Merge pull request #14 from oclay1st/develop

Refactor headers API

README.md

@@ -34,7 +34,7 @@ Filter filter = new Filter.Builder().startTime(start).endTime(end).build();
 SingleSegementRecord record = SingleSegmentRecord.parse(path, filter);
 ```
 
-Parse and filter a single-segment record by singal indices:
+Parse and filter a single-segment record by signal indices:
 ```
 Path path = Path.of(...);
 Filter filter = new Filter.Builder().signals(new int[]{0, 1, 2}).build();
@@ -49,8 +49,7 @@ MultiSegmentRecord record = MultiSegmentRecord.parse(path);
 
 Export a single-segment record:
 ```
-Path path = Path.of(...);
-Filter fiter = new Filter(...);
+...
 SingleSegmentRecord record = SingleSegmentRecord.parse(path, filter);
 Path exportPath = Path.of(...);
 record.export(exportPath);

src/main/java/io/github/oclay1st/wfdb/filters/Filter.java

@@ -84,8 +84,7 @@ public boolean equals(Object object) {
 
     @Override
     public int hashCode() {
-        int result = Objects.hash(startTime, endTime);
-        return 31 * result + Arrays.hashCode(signals);
+        return 31 * Objects.hash(startTime, endTime) + Arrays.hashCode(signals);
     }
 
     @Override

src/main/java/io/github/oclay1st/wfdb/filters/FilterProcessor.java

@@ -33,10 +33,10 @@ private FilterProcessor(Filter filter, SingleSegmentHeader header, boolean isFil
      * @return a new instance of a filter processor
      */
     public static FilterProcessor process(Filter filter, SingleSegmentHeader header) {
-        long duration = header.headerRecord().durationTime().toMillis();
+        long duration = header.record().durationTime().toMillis();
         long startMilliseconds = filter.startTime() != null ? filter.startTime() : 0;
         long endMilliseconds = filter.endTime() != null ? filter.endTime() : duration;
-        int[] indices = IntStream.range(0, header.headerSignals().length).toArray();
+        int[] indices = IntStream.range(0, header.signals().length).toArray();
         if (filter.signals() != null) {
             indices = filter.signals();
         }
@@ -54,7 +54,10 @@ public static FilterProcessor process(Filter filter, SingleSegmentHeader header)
      * @return a {@link SingleSegmentHeader} instance
      */
     public SingleSegmentHeader generateFilteredHeader() {
-        return isFilterAsDefault ? header : new SingleSegmentHeader(generateHeaderRecord(), generateHeaderSignals());
+        if (isFilterAsDefault) {
+            return header;
+        }
+        return new SingleSegmentHeader(generateHeaderRecord(), generateHeaderSignals(), header.comments());
     }
 
     /**
@@ -63,7 +66,7 @@ public SingleSegmentHeader generateFilteredHeader() {
      * @return a new {@link HeaderRecord} instance
      */
     private HeaderRecord generateHeaderRecord() {
-        HeaderRecord headerRecord = header.headerRecord();
+        HeaderRecord headerRecord = header.record();
         int numberOfSignals = filter.signals().length;
         long duration = filter.endTime() - filter.startTime();
         int numberOfSamplesPerSignal = Math.round(headerRecord.samplingFrequency() * duration / 1000);
@@ -80,7 +83,7 @@ private HeaderRecord generateHeaderRecord() {
     private HeaderSignal[] generateHeaderSignals() {
         HeaderSignal[] headerSignals = new HeaderSignal[filter.signals().length];
         for (int i = 0; i < headerSignals.length; i++) {
-            HeaderSignal headerSignal = header.headerSignals()[filter.signals()[i]];
+            HeaderSignal headerSignal = header.signals()[filter.signals()[i]];
             headerSignals[i] = new HeaderSignal(headerSignal.filename(), headerSignal.format(),
                     headerSignal.samplesPerFrame(), headerSignal.skew(), headerSignal.bytesOffset(),
                     headerSignal.adcGain(), headerSignal.baseline(), headerSignal.unit(), headerSignal.adcResolution(),
@@ -109,14 +112,15 @@ public BytesRange calculateBytesRange(HeaderSignal[] headerSignals) {
      * Calculate the byte index given the milliseconds, the bytes per sample and the
