Convert JND distances into perceptually-corrected Cartesian coordinates

Converts a coldist() output into Cartesian coordinates that are perceptually-corrected (i.e. noise-weighted Euclidean distances)

jnd2xyz(
  coldistres,
  center = TRUE,
  rotate = TRUE,
  rotcenter = c("mean", "achro"),
  ref1 = "l",
  ref2 = "u",
  axis1 = c(1, 1, 0),
  axis2 = c(0, 0, 1)
)

Arguments

coldistres: (required) the output from a coldist() call.
center: logical indicating if the data should be centered on its centroid (defaults to TRUE).
rotate: logical indicating if the data should be rotated (defaults to TRUE).
rotcenter: should the vectors for rotation be centered in the achromatic center ("achro") or the data centroid ("mean", the default)?
ref1: the cone to be used as a the first reference. May be NULL (for no first rotation in the 3-dimensional case) or must match name in the original data that was used for coldist(). Defaults to 'l'.
ref2: the cone to be used as a the second reference. May be NULL (for no first rotation in the 3-dimensional case) or must match name in the original data that was used for coldist(). Defaults to 'u'. (only used if data has 3 dimensions).
axis1: A vector of length 3 composed of 0's and 1's, with 1's representing the axes (x, y, z) to rotate around. Defaults to c(1, 1, 0), such that the rotation aligns with the xy plane (only used if data has 2 or 3 dimensions). Ignored if ref1 is NULL (in 3-dimensional case only)
axis2: A vector of length 3 composed of 0's and 1's, with 1's representing the axes (x, y, z) to rotate around. Defaults to c(0, 0, 1), such that the rotation aligns with the z axis (only used if data has 3 dimensions). Ignored if ref2 is NULL (in 3-dimensional case only)

References

Pike, T.W. (2012). Preserving perceptual distances in chromaticity diagrams. Behavioral Ecology, 23, 723-728.

Maia, R., White, T. E., (2018) Comparing colors using visual models. Behavioral Ecology, ary017 doi:10.1093/beheco/ary017

Author

Rafael Maia rm72@zips.uakron.edu

Examples

# Load floral reflectance spectra
data(flowers)

# Estimate quantum catches visual phenotype of a Blue Tit
vis.flowers <- vismodel(flowers, visual = 'bluetit')

# Estimate noise-weighted colour distances between all flowers 
cd.flowers <- coldist(vis.flowers)
#> Quantum catch are relative, distances may not be meaningful
#> Calculating noise-weighted Euclidean distances

# Convert points to Cartesian coordinates in which Euclidean distances are 
# noise-weighted.
jnd2xyz(cd.flowers)
#>                                      x          y           z
#> Goodenia_heterophylla      1.312355137 -5.3667601   6.8629524
#> Goodenia_geniculata       -0.648798700 -2.5312331  -6.5456726
#> Goodenia_gracilis         -4.834850372 10.6831212 -22.9236622
#> Xyris_operculata           3.150779009 -1.0781817  -2.8997962
#> Eucalyptus_sp             -0.082973918 -3.1963203   3.1550303
#> Faradaya_splendida        -1.266831951  0.4892355  -2.8528294
#> Gaultheria_hispida         2.274592892 -3.9525120  -1.1742262
#> Geitonoplesium_cymosum     8.033650770 -6.9198494   8.2932612
#> Euryomyrtus_ramosissima   -2.010687966 -0.3710342   4.6922247
#> Genista_linifolia         -0.617218669 -1.7069294  -2.1501789
#> Genista_monspessulana     -0.202733928 -3.0304197  -2.4820412
#> Geranium_sp                7.705016804  6.7723067  10.8297259
#> Glycine_clandestina       -0.172096284 -2.6365121  -4.2701064
#> Gompholobium_ecostatum_1   2.342604074  0.1315023   5.5688334
#> Gompholobium_ecostatum_2  -0.394030123 -2.0067259  -5.3306567
#> Gompholobium_grandiflorum -3.043177182  4.4548815  -6.5433920
#> Gompholobium_huegelii      0.731726587 -1.7597445   6.1230907
#> Gompholobium_virgatum      1.595663823 -1.1755990   5.9025137
#> Gonocarpus_humilis         0.047486608 -3.7116414  -2.6939291
#> Gonocarpus_teucrioides    -0.143737261 -2.1236747   2.1280934
#> Hibbertia_obtusifolia     -0.546715949 -1.3648630  -2.0026397
#> Zieria_arborescens        -4.374219169  8.9888446   8.7021306
#> Goodenia_lanata           -4.221201078  7.4641726 -12.6997701
#> Goodenia_ovata            -3.131626826 10.5294641   9.6861976
#> Goodenia_rotundifolia      2.743882379 -6.2826784   6.1909786
#> Grevillea_buxifolia        2.422158828 -3.4693196   1.9123426
#> Grevillea_steiglitziana   -4.435969376  5.1580526  -1.1327863
#> Grevillea_oleoides        -0.165755432 -3.0178116  -4.1570956
#> Gymnostachys_anceps       -4.457785440  9.9350339  -9.8694685
#> Hakea_actites              1.020732338 -6.3835620   8.4297774
#> Hardenbergia_violaceae    -1.543741054  0.4977253  -3.4332417
#> Hibbertia_acicularis      -0.009957462 -3.4147937   1.9458170
#> Hibbertia_bracteata        7.213297113 -2.2921695   1.6605064
#> Hibbertia_empetrifolia    -3.739762049  8.0698186   8.8247528
#> Hibbertia_procumbens       0.056155445 -3.3090457  -0.3154626
#> Hibbertia_linearis        -0.606231617 -2.0727778  -7.4312733