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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Segmentation Fault when using Teraconverter to create bigtiff file #22

Closed mary-alegro closed 6 years ago

mary-alegro commented 6 years ago

Hi everyone,

Teraconverter (Linux, binary package version 1.10.5) causes a segmentation fault when I use it to create a bigtiff file. My dataset has a single 2D image comprised of 988 tiles, about 17Gb. I've notice that it only happens when I'm creating a TIFF file. I've noticed, using the --verbose flag, that it crashes during file saving. I'm successfully able to create Vaa3D raw files. Moreover, Teraconverter works with TIFF if I stitch small datasets (about 80 images). What makes me think it has to do with the use o Big TIFF. I'd really appreciate any suggestion on how to overcome this issue. The command line I used is:

teraconverter -s="xml_merging.xml" -d="../output" --sfmt="TIFF (unstitched, 3D)" --dfmt="TIFF (series, 2D)" --libtiff_bigtiff

Thank you!

iannellog commented 6 years ago

2017-10-05 1:27 GMT+02:00 mary-alegro notifications@github.com:

Hi everyone,

Teraconverter (Linux, binary package version 1.10.5) causes a segmentation fault when I use it to create a bigtiff file. My dataset has single 2D image comprised of 988 tiles, about 17Gb. I've notice that it only happens when I'm creating a TIFF file. I'm successfully able to create Vaa3D raw files. Moreover, Teraconverter works with TIFF if I stitch small datasets (about 80 images). What makes me think it has to do with the use o Big TIFF. I'd really appreciate any suggestion on how to overcome this issue. The command line I used is:

teraconverter -s="xml_merging.xml" -d="../output" --sfmt="TIFF (unstitched, 3D)" --dfmt="TIFF (series, 2D)" --libtiff_bigtiff

Thank you!

I should have found the problem (but I cannot test it now). If you can rebuild the executables with CMake, could you please try to rebuild substituting the attached file in folder src/imagemanager ? Otherwise you should wait next week when we will update the repository

Best

-- Giulio

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google. it/citations?user=L-UJxIgAAAAJ

mary-alegro commented 6 years ago

Sure! Just one stupid question: where should I see the attachment?

iannellog commented 6 years ago

Sorry, I didn't realize that you cannot see the attachment on the GitHub issues. I have updated the source on GitHub with the corrected file (not tested however on images lager than 4 GB). Now, the last version of TeraStitcher is 1.10.7 and of TeraConverter is 3.1.14. Note that I have updated on GitHub the source only, the precompiled binaries have not been updated. If you can rebuild the binaries after downloading the new source, please check if the fix works with your 17 GB image. Thanks.

-- Giulio

2017-10-05 18:27 GMT+02:00 mary-alegro notifications@github.com:

Sure! Just one stupid question: where should I see the attachment?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/22#issuecomment-334519164, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1raW11MSzr7CgxB9WuPFsk4dGt5bks5spQOGgaJpZM4PuX4I .

--

Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

mary-alegro commented 6 years ago

Yay! Worked just fine! Thank you!