run.R

# install required packages
source("src/modules/set_up.R")
# project folder structure-------------------------------------------------------------------------
# put folders contains only .xml under "data", each folder is one batch of experiment
dir.create(file.path("./src/test"), showWarnings = FALSE)
dir.create(file.path("./data"), showWarnings = FALSE)
dir.create(file.path("./result"), showWarnings = FALSE)
# read files-------------------------------------------------------------------------
# read xml, calculate row class,
# slope and generte checking graph
system.time(
  source("src/modules/read_xml.R")
)

# run statistics-------------------------------------------------------------------------

# calculate basics statistics
system.time(
  source("src/modules/stat_analysis.R")
)

# picture wise -------------------------------------------------------------------------
system.time(
  source("src/modules/summarize_and_merge.R")
)

# NTU pipeline-------------------------------------------------------------------------

dir.create(file.path("./result/Ntu"), showWarnings = FALSE)
# put the NTU pipeline results (e.g., "res_noblurry.csv", "res_wblurry.csv") under "result/Ntu/"
# NOTICE that the unit of length, width is microum and area  is microum meter from the output of following scripts 
# remove the duplicate files -------------------------------------------------------------------------
system.time(
  source("src/modules/clean_ntu.R")
)

# match ground truth data in NTU detection-----------------------------------------------------
system.time(
  source("src/modules/check_ntu.R")
)