xform_brain should not require an explicit target specification for image data

[jefferis]

Error:

xform_brain("/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd", ref=JFRC2, sample=IS2, outfile=path.expand("~/projects/Shahar/Screen/AdditionalOutputs/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd"))

Error in basename(as.character(f)) :
argument "target" is missing, with no default

OK:

xform_brain("/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd", ref=JFRC2, sample=IS2, target=JFRC2, outfile=path.expand("~/projects/Shahar/Screen/AdditionalOutputs/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd"))
Reading transformation from studylist /Library/Frameworks/R.framework/Versions/3.2/Resources/library/nat.flybrains/extdata/bridgingregistrations/JFRC2_IS2.list
WARNING: image does not have valid orientation meta information; cannot reorient.
cmd:
'/usr/local/lib/cmtk/bin/reformatx' --verbose --outfile '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --floating '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --interpolation linear --outfile '/Volumes/teraraid/flybrain/Shahar/SplitRegistration/IS2/reformatted/JFRC2_IS2_JK733SF457-1_02_warp_m0g80c8e1e-1x26r4.nrrd' --target-grid 1024,512,218:0.622088,0.622088,0.622088:0.000000,0.000000,0.000000 '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/nat.flybrains/extdata/bridgingregistrations/JFRC2_IS2.list'

(moved from natverse/nat.flybrains#30)

[jefferis]

Could do this by adding a target argument (which is sometimes ignored) or modifying ...

see http://stackoverflow.com/questions/16321760/r-change-value-of-an-argument-in-ellipsis-and-pass-ellipsis-to-the-other-functi
for how to do that.

[jefferis]

@rrbenton this is a bug that you would like closed.

[jefferis]

@mmc46 this is interesting for you as well. Do you want to check

devtools::install_github("jefferislab/nat.templatebrains@feature/auto-target")

and see if it works for your use case without having to specify target explicitly.

[mmc46]

Yes, that works!

…

On 30 Apr 2019, at 20:38, Gregory Jefferis ***@***.***> wrote: @mmc46 <https://github.com/mmc46> this is interesting for you as well. Do you want to check devtools::install_github("jefferislab/nat.templatebrains@ feature/auto-target") and see if it works for your use case without having to specify target explicitly. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#16 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOJBU3EQZOBX553N2A56N3PTCN45ANCNFSM4BR6JW4A>.