###################################### RadDB Class #############################################
#' RadDB Class
#'
#' This is a class that creates an RCDM using an extracted RDS file.
#' Parallel processing is supported only in the current Occurrence table,
#' and it is recommended that the image table not be processed in parallel
#' because of the computer science problem that the number of images in the image table does not match.
#' Even if you set Pararell through the constructor, it is not supported by the Image method.
#'
#' @param core Number of cores to use
#' @seealso https://github.com/OHDSI/Radiology-CDM/wiki
#' @author Neon K.I.D
#' @example Examples/RadDB_Ex.R
#' @export
RadDB <- R6::R6Class(classname = "RadDB",
  private = list(
    cl = NULL,
    needFunc = c('as.bigint', 'as.float', 'getDate', 'pastePath', 'private'),
    needPkg = c('RadETL', 'rapportools'),
    mergeDfList = function(x, y) merge(x, y, all = TRUE),
    createRCDMOccurrence = function(data, ocid, idp = 2) {
      for(i in 1:length(data)) {
        if(is.empty(data[[i]]))
          stop("ERROR: There is an empty value in the data frame.")
        else {
          dcmRDS <- DicomRDS$new(data = data[[i]], idp = idp)

          # Dirpath Settings
          # Temp code, if source code open, please modify...
          sp <- strsplit(as.character(data[[i]]$path[1]), '/')
          rDirPath <- head(unlist(sp), -1)
          rDirPath <- Reduce(pastePath, rDirPath)
          #rDirPath <- file.path(rDirPath)

          #roID <- dcmRDS$createOccurrenceID()
          roID <- ocid
          studyDatetime <- dcmRDS$getStudyDateTime()

          # Searching AcquisitionDateTime...
          duringTime <- ''
          for(k in length(data):i) {
            dcmRDSk <- DicomRDS$new(data = data[[k]], idp = idp)
            duringTime <- dcmRDSk$getDuringTime(studyDateTime = studyDatetime)
            if(!is.empty(duringTime)) break else duringTime <- NA
            dcmRDSk$finalize()
          }

          pID <- dcmRDS$getPatientID()
          if(is.na(pID) || is.character(pID)) pID <- dcmRDS$getDirectoryID()
          coID <- 0
          dcID <- dcmRDS$getDeviceID()
          modality <- dcmRDS$getModality()
          pocID <- dcmRDS$getPosition()
          oriID <- dcmRDS$getOrientation()

          # Contrast Information,,
          # Reference is RadEx v4.0
          # 28768: Imaging without iv contrast
          # 28771: Imaging without then with IV contrast
          rpcID <- 10392
          for(j in i:length(data)) {
            dcmRDSj <- DicomRDS$new(data[[j]], idp)
            if(dcmRDSj$isPost4BrainCT()) {
              rpcID <- 10371
              break
            }
            dcmRDSj$finalize()
          }

          tCount <- length(data)
          ascID <- 6434           # is Brain CT
          imgComment <- dcmRDS$getComment()
          dosage <- dcmRDS$getDosageunit(modality = modality)
          dosageNum <- dcmRDS$getDosage(dosageUnit = dosage)
          timeUnit <- "sec"
          voID <- 0
          break
        }
      }

      radiology_occurrence_ID <- as.bigint(roID, 4)
      radiology_occurrence_date <- as.Date(getDate(dcmRDS$getStudyDate()))
      radiology_occurrence_datetime <- as.POSIXct(studyDatetime)

      Person_ID <- as.bigint(pID, 4)
      Condition_occurrence_id <- as.integer(coID)
      Device_concept_id <- as.bigint(dcID, 4)

      radiology_modality_concept_ID <- modality  # VARCHAR -> int
      Person_position_concept_id <- pocID        # VARCHAR -> Int
      Person_orientation_concept <- oriID        # VARCHAR -> will deprecate
      radiology_protocol_concept_id <- rpcID     # VARCHAR -> int

      Image_total_count <- as.integer(tCount)
      Anatomic_site_concept_id <- as.integer(ascID)
      radiology_Comment <- imgComment

      Image_dosage_unit_concept <- dosage
      Dosage_value_as_number <- as.numeric(dosageNum)
      Image_exposure_time_unit_concept <- timeUnit
      Image_exposure_time <- as.float(x = duringTime, digits = 5)

      Radiology_dirpath <- rDirPath
      Visit_occurrence_id <- as.bigint(voID, 4)

      data.frame(
        radiology_occurrence_ID,
        radiology_occurrence_date,
        radiology_occurrence_datetime,
        Person_ID,
        Condition_occurrence_id,
        Device_concept_id,
        radiology_modality_concept_ID,
        # Person_orientation_concept,
        radiology_protocol_concept_id,
        Person_position_concept_id,
        Image_total_count,
        Anatomic_site_concept_id,
        radiology_Comment,
        Image_dosage_unit_concept,
        Dosage_value_as_number,
        Image_exposure_time_unit_concept,
        Image_exposure_time,
        Visit_occurrence_id,
        Radiology_dirpath,
        stringsAsFactors = FALSE
      )
    },

    createRCDMImage = function(data, ocid, idp, validpixelonly = FALSE) {
      Radiology_occurrence_ID <- c()
      Person_ID <- c()
      Person_orientation_concept <- c()
      Image_type <- c()
      Radiology_phase_concept_id <- c()
      Image_no <- c()
      Phase_total_no <- c()
      image_resolution_Rows <- c()
      image_Resolution_Columns <- c()
      Image_Window_Level_Center <- c()
      Image_Window_Level_Width <- c()
      Image_slice_thickness <- c()
      image_filepath <- c()

      num <- 1
      pNum <- 1
      rID <- NA
      reNum <- 1

      # Current imageType, radiology_phase_concept
      curimType <- NA
      curPCID <- NA

      for(i in 1:length(data)) {
        if(!is.null(data[[i]])) {
          dcmRDS <- DicomRDS$new(data[[i]], idp)
          if(validpixelonly) {
            if(!dcmRDS$isPixelData())
              next
          }
          Person_ID[num] <- as.bigint(dcmRDS$getDirectoryID(), 4)

