## ----echo = F, message = F-----------------------------------------------
api_key <- Sys.getenv("TCIA_API_KEY")
if(identical(api_key, "")) {
  knitr::opts_chunk$set(eval = FALSE)
  message("Note: code examples will not be evaluated because the system does not have a valid API key installed.")
}

## ------------------------------------------------------------------------
#  library(TCIApathfinder)
#  
#  # Pick a patient of interest
#  patient <- "TCGA-AR-A1AQ"
#  
#  # Get information on all image series for this patient
#  series <- get_series_info(patient_id = patient)
#  
#  # Pick an image series to download
#  series_instance_uid <- as.character(series$series[1, "series_instance_uid"])
#  
#  # Download and unzip the image series
#  ser <- save_extracted_image_series(series_instance_uid = series_instance_uid)
#  dicom_dir <- ser$dirs

## ------------------------------------------------------------------------
#  suppressPackageStartupMessages(library(oro.dicom))
#  
#  # Read in the DICOM images and create a 3D array of intensities
#  dicom_list <- readDICOM(dicom_dir)
#  img_array_3d <- create3D(dicom_list)
#  
#  # Check the dimensions of the 3D array
#  dim(img_array_3d)