prepImageData | R Documentation |
Forms the prime traits by selecting a subset of the traits in a data.frame of
imaging data produced by the Lemna Tec Scanalyzer. The imaging traits to be retained
are specified using the traits
and labsCamerasViews
arguments. Some imaging
traits are divided by 1000 to convert them from pixels to kilopixels.
Also added are factor
s and explanatory variates that might be of use in an
analysis of the data.
prepImageData(data, cartId = "Snapshot.ID.Tag",
imageTimes = "Snapshot.Time.Stamp",
timeAfterStart = "Time.after.Planting..d.",
PSAcolumn = "Projected.Shoot.Area..pixels.",
idcolumns = c("Genotype.ID","Treatment.1"),
traits = list(all = c("Area",
"Boundary.Points.To.Area.Ratio",
"Caliper.Length", "Compactness",
"Convex.Hull.Area"),
side = c("Center.Of.Mass.Y",
"Max.Dist.Above.Horizon.Line")),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
side = c("SV1", "SV2")),
smarthouse.lev = NULL,
calcWaterUse = TRUE)
data |
A Smarthouse, Lane, Position, Weight.Before, Weight.After, Water.Amount, Projected.Shoot.Area..pixels. The defaults for the arguments to Smarthouse, Lane, Position, Weight.Before, Weight.After, Water.Amount, Projected.Shoot.Area..pixels., Area.SV1, Area.SV2, Area.TV, Boundary.Points.To.Area.Ratio.SV1, Boundary.Points.To.Area.Ratio.SV2, Boundary.Points.To.Area.Ratio.TV, Caliper.Length.SV1, Caliper.Length.SV2, Caliper.Length.TV, Compactness.SV1, Compactness.SV2, Compactness.TV, Convex.Hull.Area.SV1, Convex.Hull.Area.SV2, Convex.Hull.Area.TV, Center.Of.Mass.Y.SV1, Center.Of.Mass.Y.SV2, Max.Dist.Above.Horizon.Line.SV1, Max.Dist.Above.Horizon.Line.SV2. |
cartId |
A |
imageTimes |
A |
timeAfterStart |
A |
PSAcolumn |
A |
idcolumns |
A |
traits |
A |
labsCamerasViews |
A |
smarthouse.lev |
A |
calcWaterUse |
A |
The columns are copied from data
, except for those columns that are calculated from the columns in data
; those columns that are calculated have ‘(calculated)’ appended in the list under Value.
A data.frame
containing the columns specified by cartId
,
imageTimes
, timeAfterStart
, idcolumns
, traits
and
cameras
. The defaults will result in the following columns:
Smarthouse: factor
with levels for the Smarthouse
Lane: factor
for lane number in a smarthouse
Position: factor
for east/west position in a lane
DAP: factor
for the number of Days After Planting
xDAP: numeric for the DAP (calculated)
cartId
: unique code for each cart
imageTimes
: time at which an image was taken in POSIXct format
Hour: hour of the day, to 2 decimal places, at which the image was taken (calculated)
Reps: factor
indexing the replicates for each combination of the factor
s in idcolumns
(calculated)
idcolumns
: the columns listed in idcolumns
that have been converted to factor
s
Weight.Before: weight of the pot before watering (only if calcWaterUse
is TRUE
)
Weight.After: weight of the pot after watering (only if calcWaterUse
is TRUE
)
Water.Amount: the weight of the water added (= Water.After - Water.Before) (calculated)
WU: the water use calculated as the difference between Weight.Before for the current imaging and the Weight.After for the previous imaging (calculated unless calcWaterUse
is FALSE
)
PSA: the Projected.Shoot.Area..pixels. divided by 1000 (calculated)
PSA.SV1: the Projected.Shoot.Area from Side View 1 divided by 1000 (calculated)
PSA.SV2: the Projected.Shoot.Area from Side View 2 divided by 1000 (calculated)
PSA.TV: the Projected.Shoot.Area from Top View divided by 1000 (calculated)
Boundary.To.PSA.Ratio.SV1
Boundary.To.PSA.Ratio.SV2
Boundary.To.PSA.Ratio.TV
Caliper.Length.SV1
Caliper.Length.SV2
Caliper.Length.TV
Compactness.SV1 from Side View 1
Compactness.SV2 from Side View 2
Compactness.TV: from Top View
Convex.Hull.PSA.SV1: area of Side View 1 Convex Hull divided by 1000 (calculated)
Convex.Hull.PSA.SV2: area of Side View 2 Convex Hull divided by 1000 (calculated)
Convex.Hull.PSA.TV: Convex.Hull.Area.TV divided by 1000 (calculated)
Center.Of.Mass.Y.SV1: Centre of Mass from Side View 1
Center.Of.Mass.Y.SV2: Centre of Mass from Side View 2
Max.Dist.Above.Horizon.Line.SV1: the Max.Dist.Above.Horizon.Line.SV1 divided by 1000 (calculated)
Max.Dist.Above.Horizon.Line.SV2: the Max.Dist.Above.Horizon.Line.SV2 divided by 1000 (calculated)
Chris Brien
data(exampleData)
longi.dat <- prepImageData(data=raw.dat, smarthouse.lev=1)
longi.dat <- prepImageData(data=raw.dat, smarthouse.lev=1,
traits = list(a = "Area", c = "Compactness"),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
t = "TV"))
longi.dat <- prepImageData(data=raw.dat, smarthouse.lev=1,
traits = c("Area.SV1", "Area.SV2", "Area.TV",
"Compactness.TV"),
labsCamerasViews = NULL)
longi.dat <- prepImageData(data=raw.dat, smarthouse.lev=1,
calcWaterUse = FALSE,
traits = list(img = c("Area", "Compactness"),
H20 = c("Weight.Before","Weight.After",
"Water.Amount")),
labsCamerasViews = list(all = c("SV1", "SV2", "TV"),
H2O = NULL))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.