Error using extract vignettes to prediction folder

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Error using extract vignettes to prediction folder

Post  msutor on Tue Jun 09, 2009 9:23 pm

I have just upgraded to Version 6.11--the View vignettes error I reported earlier is fixed, thanks Marc. I am experiencing a new error. When I attept to extract vignettes to the prediction folder (utilizing my results from Plankton Identifier), I get the following message while Zooprocess is attempting to open what I believe is the vis1 zipped file in the work folder.

Zip Decoder
java.lang.NullPointerException

I do have Image J version 1.41o, perhaps there is something else I need to ensure if upgraded on the computer? Thanks again

Malinda

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Error extracting vignettes for Plankton identifier

Post  picheral on Fri Jun 12, 2009 6:45 pm

Dear Malinda,
I never got this error message when I extracted the vignettes.
Did you change any of the vignette quality settings ?
Can you try it again keeping the default parametres ?
I will check again this using large frame images as you are probably doing. Can you confirm that you are using these large images ?
Regards
Marc P.

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Re: Error using extract vignettes to prediction folder

Post  msutor on Sun Jun 14, 2009 5:27 pm

Marc,

I am using an image that was scanned with the large frame. It is actually the image that you scanned at the SCOR workshop. I have looked at the log to confirm the scan area and the image resolution, and it is confirmed as the large frame, and I assume that it is a 2400 dpi image. I am not certain looking at the log file as the scan resolution is = 3. Can you confirm that a value of 3 means that the image was scanned at 2400 dpi? Or perhaps there is somewhere else I should look to confirm the raw scan image resolution.

I have been using the default parameters when I attempt to extract the vignettes. The one other piece of information I can give you is the portion of the error that I can read in the Zooscan log window (I am unable to increase the size of the window to read the full message and the log file that is saved only has the name of the image file listed and no other text). The message reads

java.io.EOFException: Unexpected end of ZLIB input........

This may very well be operator error, but I can't quite find what I might be doing incorrectly. Thank you for your help!

Malinda

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Zlib error in ImageJ and Zooprocess

Post  picheral on Sun Jun 14, 2009 5:45 pm

Dear Malinda,
The Zlib error occurs when trying to open a corrupted zip archive...
Can you please try to open manually the vis1.zip images that makes the error ? Try then to extract it manually ?
You can also drag the vis1.zip file to ImageJ. It will be openned automatically if the zip archive is OK.
If you experience any problem doing one of these tests, the zipped image is corrupted ! Delete it and reprocess the sample (process in batch using defaults settings). Try then again the extract vignettes tool.
Regards
Marc P.

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Re: Error using extract vignettes to prediction folder

Post  msutor on Fri Jun 19, 2009 8:10 pm

Marc,

Thank you for the information. The problem was indeed a corrupt zip file. I am still a little perplexed as I was able to successfully extract vignettes for use in Plankton Identifier, but I got the error when I tried to extract vignettes to the predictions and vis folders utilizing the results I had generated from Plankton Identifier. Is the same zip file used for all vignette extraction tools? Thank you

Malinda

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Re: Error using extract vignettes to prediction folder

Post  vatansever223 on Wed Nov 03, 2010 8:12 am

Can you please try to open manually the vis1.zip images that makes the error ? Try then to extract it manually ?

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extract vignettes to prediction or validation error

Post  clementine on Fri Mar 01, 2013 1:24 pm

Hi zooscan users,

I'm a new user and I have a problem when I try to "extract vignettes in folders according to prediction or validation".

First, I created a new project and I scanned backgrounds and samples (10) with the 4800 dpi resolutions, without problem. Then, I had converted and processed in batch mode during the night, without problem too. I used Plankton identifier to realise prediction, I retrieved a .txt in the prediction folder, so I copied and pasted this .txt into the Pid_results, wihtout errors (I have choosen the Spv method learning 4).

But when I used ImageJ to extract the vignettes, I chose "extract PREDICTED files from "Pid_results" folder" and the first .txt created and Image resolution 4800 but I obtained this error :

"resolution differs from settings in files :
blabla.txt file resolution: 4800.0"

I don't understand where the problem is, I checked the config file of the project, It's a 4800 dpi resolution, so I don't understand.

Any information you could provide would be greatly appreciated. Thanks!

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Re: Error using extract vignettes to prediction folder

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