Add reset methods for each option

build.gradle

@@ -31,7 +31,7 @@ repositories {
 dependencies {
     implementation 'net.java.dev.jna:jna:5.10.0'
     implementation 'dev.zarr:jzarr:0.4.2'
-    implementation 'info.picocli:picocli:4.2.0'
+    implementation 'info.picocli:picocli:4.7.5'
     implementation 'me.tongfei:progressbar:0.9.0'
     implementation 'ome:formats-bsd:7.0.0'
     implementation 'com.glencoesoftware:bioformats2raw:0.8.0-rc1'

src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java

@@ -123,13 +123,13 @@ public class PyramidFromDirectoryWriter implements Callable<Void> {
   /** Where to write? */
   Path outputFilePath;
   Path inputDirectory;
-  private volatile String logLevel = "WARN";
+  private volatile String logLevel;
   private volatile boolean progressBars = false;
   boolean printVersion = false;
-  CompressionType compression = CompressionType.LZW;
+  CompressionType compression;
   CodecOptions compressionOptions;
   boolean legacy = false;
-  int maxWorkers = Runtime.getRuntime().availableProcessors();
+  int maxWorkers;
   boolean rgb = false;
 
   private List<PyramidSeries> series = new ArrayList<PyramidSeries>();
@@ -148,7 +148,6 @@ public class PyramidFromDirectoryWriter implements Callable<Void> {
    * Construct a writer for performing the pyramid conversion.
    */
   public PyramidFromDirectoryWriter() {
-    tileQueue = new LimitedQueue<Runnable>(maxWorkers);
   }
 
   /**
@@ -159,11 +158,17 @@ public PyramidFromDirectoryWriter() {
   @Parameters(
       index = "1",
       arity = "1",
-      description = "Relative path to the output OME-TIFF file"
+      description = "Relative path to the output OME-TIFF file",
+      defaultValue = Option.NULL_VALUE
   )
   public void setOutputPath(String output) {
     // could be expanded to allow other output locations
-    outputFilePath = Paths.get(output);
+    if (output != null) {
+      outputFilePath = Paths.get(output);
+    }
+    else {
+      outputFilePath = null;
+    }
   }
 
   /**
@@ -174,11 +179,17 @@ public void setOutputPath(String output) {
   @Parameters(
       index = "0",
       arity = "1",
-      description = "Directory containing pixel data to convert"
+      description = "Directory containing pixel data to convert",
+      defaultValue = Option.NULL_VALUE
   )
   public void setInputPath(String input) {
     // could be expanded to allow other input locations
-    inputDirectory = Paths.get(input);
+    if (input != null) {
+      inputDirectory = Paths.get(input);
+    }
+    else {
+      inputDirectory = null;
+    }
   }
 
   /**
@@ -208,7 +219,8 @@ public void setLogLevel(String level) {
   @Option(
     names = {"-p", "--progress"},
     description = "Print progress bars during conversion",
-    help = true
+    help = true,
+    defaultValue = "false"
   )
   public void setProgressBars(boolean useProgressBars) {
     progressBars = useProgressBars;
@@ -223,7 +235,8 @@ public void setProgressBars(boolean useProgressBars) {
   @Option(
       names = "--version",
       description = "Print version information and exit",
-      help = true
+      help = true,
+      defaultValue = "false"
   )
   public void setPrintVersionOnly(boolean versionOnly) {
     printVersion = versionOnly;
@@ -271,7 +284,8 @@ public void setCompression(CompressionType compressionType) {
   @Option(
       names = "--quality",
       converter = CompressionQualityConverter.class,
-      description = "Compression quality"
+      description = "Compression quality",
+      defaultValue = Option.NULL_VALUE
   )
   public void setCompressionOptions(CodecOptions options) {
     compressionOptions = options;
@@ -286,7 +300,8 @@ public void setCompressionOptions(CodecOptions options) {
    */
   @Option(
       names = "--legacy",
-      description = "Write a Bio-Formats 5.9.x pyramid instead of OME-TIFF"
+      description = "Write a Bio-Formats 5.9.x pyramid instead of OME-TIFF",
+      defaultValue = "false"
   )
   public void setLegacyTIFF(boolean legacyTIFF) {
     legacy = legacyTIFF;
@@ -300,26 +315,36 @@ public void setLegacyTIFF(boolean legacyTIFF) {
   @Option(
       names = "--split",
       description =
-        "Split output into one OME-TIFF file per OME Image/Zarr group"
+        "Split output into one OME-TIFF file per OME Image/Zarr group",
+      defaultValue = "false"
   )
   public void setSplitTIFFs(boolean split) {
     splitBySeries = split;
   }
 
