.replace(sb.length() - 2, sb.length(), "");
             sb.append("\n");
             sb.append(String.format("%30s", "Block count: "))
-                    .append(String.format("%-3s", massSpecExtractedData.getBlocksDataLite().size()))
-                    .append(String.format("%-3s", "each with " + massSpecExtractedData.getBlocksDataLite().get(1).cycleData().length) + " cycles");
+                    .append(String.format("%-3s", massSpecExtractedData.getBlocksDataLite().size()));
+            if (massSpecExtractedData.getBlocksDataLite().size() > 0) {
+                sb.append(String.format("%-3s", "each with " + massSpecExtractedData.getBlocksDataLite().get(1).cycleData().length) + " cycles");
+            }
             sb.append("\n");
         } else {
             sb.append(String.format("%30s", "Column headers: "));
-            for (String header : massSpecExtractedData.getColumnHeaders()) {
+            for (String header : massSpecExtractedData.getUsedColumnHeaders()) {
                 sb.append(header + ", ");
             }
             sb.replace(sb.length() - 2, sb.length(), "");

TripoliCore/src/main/java/org/cirdles/tripoli/sessions/analysis/massSpectrometerModels/dataModels/dataLiteOne/initializers/AllBlockInitForDataLiteOne.java

@@ -45,11 +45,11 @@ public static AllBlockInitForMCMC.PlottingData initBlockModels(AnalysisInterface
             }
         }
 
-        return new AllBlockInitForMCMC.PlottingData(
+        return (countOfBlocks > 0) ? new AllBlockInitForMCMC.PlottingData(
                 null,
                 null,
                 singleBlockRawDataLiteSetRecords,
-                singleBlockRawDataLiteSetRecords[0].blockRawDataLiteArray().length, true, 1);
+                singleBlockRawDataLiteSetRecords[0].blockRawDataLiteArray().length, true, 1) : null;
     }
 
     private static SingleBlockRawDataLiteSetRecord prepareSingleBlockDataLiteCaseOne(int blockID, MassSpecExtractedData massSpecExtractedData) {

TripoliCore/src/main/java/org/cirdles/tripoli/sessions/analysis/massSpectrometerModels/dataSourceProcessors/MassSpecExtractedData.java

@@ -190,6 +190,12 @@ public int[] assignBlockIdToSessionTimeLite() {
         return blockIDs;
     }
 
+    public void expandCycleDataForUraniumOxideCorrection(int r270_267ColumnIndex, int r265_267ColumnIndex, double r18O_16O) {
+        for (Integer blockID : blocksDataLite.keySet()) {
+            blocksDataLite.put(blockID, blocksDataLite.get(blockID).expandForUraniumOxideCorrection(r270_267ColumnIndex, r265_267ColumnIndex, r18O_16O));
+        }
+    }
+
     public MassSpectrometerContextEnum getMassSpectrometerContext() {
         return massSpectrometerContext;
     }
@@ -214,6 +220,16 @@ public void setColumnHeaders(String[] columnHeaders) {
         this.columnHeaders = columnHeaders;
     }
 
+    public String[] getUsedColumnHeaders() {
+        List<String> usedColumnHeadersList = new ArrayList<>();
+        for (String ch : columnHeaders) {
+            if (ch != null) {
+                usedColumnHeadersList.add(ch);
+            }
+        }
+        return usedColumnHeadersList.toArray(new String[0]);
+    }
+
     public DetectorSetup getDetectorSetup() {
         return detectorSetup;
     }

TripoliCore/src/main/java/org/cirdles/tripoli/sessions/analysis/massSpectrometerModels/dataSourceProcessors/MassSpecOutputBlockRecordLite.java

@@ -26,5 +26,19 @@ public record MassSpecOutputBlockRecordLite(
         int blockID,
         double[][] cycleData
 ) implements Serializable {
+    public MassSpecOutputBlockRecordLite expandForUraniumOxideCorrection(int r270_267ColumnIndex, int r265_267ColumnIndex, double r18O_16O) {
+        double[][] cycleDataExpand = new double[cycleData.length][];
+        for (int row = 0; row < cycleData.length; row++) {
+            cycleDataExpand[row] = new double[cycleData[row].length + 3];
+            System.arraycopy(cycleData[row], 0, cycleDataExpand[row], 0, cycleData[row].length);
 
