How to extract

Extraction Sequence

Use the library function to include the RadETL package.

library(RadETL)

1. Use the DcmFileModule class to extract metadata from a DICOM image file into an RDS file

   # Example
   DFM <- DcmFileModule$new(path, savePathRoot, core)
   res <- DFM$dcmToRDS(rootPathCount = 4, verbose = FALSE)
   
   # If you want to see the saving status..
   View(res)  # List

   

2. Read the extracted metadata RDS file using the Radiology CDM generation function. (Using createRadiology family function)

   # Example 
   
   # Create Radiology_Occurrence table for rds Path
   rdsPath <- "/home/ohdsi/Radiology/rdsfiles"
   
   # Create RadDB object,,
   # If using pararell, require pararell package
   RDB <- RadDB$new(core = parallel::detectCores() - 1)
   
   # Get Radiology_Occurrence table
   occur <- RDB$createRadiologyOccurrence(path = rdsPath)
   
   # Create Radiology_Image table for read RDS file
   rdsFile <- "/home/ohdsi/DICOM-header/header.rds"
   data <- readRDS(file = rdsFile)
   
   # Get Radiology_Image table
   img <- RDB$createRadiologyImage(data = data)

   

3. Loads data from the RDS file into the RDBMS. (Using DBMSIO Class. Option A)

   # Example
   dbms <- "sql server"
   user <- Sys.getenv("user")
   pw <- Sys.getenv("pw")
   server <- Sys.getenv("dbServer")
   
   # Connect DBMS...
   db <- DBMSIO$new(server = server, user = user, pw = pw, dbms = dbms)
   
   # df is radiology Data frame,,
   db$insertDB(dbS = databaseSchema, data = df)
   db$finalize()

   

4. Loads data from the RDS file into the RDBMS. (Using DatabaseConnector and SqlRender, Option B)

   # Example
   dbms <- "sql server"
   user <- Sys.getenv("user")
   pw <- Sys.getenv("pw")
   server <- Sys.getenv("dbServer")
   
   # Write connect information
   conDetails <- DatabaseConnector::createConnectionDetails(dbms = dbms, user = user, password = pw, server = server)
   
   # Connect DBMS
   con <- DatabaseConnector::connect(connectionDetails = conDetails)
   
   # insert tables...
   DatabaseConnector::insertTable(connection = con, tableName = paste0(databaseSchema, tbSchema), data = df)
   
   # if want disconnect
   DatabaseConnector::disconnect(connection = con)