OMEPyramidWriter and ConvertCommand improvements

Fixes for
* qupath#857
* qupath#858
This introduces the ability to write some other file formats using OMEPyramidWriter.
It also adds the ability to specify --big-tif with the convert-ome command.

CHANGELOG.md

@@ -17,7 +17,10 @@ List of bugs fixed:
 * 'Automate -> Show workflow command history' displays empty workflow (https://github.com/qupath/qupath/pull/851)
 * Extensions are sometimes loaded too late when running command line scripts (https://github.com/qupath/qupath/issues/852)
 * ICC Profiles could not be set in the viewer (unused preview feature, https://github.com/qupath/qupath/pull/850)
-* convert-ome command doesn't report when it is finished (https://github.com/qupath/qupath/issues/859)
+* Image writing fixes, including
+  * convert-ome command doesn't report when it is finished (https://github.com/qupath/qupath/issues/859)
+  * OMEPyramidWriter ignores file extension to always write ome.tif (https://github.com/qupath/qupath/issues/857)
+  * OMEPyramidWriter logic for bigtiff can fail for image pyramids (https://github.com/qupath/qupath/issues/858)
 
 ### Dependency updates
 * JavaFX 17.0.1

qupath-extension-bioformats/src/main/java/qupath/lib/images/writers/ome/ConvertCommand.java

@@ -43,7 +43,6 @@
 import qupath.lib.images.servers.bioformats.BioFormatsServerBuilder;
 import qupath.lib.images.writers.ome.OMEPyramidWriter.Builder;
 import qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType;
-import qupath.lib.regions.RegionRequest;
 
 /**
  * Allows command line option to convert an input image to OME-TIFF
@@ -81,6 +80,10 @@ public class ConvertCommand implements Runnable, Subcommand {
 			"Each pyramidal level is scaled down by the specified factor (> 1)."})
 	private double pyramid;
 
+	@Option(names = {"--big-tiff"}, defaultValue = Option.NULL_VALUE, description = {"Request to write a big tiff, which is required when writing a TIFF images > 4GB.",
+			"Default is to automatically decide based on image size. Choose --big-tiff=false to force a non-big-tiff to be written."})
+	private Boolean bigTiff;
+
 	@Option(names = {"--tile-size"}, defaultValue = "-1", description = "Set the tile size (of equal height and width).")
 	private int tileSize;
 
@@ -170,6 +173,9 @@ public void run() {
 					.tileSize(tileWidth, tileHeight)
 					.parallelize(parallelize);
 
+			if (bigTiff != null)
+				builder = builder.bigTiff(bigTiff.booleanValue());
+
 			// Make pyramidal, if requested
 			if (downsample < 1)
 				downsample = server.getDownsampleForResolution(0);
@@ -239,7 +245,7 @@ else if (tStart > tEnd) {
 				}
 			}
 
-			builder.build().writePyramid(outputFile.getPath());
+			builder.build().writeSeries(outputFile.getPath());
 
 			long duration = System.currentTimeMillis() - startTime;
 			logger.info(String.format("%s written in %.1f seconds", outputFile.getAbsolutePath(), duration/1000.0));