error adding image

[alfonsosaera]

Hi,

I am trying to add a high resolution image to my spe object as follows

spe <- addImg( spe, 
               sample_id = "section1", 
               image_id = "HR_img",
               imageSource = "/path/to/img/Hres.tif", 
               scaleFactor = NA_real_, 
               load = TRUE
             )

but I get this error

Error: R: width or height exceeds limit `/path/to/img/Hres.tif' @ error/cache.c/OpenPixelCache/3909

Thanks for your help!

Alfonso

[drighelli]

Hi Alfonso @alfonsosaera,

thanks for notifying us about this, but it seems related to the magick library, which seems to have a caching limit on the images it loads. And we depend on magick for the image loading in the class.

How big is your image? (WxH and in Mb/Gb?)

Reference topic from the internet: https://processwire.com/talk/topic/25280-width-or-height-exceeds-limit-in-openpixelcache3911/

[alfonsosaera]

Thanks for the answer @drighelli

The image is prety big, 2GB (20045 x 18433). Is it possible to increase the limit of the magick library?

Thanks

[drighelli]

I really don't know, but maybe this stack overflow thread could help

https://unix.stackexchange.com/questions/329530/increasing-imagemagick-memory-disk-limits

[alfonsosaera]

Thanks again for your reply.

I followed the suggestion in the answer of the stackexchange post and modified the limits of the policy.xml file.

$ identify -list resource
Resource limits:
  Width: 25KP
  Height: 25KP
  List length: unlimited
  Area: 800MP
  Memory: 4GiB
  Map: 8GiB
  Disk: 4GiB
  File: 768
  Thread: 80
  Throttle: 0
  Time: unlimited

However I still get an error when I try to add the image. The error is the wether I try to load the image in Rstudio or in the R terminal. However it is not the same error as before.

Error: rsession: cache resources exhausted `' @ error/cache.c/OpenPixelCache/4095

Now seems to talk about cache but the limits seem enough for me.

I guess it is not an R related issue since I can load the image perfectly using the tiff package.

> library(tiff)
> image <- readTIFF(img.file) # same img.file as in addImg

Any advide is highly appreciated.

Here my session info (before using tiff package)

> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggspavis_1.4.0              ggplot2_3.4.4               SpatialExperiment_1.8.1     SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0 Biobase_2.58.0             
 [7] GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0              S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0      
[13] matrixStats_1.0.0          

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11               locfit_1.5-9.8            lattice_0.22-5            digest_0.6.33             utf8_1.2.4                R6_2.5.1                 
 [7] evaluate_0.22             pillar_1.9.0              sparseMatrixStats_1.10.0  zlibbioc_1.44.0           rlang_1.1.2               rstudioapi_0.15.0        
[13] magick_2.8.1              R.utils_2.12.2            R.oo_1.25.0               Matrix_1.6-1.1            rmarkdown_2.25            BiocParallel_1.32.6      
[19] RCurl_1.98-1.12           munsell_0.5.0             beachmat_2.14.2           ggside_0.2.2              DelayedArray_0.24.0       HDF5Array_1.26.0         
[25] compiler_4.2.2            xfun_0.40                 DropletUtils_1.18.1       pkgconfig_2.0.3           htmltools_0.5.6.1         tidyselect_1.2.0         
[31] tibble_3.2.1              GenomeInfoDbData_1.2.9    edgeR_3.40.2              codetools_0.2-19          fansi_1.0.5               withr_2.5.2              
[37] dplyr_1.1.4               rhdf5filters_1.10.1       bitops_1.0-7              R.methodsS3_1.8.2         grid_4.2.2                gtable_0.3.4             
[43] lifecycle_1.0.4           magrittr_2.0.3            scales_1.2.1              dqrng_0.3.1               cli_3.6.1                 scuttle_1.8.4            
[49] XVector_0.38.0            limma_3.54.2              generics_0.1.3            DelayedMatrixStats_1.20.0 vctrs_0.6.4               Rhdf5lib_1.20.0          
[55] rjson_0.2.21              tools_4.2.2               glue_1.6.2                parallel_4.2.2            fastmap_1.1.1             yaml_2.3.7               
[61] colorspace_2.1-0          rhdf5_2.42.1              knitr_1.44   

[drighelli]

I don't know what else to suggest...

Have you also tried to restart your computer after setting the new limits?

This could be a runtime loading at the system start.

[alfonsosaera]

Thanks again for your response, @drighelli.

I am working on a shared server, so restarting is not as straightforward. What I did was reconnecting to the server via SSH and starting a new RStudio session.

In any case, I assume the system 'knows' about the settings change, as I can see them when running identify -list resource.

I hope someone has an idea on how to solve this.

[drighelli]

maybe you can also try to open an issue or write to the imagemagick authors