      * number of signals
      *
-     * @param milliseconds the value of the milliseconds
-     * @param bytesPerSample the value of the bytes per sample
+     * @param milliseconds    the value of the milliseconds
+     * @param bytesPerSample  the value of the bytes per sample
      * @param numberOfSignals the value of number of signals
      * @return the byte index value
      */
     private long calculateByteIndex(long milliseconds, float bytesPerSample, int numberOfSignals) {
-        int numberOfSamplesPerSignal = Math.round(header.headerRecord().samplingFrequency() * milliseconds / 1000);
+        int numberOfSamplesPerSignal = Math.round(header.record().samplingFrequency() * milliseconds / 1000);
         int numberOfSamples = numberOfSamplesPerSignal * numberOfSignals;
         return (int) Math.ceil(numberOfSamples * bytesPerSample);
     }
+
 }

src/main/java/io/github/oclay1st/wfdb/records/MultiSegmentHeader.java

@@ -12,12 +12,12 @@
 /**
  * Represent the info from a multi-segment header
  *
- * @param headerRecord   the header record
- * @param headerSegments the array of header segments
+ * @param record   the header record
+ * @param segments the array of header segments
  * @see HeaderRecord
  * @see HeaderSegment
  */
-public record MultiSegmentHeader(HeaderRecord headerRecord, HeaderSegment[] headerSegments) {
+public record MultiSegmentHeader(HeaderRecord record, HeaderSegment[] segments, String comments) { // NOSONAR
 
     /**
      * Parse the multi-segment header from an input form.
@@ -43,12 +43,15 @@ public static MultiSegmentHeader parse(InputStream input) throws IOException, Pa
         int segmentIndex = 0;
         String headerLine;
         boolean headerRecordProcessed = false;
+        StringBuilder commentsBuilder = new StringBuilder();
         while ((headerLine = reader.readLine()) != null) {
             String stripedHeaderLine = headerLine.strip();
-            if (stripedHeaderLine.isEmpty() || stripedHeaderLine.charAt(0) == '#') {
+            if (stripedHeaderLine.isEmpty()) {
                 continue;
             }
-            if (!headerRecordProcessed) {
+            if (stripedHeaderLine.charAt(0) == '#') {
+                commentsBuilder.append('\n').append(stripedHeaderLine);
+            } else if (!headerRecordProcessed) {
                 headerRecord = HeaderRecord.parse(stripedHeaderLine);
                 headerSegments = new HeaderSegment[headerRecord.numberOfSegments()];
                 headerRecordProcessed = true;
@@ -57,7 +60,7 @@ public static MultiSegmentHeader parse(InputStream input) throws IOException, Pa
                 segmentIndex++;
             }
         }
-        return new MultiSegmentHeader(headerRecord, headerSegments);
+        return new MultiSegmentHeader(headerRecord, headerSegments, commentsBuilder.toString());
     }
 
     /**
@@ -67,29 +70,28 @@ public static MultiSegmentHeader parse(InputStream input) throws IOException, Pa
      */
     public String toTextBlock() {
         StringBuilder builder = new StringBuilder();
-        builder.append(headerRecord.toTextLine());
-        for (HeaderSegment headerSegment : headerSegments) {
-            builder.append("\n");
-            builder.append(headerSegment.toTextLine());
+        builder.append(record.toTextLine());
+        for (HeaderSegment headerSegment : segments) {
+            builder.append('\n').append(headerSegment.toTextLine());
         }
         return builder.toString();
     }
 
     @Override
     public String toString() {
-        return "MultiSegmentHeader [headerRecord = " + headerRecord + ", headerSegments = "
-                + Arrays.toString(headerSegments) + "]";
+        return "MultiSegmentHeader [headerRecord = " + record + ", headerSegments = "
+                + Arrays.toString(segments) + "]";
     }
 
     @Override
     public boolean equals(Object object) {
-        return object instanceof MultiSegmentHeader instance && headerRecord.equals(instance.headerRecord)
