tests/testthat/testprepImageData.r
In briencj/growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
cat("#### Test prepImageData\n")
test_that("prepImageData", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A set of RGB images with all names using defaults
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"))
testthat::expect_equal(nrow(longi.RGB), 2)
testthat::expect_equal(ncol(longi.RGB), 35)
testthat::expect_true("Reps" %in% names(longi.RGB))
# Area RGB images with some imaging traits and copying Water traits
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"),
calcWaterUse = FALSE,
traits = list(img = c("Area", "Compactness"),
H2O = c("Weight.Before","Weight.After",
"Water.Amount")),
labsCamerasViews = list(img = c("SV1", "SV2", "TV"),
H2O = NULL))
testthat::expect_equal(nrow(longi.RGB), 2)
testthat::expect_equal(ncol(longi.RGB), 21)
#Check cameraType = FLUO and keepCameraType
raw.FLUO.dat <- suppressWarnings(importExcel(file = "./data/rawFLUOdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE,
cameraType = "FLUO",
keepCameraType = TRUE))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("Area.FLUO_SV1", "Area.FLUO_SV2")))
raw.FLUO.dat <- rbind(raw.FLUO.dat, raw.FLUO.dat)
longi.FLUO <- prepImageData(data = raw.FLUO.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"),
traits = list(all = "Area"),
labsCamerasViews = list(all = c("FLUO_SV1", "FLUO_SV2")))
testthat::expect_equal(nrow(longi.FLUO), 2)
testthat::expect_equal(ncol(longi.FLUO), 18)
testthat::expect_lt(abs(longi.FLUO$PSA[1] - 13.43), 1e-02)
testthat::expect_lt(abs(longi.FLUO$PSA.FLUO_SV1[1] - 6.41), 1e-02)
camview.labels <- c("SF0", "SL0", "SU0", "TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0",
"RGB_Side_Upper_0", "RGB_TV_0")
#Test name change with move to suffix and supply characters instead of lists
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = "Area",
labsCamerasViews = camview.labels)
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.SF0[1] - 1.18), 1e-02)
#Test name change with move to suffix and pass through just the names to retain
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0"),
labsCamerasViews = NULL)
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.SF0[1] - 1.18), 1e-02)
#Test remove cameraType with move to suffix
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
cameraType = "RGB",
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.Side_Far_0", "Area.Side_Lower_0", "Area.Side_Upper_0",
"Area.TV_0") %in% names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = list(t = "Area"),
labsCamerasViews = list(c = c("Side_Far_0", "Side_Lower_0",
"Side_Upper_0", "TV_0")))
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.Side_Far_0[1] - 1.18), 1e-02)
})
cat("#### Test prepImageData Replicates\n")
test_that("prepImageData Replicates", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A set of RGB images with all names using defaults
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB.Rep <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment", "Replicate"))
testthat::expect_equal(nrow(longi.RGB.Rep), 2)
testthat::expect_equal(ncol(longi.RGB.Rep), 35)
testthat::expect_true(!("Reps" %in% names(longi.RGB.Rep)))
testthat::expect_true(is.factor(longi.RGB.Rep$Replicate))
longi.RGB.Rep <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment"))
testthat::expect_equal(nrow(longi.RGB.Rep), 2)
testthat::expect_equal(ncol(longi.RGB.Rep), 34)
testthat::expect_true(!("Reps" %in% names(longi.RGB.Rep)))
testthat::expect_true(!("Replicate" %in% names(longi.RGB.Rep)))
#Test when no Replicate in data.frame
tmp <- raw.RGB.dat[, -match("Replicate", names(raw.RGB.dat))]
testthat::expect_error(
longi.RGB.Rep <- prepImageData(data = tmp,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment", "Replicate")),
regexp = "The following variables are not present in data: Replicate")
})
cat("#### Test prepImageData exampleData\n")
test_that("prepImageData exampleData", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
longi.dat <- prepImageData(data=raw.dat,
traits= list(all = "Area"),
labsCamerasViews = list(all = NULL),
potIDcolumns = c("Genotype.ID", "Treatment.1", "Replicate" ),
smarthouse.lev=1)
testthat::expect_true(all(c("Genotype.ID", "Treatment.1", "Replicate" ) %in% names(longi.dat)))
testthat::expect_true(!("Reps" %in% names(longi.dat)))
testthat::expect_true(!("Treatment.2" %in% names(longi.dat)))
})
briencj/growthPheno documentation built on April 14, 2025, 6:17 p.m.
