Conversion of image with uneven dimensions fails #139
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Thanks for reporting this, @korseby. The error messages you are seeing mean that blosc is either not installed or not found. #101 (comment) and the |
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Hi @melissalinkert , blosc is installed and bioformats2raw is working as expected for other files. This time I used a tiff-file. Below is the full error message: |
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The latest output shows several different things going wrong. I can reproduce the The various The blosc errors may be a result of the |
melissalinkert
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Mar 15, 2022
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I am using the default recommended setting for blosc: The Would it make a difference in using a different Java version? What version would you recommend? |
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At this point, if you can send the TIFF file that would be helpful. If I understand correctly, it was converted from the JPEG referenced in #138? If so, it would also help to have the original JPEG and the exact command used to convert from JPEG to TIFF. If you need somewhere to upload files, we suggest Zenodo. ome/bioformats#3796 proposes a fix for the |
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Can you try this file? It is "just" a photo of the voucher of the specimen. The data will be uploaded on IDR soon. https://www.korseby.net/riccia_sorocarpa_voucher_specimen1.zip |
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Thanks for sending the files, @korseby. I am able to convert both of these files, as well as a pattern file that only references On Linux, with Java 11 and blosc installed according to the readme, bioformats2raw 0.4.0 "just works" with no errors or warnings. Since you're using a Mac, please check whether you have an M1 or not. The If you don't have an M1, I would just double-check that On an M1 Mac, I was able to reproduce the errors in #139 (comment), and these steps seemed to solve it:
I'm still confused how you were able to convert other files without seeing blosc errors, assuming all conversions were done on the same machine. Can you clarify what kind of Mac you have, and whether the working conversions were done somewhere else? |
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Hi, I really hope that the 14 TB I just finished uploading for almost 3 months to IDR were not pointless. We checked a few generated ome.tiff files and they were fine even with all the blosc errors. ;) Let's take this step by step. I am still on a Mac Pro. I installed Java 11 and with that version I am unable to convert any file. See below. With the patch(es) you have applied, do I need to recompile the entire |
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Thanks for the additional info, you can ignore everything I said above about M1 Macs. This warning does not mean that the conversion failed. It is expected, and can be ignored. Is that the complete output? |
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I upgraded to the latest macOS and upgraded brew and macports. Sadly, same errors. Using When trying to process the "problematic" tiff file, same errors appear. Should I try a development version? |
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Does removing all |
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Hi @melissalinkert , I got it to work but ONLY when putting the If that is not the case, or I put the Strange thing is, why does it work for the other |
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Can you paste the output of |
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Hi, the directory looks like this: |
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OK, I think I see the problem, but just to be sure: if you copy just |
melissalinkert
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Mar 22, 2022
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Yes. That is exactly the case. Any other tiff file in that same subdirectory will also result in the error. |
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Great, that's what I would have expected. We have a proposed fix for this problem in ome/bioformats#3801, but that won't help you immediately. Three ways to work around the problem now:
The first option is what I would suggest. There is no advantage to using a pattern file that references a single file, as pattern files are meant for grouping multiple files together. |
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Okay. I can confirm that conversion works for using the TIFF files directly. I close this issue now. Thanks. :) |
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Mar 28, 2022
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Hi,
I am trying to convert a single image to ome.tiff. I tried tiff and jpeg formats but the conversion constantly fails. The image has the following properties:
I am on a Mac and this is what I am doing:
This causes the following error:
I am using this java version:
The conversion also fails for other images with similar uneven dimensions. As I am preparing a large upload to IDR, I can send you the files for testing.
Is the error in my side or is this a bug?
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