          # PatientPosition is null .... blank
          pocID <- dcmRDS$getOrientation()

          # Get ImageType, ORIGINAL is PRIMARY, DERIVED is SECONDARY
          imType <- dcmRDS$getImageType()
          modality <- dcmRDS$getModality()

          # Reference is RadEx v4.0
          # 28833: Imaging without iv contrast
          # 28694: Imaging without then with IV contrast
          rpcID <- 28833
          if(pmatch(x = imType, "SECONDARY", nomatch = FALSE) == 1) rpcID <- 5901
          else if(dcmRDS$isPost4BrainCT()) rpcID <- 28694

          Radiology_phase_concept_id[num] <- rpcID
          thickness <- dcmRDS$getThickness()
          Phase_total_no[num] <- 0

          rows <- dcmRDS$getImgRows()
          columns <- dcmRDS$getImgCols()

          # Checking Phase number..
          if(num == 1) {
            rID <- ocid
            curimType <- imType
            curPCID <- rpcID
          } else if(is.na(pmatch(x = rpcID, curPCID, nomatch = NA_character_))
                    || is.na(pmatch(x = imType, curimType, nomatch = NA_character_))) {
            for(k in reNum:num)
              Phase_total_no[k] <- pNum - 1

            curimType <- imType
            curPCID <- rpcID

            reNum <- num
            pNum <- 1
          } else if(i == length(data)) {
            for(k in reNum:num)
              Phase_total_no[k] <- pNum
          }

          Image_no[num] <- as.integer(pNum)
          Radiology_occurrence_ID[num] <- as.bigint(rID, 4)
          image_resolution_Rows[num] <- as.integer(rows)
          image_Resolution_Columns[num] <- as.integer(columns)
          Image_Window_Level_Center[num] <- dcmRDS$getWindowCenter()
          Image_Window_Level_Width[num] <- dcmRDS$getWindowWidth()
          Image_slice_thickness[num] <- if(is.empty(thickness)) '' else as.numeric(thickness)
          Image_type[num] <- imType
          Person_orientation_concept[num] <- pocID
          image_filepath[num] <- as.character(data[[i]]$path[1])

          num <- num + 1
          pNum <- pNum + 1
        }
      }

      Radiology_Image <- data.frame(
        Radiology_occurrence_ID,
        Person_ID,
        # Person_orientation_concept,
        Image_type,
        Radiology_phase_concept_id,
        Image_no,
        Phase_total_no,
        image_resolution_Rows,
        image_Resolution_Columns,
        Image_Window_Level_Center,
        Image_Window_Level_Width,
        Image_slice_thickness,
        image_filepath,
        stringsAsFactors = FALSE
      )
      return(Radiology_Image)
    }
  ),

  public = list(
    initialize = function(core, logfile = NA) {
      library(foreach)

      if(is.na(logfile))
        logfile <- switch(getOS(), cpm = 'C:/TEMP/radiologyDB.log', '/tmp/radiologyDB.log')

      # Parallel Processing
      private$cl <- parallel::makePSOCKcluster(core, outfile = logfile)
      doSNOW::registerDoSNOW(private$cl)
    },

    createRadiologyDB = function(path, idp = 2, o_start = 1) {
      fileList <- list.files(path = path, recursive = T, full.names = T, pattern = "\\.rds$")
      pb <- txtProgressBar(min = 0, max = length(fileList), style = 3)

      progress <- function(n) setTxtProgressBar(pb, n)
      opts <- list(progress=progress)

      # Occurrence
      ro <- data.frame()
      writeLines('Create Radiology Occurrence Data frame....')
      ocid <- o_start - 1
      ro <- foreach(f = 1:length(fileList), .options.snow = opts, .packages = private$needPkg, .export = private$needFunc) %dopar% {
        data <- readRDS(file = fileList[f])
        Sys.sleep(0.01)

        ocid <- ocid + f
        private$createRCDMOccurrence(data = data, ocid = ocid, idp = idp)
      }
      res_ocur <- Reduce(private$mergeDfList, ro)

      # Image
      ri <- data.frame()
      writeLines('Create Radiology Image Data frame....')
      ocid <- o_start - 1
      ri <- foreach(f = 1:length(fileList), .options.snow = opts, .packages = private$needPkg, .export = private$needFunc) %dopar% {
        data <- readRDS(file = fileList[f])
        Sys.sleep(0.01)

        ocid <- ocid + f
        private$createRCDMImage(data = data, ocid = ocid, idp = idp)
      }
      res_img <- Reduce(private$mergeDfList, ri)

      return(list(res_ocur, res_img))
    },

    finalize = function() {
      parallel::stopCluster(cl = private$cl)  # Requirement
    }
  )
)