Here is a short example to guide you step by step through the extraction of crown scale data. All you need to start it is a RGB orthomosaics time serie and a shape file of the crown delineations. To run the following code you can use the outputs of the of the Generate ans align orthomosaics article or directly download the test data (link is coming).
############## Load libraries --------------------------------------------------
library(canObsR)
library(tidyverse)
library(sf)
library(openxlsx)Set parameters
Set your parameters, the path to the CanObsR_data folder,
the Tmpfiles_directory if you want to store the temporary files
in a specific folder and N_cores the number of cores you want
to allocate for the function extract_crownsImages() and
extract_rgbValues().
Note : The functions extract_crownsImages() and
extract_rgbValues() can produce a lot of temporary files
and need several GB of memory depending on the size, the resolution and
the number of mosaics. You can specify where you want to store the
temporary files.
############## Set variables ---------------------------------------------------
# Path to the main directory
path = 'XXXX/canObsR_data'
# Path to store the temp files
Tmpfiles_directory = 'XXX/R_tmpdir' # NULL if you want to use the default folder
# Number of cores used for the paralelized functions
N_cores = 10If you are using the test data or if you follow the same files architecture just run the following code.
# Path to the mosaics
imgs <- list.files(file.path(path,'3_orthomosaics_aligned'), full.names = T)
# Extract the dates of the images
dates <-
extr_dates(names_img = basename(imgs), n = 2, sep = '_', extension = '.gpkg')First step : Make the crowns shape file compatible
The first step is to check the crowns file compatibility with the
function check_crownsFile. To be compatible with the
package functions the shape file must have :
- at least the variables ‘id’, ‘species’, ‘genus’ and ‘family’
- ‘species’, ‘genus’ and ‘family’ should not have NA. Replce them by ‘indet’
- ‘id’ should not have duplicated values.
############## STEP 1 Check and modify the crowns file ------------------------
# Check the crowns file compatibility
check_crownsFile(path_crowns = file.path(path,'crowns.gpkg'))
# Rename variables
sf::read_sf(file.path(path,'crowns.gpkg')) %>% # Load the file
rename(
family = tax_fam, # Rename the corresponding variable as 'family'
genus = tax_gen, # Rename the corresponding variable as 'genus'
species = tx_sp_lvl # Rename the corresponding variable as 'species'
) %>%
sf::write_sf(.,file.path(path,'crowns_corrected.gpkg')) # And save the file
# Check the new crowns file compatibility
check_crownsFile(path_crowns = file.path(path,'crowns_corrected.gpkg'))
# Rename NA to 'indet'
sf::read_sf(file.path(path,'crowns_corrected.gpkg')) %>% # Load the new file
mutate(
# Rename NA to 'indet' in the family variable
family = case_when(is.na(family)~ 'indet', TRUE ~ family),
# Same for genus
genus = case_when(is.na(genus)~ 'indet', TRUE ~ genus),
# Same for species
species = case_when(is.na(species)~ paste(genus, 'indet'), TRUE ~ species)
) %>%
sf::write_sf(.,file.path(path,'crowns_corrected.gpkg')) # And save the file
# Re-check the new crowns file compatibility
check_crownsFile(path_crowns = file.path(path,'crowns_corrected.gpkg'))
# File compatibility should be OK
############## STEP 2 Extract crowns images ------------------------------------
extract_crownsImages(
path_images = imgs, # Path to mosaics
path_crowns = file.path(path,'crowns_corrected.gpkg'), # Path to crowns file
out_dir_path = file.path(path,'4_crowns_img'), # Path to output folder
tempdir_custom = Tmpfiles_directory, # Path to tmp file directory
site = NULL, # If NULL, will be extract from the path_images
dates = NULL, # If NULL, will be extract from the path_images
N_cores = N_cores, # Number of cores
width = 720, # By default it is 720
height = 825 # By default it is 720
)
############## STEP 3 Extract spectral indices from mosaic at the crown scale --
rgb_data <- extract_rgbValues (
path_images = imgs, # Path to mosaics
path_crowns = file.path(path,'crowns_corrected.gpkg'), # Path to crowns file
out_dir_path = path, # Path to output folder
tempdir_custom = Tmpfiles_directory, # Path to tmp file directory
ncor = N_cores, # Number of cores
sites = NULL, # If NULL, will be extract from the path_images
dates = NULL, # If NULL, will be extract from the path_images
file_type = '.xlsx' # Could be '.csv' or '.xlsx' or 'RData'
)
############## STEP 4 Create file to do the labeling --------------------------
create_labelingFile(
path_crowns = file.path(path,'crowns_corrected.gpkg'), # Path to crowns file
site = 'Bouamir', # Site name
dates = dates, # Dates of the RGB survey
out_dir_path = path) # Path to output folder
# open it
openXL(file.path(path,paste(site,'labelingFile',paste0(format(as.Date(Sys.Date(),format="%Y-%m-%d"), format = "%Y%m%d"), '.xlsx'), sep = '_' )))
############## STEP 5 Fill the labelingFile with shiny app --------------------
# Import the labelingFile
labeling_file <- read.xlsx(
file.path(
path,
paste(
'Bouamir_labelingFile',
paste0(format(as.Date(Sys.Date(),format="%Y-%m-%d"), format = "%Y%m%d"), '.xlsx'),
sep = '_' )
)
)
# Start the app
shiny_labels(
data_labeling = labeling_file,
newFile = 'E:/new.xlsx',
imgFolder = file.path(path,'4_crowns_img') # Path to the crowns images folder
)