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tlnagy / OMETIFF.jl

I/O operations for OME-TIFF files in Julia
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Broken JSON metadata blocks file loading #98

Open tlnagy opened 2 years ago

tlnagy commented 2 years ago

I need to thoroughly diagnose this, but I have multiple MicroManager images that have broken embedded JSON comments that cause the loading to come to a screeching halt at

https://github.com/tlnagy/OMETIFF.jl/blob/7134699511ba12864a3b1a3b74331f40636e8f1c/src/files.jl#L200

Examples (for later reference) include

/mnt/eurekapool/data/2022/220720_fxm_collagen_minimalprocess/exp2_collagen_fxm_chemotaxis_1/exp2_collagen_fxm_chemotaxis_1_MMStack.ome.tif

While the longer term fix is clearly to identify why this is happening, the shorter term fix is to abort and throw a warning. This is solely for nice-to-have metadata and is fine if it can't be read.