-                && Arrays.equals(headerSegments, instance.headerSegments);
+        return object instanceof MultiSegmentHeader instance && record.equals(instance.record)
+                && Arrays.equals(segments, instance.segments);
     }
 
     @Override
     public int hashCode() {
-        int result = Objects.hash(headerRecord);
-        return 31 * result + Arrays.hashCode(headerSegments);
+        return 31 * Objects.hash(record) + Arrays.hashCode(segments);
     }
+
 }

src/main/java/io/github/oclay1st/wfdb/records/MultiSegmentRecord.java

@@ -31,9 +31,9 @@ public static MultiSegmentRecord parse(Path recordPath) throws IOException, Pars
             // Parse the multi-segment header file
             MultiSegmentHeader header = MultiSegmentHeader.parse(inputStream);
             int recordIndex = 0;
-            SingleSegmentRecord[] singleSegmentRecords = new SingleSegmentRecord[header.headerRecord()
+            SingleSegmentRecord[] singleSegmentRecords = new SingleSegmentRecord[header.record()
                     .numberOfSamplesPerSignal()];
-            for (HeaderSegment segment : header.headerSegments()) {
+            for (HeaderSegment segment : header.segments()) {
                 Path segmentRecordPath = recordPath.resolveSibling(segment.name());
                 SingleSegmentRecord singleSegmentRecord = SingleSegmentRecord.parse(segmentRecordPath);
                 singleSegmentRecords[recordIndex] = singleSegmentRecord;
@@ -51,8 +51,7 @@ public boolean equals(Object object) {
 
     @Override
     public int hashCode() {
-        int result = Objects.hash(header);
-        return 31 * result + Arrays.hashCode(records);
+        return 31 * Objects.hash(header) + Arrays.hashCode(records);
     }
 
     @Override

src/main/java/io/github/oclay1st/wfdb/records/SingleSegmentHeader.java

@@ -16,10 +16,10 @@
 /**
  * Represents a single-segment record header.
  *
- * @param headerRecord  the header record
- * @param headerSignals the array of header signals
+ * @param record  the header record
+ * @param signals the array of header signals
  */
-public record SingleSegmentHeader(HeaderRecord headerRecord, HeaderSignal[] headerSignals) {
+public record SingleSegmentHeader(HeaderRecord record, HeaderSignal[] signals, String comments) { // NOSONAR
 
     /**
      * Parse the single-segment header from an input form.
@@ -47,12 +47,15 @@ public static SingleSegmentHeader parse(InputStream input) throws IOException, P
         int signalIndex = 0;
         String headerLine;
         boolean headerRecordProcessed = false;
+        StringBuilder commentsBuilder = new StringBuilder();
         while ((headerLine = reader.readLine()) != null) {
             String stripedHeaderLine = headerLine.strip();
-            if (stripedHeaderLine.isEmpty() || stripedHeaderLine.charAt(0) == '#') {
+            if (stripedHeaderLine.isEmpty()) {
                 continue;
             }
-            if (!headerRecordProcessed) {
+            if (stripedHeaderLine.charAt(0) == '#') {
+                commentsBuilder.append('\n').append(stripedHeaderLine);
+            } else if (!headerRecordProcessed) {
                 headerRecord = HeaderRecord.parse(stripedHeaderLine);
                 headerSignals = new HeaderSignal[headerRecord.numberOfSignals()];
                 headerRecordProcessed = true;
@@ -61,7 +64,7 @@ public static SingleSegmentHeader parse(InputStream input) throws IOException, P
                 signalIndex++;
             }
         }
-        return new SingleSegmentHeader(headerRecord, headerSignals);
+        return new SingleSegmentHeader(headerRecord, headerSignals, commentsBuilder.toString());
     }
 
     /**
@@ -70,7 +73,7 @@ public static SingleSegmentHeader parse(InputStream input) throws IOException, P
      * @return the group of header signals
      */
     public Map<String, List<HeaderSignal>> groupHeaderSignalsByFilename() {
-        return Arrays.stream(headerSignals)
+        return Arrays.stream(signals)
