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b/tests/testthat/test-image.R |
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test_that("image", { |
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# get data |
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data("visium_data") |
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# get image |
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images <- vrImages(visium_data) |
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images <- vrImages(visium_data, name = "main") |
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expect_error(images <- vrImages(visium_data, name = "main2")) |
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images <- vrImages(visium_data, name = "main", channel = "H&E") |
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expect_warning(images <- vrImages(visium_data, name = "main", channel = "H&E2")) |
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# manipulate image |
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visium_data_resize <- resizeImage(visium_data, size = 400) |
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visium_data_modulate <- modulateImage(visium_data, brightness = 400) |
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# add new image |
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visium_data[["Assay1"]]@image[["new_image"]] <- vrImages(visium_data_resize) |
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# get image names |
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expect_equal(vrImageNames(visium_data), c("main", "new_image")) |
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# get main image |
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expect_equal(vrMainImage(visium_data[["Assay1"]]), "main") |
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expect_equal(vrMainSpatial(visium_data[["Assay1"]]), "main") |
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# change main image |
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vrMainImage(visium_data[["Assay1"]]) <- "new_image" |
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vrMainSpatial(visium_data[["Assay1"]]) <- "new_image" |
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expect_equal(vrMainImage(visium_data[["Assay1"]]), "new_image") |
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expect_equal(vrMainSpatial(visium_data[["Assay1"]]), "new_image") |
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# return |
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expect_equal(1,1L) |
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}) |
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test_that("import image voltron data", { |
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# get image |
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imgfile <- system.file("extdata", "DAPI.tif", package = "VoltRon") |
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# tile size |
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imgdata <- importImageData(imgfile, tile.size = 4, image_name = "main") |
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imgdata <- importImageData(imgfile, tile.size = 1, image_name = "main") |
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imgdata <- importImageData(imgfile, tile.size = 200, image_name = "main") |
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expect_equal(vrImageChannelNames(imgdata)$Spatial, "main") |
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expect_error(imgdata <- importImageData("", tile.size = 200, image_name = "main")) |
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# channel names |
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imgdata <- importImageData(imgfile, tile.size = 200, image_name = "main", channel_names = "DAPI") |
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expect_equal(vrImageChannelNames(imgdata)$Channels, "DAPI") |
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# multiple images |
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imgfile <- c(imgfile, imgfile) |
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imgdata <- importImageData(imgfile, tile.size = 4) |
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expect_equal(vrImageChannelNames(imgdata)$Channels, "channel_1,channel_2") |
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imgdata <- importImageData(imgfile, tile.size = 4, channel_names = c("DAPI", "DAPI2")) |
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expect_equal(vrImageChannelNames(imgdata)$Channels, "DAPI,DAPI2") |
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# return |
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expect_equal(1,1L) |
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}) |