require(Momocs)
require(gridExtra)

lf1 <- list.files('C:/Users/Viktor Baranov/Documents/Baranov/my papers/in work/22.stratiomyomiomorpha larvae/masks stratiomyomorpha/new masks', full.names=TRUE)

#path to files
#coo <- import_jpg(lf)#import
coo <- import_jpg(lf1)#import
Out(coo)#conversion to outlines


dat=Out(coo)# outlines saved as cash object



panel(dat)#plotting outlines
#stack(dat)#stacking the shapes together

#dat %>% 
 # coo_center %>% coo_scale %>% 
  #coo_alignxax() %>% coo_slidedirection("right") %T>% 
  #print() %>% stack() #centering and un-directioning stack
b <- coo_rotate(dat[1], pi/6) # dummy example just to make it obvious
coo_plot(b)
coo_plot(coo_slidedirection(b, "up"))
coo_plot(coo_slidedirection(b, "right"))
coo_plot(coo_slidedirection(b, "left"))
coo_plot(coo_slidedirection(b, "down"))
b <- dat %>% slice(1:69) # for speed sake
stack(b)


dat %>% slice(1:69)%>%
coo_center %>% coo_scale %>% 
coo_alignxax()%>% 
stack(b) #centering and un-directioning stack


#dat.ld<- def_ldk(dat, 3, close = T, points = T) # define 3 landmarks
#dat.ld <- def_ldk(dat, 4) 
dat.ld=dat

dat.ld$fake <- factor(c("Xylophagous",
                      "Xylophagous",
                      "Xylophagous",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "Xylophagous",
                      "aquatic",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "unknown",
                      "terrestrial",
                      "unknown",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "terrestrial",
                      "terrestrial",
                      "unknown",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "unknown",
                      "unknown",
                      "unknown",
                      "unknown",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "aquatic",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "unknown",
                      "terrestrial",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "aquatic",
                      "terrestrial",
                      "unknown",
                      "terrestrial",
                      "unknown",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial",
                      "terrestrial"))


dat.ld$fake2 <- factor(c(	"extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "burmese",
                          "extant",
                          "messel",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "burmese",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "baltic",
                          "burmese",
                          "burmese",
                          "burmese",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "slovenian shales",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          "extant",
                          " Limestone Montsech",
                          "extant",
                          "dominican",
                          "extant",
                          "extant",
                          "extant",
                          "extant"))
#id of the fossils
dat.ld$fake3 <- factor(c("extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "Liu et al. 2019 mt 1",
                         "extant",
                         "Messel specimen",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "NHMLA spec 2",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "ped01",
                         "ped0041",
                         "ped0362",
                         "ped0031",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "slovenian shales",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         "extant",
                         " Limestone Montsech",
                         "extant",
                         "dominican",
                         "extant",
                         "extant",
                         "extant",
                         "extant"))

  coo_oscillo(dat.ld[1], "efourier")
Ptolemy(dat.ld[1])


dat.f <- efourier(dat.ld)
dat.f <- efourier(dat.ld, nb.h=36)
dat.p <- PCA(dat.f)
m=MANOVA(dat.p, dat.ld$fake)

m <- manova(dat.p$x[, 1:69] ~  dat.ld$fake2)
summary.aov(m)

plot(dat.p)
library(ggplot2)
library(grid)
library(gridExtra)
library(ggfortify)
df_out <- as.data.frame(dat.p$x)


plot(dat.p, dat.ld$fake,chull=TRUE, ellipses=TRUE, conf_ellipses = 0.9)
plot(dat.p, dat.ld$fake2,chull=TRUE, ellipses=TRUE, conf_ellipses = 0.9)
plot(dat.p, dat.ld$fake3,chull=TRUE, ellipses=TRUE, conf_ellipses = 0.9)

hist(dat.f, drop=0)
boxplot(dat.f, drop=1)
dat.p <- PCA(dat.f)
class(dat.p)        # a PCA object, let's plot it
plot(dat.p)

#coo_plot(coo_slidedirection(b, "up"))
#coo_plot(coo_slidedirection(b, "right"))
#coo_plot(coo_slidedirection(b, "left"))
#coo_plot(coo_slidedirection(b, "down"))

ading
#(dat, title = "Non-aligned head")
#dat.al <- fgProcrustes(dat, tol = 1e-4) %>% coo_slidedirection(b, "right")
#stack(dat.al, title="Aligned heads")


#




plot(dat.p, dat$fake)
plot(dat.p, dat.ld$fake, 1, pos.shp="circle", stars=TRUE, chull.filled=TRUE, palette=col_spring)


PCcontrib(dat.p)


dat.l <- LDA(dat.p,dat$fake)
MANOVA_PW(dat.p, "fake")
KMEANS(dat.p, centers = 10)
dat.f %>% mshapes() %>% coo_plot()


dat %>% efourier(norm=TRUE) %>% PCA() %>% plot("fake")