tests/testthat/test-zeiss.R

In hmbotelho/htmrenamer: File Renaming Tools for High Throughput Microscopy

library(htmrenamer)
source("./helper_functions.R")
# context("renaming files and checking results - Zeiss")



test_that("Renaming Zeiss confocal files #01: T dataset", {

    # Download data
    testdir <- tempdir()
    cat("Test folder:", testdir)
    download_test_data2(testfolder = testdir,
                        zip_raw_url = "https://github.com/hmbotelho/htmrenamer_testdata/raw/master/zeiss/01_T/raw.zip",
                        zip_ren_url = "https://github.com/hmbotelho/htmrenamer_testdata/raw/master/zeiss/01_T/renamed.zip",
                        delete_zip_files = TRUE)

    # Rename files
    path_raw_img <- paste0(testdir, "/raw")
    path_infile  <- paste0(testdir, "/testplate.txt")
    rename_zeiss(sourcefolder = path_raw_img,
                 targetfolder = testdir,
                 infilepath = path_infile,
                 numrow = 8,
                 numcol = 12,
                 REGEXvalidimages = "^.*?s.*?t.*?\\.tif$",
                 REGEXscenenum = "^.*/.*_s(.*)t.*\\.tif$",
                 REGEXtimenum = "^.*/.*_s.*t(.*)\\.tif$",
                 printMessages = FALSE,
                 printFiles = FALSE,
                 printToGUI = FALSE,
                 move = FALSE)


    # Compare outputs
    path_ren_img <- paste0(testdir, "/testplate")
    path_ref_img <- paste0(testdir, "/renamed")
    mismatches <- compare_datasets(dir1 = path_ref_img,
                                   dir2 = path_ren_img,
                                   exclude_regex = "/renamer\\.log$")

    # Clean up
    if(dir.exists(path_raw_img)) unlink(path_raw_img, recursive = T)
    if(dir.exists(path_ren_img)) unlink(path_ren_img, recursive = T)
    if(dir.exists(path_ref_img)) unlink(path_ref_img, recursive = T)
    if(file.exists(path_infile)) unlink(path_infile)

    expect_identical(mismatches, character(0))
})