tests/testthat/testImportXL.r
In briencj/growthPheno: Functional Analysis of Phenotypic Growth Data to Smooth and Extract Traits
cat("#### Test importExcel arguments\n")
test_that("importXLRename", {
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")))
#Check keepCameraType
raw.RGB.dat <- 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,
keepCameraType = TRUE)
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.RGB_SV1", "Area.RGB_SV2", "Area.RGB_TV")))
#Check cameraType = FLUO
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"))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("Area.SV1", "Area.SV2")))
#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")))
#Check no cameraType and keepCameraType (can only move if can recognize camera type)
testthat::expect_warning(raw.FLUO.dat <- 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,
keepCameraType = TRUE))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("FLUO_SV1.Area", "FLUO_SV2.Area")))
#Test do nothing
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",
plotImagetimes = FALSE,
prefix2suffix = FALSE, keepCameraType = TRUE))
testthat::expect_true(all(c("RGB_Side_Far_0.Area", "RGB_Side_Lower_0.Area",
"RGB_Side_Upper_0.Area", "RGB_TV_0.Area") %in% names(raw.19.dat)))
#Test do nothing except remove cameraType
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",
prefix2suffix = FALSE,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Side_Far_0.Area", "Side_Lower_0.Area",
"Side_Upper_0.Area", "TV_0.Area") %in% names(raw.19.dat)))
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 only
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",
prefix2suffix = FALSE,
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("SF0.Area", "SL0.Area", "SU0.Area", "TV0.Area") %in%
names(raw.19.dat)))
#Test name change 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",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
#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)))
#Test name change with retain cameraType and move to suffix
camview.labels <- c("RGB_SF0", "RGB_SL0", "RGB_SU0", "RGB_TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0", "RGB_Side_Upper_0",
"RGB_TV_0")
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,
keepCameraType = TRUE,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.RGB_SF0", "Area.RGB_SL0", "Area.RGB_SU0",
"Area.RGB_TV0") %in% names(raw.19.dat)))
#Test name change with remove cameraType and move to suffix
camview.labels <- c("RGB_SF0", "RGB_SL0", "RGB_SU0", "RGB_TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0", "RGB_Side_Upper_0",
"RGB_TV_0")
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)))
})
cat("#### Test importExcel times\n")
test_that("importXLRename", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
camera.names <- c("SV1", "SV2", "TV")
names(camera.names) <- paste(c("RGB_Side_Far_0", "RGB_Side_Far_4", "RGB_TV"), "Result", sep=".")
#Cannot test xlsx files because these cannot be included in a package
#Test for csv file
#The warning occurs because the first Snaopshot.ID.Tag does not have a DAP15
testthat::expect_warning(raw.dat <- importExcel(file = "./data/0498_Rice_Plett_test.csv",
startTime = "27/02/2020 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camera.names))
testthat::expect_true(all(dim(raw.dat) == c(863, 26)))
testthat::expect_true(all(c("area.SV1", "area.SV2", "area.TV") %in% names(raw.dat)))
testthat::expect_true(all(table(raw.dat$Time.after.Planting..d.) == c(215,216,216,216)))
#Non-matching time formats is a problem for csv files
testthat::expect_warning(testthat::expect_error(
raw.dat <- importExcel(file = "./data/0498_Rice_Plett test.csv",
startTime = "2020-02-27 0:00 AM",
timeFormat = "%Y-%m-%d %H:%M",
labsCamerasViews = camera.names)))
})
briencj/growthPheno documentation built on April 14, 2025, 6:17 p.m.
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cat("#### Test importExcel arguments\n")
test_that("importXLRename", {
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")))
#Check keepCameraType
raw.RGB.dat <- 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,
keepCameraType = TRUE)
testthat::expect_true(all(names(raw.RGB.dat)[c(18,56,94)] ==
c("Area.RGB_SV1", "Area.RGB_SV2", "Area.RGB_TV")))
#Check cameraType = FLUO
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"))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("Area.SV1", "Area.SV2")))
#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")))
#Check no cameraType and keepCameraType (can only move if can recognize camera type)
testthat::expect_warning(raw.FLUO.dat <- 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,
keepCameraType = TRUE))
testthat::expect_true(all(names(raw.FLUO.dat)[c(18,54)] ==
c("FLUO_SV1.Area", "FLUO_SV2.Area")))
#Test do nothing
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",
plotImagetimes = FALSE,
prefix2suffix = FALSE, keepCameraType = TRUE))
testthat::expect_true(all(c("RGB_Side_Far_0.Area", "RGB_Side_Lower_0.Area",
"RGB_Side_Upper_0.Area", "RGB_TV_0.Area") %in% names(raw.19.dat)))
#Test do nothing except remove cameraType
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",
prefix2suffix = FALSE,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Side_Far_0.Area", "Side_Lower_0.Area",
"Side_Upper_0.Area", "TV_0.Area") %in% names(raw.19.dat)))
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 only
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",
prefix2suffix = FALSE,
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("SF0.Area", "SL0.Area", "SU0.Area", "TV0.Area") %in%
names(raw.19.dat)))
#Test name change 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",
labsCamerasViews = camview.labels,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.SF0", "Area.SL0", "Area.SU0", "Area.TV0") %in%
names(raw.19.dat)))
#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)))
#Test name change with retain cameraType and move to suffix
camview.labels <- c("RGB_SF0", "RGB_SL0", "RGB_SU0", "RGB_TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0", "RGB_Side_Upper_0",
"RGB_TV_0")
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,
keepCameraType = TRUE,
plotImagetimes = FALSE))
testthat::expect_true(all(c("Area.RGB_SF0", "Area.RGB_SL0", "Area.RGB_SU0",
"Area.RGB_TV0") %in% names(raw.19.dat)))
#Test name change with remove cameraType and move to suffix
camview.labels <- c("RGB_SF0", "RGB_SL0", "RGB_SU0", "RGB_TV0")
names(camview.labels) <- c("RGB_Side_Far_0", "RGB_Side_Lower_0", "RGB_Side_Upper_0",
"RGB_TV_0")
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)))
})
cat("#### Test importExcel times\n")
test_that("importXLRename", {
skip_if_not_installed("growthPheno")
skip_on_cran()
library(dae)
library(ggplot2)
library(growthPheno)
camera.names <- c("SV1", "SV2", "TV")
names(camera.names) <- paste(c("RGB_Side_Far_0", "RGB_Side_Far_4", "RGB_TV"), "Result", sep=".")
#Cannot test xlsx files because these cannot be included in a package
#Test for csv file
#The warning occurs because the first Snaopshot.ID.Tag does not have a DAP15
testthat::expect_warning(raw.dat <- importExcel(file = "./data/0498_Rice_Plett_test.csv",
startTime = "27/02/2020 0:00 AM",
timeFormat = "%d/%m/%Y %H:%M",
labsCamerasViews = camera.names))
testthat::expect_true(all(dim(raw.dat) == c(863, 26)))
testthat::expect_true(all(c("area.SV1", "area.SV2", "area.TV") %in% names(raw.dat)))
testthat::expect_true(all(table(raw.dat$Time.after.Planting..d.) == c(215,216,216,216)))
#Non-matching time formats is a problem for csv files
testthat::expect_warning(testthat::expect_error(
raw.dat <- importExcel(file = "./data/0498_Rice_Plett test.csv",
startTime = "2020-02-27 0:00 AM",
timeFormat = "%Y-%m-%d %H:%M",
labsCamerasViews = camera.names)))
})
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