Conversion Error: Conversion from numpy array type 20 is not supported #45
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Hi @const-ae Thanks for the issue (and giving zellkonverter a go)! It definitely could be whatever is in |
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Ok, I have spent some time looking into this. First I can confirm this is an issue (using the smaller For zellkonverter there are a couple of things that need to be done:
Should be able to get at least the conversion check into the next release, not so sure about the |
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This is great. Thank you so much for your effort :) |
lazappi
added a commit
that referenced
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May 3, 2021
Centralised in a new .convert_anndata_slot() function. Related to #45.
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Ok, I've added checks that should prevent this error in the current dev version (v1.1.8) but without any conversion. I would like to be able to handle the conversion as well but I think that will require rewriting some things so might not happen for this release. |
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This is already great. Thank you for the effort :) |
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I'm having a similar issue Error is similar to OP: I did try rolling back to Zellkonverter 1.6.0 and the error is not present. Is this perhaps an anndata version issue? |
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There shouldn't be any major differences between {zellkonverter} v1.6.0 and v1.6.4. Could you please post the output with |
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Traceback on error: I can't attach the object but here's the content |
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Ok, so it seems like something to do with |
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I encountered it once as well with the cache <- BiocFileCache::BiocFileCache(ask = FALSE)
example_file <- BiocFileCache::bfcrpath(
cache, "https://ndownloader.figshare.com/files/30462915"
)
sce <- readH5AD(example_file, raw = TRUE)One approach we could try to use is to add an explicit converter along the lines of: # workaround for Error in py_ref_to_r(x) :
# Conversion from numpy array type 20 is not supported
# see https://github.com/theislab/zellkonverter/issues/45
py_to_r.numpy.ndarray <- function(x) {
disable_conversion_scope(x)
if (x$dtype$num == 20) {
np <- import("numpy", convert = TRUE)
out <-
tryCatch({
# assuming is float
x$dtype <- np$dtype("float32")
py_to_r(x)
}, error = function(e) {
warning("Could not convert numpy array type 20, skipping conversion")
NULL
})
return(out)
}
# no special handler found; delegate to next method
NextMethod()
}(This solution is 100% untested ;)) |
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Hi Luke,
I tried to load a single cell dataset from https://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples#study-summary, however I get the following error
in line
zellkonverter/R/konverter.R
Line 160 in 069239e
I assume that the problem is the COMPOUND datatype in
/varm, however I am not quite sure.I could try to provide a reduced file as the original is quite big (1,5GB), but I am not sure what is the best way to reduce the size of a h5ad file.
Best,
Constantin
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