Add reset methods for each option

[melissalinkert]

Corresponds to glencoesoftware/bioformats2raw#219

[DavidStirling]

Changes look fine, though between this and the getters/setters could I check whether the tileQueue size limit should be being adjusted when maxWorkers is changed? It currently looks like this is only set when the class is initialised.

raw2ometiff/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java

Lines 150 to 152 in 6cd57d7

	public PyramidFromDirectoryWriter() {
	tileQueue = new LimitedQueue<Runnable>(maxWorkers);
	}

[melissalinkert]

Changes look fine, though between this and the getters/setters could I check whether the tileQueue size limit should be being adjusted when maxWorkers is changed? It currently looks like this is only set when the class is initialised.

Good catch; a0dafc7 should reset tileQueue to match maxWorkers when the setter or resetter actually changes the value of maxWorkers.

[DavidStirling]

I'm a bit lost here now, how are we meant to reset values if not using the CLI?

[DavidStirling]

While cmd.parseArgs() works well as a resetter in the bioformats2raw PR, trying to call it with raw2ometiff is generating the following error:

picocli.CommandLine$MissingParameterException: Missing required parameters: '<inputPath>', '<outputPath>'
	at picocli.CommandLine$Interpreter.assertNoMissingParameters(CommandLine.java:14918)
	at picocli.CommandLine$Interpreter.validateConstraints(CommandLine.java:13653)
	at picocli.CommandLine$Interpreter.parse(CommandLine.java:13614)
	at picocli.CommandLine$Interpreter.parse(CommandLine.java:13559)
	at picocli.CommandLine$Interpreter.parse(CommandLine.java:13454)
	at picocli.CommandLine.parseArgs(CommandLine.java:1552)
	at com.glencoesoftware.convert.tasks.CreateTiff.<init>(CreateTiff.java:64)
	at com.glencoesoftware.convert.workflows.ConvertToTiff.<init>(ConvertToTiff.java:25)
	... 43 more

I can't see anything significantly different in the CLI implementation, aside from the underlying i/o variables being Path objects instead of Strings. Not sure if that could be causing it to reject.

[melissalinkert]

@DavidStirling: sorry, the build was failing quietly here due to a merge conflict, so it's likely you're seeing MissingParameterException because the relevant default value changes weren't included. f996b88 fixes the conflict and builds now pass, so see if it works after updating?

[DavidStirling]

Working now, thanks!

[sbesson]

Thanks @melissalinkert. Looks good to me and happy to move forward with this strategy together with glencoesoftware/bioformats2raw#226 in the upcoming 0.6.0 release of raw2ometiff

Before merging, could we add a simple testResetOptions unit test demonstrating and covering the usage of the API to reset options similarly to https://github.com/glencoesoftware/bioformats2raw/pull/226/files#diff-3bf686322477afd2500c0b42697eb037dd07ae3fc65e17ece2facd25bf5c6081R1997-R2035?