Fixes #44 - Retrieve unit from .ch file (#45)

Read unit from .ch file and convert from it to picoampere when reading values

pom.xml

@@ -81,6 +81,11 @@
             <artifactId>ASMUtils</artifactId>
             <version>1.0</version>
         </dependency>
+        <dependency>
+            <groupId>org.jscience</groupId>
+            <artifactId>jscience</artifactId>
+            <version>4.3.1</version>
+        </dependency>
     </dependencies>
 
     <build>

src/main/java/fr/ifpen/allotropeconverters/gc/chemstation/chfile/ChFile.java

@@ -1,5 +1,9 @@
 package fr.ifpen.allotropeconverters.gc.chemstation.chfile;
 
+import javax.measure.quantity.ElectricCurrent;
+import javax.measure.quantity.Quantity;
+import javax.measure.unit.SI;
+import javax.measure.unit.Unit;
 import java.io.IOException;
 import java.io.RandomAccessFile;
 import java.util.List;
@@ -9,24 +13,29 @@
 
 public abstract class ChFile {
 
+    protected static final Unit<ElectricCurrent> PICO_AMPERE_UNIT = SI.PICO(SI.AMPERE);
+
     protected List<Double> values;
     protected Float startTime;
     protected Float endTime;
+    protected Unit<ElectricCurrent> unit;
     protected Double yScaling;
     protected Double yOffset;
     protected String detector;
 
-    int dataStart;
-    int startTimePosition;
-    int endTimePosition;
-    int yOffsetPosition;
-    int yScalingPosition;
-    int detectorPosition;
+    protected final int dataStart; // Has no use for now
+    protected final int startTimePosition;
+    protected final int endTimePosition;
+    protected final int unitsPosition;
+    protected final int yOffsetPosition;
+    protected final int yScalingPosition;
+    protected final int detectorPosition;
 
-    protected ChFile(RandomAccessFile input, int dataStart, int startTimePosition, int endTimePosition, int yOffsetPosition, int yScalingPosition, int detectorPosition) throws IOException {
+    protected ChFile(RandomAccessFile input, int dataStart, int startTimePosition, int endTimePosition, int unitsPosition, int yOffsetPosition, int yScalingPosition, int detectorPosition) throws IOException {
         this.dataStart = dataStart;
         this.startTimePosition = startTimePosition;
         this.endTimePosition = endTimePosition;
+        this.unitsPosition = unitsPosition;
         this.yOffsetPosition = yOffsetPosition;
         this.yScalingPosition = yScalingPosition;
         this.detectorPosition = detectorPosition;
@@ -37,48 +46,54 @@ protected ChFile(RandomAccessFile input, int dataStart, int startTimePosition, i
 
     protected abstract void parseData(RandomAccessFile input) throws IOException;
 
+    /**
+     * Returns the values found in the .ch file, converted to picoampere as the standard imposes.
+     */
     public List<Double> getValues() {
         return values;
     }
 
-    protected void setValues(List<Double> values) {
-        this.values = values;
-    }
-
     public Float getStartTime() {
         return startTime;
     }
 
-    private void setStartTime(Float startTime) {
-        this.startTime = startTime;
-    }
-
     public Float getEndTime() {
         return endTime;
     }
 
-    private void setEndTime(Float endTime) {
-        this.endTime = endTime;
-    }
-
     public String getDetector() {
         return detector;
     }
 
-    private void setDetector(String detector) {
-        this.detector = detector;
+    /**
+     * Returns the unit found in the .ch file.<br>
+     * Warning: the values stored in this class are converted to picoampere, as the standard imposes.
+     */
+    protected Unit<ElectricCurrent> getUnit() {
+        return unit;
+    }
+
+    private void setUnit(String unit) {
+        Unit<? extends Quantity> localUnit = Unit.valueOf(unit);
+
+        if (!PICO_AMPERE_UNIT.isCompatible(localUnit)) {
+            throw new IllegalArgumentException("Unsupported unit: " + unit);
+        }
+
+        this.unit = localUnit.asType(ElectricCurrent.class);
     }
 
     protected void readMetadata(RandomAccessFile input) throws IOException {
-        setStartTime(readMetadataTime(input, startTimePosition));
-        setEndTime(readMetadataTime(input, endTimePosition));
+        startTime = readMetadataTime(input, startTimePosition);
+        endTime = readMetadataTime(input, endTimePosition);
+        setUnit(readStringAtPosition(input, unitsPosition, true));
 
         input.seek(yOffsetPosition);
         yOffset = input.readDouble();
 
         input.seek(yScalingPosition);
         yScaling = input.readDouble();
 
