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niaid / image_portal_workflows

Workflows related to project previously referred to as "Hedwig"
BSD 3-Clause "New" or "Revised" License
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One 2D RGB sample file failed the processing of the Irg_2D pipeline in QA on 12/12/2023 #405

Closed NetaFG closed 10 months ago

NetaFG commented 10 months ago

Pipeline run: https://prefect1.hedwig-workflow-api.niaidqa.net/default/flow-run/a06c3900-50f4-4084-9a62-f9b39d9b7f64 Hedwig interface: https://hedwig2qa.niaid.nih.gov/sessions/U2Vzc2lvbjozMzEy/records File system: \ai-fas12.niaid.nih.gov\RMLSOHedwigQA\Projects\RTB\darrellh\kaladik2-2023-1117-Testkeyword\Protein-2023-1117-testtag-Registration_samples\ROI_Images

Sample IA_P2_S2 - failed All other three samples passed and tested using the Hedwig interface.

philipmac commented 10 months ago

see: ("ERROR : convert: no images defined `/gs1/Scratch/hedwig_qa_scratch/tmp2lmx8g0d/IA_P2_S2.tiff' @ error/convert.c/ConvertImageCommand/3235.\n -- ")

suspect input tiff file exceeds allowable input dims for convert

philipmac commented 10 months ago

input file with problem: /mnt/ai-fas12/RMLSOHedwigQA/Projects/RTB/darrellh/kaladik2-2023-1117-Testkeyword/Protein-2023-1117-testtag-Registration_samples/ROI_Images/IA_P2_S2.png

$ convert /mnt/ai-fas12/RMLSOHedwigQA/Projects/RTB/darrellh/kaladik2-2023-1117-Testkeyword/Protein-2023-1117-testtag-Registration_samples/ROI_Images/IA_P2_S2.png -define tiff:tile-geometry=128x128 -background white -alpha remove -alpha off  /gs1/Scratch/hedwig_qa_scratch/philip_t.tiff
convert: no images defined `/gs1/Scratch/hedwig_qa_scratch/philip_t.tiff' @ error/convert.c/ConvertImageCommand/3235.

info about this file:

$ identify /mnt/ai-fas12/RMLSOHedwigQA/Projects/RTB/darrellh/kaladik2-2023-1117-Testkeyword/Protein-2023-1117-testtag-Registration_samples/ROI_Images/IA_P2_S2.png

/.../IA_P2_S2.png PNG 9720x18772 9720x18772+0+0 8-bit sRGB 99.6827MiB 0.000u 0:00.000

strangely, another, bigger file, converts without issue:

$ identify /mnt/ai-fas12/RMLSOHedwigQA/Projects/RTB/darrellh/kaladik2-2023-1117-Testkeyword/Protein-2023-1117-testtag-Registration_samples/ROI_Images/IA_P2_S1.png

/.../IA_P2_S1.png PNG 9813x19261 9813x19261+0+0 8-bit sRGB 200.981MiB 0.000u 0:00.000

https://stackoverflow.com/questions/64791630/imagemagick-no-images-defined-for-output-filename

updated policy.xml

from 10KP -> 30KP

philipmac commented 10 months ago

debug convert https://gist.github.com/philipmac/555837dc5b5406af61de5e56d8b2223e

philipmac commented 10 months ago

libpng-1.5.13 error: invalid stored block lengths

this is fixed in libpng-1.6.3 on - can also be fixed with libpng's "contrib/tools/pngfix" or pngcrush

philipmac commented 10 months ago

Issue with input PNG - user recreated input file and pipeline runs without issue