                 .collect(Collectors.groupingBy(HeaderSignal::filename, LinkedHashMap::new, Collectors.toList()));
     }
 
@@ -81,24 +84,23 @@ public Map<String, List<HeaderSignal>> groupHeaderSignalsByFilename() {
      */
     public String toTextBlock() {
         StringBuilder builder = new StringBuilder();
-        builder.append(headerRecord.toTextLine());
-        for (HeaderSignal headerSignal : headerSignals) {
-            builder.append("\n");
-            builder.append(headerSignal.toTextLine());
+        builder.append(record.toTextLine());
+        for (HeaderSignal headerSignal : signals) {
+            builder.append('\n').append(headerSignal.toTextLine());
         }
         return builder.toString();
     }
 
     /**
-     * Generate a copy of the header with the checksum of the singals.
+     * Generate a copy of the header with the checksum of the signals.
      *
-     * @param samplesPerSignal the array of samples per singal
+     * @param samplesPerSignal the array of samples per signal
      * @return a new {@link SingleSegmentHeader} instance
      */
     public SingleSegmentHeader generateChecksumCopy(int[][] samplesPerSignal) {
-        HeaderSignal[] newHeaderSignals = new HeaderSignal[headerSignals.length];
-        for (int i = 0; i < headerSignals.length; i++) {
-            HeaderSignal headerSignal = headerSignals[i];
+        HeaderSignal[] newHeaderSignals = new HeaderSignal[signals.length];
+        for (int i = 0; i < signals.length; i++) {
+            HeaderSignal headerSignal = signals[i];
             int initialValue = samplesPerSignal[i][0];
             int checksum = HeaderSignal.calculateChecksum(samplesPerSignal[i]);
             newHeaderSignals[i] = new HeaderSignal(headerSignal.filename(), headerSignal.format(),
@@ -107,24 +109,24 @@ public SingleSegmentHeader generateChecksumCopy(int[][] samplesPerSignal) {
                     headerSignal.adcZero(), initialValue, checksum, headerSignal.blockSize(),
                     headerSignal.description());
         }
-        return new SingleSegmentHeader(headerRecord, newHeaderSignals);
+        return new SingleSegmentHeader(record, newHeaderSignals, comments);
     }
 
     @Override
     public String toString() {
-        return "SingleSegmentHeader [headerRecord = " + headerRecord + ", headerSignals = "
-                + Arrays.toString(headerSignals) + "]";
+        return "SingleSegmentHeader [headerRecord = " + record + ", headerSignals = "
+                + Arrays.toString(signals) + "]";
     }
 
     @Override
     public boolean equals(Object object) {
-        return object instanceof SingleSegmentHeader instance && headerRecord.equals(instance.headerRecord)
-                && Arrays.equals(headerSignals, instance.headerSignals);
+        return object instanceof SingleSegmentHeader instance && record.equals(instance.record)
+                && Arrays.equals(signals, instance.signals);
     }
 
     @Override
     public int hashCode() {
-        int result = Objects.hash(headerRecord);
-        return 31 * result + Arrays.hashCode(headerSignals);
+        return 31 * Objects.hash(record) + Arrays.hashCode(signals);
     }
+
 }

src/main/java/io/github/oclay1st/wfdb/records/SingleSegmentRecord.java

@@ -51,7 +51,7 @@ public static SingleSegmentRecord parse(Path recordPath, Filter filter) throws I
         SingleSegmentHeader header = parseHeaderFile(recordPath);
         FilterProcessor filterProcessor = FilterProcessor.process(filter, header);
         SingleSegmentHeader filteredHeader = filterProcessor.generateFilteredHeader();
-        int numberOfSignals = filteredHeader.headerRecord().numberOfSignals();
+        int numberOfSignals = filteredHeader.record().numberOfSignals();
         int[][] samplesPerSignal = new int[numberOfSignals][0];
         int samplesPerSignalIndex = 0;
         // Group the signals by filename
@@ -148,7 +148,7 @@ private static SignalFormatter resolveSignalFormatter(HeaderSignal[] headerSigna
     /**
      * Export the single-segment record. Generate the header and signal(s) files.
