context("importImzMl") test_that("importImzMl continuous", { expect_error(MALDIquantForeign:::.importImzMl("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny_continuous.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importImzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="imzML", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny_continuous.imzML") expect_equal(mass(s[[2]]), 1:5) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny_continuous.imzML") }) test_that("importImzMl processed", { path <- normalizePath(system.file( file.path("exampledata", "tiny_processed.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importImzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="imzML", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny_processed.imzML") expect_equal(mass(s[[2]]), 6:10) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny_processed.imzML") }) test_that("importImzMl coordinates", { path <- normalizePath(system.file( file.path("exampledata", "tiny_continuous.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, importImzMl(path, coordinates=cbind(1:2, c(1, 1)), verbose=FALSE)) expect_equal(s[1], importImzMl(path, coordinates=cbind(1, 1), verbose=FALSE)) expect_equal(s[[2]], importImzMl(path, coordinates=cbind(2, 1), verbose=FALSE)[[1]]) expect_error(importImzMl(path, coordinates=3, verbose=FALSE), "The .*coordinates.* argument has to be a matrix with two columns") expect_warning(importImzMl(path, coordinates=cbind(1:3, 2:0), verbose=FALSE), "The following rows contain invalid coordinates: 1, 3") })
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