Error produced while loading images

[Micha Eichmann]

Hi Pete, hi guys

I got an error (see attachment) in a project I had saved in November 2016. The project includes three de-arrayed TMA slide images, cell detections, and classifications. While the first image loads and displays correctly, the other two produce the attached error when loading. The images eventually display, but without any annotations.

What could cause this?

I used the last release before the current one when saving the project for the last time. Could it be an update issue?

Thank you very much in advance for your answers!

Best,

Micha

[Pete]

Hi Micha,

Oh dear, I'm afraid it looks like the file may be corrupt/incomplete.  The crucial line in the log is

ERROR: Reached end of file...

which the stack trace shows happens when trying to read the .qpdata file.

I have seen this problem before, but not for a long time and I thought it had been fixed.  It could occur if QuPath is shut down before saving the data is complete, but under normal circumstances this shouldn't happen and I recall incorporating steps that try to reduce the risk.  Although I'm not sure in which version of QuPath I made these changes.

If you find that the problem occurs with the latest version of QuPath, and especially if you find a way to make it happen reproducibly, please do let me know.

As it is, I'm afraid that I do not know if it will be possible to recover the data from your existing files, but it is worth trying.  Your project directory should contain a 'data' subdirectory containing several files with the extension '.qpdata', and a filename dependent upon the original image name.

If you look in the directory, can you see these .qpdata files?  If so, do they have sufficiently large file sizes to suggest that they contain anything interesting?  Are any backup files present in that directory as well?

If you are able to send me any .qpdata files then I would see if I can recover data from them by modifying the file reading code.  I am not sure if this will be successful, but certainly I am happy to try.

Pete

[Micha Eichmann]

Hi Pete,

Thank you for your answer and for looking into this, I highly appreciate it!

The data folder contains the files

which I uploaded here. You were right in the VA case regarding not containing useful information.

So far, I haven't been able to reproduce the error with the updated QuPath version and it hopefully stays that way :-)

In case it's a lot of work for you, we probably better just redo the analysis!

Best,

Micha

[Pete]

Hi Micha,

Thanks for your reply - sorry for the delay in getting back to you, it took a while before I was at a computer where I could explore this.

It does look like there is nothing to recover from VA, unfortunately.

For IIIA, the main .qpdata file is indeed incomplete.  However you should be able to swap it for the previous saved version by simply removing '.backup' from the similarly-named file.

When writing a .qpdata file, QuPath first checks to see if there is any existing file with that name - if so, it keeps the old file and appends '.backup' to its name.  It then writes the new file and, if successful, deletes the one with .backup at the end.

I don't actually remember seeing a time when this was useful, because usually writing the file works ok and the .backup file is deleted.  So I'm not sure what happened in your case, but hopefully this helps to recover some of the information.

Pete