Closed BioTurboNick closed 1 year ago
Side issue - even if I do rename it, OMETIFF isn't able to load the OME XML.
BioFormats in ImageJ can load the metadata just fine.
Given that there is essentially no difference between OMETIFFs and regular TIFFs beside the presence of the OMEXML data, FileIO uses the file-ending as a crutch. We could be more flexible with checking the file endings to allow people to do something like the following:
julia> f = "colorized-1.tif" # a standard tiff
julia> img = FileIO.load(Stream{format"OMETIFF"}(open(f), f)) # Force FileIO to delegate to OMETIFF
Currently this doesn't work (EDIT: see below) because we have a secondary check at https://github.com/tlnagy/OMETIFF.jl/blob/7134699511ba12864a3b1a3b74331f40636e8f1c/src/loader.jl#L30-L32 which is quite over the top.
Could you post the error with the metadata? It's hard to diagnose without an error message or a minimal working example.
Once I merge #102 and push OMETIFF v0.4.3 out you'll be able to do:
julia> f = "rename_test.ome.tif" # a standard ome file
"rename_test.ome.tif"
julia> newf = cp(f, "rename_test.tif", force = true) # rename without ome extension
"rename_test.tif"
julia> img = FileIO.load(Stream{format"OMETIFF"}(open(newf), newf)) # force fileio to use ometiff to open it
Gray ImageMeta with:
data: 2-dimensional AxisArray{Gray{Q0f7},2,...} with axes:
:y, 1:167
:x, 1:439
And data, a 167×439 Array{Gray{Q0f7},2} with eltype ColorTypes.Gray{FixedPointNumbers.Q0f7}
properties:
Description:
Elapsed_Times: Array{Quantity{Float64, 𝐓, FreeUnits{(s,), 𝐓, nothing}}, 0}(UndefInitializer())
OMETIFF v0.4.3
is in the next round for release with the aforementioned ability to open file with alternative file endings. Please open a new issue with more details about the metadata problem that you ran into and I'll do my best to diagnose it.
Will do, thanks!
Simple question: How?
FileIO.load just sees .tif and uses TiffImages.
I don't want to rename all the files I need to open.