Add reset methods for each option

src/main/java/com/glencoesoftware/bioformats2raw/Converter.java

@@ -799,13 +799,256 @@ public void setDimensionOrder(DimensionOrder order) {
     dimensionOrder = order;
   }
 
+  // Option resetters - reset to defaults
+
+  /**
+   * Reset all options to their default values.
+   */
+  public void resetOptions() {
+    resetInputPath();
+    resetOutputPath();
+    resetOutputOptions();
+    resetResolutions();
+    resetSeriesList();
+    resetTileWidth();
+    resetTileHeight();
+    resetChunkDepth();
+    resetLogLevel();
+    resetProgressBars();
+    resetPrintVersionOnly();
+    resetMaxWorkers();
+    resetMaxCachedTiles();
+    resetCompression();
+    resetCompressionProperties();
+    resetExtraReaders();
+    resetCalculateOMEROMetadata();
+    resetNested();
+    resetPyramidName();
+    resetScaleFormat();
+    resetAdditionalScaleFormatCSV();
+    resetMemoDirectory();
+    resetKeepMemoFiles();
+    resetDownsampling();
+    resetOverwrite();
+    resetFillValue();
+    resetReaderOptions();
+    resetNoHCS();
+    resetNoOMEMeta();
+    resetNoRootGroup();
+    resetReuseExistingResolutions();
+    resetMinImageSize();
+    resetDimensionOrder();
+  }
+
+  /**
+   */
+  public void resetInputPath() {
+    inputPath = null;
+  }
+
+  /**
+   */
+  public void resetOutputPath() {
+    outputLocation = null;
+  }
+
+  /**
+   */
+  public void resetOutputOptions() {
+    outputOptions = null;
+  }
+
+  /**
+   */
+  public void resetResolutions() {
+    pyramidResolutions = null;
+  }
+
+  /**
+   */
+  public void resetSeriesList() {
+    seriesList = new ArrayList<Integer>();
+  }
+
+  /**
+   */
+  public void resetTileWidth() {
+    tileWidth = 1024;
+  }
+
+  /**
+   */
+  public void resetTileHeight() {
+    tileHeight = 1024;
+  }
+
+  /**
+   */
+  public void resetChunkDepth() {
+    chunkDepth = 1;
+  }
+
+  /**
+   */
+  public void resetLogLevel() {
+    logLevel = "WARN";
+  }
+
+  /**
+   */
+  public void resetProgressBars() {
+    progressBars = false;
+  }
+
+  /**
+   */
+  public void resetPrintVersionOnly() {
+    printVersion = false;
+  }
+
+  /**
+   */
+  public void resetMaxWorkers() {
+    maxWorkers = (int) Math.min(4, Runtime.getRuntime().availableProcessors());
+  }
+
+  /**
+   */
+  public void resetMaxCachedTiles() {
+    maxCachedTiles = 64;
+  }
+
+  /**
+   */
+  public void resetCompression() {
+    compressionType = ZarrCompression.blosc;
+  }
+
+  /**
+   */
+  public void resetCompressionProperties() {
+    compressionProperties = new HashMap<String, Object>();
+  }
+
+  /**
+   */
+  public void resetExtraReaders() {
+    extraReaders = new Class[] {
+      PyramidTiffReader.class, MiraxReader.class,
+      BioTekReader.class, ND2PlateReader.class
+    };
+  }
+
+  /**
+   */
+  public void resetCalculateOMEROMetadata() {
+    omeroMetadata = true;
+  }
+
+  /**
+   */
+  public void resetNested() {
+    nested = true;
+  }
+
+  /**
+   */
+  public void resetPyramidName() {
+    pyramidName = null;
+  }
+
+  /**
+   */
+  public void resetScaleFormat() {
+    scaleFormatString = "%d/%d";
+  }
+
+  /**
+   */
+  public void resetAdditionalScaleFormatCSV() {
+    additionalScaleFormatStringArgsCsv = null;
+    additionalScaleFormatStringArgs = null;
+  }
+
+  /**
+   */
+  public void resetMemoDirectory() {
+    memoDirectory = null;
+  }
+
+  /**
+   */
+  public void resetKeepMemoFiles() {
+    keepMemoFiles = false;
+  }
+
+  /**
+   */
+  public void resetDownsampling() {
+    downsampling = Downsampling.SIMPLE;
+  }
+
+  /**
+   */
+  public void resetOverwrite() {
+    overwrite = false;
+  }
+
+  /**
+   */
+  public void resetFillValue() {
+    fillValue = null;
+  }
+
+  /**
+   */
+  public void resetReaderOptions() {
+    readerOptions = new ArrayList<String>();
+  }
+
+  /**
+   */
+  public void resetNoHCS() {
+    noHCS = false;
+  }
+
+  /**
+   */
+  public void resetNoOMEMeta() {
+    noOMEMeta = false;
+  }
+
+  /**
+   */
+  public void resetNoRootGroup() {
+    noRootGroup = false;
+  }
+
+  /**
+   */
+  public void resetReuseExistingResolutions() {
+    reuseExistingResolutions = false;
+  }
+
+  /**
+   */
+  public void resetMinImageSize() {
+    minSize = MIN_SIZE;
+  }
+
+  /**
+   */
+  public void resetDimensionOrder() {
+    dimensionOrder = DimensionOrder.XYZCT;
+  }
+
   // Option getters
 
   /**
    * @return path to input data
    */
   public String getInputPath() {
-    return inputPath.toString();
+    return inputPath == null ? null : inputPath.toString();
   }
 
   /**

src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java

@@ -1983,6 +1983,40 @@ public void testOptionsAPI() throws Exception {
     }
   }
 
+  /**
+   * Check that setting and resetting options via API will reset options to
+   * their default values.
+   */
+  @Test
+  public void testResetOptions() throws Exception {
+    input = fake("series", "2", "sizeX", "4096", "sizeY", "4096");
+
+    Converter apiConverter = new Converter();
+    apiConverter.setInputPath(input.toString());
+    apiConverter.setOutputPath(output.toString());
+    apiConverter.setSeriesList(Collections.singletonList(1));
+    apiConverter.setTileWidth(128);
+    apiConverter.setTileHeight(128);
+
+    assertEquals(apiConverter.getInputPath(), input.toString());
+    assertEquals(apiConverter.getOutputPath(), output.toString());
+    assertEquals(apiConverter.getSeriesList(), Collections.singletonList(1));
+    assertEquals(apiConverter.getTileWidth(), 128);
+    assertEquals(apiConverter.getTileHeight(), 128);
+
+    apiConverter.resetInputPath();
+    assertEquals(apiConverter.getInputPath(), null);
+
+    apiConverter.setInputPath(input.toString());
+
+    apiConverter.resetOptions();
+    assertEquals(apiConverter.getInputPath(), null);
+    assertEquals(apiConverter.getOutputPath(), null);
+    assertEquals(apiConverter.getSeriesList().size(), 0);
+    assertEquals(apiConverter.getTileWidth(), 1024);
+    assertEquals(apiConverter.getTileHeight(), 1024);
+  }
+
   /**
    * @param root dataset root path
    * @param rowCount total rows the plate could contain