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quantixedquantixed
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v0.4.0
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‎DESCRIPTION‎

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Package: TrackMateR
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Type: Package
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Title: Working with TrackMate outputs in R
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Version: 0.3.15
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Version: 0.4.0
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Authors@R:
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person(given = "Stephen J",
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family = "Royle",
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xml2,
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zoo
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Suggests:
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knitr,
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rmarkdown
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knitr,
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rmarkdown,
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testthat (>= 3.0.0)
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URL: https://quantixed.github.io/TrackMateR/
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Config/testthat/edition: 3

‎NEWS.md‎

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# TrackMateR
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# TrackMateR 0.4.0
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- Testing framework added. Bumping to 0.4.0 to reflect this major change.
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# TrackMateR 0.3.15
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- Added `convertTrackMateXML2CSV()` to convert TrackMate XML fles to csv.
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# TrackMateR 0.3.14

‎tests/testthat.R‎

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# This file is part of the standard setup for testthat.
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# It is recommended that you do not modify it.
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#
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# Where should you do additional test configuration?
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# Learn more about the roles of various files in:
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# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
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# * https://testthat.r-lib.org/articles/special-files.html
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library(testthat)
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library(TrackMateR)
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test_check("TrackMateR")

‎tests/testthat/test-readTrackMateXML.R‎

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test_that("readTrackMateXML handles non-existent file gracefully", {
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res <- tryCatch(readTrackMateXML("nonexistent.xml"), error = function(e) e)
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expect_true(is.null(res) || inherits(res, "error"))
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})
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test_that("readTrackMateXML handles wrong file suffix", {
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tmp <- tempfile(fileext = ".csv")
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file.create(tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) e)
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expect_true(is.null(res) || inherits(res, "error"))
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})
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test_that("readTrackMateXML handles XML with no tracks", {
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xml_content <- '<?xml version="1.0" encoding="UTF-8"?>
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<TrackMate>
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<Model spatialunits="pixel" timeunits="sec"/>
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<AllSpots/>
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</TrackMate>'
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tmp <- tempfile(fileext = ".xml")
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writeLines(xml_content, tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) e)
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expect_true(is.null(res) || inherits(res, "error"))
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})
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test_that("readTrackMateXML handles XML with no filtered tracks", {
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xml_content <- '<?xml version="1.0" encoding="UTF-8"?>
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<TrackMate>
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<Model spatialunits="pixel" timeunits="sec"/>
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<AllSpots/>
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<AllTracks>
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<Track TRACK_ID="0"/>
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</AllTracks>
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<FilteredTracks/>
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</TrackMate>'
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tmp <- tempfile(fileext = ".xml")
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writeLines(xml_content, tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) e)
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expect_true(is.null(res) || inherits(res, "error"))
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})
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test_that("readTrackMateXML parses valid XML correctly", {
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xml_content <- '<?xml version="1.0" encoding="UTF-8"?>
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<TrackMate>
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<Model spatialunits="micron" timeunits="sec"/>
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<AllSpots>
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<SpotsInFrame frame="0">
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<Spot ID="1" POSITION_X="10.0" POSITION_Y="20.0" POSITION_Z="0.0" POSITION_T="0.0" FRAME="0" RADIUS="2.5" QUALITY="100"/>
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<Spot ID="2" POSITION_X="15.0" POSITION_Y="25.0" POSITION_Z="0.0" POSITION_T="0.5" FRAME="1" RADIUS="2.5" QUALITY="100"/>
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</SpotsInFrame>
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</AllSpots>
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<AllTracks>
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<Track TRACK_ID="0">
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<Edge SPOT_SOURCE_ID="1" SPOT_TARGET_ID="2"/>
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</Track>
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</AllTracks>
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<FilteredTracks>
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<TrackID TRACK_ID="0"/>
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</FilteredTracks>
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</TrackMate>'
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tmp <- tempfile(fileext = ".xml")
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writeLines(xml_content, tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) { skip(paste("readTrackMateXML failed:", e$message)) })
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# result is expected to be a list: first element the data frame, second calibration
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expect_true(is.list(res))
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result <- res[[1]]
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expect_true(is.data.frame(result))
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expect_true(all(c("track", "frame", "x", "y", "z", "time") %in% names(result)))
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})
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test_that("readTrackMateXML only includes filtered tracks", {
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xml_content <- '<?xml version="1.0" encoding="UTF-8"?>
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<TrackMate>
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<Model spatialunits="micron" timeunits="sec"/>
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<AllSpots>
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<SpotsInFrame frame="0">
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<Spot ID="1" POSITION_X="10.0" POSITION_Y="20.0" POSITION_Z="0.0" POSITION_T="0.0" FRAME="0"/>
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<Spot ID="2" POSITION_X="15.0" POSITION_Y="25.0" POSITION_Z="0.0" POSITION_T="1.0" FRAME="1"/>
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<Spot ID="3" POSITION_X="100.0" POSITION_Y="200.0" POSITION_Z="0.0" POSITION_T="0.0" FRAME="0"/>
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<Spot ID="4" POSITION_X="105.0" POSITION_Y="205.0" POSITION_Z="0.0" POSITION_T="1.0" FRAME="1"/>
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</SpotsInFrame>
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</AllSpots>
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<AllTracks>
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<Track TRACK_ID="0">
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<Edge SPOT_SOURCE_ID="1" SPOT_TARGET_ID="2"/>
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</Track>
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<Track TRACK_ID="1">
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<Edge SPOT_SOURCE_ID="3" SPOT_TARGET_ID="4"/>
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</Track>
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</AllTracks>
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<FilteredTracks>
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<TrackID TRACK_ID="0"/>
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</FilteredTracks>
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</TrackMate>'
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tmp <- tempfile(fileext = ".xml")
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writeLines(xml_content, tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) { skip(paste("readTrackMateXML failed:", e$message)) })
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result <- res[[1]]
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expect_equal(nrow(result), 2)
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expect_equal(nlevels(result$track), 1)
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expect_equal(as.character(unique(result$track)), "0")
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expect_false(any(result$x > 50))
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})
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test_that("readTrackMateXML warns on duplicate track-frame combinations", {
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xml_content <- '<?xml version="1.0" encoding="UTF-8"?>
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<TrackMate>
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<Model spatialunits="micron" timeunits="sec"/>
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<AllSpots>
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<SpotsInFrame frame="0">
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<Spot ID="1" POSITION_X="10.0" POSITION_Y="20.0" POSITION_Z="0.0" POSITION_T="0.0" FRAME="0"/>
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<Spot ID="2" POSITION_X="15.0" POSITION_Y="25.0" POSITION_Z="0.0" POSITION_T="0.0" FRAME="0"/>
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</SpotsInFrame>
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</AllSpots>
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<AllTracks>
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<Track TRACK_ID="0">
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<Edge SPOT_SOURCE_ID="1" SPOT_TARGET_ID="2"/>
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</Track>
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</AllTracks>
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<FilteredTracks>
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<TrackID TRACK_ID="0"/>
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</FilteredTracks>
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</TrackMate>'
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tmp <- tempfile(fileext = ".xml")
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writeLines(xml_content, tmp)
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on.exit(unlink(tmp))
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res <- tryCatch(readTrackMateXML(tmp), error = function(e) { skip(paste("readTrackMateXML failed:", e$message)) })
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expect_output(invisible(res <- readTrackMateXML(tmp)), "duplicate")
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})

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