-        setDetector(readStringAtPosition(input, detectorPosition, true));
+        detector = readStringAtPosition(input, detectorPosition, true);
     }
 }

src/main/java/fr/ifpen/allotropeconverters/gc/chemstation/chfile/ChFile179.java

@@ -1,33 +1,40 @@
 package fr.ifpen.allotropeconverters.gc.chemstation.chfile;
 
-import java.io.*;
+import javax.measure.converter.UnitConverter;
+import java.io.IOException;
+import java.io.RandomAccessFile;
 import java.util.ArrayList;
 
 import static fr.ifpen.allotropeconverters.gc.chemstation.chfile.ReadHelpers.readLittleEndianDouble;
 
 class ChFile179 extends ChFile {
+
     private static final int DATA_START = 6144; // https://github.com/CINF/PyExpLabSys/blob/master/PyExpLabSys/file_parsers/chemstation.py
     private static final int START_TIME_POSITION = 282;
     private static final int END_TIME_POSITION = 286;
+    private static final int UNITS_POSITION = 4172;
     private static final int Y_OFFSET_POSITION = 4724;
     private static final int Y_SCALING_POSITION = 4732;
     private static final int DETECTOR_POSITION = 4213;
 
     ChFile179(RandomAccessFile input) throws IOException {
-        super(input, DATA_START, START_TIME_POSITION, END_TIME_POSITION, Y_OFFSET_POSITION, Y_SCALING_POSITION, DETECTOR_POSITION);
+        super(input, DATA_START, START_TIME_POSITION, END_TIME_POSITION, UNITS_POSITION, Y_OFFSET_POSITION, Y_SCALING_POSITION, DETECTOR_POSITION);
     }
 
-
     @Override
     protected void parseData(RandomAccessFile input) throws IOException {
-
         long numberOfPoints = (input.length() - DATA_START) / 8;
+        if (numberOfPoints > Integer.MAX_VALUE) {
+            throw new IllegalArgumentException("Input too large to parse");
+        }
+
+        values = new ArrayList<>((int) numberOfPoints);
+        UnitConverter unitConverter = unit.getConverterTo(PICO_AMPERE_UNIT);
 
         input.seek(DATA_START);
 
-        setValues(new ArrayList<>());
-        for(int i=0; i<numberOfPoints;i++){
-            getValues().add(readLittleEndianDouble(input) * yScaling);
+        for (int i = 0; i < numberOfPoints; i++) {
+            values.add(unitConverter.convert(readLittleEndianDouble(input) * yScaling));
         }
     }
 }

src/main/java/fr/ifpen/allotropeconverters/gc/chemstation/chfile/ChFile181.java

@@ -1,48 +1,51 @@
 package fr.ifpen.allotropeconverters.gc.chemstation.chfile;
 
+import javax.measure.converter.UnitConverter;
 import java.io.EOFException;
 import java.io.IOException;
 import java.io.RandomAccessFile;
 import java.util.ArrayList;
 
 class ChFile181 extends ChFile {
+
     private static final int DATA_START = 6144; // https://github.com/chemplexity/chromatography/blob/master/Development/File%20Conversion/ImportAgilentFID.m
     private static final int START_TIME_POSITION = 282;
     private static final int END_TIME_POSITION = 286;
+    private static final int UNITS_POSITION = 4172;
     private static final int Y_OFFSET_POSITION = 4724;
     private static final int Y_SCALING_POSITION = 4732;
     private static final int DETECTOR_POSITION = 4213;
 