+            cycleDataExpand[row][cycleData[row].length + 0]
+                    = cycleData[row][r265_267ColumnIndex] / (1.0 - 2.0 * r18O_16O * cycleData[row][r265_267ColumnIndex]);
+            cycleDataExpand[row][cycleData[row].length + 1]
+                    = cycleData[row][r270_267ColumnIndex] / (1.0 - 2.0 * r18O_16O * cycleData[row][r270_267ColumnIndex]);
+            cycleDataExpand[row][cycleData[row].length + 2]
+                    = cycleDataExpand[row][cycleData[row].length + 1] / cycleDataExpand[row][cycleData[row].length + 0];
+        }
+        return new MassSpecOutputBlockRecordLite(blockID, cycleDataExpand);
+    }
 }

TripoliCore/src/main/java/org/cirdles/tripoli/sessions/analysis/massSpectrometerModels/dataSourceProcessors/phoenix/PhoenixMassSpec.java

@@ -33,6 +33,8 @@
 import java.util.*;
 import java.util.stream.Collectors;
 
+import static java.lang.StrictMath.ceil;
+
 /**
  * @author James F. Bowring
  */
@@ -73,11 +75,29 @@ public static MassSpecExtractedData extractMetaDataAndBlockDataFromIonvantageXLS
             }
         }
 
+        String localDateTimeZero = lines[startCtrlSheet + 21].split("\t")[2];
+
 //            String sampleName = lines[startCtrlSheet + 7].split("\t")[3];
         String methodName = lines[startCtrlSheet + 11].split("\t")[2];
         int cyclesPerBlock = Integer.parseInt(lines[startCtrlSheet + 12].split("\t")[3]);
-        int blockCount = Integer.parseInt(lines[startCtrlSheet + 13].split("\t")[3]);
-        String localDateTimeZero = lines[startCtrlSheet + 21].split("\t")[2];
+
+        // April 2024 to handle aborted runs, find end of cycles and divide by cyclesperblock
+        int cyclesStart = startCycleSheet + 16;
+        int startBlockSheet = 0;
+        for (int i = startCycleSheet; i < lines.length; i++) {
+            if (lines[i].trim().compareTo("BLOCK") == 0) {
+                startBlockSheet = i;
+                break;
+            }
+        }
+
+        int lastCycleNumber;
+        if (lines[startBlockSheet - 2].startsWith("0")) {
+            lastCycleNumber = 0;
+        } else {
+            lastCycleNumber = Integer.parseInt(lines[startBlockSheet - 2].split("\t")[0]);
+        }
+        int blockCount = (int) ceil(lastCycleNumber / cyclesPerBlock) + (int) Math.signum(lastCycleNumber % cyclesPerBlock);
 
         MassSpecExtractedData.MassSpecExtractedHeader header = new MassSpecExtractedData.MassSpecExtractedHeader(
                 "IonVantage",
@@ -90,12 +110,14 @@ public static MassSpecExtractedData extractMetaDataAndBlockDataFromIonvantageXLS
         );
         massSpecExtractedData.setHeader(header);
 
-        int cyclesStart = startCycleSheet + 16;
         List<List<String>> dataByBlocks = new ArrayList<>();
         for (int blockID = 1; blockID <= blockCount; blockID++) {
+
             List<String> dataByBlock = new ArrayList<>();
             for (int cycleNum = 1; cycleNum <= cyclesPerBlock; cycleNum++) {
-                dataByBlock.add(lines[cyclesStart + (blockID - 1) * cyclesPerBlock + cycleNum]);
+                if ((lastCycleNumber % cyclesPerBlock) == 0 || (lastCycleNumber % cyclesPerBlock) > cycleNum) {
+                    dataByBlock.add(lines[cyclesStart + (blockID - 1) * cyclesPerBlock + cycleNum]);
+                }
             }
             dataByBlocks.add(dataByBlock);
             List<String[]> cycleDataByLineSplit = new ArrayList<>();