Shiny barfs on zyx oriented minc files

[gdevenyi]

Can't quite follow the logic in server.R, but somewhere an assumption is being made about the orientation of inputs. I can use mincPlotSliceSeries properly, but shiny fails to properly produce figures:

Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning: Error in [: subscript out of bounds
  171: getSlice
  170: mincImage
  169: FUN
  168: lapply
  167: <Anonymous>
  165: mincPlotSliceSeries
  164: renderPlot [/opt/quarantine/RMINC/1.5.2.0^minc-toolkit-1.9.16^R-3.5.0/install/RMINC/shinyRMINC/server.R#217]
  162: func
  122: drawPlot
  108: <reactive:plotObj>
   92: drawReactive
   79: origRenderFunc
   78: output$seriesPlot
    2: shiny::runApp
    1: launch_shinyRMINC

[gdevenyi]

Followup, after mincreshaping the files, shiny still fails.

What might be of relevance here is that this is 1x1x1 Human T1s.

[cfhammill]

I'm surprised, could you send me a reproducible example?

[gdevenyi]

Is a anat file + RData of the model environment sufficient?

[cfhammill]

yeah that should be fine

[gdevenyi]

User will provide tomorrow.

[cfhammill]

great, thanks.

[gdevenyi]

Full runtime error:

[gdevenyi]

https://we.tl/t-VvEv6YnudA

[gdevenyi]

.RData includes the model and the anat object loaded with mincArray(mincGetVolume).

[cfhammill]

I think I also need an empty volume with the right dimensions to use as a likeFile

[gdevenyi]

You'll have it monday!

[gdevenyi]

https://we.tl/t-9KptBZGIyS

[cfhammill]

hmm, this worked fine for me:

launch_shinyRMINC(vs, anat, anatLow = 1, anatHigh = 10
  , plotcolumns = demographics[, c("Group", "Age_MRI1", "M/F", "MR Delay")]
  , fdr = FDR)

what happens if you use:

likeVolume(vs) <- "secondlevel_template0.mnc"

before the run?

Failing that, have you tried with the develop branch? I don't think I've touched any of this code since the last release, but maybe...

EDIT: I have not.

[gdevenyi]

No change trying that.

Perhaps this is a version issue. We're on minc-toolkit 1.9.16 built from source.

[cfhammill]

Hmm, it would surprise me if the toolkit was the issue. Especially since sliceSeries works.

Could you try updating shiny? Also could you send me a screen capture of failed plot, or describe it? Is it all missing or just the anatomy or something like that.

[gdevenyi]

Re shiny:

library(shiny)
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /opt/quarantine/R/3.5.0/install/opt/microsoft/ropen/3.5.0/lib64/R/lib/libRblas.so
LAPACK: /opt/quarantine/R/3.5.0/install/opt/microsoft/ropen/3.5.0/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shiny_1.1.0          RevoUtils_11.0.0     RevoUtilsMath_11.0.0

loaded via a namespace (and not attached):
 [1] compiler_3.5.0  magrittr_1.5    R6_2.2.2        promises_1.0.1 
 [5] later_0.7.3     htmltools_0.3.6 Rcpp_0.12.17    digest_0.6.15  
 [9] xtable_1.8-2    httpuv_1.4.4.2  mime_0.5       

Looks like I have the latest version.

[gdevenyi]

Screenshot: there's an red "error subscript out of bounds" in the plot section before the broken image replaces it

[cfhammill]

And in the browser?

[gdevenyi]

Same out of bounds thing and broken display.

[gdevenyi]

Any progress here? Anything you can suggest?

[cfhammill]

Sorry lost track of this. I'm totally stumped, I can't reproduce on my system so it will be tough to debug. Any way I could ssh/vnc into your system and debug there?

[gdevenyi]

We can probably figure that out. Let me try this test data on an install from a different family of systems and see if it goes away for me too.

[cfhammill]

Any progress on this @gdevenyi?

[gdevenyi]

Last I checked it was still broken. We transitioned to mricrotome images so haven't tried shiny again. Will update things and check. I should try the VM