Fix DICOM export in ImageJ

[melissalinkert]

See https://forum.image.sc/t/exporting-a-dicom-stack/99400/6

I was able to reproduce the exception in that thread using ImageJ + Bio-Formats 7.3.1 by selecting File > Open Samples > Organ of Corti..., then Plugins > Bio-Formats > Bio-Formats Exporter and saving to a file with the .dcm extension.

With this change, the same test should result in a converted .dcm file (with no exception) that can be re-opened.

[imagesc-bot]

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/exporting-a-dicom-stack/99400/8

[sbesson]

Using the current release JARS (7.3.1) shipped in the Java-8 distribution, I was able to reproduce the exception described in the PR while exporting the sample file as a DICOM.

Using the JARs built from this branch and replacing them in my local distribution, the same sample file exports successfully using the exporter and can be reopened with the plugin.

Testing the export of a few other sample files, I came across another NPE using ``File > Open Samples > Cardio (RGB DICOM)` and selecting the Bio-Formats exporter to create a DICOM

java.lang.NullPointerException
	at loci.formats.out.DicomWriter.setId(DicomWriter.java:1057)
	at loci.formats.FormatWriter.changeOutputFile(FormatWriter.java:123)
	at loci.plugins.out.Exporter.run(Exporter.java:815)
	at loci.plugins.LociExporter.run(LociExporter.java:75)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:246)
	at ij.IJ.runPlugIn(IJ.java:210)
	at ij.IJ.runPlugIn(IJ.java:199)
	at loci.plugins.shortcut.ShortcutPanel$1.run(ShortcutPanel.java:189)
	Suppressed: java.lang.NullPointerException
		at loci.formats.out.DicomWriter.writeIFDs(DicomWriter.java:2008)
		at loci.formats.out.DicomWriter.close(DicomWriter.java:1402)
		at loci.plugins.out.Exporter.run(Exporter.java:343)
		... 7 more

Is that something we also want to fix as part of this PR?

[melissalinkert]

Testing the export of a few other sample files, I came across another NPE using ``File > Open Samples > Cardio (RGB DICOM)` and selecting the Bio-Formats exporter to create a DICOM

ab8234f is one way to handle, but open to other ideas.

[sbesson]

ab8234f is one way to handle, but open to other ideas.

No objections to this approach from my side. The proposal is very similar to glencoesoftware/omero-ms-image-region#99 which was addressing a very similar use case. In the same spirit, could the private method handle separately the null case from the unsupported length units case and log a warning level statement in the latter case to communicate that metadata is lost on conversion?

[sbesson]

Successfully tested by exporting a few ImageJ samples (Cardio (RGB DICOM), CT (16-bit DICOM), Organ of Corti (4D stack)) as DICOM and rereading them in Fiji modified with the JARs built from this PR.

Noticed that if all DICOM files are exported in the same folder, the initialization fails as I assume the reader tries to read multiple DICOM files in the same directory. But this is the current behavior and was not introduced by this PR