     ChFile181(RandomAccessFile input) throws IOException {
-        super(input, DATA_START, START_TIME_POSITION, END_TIME_POSITION, Y_OFFSET_POSITION, Y_SCALING_POSITION, DETECTOR_POSITION);
+        super(input, DATA_START, START_TIME_POSITION, END_TIME_POSITION, UNITS_POSITION, Y_OFFSET_POSITION, Y_SCALING_POSITION, DETECTOR_POSITION);
     }
 
     @Override
     protected void parseData(RandomAccessFile input) throws IOException {
         input.seek(DATA_START);
 
         values = new ArrayList<>();
-        long[] buffer = new long[]{0,0,0};
+        long[] buffer = new long[]{0, 0, 0};
+
+        UnitConverter unitConverter = unit.getConverterTo(PICO_AMPERE_UNIT);
 
         boolean endOfFile = false;
 
-        while(!endOfFile){
-            try{
-                buffer[2]= input.readShort();
+        while (!endOfFile) {
+            try {
+                buffer[2] = input.readShort();
 
-                if(buffer[2] != 32767){
-                    buffer[1]=buffer[2]+buffer[1];
-                    buffer[0]=buffer[1]+buffer[0];
+                if (buffer[2] != 32767) {
+                    buffer[1] = buffer[2] + buffer[1];
+                    buffer[0] = buffer[1] + buffer[0];
                 } else {
                     buffer[0] = (long) input.readShort() << 32;
                     buffer[0] = input.readInt() + buffer[0];
                     buffer[1] = 0;
                 }
 
-                values.add(buffer[0] * yScaling + yOffset);
-
-            }
-            catch (EOFException e){
+                values.add(unitConverter.convert(buffer[0] * yScaling + yOffset));
+            } catch (EOFException e) {
                 endOfFile = true;
             }
         }

src/test/java/fr/ifpen/allotropeconverters/gc/chemstation/chfile/ChFile179Tests.java

@@ -3,15 +3,17 @@
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
+import javax.measure.unit.SI;
 import java.io.File;
 import java.io.IOException;
 import java.io.RandomAccessFile;
 import java.net.URI;
 import java.util.List;
 
 class ChFile179Tests {
+
     @Test
-    void GetVersionReturnsExpected() throws IOException {
+    void getVersionReturnsExpected() throws IOException {
         URI uri = new File("src/test/resources/V179.D/FID1A.ch").toURI();
         RandomAccessFile file = new RandomAccessFile(uri.getPath(), "r");
         ChFile chFile = new ChFile179(file);
@@ -20,5 +22,7 @@ void GetVersionReturnsExpected() throws IOException {
 
         Assertions.assertEquals(71840, values.size());
         Assertions.assertEquals(2.165234, values.get(0), 0.001);
+
+        Assertions.assertEquals(SI.PICO(SI.AMPERE), chFile.getUnit());
     }
 }

src/test/java/fr/ifpen/allotropeconverters/gc/chemstation/chfile/ChFile181Tests.java

@@ -1,19 +1,19 @@
 package fr.ifpen.allotropeconverters.gc.chemstation.chfile;
 
-import fr.ifpen.allotropeconverters.gc.chemstation.chfile.ChFile;
-import fr.ifpen.allotropeconverters.gc.chemstation.chfile.ChFile181;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
+import javax.measure.unit.SI;
 import java.io.File;
 import java.io.IOException;
 import java.io.RandomAccessFile;
 import java.net.URI;
 import java.util.List;
 
 class ChFile181Tests {
+
     @Test
-    void GetVersionReturnsExpected() throws IOException {
+    void getVersionReturnsExpected() throws IOException {
         URI uri = new File("src/test/resources/V181.D/V181.ch").toURI();
         RandomAccessFile file = new RandomAccessFile(uri.getPath(), "r");
         ChFile chFile = new ChFile181(file);
@@ -22,5 +22,7 @@ void GetVersionReturnsExpected() throws IOException {
 
         Assertions.assertEquals(5914, values.size());
         Assertions.assertEquals(2.1010, values.get(0), 0.001);
+
+        Assertions.assertEquals(SI.PICO(SI.AMPERE), chFile.getUnit());
     }
-}
+}