      *
-     * @param recordPath the path of the record 
+     * @param recordPath the path of the record
      * @throws IOException if the record can't be exported.
      */
     public void export(Path recordPath) throws IOException {

src/test/java/io/github/oclay1st/wfdb/records/MultiSegmentHeaderTest.java

@@ -27,17 +27,17 @@ void shouldParseTheMultiSegmentHeader() throws IOException, ParseException {
         ByteArrayInputStream headerInput = new ByteArrayInputStream(headerText.getBytes());
         MultiSegmentHeader header = MultiSegmentHeader.parse(headerInput);
         assertNotNull(header);
-        assertNotNull(header.headerRecord());
-        assertTrue(header.headerRecord().isMultiSegment());
-        assertEquals("multi", header.headerRecord().name());
-        assertEquals(4, header.headerRecord().numberOfSignals());
-        assertEquals(360, header.headerRecord().samplingFrequency());
-        assertEquals(45000, header.headerRecord().numberOfSamplesPerSignal());
-        assertEquals(2, header.headerSegments().length);
-        assertEquals("test", header.headerSegments()[0].name());
-        assertEquals(22500, header.headerSegments()[0].numberOfSamplesPerSignal());
-        assertEquals("other", header.headerSegments()[1].name());
-        assertEquals(22500, header.headerSegments()[1].numberOfSamplesPerSignal());
+        assertNotNull(header.record());
+        assertTrue(header.record().isMultiSegment());
+        assertEquals("multi", header.record().name());
+        assertEquals(4, header.record().numberOfSignals());
+        assertEquals(360, header.record().samplingFrequency());
+        assertEquals(45000, header.record().numberOfSamplesPerSignal());
+        assertEquals(2, header.segments().length);
+        assertEquals("test", header.segments()[0].name());
+        assertEquals(22500, header.segments()[0].numberOfSamplesPerSignal());
+        assertEquals("other", header.segments()[1].name());
+        assertEquals(22500, header.segments()[1].numberOfSamplesPerSignal());
     }
 
     @Test
@@ -54,9 +54,9 @@ void shouldIgnoreCommentsAndBlankLines() throws IOException, ParseException {
         ByteArrayInputStream headerInput = new ByteArrayInputStream(headerText.getBytes());
         MultiSegmentHeader header = MultiSegmentHeader.parse(headerInput);
         assertNotNull(header);
-        assertNotNull(header.headerRecord());
-        assertTrue(header.headerRecord().isMultiSegment());
-        assertEquals(3, header.headerSegments().length);
+        assertNotNull(header.record());
+        assertTrue(header.record().isMultiSegment());
+        assertEquals(3, header.segments().length);
     }
 
     @ParameterizedTest(name = "in {0}")

src/test/java/io/github/oclay1st/wfdb/records/MultiSegmentRecordTest.java

@@ -19,7 +19,7 @@ void shouldParseMultiSegmentRecord() throws IOException, ParseException {
         Path recordPath = Path.of("src", "test", "resources", "multi-segment", "v102s", "v102s");
         MultiSegmentRecord multiSegmentRecord = MultiSegmentRecord.parse(recordPath);
         assertNotNull(multiSegmentRecord);
-        assertEquals(3, multiSegmentRecord.header().headerSegments().length);
+        assertEquals(3, multiSegmentRecord.header().segments().length);
     }
 
 }