There is a shortage of ideas from others about the "whether" I'm afraid! From the client, one's principal clues are image dimensions and format and if there is an associated fileset. In HQL, to find the images that do not have a fileset, thus probably do have a file under the Pixels directory,
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SELECT id FROM Image WHERE fileset IS NULL
For images with filesets, for which only large enough images in certain formats will have a file under the Pixels directory, there will generally also be a Bio-Formats reader already noted for them, permitting in SQL,
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SELECT i.id, p.sizex, p.sizey, vi.value FROM image i, pixels p, fileset f, filesetjoblink fjl, uploadjob uj, uploadjob_versioninfo vi WHERE i.id = p.image AND i.fileset = f.id AND fjl.parent = f.id AND fjl.child = uj.job_id AND uj.job_id = vi.uploadjob_id AND vi.name = 'bioformats.reader'
Unfortunately, what that latter query would be in HQL, I've no idea; since the latest changes for 5.1 I do not yet know how to query the new map values' key-value pairs from HQL in this kind of situation. However, it has to be possible, even if it is best split up into multiple queries.
If you have further questions or ideas on this issue please do feel free to bounce them off us. I will make a note that we should look again at the Pixels directory issue, especially for your use case, and I'll check again if someone else can add more to this thread here.
Cheers,
Mark