Posted by
Kenneth Sloan-2 on
URL: http://imagej.273.s1.nabble.com/vsi-file-corruption-Mac-tp5018990.html
This one is strange.
Environment: Mac, OS/X (may be specific to iMacs running slightly older version of OS/X, may be specific to the use of an external disk drive.
We have .vsi files which contain two series. One series is a depth stack of ~20 16bit grayscale images. The other is at lower resolution and contains 3 planes. We are using the first series.
With a well-formed .vsi file, manually running BioFormats prompts for a choice of which series to use. Running BioFormats Importer from an ImageJ java plugin, we can successfully import the correct series.
With a CORRUPTED .vsi file, manually runnint BioFormats simply opens the second series (the first one is invisible)
Running BioFormats Importer from an ImageJ java plugin produces the second series (which is not useful).
Looking at the meta-date, it appears that the CORRUPTED files contain LESS meta-data (details available to anyone who knows what to do with it).
How do the files become CORRUPTED? It seems that simply copying the file (either to another disk, or even to the same disk, will SOMETIMES corrupt the file. Some copies have been successful - but some (probably most) have produced corrupted files.
Both the well-formed and corrupted files are exactly the same length.
It looks to me as if some character in the middle of the meta-data becomes mangled.
NOTE: I have seen the corrupting AND correct copying behavior on the SAME FILE.
I’m stumped. I’ll probably try to get hex dumps of a correct and a mangled file to try to generate more clues.
Does this ring any bells? Is there a .vsi file expert out there? With some effort, I think I can provide a correct, and mangled, version of one of these files to anyone who has the necessary knowledge.
Note that this *may* be either a Mac issue, or a disk issue. As near as I can make out, all the offending copies were FROM a specific external drive, and done on one of two iMacs.
One last twist…the person who generated most of these files was German, and may have used a Mac with German settings at some point.
But…note that I have personally done two copies FROM the primary external drive TO a different external drive. One corrupted…and the second one did not. So, whatever is going on is intermittent.
It’s *possible* that there may be a way to REPAIR the damage, once done. That’s what I’ll be working on right now - comparing good and bad copies to see if there is an easy way to patch the bad copies. I’m not really optimistic about that.
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Kenneth Sloan
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Vision is the art of seeing what is invisible to others.
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