   /**
    * Set the maximum number of workers to use for converting tiles.
-   * Defaults to the number of detected CPUs.
+   * Defaults to 4 or the number of detected CPUs, whichever is smaller.
    *
    * @param workers maximum worker count
    */
   @Option(
       names = "--max_workers",
-      description = "Maximum number of workers (default: ${DEFAULT-VALUE})"
+      description = "Maximum number of workers (default: ${DEFAULT-VALUE})",
+      defaultValue = "4"
   )
   public void setMaxWorkers(int workers) {
-    if (workers > 0) {
+    int availableProcessors = Runtime.getRuntime().availableProcessors();
+    int prevWorkers = getMaxWorkers();
+    if (workers > availableProcessors) {
+      maxWorkers = availableProcessors;
+    }
+    else if (workers > 0 && workers != maxWorkers) {
       maxWorkers = workers;
     }
+    if (prevWorkers != maxWorkers) {
+      tileQueue = new LimitedQueue<Runnable>(maxWorkers);
+    }
   }
 
   /**
@@ -332,7 +357,8 @@ public void setMaxWorkers(int workers) {
   @Option(
       names = "--rgb",
       description = "Attempt to write channels as RGB; " +
-                    "channel count must be a multiple of 3"
+                    "channel count must be a multiple of 3",
+      defaultValue = "false"
   )
   public void setRGB(boolean isRGB) {
     rgb = isRGB;
@@ -342,13 +368,19 @@ public void setRGB(boolean isRGB) {
    * @return path to output data
    */
   public String getOutputPath() {
+    if (outputFilePath == null) {
+      return null;
+    }
     return outputFilePath.toString();
   }
 
   /**
    * @return path to input data
    */
   public String getInputPath() {
+    if (inputDirectory == null) {
+      return null;
+    }
     return inputDirectory.toString();
   }
 

src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java

@@ -661,10 +661,68 @@ public void testOptionsAPI() throws Exception {
 
     outputOmeTiff = output.resolve("output.ome.tiff");
     PyramidFromDirectoryWriter apiConverter = new PyramidFromDirectoryWriter();
+    CommandLine cmd = new CommandLine(apiConverter);
+    cmd.parseArgs();
+
+    apiConverter.setInputPath(output.toString());
+    apiConverter.setOutputPath(outputOmeTiff.toString());
+    apiConverter.setCompression(CompressionType.UNCOMPRESSED);
+    apiConverter.setRGB(true);
+    apiConverter.call();
+
+    iteratePixels();
+  }
+
+  /**
+   * Test resetting options to their default values.
+   */
+  @Test
+  public void testResetAPI() throws Exception {
+    input = fake("sizeC", "12", "rgb", "3");
+    assertBioFormats2Raw();
+
+    outputOmeTiff = output.resolve("output.ome.tiff");
+
+    // make sure default options are set
+    PyramidFromDirectoryWriter apiConverter = new PyramidFromDirectoryWriter();
+    CommandLine cmd = new CommandLine(apiConverter);
+    cmd.parseArgs();
+
+    Assert.assertEquals(apiConverter.getInputPath(), null);
+    Assert.assertEquals(apiConverter.getOutputPath(), null);
+    Assert.assertEquals(apiConverter.getCompression(), CompressionType.LZW);
+    Assert.assertEquals(apiConverter.getRGB(), false);
+    Assert.assertEquals(apiConverter.getLegacyTIFF(), false);
+    Assert.assertEquals(apiConverter.getSplitTIFFs(), false);
+
+    // override default options, as though to start a conversion
     apiConverter.setInputPath(output.toString());
     apiConverter.setOutputPath(outputOmeTiff.toString());
     apiConverter.setCompression(CompressionType.UNCOMPRESSED);
     apiConverter.setRGB(true);
+
+    // change our minds and reset the options to defaults again
+    cmd.parseArgs();
+
+    Assert.assertEquals(apiConverter.getInputPath(), null);
+    Assert.assertEquals(apiConverter.getOutputPath(), null);
+    Assert.assertEquals(apiConverter.getCompression(), CompressionType.LZW);
+    Assert.assertEquals(apiConverter.getRGB(), false);
+    Assert.assertEquals(apiConverter.getLegacyTIFF(), false);
+    Assert.assertEquals(apiConverter.getSplitTIFFs(), false);
+
+    // update options, make sure they were set, and actually convert
+    apiConverter.setInputPath(output.toString());
+    apiConverter.setOutputPath(outputOmeTiff.toString());
+    apiConverter.setCompression(CompressionType.UNCOMPRESSED);
+    apiConverter.setRGB(true);
+
+    Assert.assertEquals(apiConverter.getInputPath(), output.toString());
+    Assert.assertEquals(apiConverter.getOutputPath(), outputOmeTiff.toString());
+    Assert.assertEquals(apiConverter.getCompression(),
+      CompressionType.UNCOMPRESSED);
+    Assert.assertEquals(apiConverter.getRGB(), true);
+
     apiConverter.call();
 
     iteratePixels();