CODEWITHSUNDEEP
rrasterr-raster
Rob
Rob

Reputation: 1

File not found in R raster loop

Here I am trying to import tiff files of CT images to R for analysis. I have about 250 tiff files that I am trying to analyze on a loop. The analysis starts by cropping, then thresholding, then calculating porosity based on pixel intensity values. Currently I am getting this error:

Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", : Cannot create a RasterLayer object from this file. (file does not exist) 

`library(raster)
 library(rgdal)
 library(sp)`


    `project_files <- dir("/Users/Rob/Documents/BMBT5130/Data")
    for (jj in 1:length(mget(project_files)))  {
    x[jj] <- raster(paste0(project_files[jj]))
    x1 <- crop(x, extent(800,1600,700,1600))
    x[x<=35]=0
    plot(x1)
    Porosity[jj] <- (length(x1[x1<=35]))/length(x1[x1>=0])`

The working directory is the directory used above

Sessioninfo:

R version 3.3.3 (2017-03-06) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X El Capitan 10.11.6

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] RBioFormats_0.0.30 rJava_0.9-8 EBImage_4.16.0 imager_0.40.2 magrittr_1.5 [6] plyr_1.8.4 ROI_0.2-1 rgdal_1.2-6 raster_2.5-8 sp_1.2-4 [11] tiff_0.1-5

loaded via a namespace (and not attached): [1] Rcpp_0.12.10 knitr_1.15.1 BiocGenerics_0.20.0 lattice_0.20-35 jpeg_0.1-8 [6] stringr_1.2.0 tools_3.3.3 parallel_3.3.3 grid_3.3.3 png_0.1-7 [11] registry_0.3 abind_1.4-5 bmp_0.2 purrr_0.2.2 fftwtools_0.9-8 [16] slam_0.1-40 readbitmap_0.1-4 stringi_1.1.5 locfit_1.5-9.1

Any help fixing this will be much appreciated.
Best,
Rob

Upvotes: 0

Views: 678

Answers (1)

maRtin
maRtin

Reputation: 6516

As already mentioned in the comments:

list.files("/Users/Rob/Documents/BMBT5130/Data", full.names=T, pattern="tif$")

should make your code work.

Make sure to set full.names=T to ensure that you get the entire path name and if you are working woth tif files, think about only searching files that end with "tif" (i.e. exclude tix.aux files).

Upvotes: 1

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