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cat("#### Test prepImageData\n")
test_that("prepImageData", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A set of RGB images with all names using defaults
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"))
testthat::expect_equal(nrow(longi.RGB), 2)
testthat::expect_equal(ncol(longi.RGB), 35)
testthat::expect_true("Reps" %in% names(longi.RGB))
# Area RGB images with some imaging traits and copying Water traits
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"),
calcWaterUse = FALSE,
traits = list(img = c("Area", "Compactness"),
H2O = c("Weight.Before","Weight.After",
"Water.Amount")),
labsCamerasViews = list(img = c("SV1", "SV2", "TV"),
H2O = NULL))
testthat::expect_equal(nrow(longi.RGB), 2)
testthat::expect_equal(ncol(longi.RGB), 21)
#Check cameraType = FLUO and keepCameraType
raw.FLUO.dat <- suppressWarnings(importExcel(file = "./data/rawFLUOdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE,
cameraType = "FLUO",
keepCameraType = TRUE))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("Area.FLUO_SV1", "Area.FLUO_SV2")))
raw.FLUO.dat <- rbind(raw.FLUO.dat, raw.FLUO.dat)
longi.FLUO <- prepImageData(data = raw.FLUO.dat,
timeAfterStart = "Time.after.Plantind..d.",
idcolumns = c("Genotype.ID", "Treatment"),
traits = list(all = "Area"),
labsCamerasViews = list(all = c("FLUO_SV1", "FLUO_SV2")))
testthat::expect_equal(nrow(longi.FLUO), 2)
testthat::expect_equal(ncol(longi.FLUO), 18)
testthat::expect_lt(abs(longi.FLUO$PSA[1] - 13.43), 1e-02)
testthat::expect_lt(abs(longi.FLUO$PSA.FLUO_SV1[1] - 6.41), 1e-02)
camview.labels <- c("SF0", "SL0", "SU0", "TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0",
"RGB_Side_Upper_0", "RGB_TV_0")
#Test name change with move to suffix and supply characters instead of lists
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = "Area",
labsCamerasViews = camview.labels)
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.SF0[1] - 1.18), 1e-02)
#Test name change with move to suffix and pass through just the names to retain
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0"),
labsCamerasViews = NULL)
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.SF0[1] - 1.18), 1e-02)
#Test remove cameraType with move to suffix
raw.19.dat <- suppressWarnings(importExcel(file = "./data/raw19datarow.csv",
individualId = "Snapshot.ID.Tags",
startTime = "06/10/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
cameraType = "RGB",
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.Side_Far_0", "Area.Side_Lower_0", "Area.Side_Upper_0",
"Area.TV_0") %in% names(raw.19.dat)))
raw.19.dat <- rbind(raw.19.dat, raw.19.dat)
longi.19 <- prepImageData(data = raw.19.dat,
individualId = "Snapshot.ID.Tags",
idcolumns = c("Plant.Species", "Mycorrhiza", "Zn"),
calcWaterUse = FALSE,
traits = list(t = "Area"),
labsCamerasViews = list(c = c("Side_Far_0", "Side_Lower_0",
"Side_Upper_0", "TV_0")))
testthat::expect_equal(nrow(longi.19), 2)
testthat::expect_equal(ncol(longi.19), 17)
testthat::expect_lt(abs(longi.19$PSA[1] - 6.73), 1e-02)
testthat::expect_lt(abs(longi.19$PSA.Side_Far_0[1] - 1.18), 1e-02)
})
cat("#### Test prepImageData Replicates\n")
test_that("prepImageData Replicates", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
# A set of RGB images with all names using defaults
raw.RGB.dat <- suppressWarnings(importExcel(file = "./data/rawRGBdatarow.csv",
timeAfterStart = "Time.after.Plantind..d.",
startTime = "09/01/2017 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
plotImagetimes = FALSE))
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.SV1", "Area.SV2", "Area.TV")))
raw.RGB.dat <- rbind(raw.RGB.dat, raw.RGB.dat)
longi.RGB.Rep <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment", "Replicate"))
testthat::expect_equal(nrow(longi.RGB.Rep), 2)
testthat::expect_equal(ncol(longi.RGB.Rep), 35)
testthat::expect_true(!("Reps" %in% names(longi.RGB.Rep)))
testthat::expect_true(is.factor(longi.RGB.Rep$Replicate))
longi.RGB.Rep <- prepImageData(data = raw.RGB.dat,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment"))
testthat::expect_equal(nrow(longi.RGB.Rep), 2)
testthat::expect_equal(ncol(longi.RGB.Rep), 34)
testthat::expect_true(!("Reps" %in% names(longi.RGB.Rep)))
testthat::expect_true(!("Replicate" %in% names(longi.RGB.Rep)))
#Test when no Replicate in data.frame
tmp <- raw.RGB.dat[, -match("Replicate", names(raw.RGB.dat))]
testthat::expect_error(
longi.RGB.Rep <- prepImageData(data = tmp,
timeAfterStart = "Time.after.Plantind..d.",
potIDcolumns = c("Genotype.ID", "Treatment", "Replicate")),
regexp = "The following variables are not present in data: Replicate")
})
cat("#### Test prepImageData exampleData\n")
test_that("prepImageData exampleData", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(growthPheno)
data(exampleData)
longi.dat <- prepImageData(data=raw.dat,
traits= list(all = "Area"),
labsCamerasViews = list(all = NULL),
potIDcolumns = c("Genotype.ID", "Treatment.1", "Replicate" ),
smarthouse.lev=1)
testthat::expect_true(all(c("Genotype.ID", "Treatment.1", "Replicate" ) %in% names(longi.dat)))
testthat::expect_true(!("Reps" %in% names(longi.dat)))
testthat::expect_true(!("Treatment.2" %in% names(longi.dat)))
})
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