fetch mesh from CATMAID

artxz commented 5 years ago

catmaid_get_volume()gives an error when the argument is, instead of id, character name:

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 559, 638

Also the first example in the function's documentation, v375=catmaid_get_volume(375), seems outdated (couldn't find matching volume with id = 375)

jefferis commented 5 years ago

Hi @artxz

can you check what version of the catmaid package you have? You could paste the result of devtools::session_info()
can you confirm the exact command that failed when you were requesting a volume by name rather than id?
can you confirm which server you are using?
I will fix the example – using numeric ids is not a great Idea because they can indeed change.

artxz commented 5 years ago

Session info ---------------------------------------------------------------------------------------------------------------------------------------------------------------- setting value
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language (EN)
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tz America/New_York
date 2019-07-31
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callr 3.2.0 2019-03-15 [1] CRAN (R 3.4.4)
catmaid 0.9.8 2019-04-26 [1] Github (jefferis/rcatmaid@a720f81)
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This fails with the error in the first post catmaid_get_volume("v14.neuropil")

catmaid.server="https://neuropil.janelia.org/tracing/fafb/v14"

jefferis commented 5 years ago

Thanks. There is an updated version, so I recommend installing that as usual. I note that your version of R is starting to get old (3.4.2) but I don't know of a reason why that should be a problem.

Can you give me the result of traceback() because I cannot reproduce your error with catmaid_get_volume("v14.neuropil") (It works perfectly for me).

Finally with the latest version of the package

> v375=catmaid_get_volume(375)
 Error: catmaid_get_volume of type: ValueError
  Could not find volume 375

already gives a better error.

artxz commented 5 years ago

Thanks @jefferis !

The traceback() result is very long, more the 1000 lines. I think i'll try updating the packages. If the error persists i'll somehow send the traceback() result.

jefferis commented 5 years ago

OK. You can attach the traceback as a text file by drag and drop.

jefferis commented 5 years ago

I'm closing this because it seems to have been fixed by an upgrade.

natverse / rcatmaid

fetch mesh from CATMAID #133