server.R

library(oro.dicom)
library(oro.nifti)
library(shiny)
library(shinyIncubator)
options(shiny.maxRequestSize = -1)
shinyServer(function(input, output, session) {
  # output$filetable <- renderTable({
  makenii = reactive({
    rimg = c(0, 100)    
    nii = NULL
    if (!is.null(input$files)) {
        # User has not uploaded a file yet
     
        filenames = input$files
        # print(input$files)
        filenames = file.path(filenames$datapath)
        # print(filenames)

        nfiles <- length(filenames)
        nch <- nchar(as.character(nfiles))
        headers <- images <- vector("list", nfiles)
        names(images) <- names(headers) <- filenames
            # cat(" ", nfiles, "files to be processed by readDICOM()", 
            #     fill = TRUE)
          withProgress(session, min=0, max=nfiles, {            
              setProgress(message="Reading Data")
          for (i in 1:nfiles) {
              setProgress(value =i)
              dcm <<- rereadDICOMFile(filenames[i])
              images[[i]] <<- dcm$img
              headers[[i]] <<- dcm$hdr
          }
          })
          dcm = list(hdr = headers, img = images)
          # print(head(dcm$hdr))

        ### rescaling on my own
        dcmtable = dicomTable(dcm$hdr)
        keepcols = grepl("RescaleIntercept|RescaleSlope|PixelSpacing", 
                         colnames(dcmtable))
        dcmtab = dcmtable[, 
          c("0028-1052-RescaleIntercept", 
            "0028-1053-RescaleSlope", 
            "0028-0030-PixelSpacing"),
          drop=FALSE]
        stopifnot(ncol(dcmtab) == 3)
        colnames(dcmtab) = c("intercept", "slope", "pixelspacing")


        for (iimg in 1:length(dcm$img)){
          inter = as.numeric(dcmtab$intercept[iimg])
          slope = as.numeric(dcmtab$slope[iimg])
          dcm$img[[iimg]] = dcm$img[[iimg]] * slope + inter
          x = dcm$img[[iimg]]
          # if (verbose) print(range(dcm$img[[iimg]]))
          dcm$img[[iimg]][x < -1024] = -1024
          dcm$img[[iimg]][x > 3071] = 3071
      #http://www.medical.siemens.com/siemens/en_GLOBAL/rg_marcom_FBAs/files/brochures/DICOM/ct/DICOM_VA70C.pdf 
          # for 4095 ranges
        }

            nii = dicom2nifti(dcm, rescale=FALSE, reslice=FALSE, 
            descrip = NULL)
            rimg = range(nii, na.rm=TRUE)
              "Finished converting"
    }
      return(list(nii=nii, rimg=rimg))
  })



	# Partial example
	output$sld_window <- renderUI({
    rimg = makenii()$rimg

		sliderInput("window", "Range of Data:",
                min = rimg[1], max = rimg[2], value = rimg)
	})  
	

	output$ortho = renderPlot({
    window = input$window
    nii = makenii()$nii
    # print(window)
    # print(nii)
    if (!is.null(nii)){
      img = nii
      print("img is ")
      print(img)
      img@cal_min = window[1]
      img@cal_max = window[2]

      img[ img < window[1] ] = window[1]
      img[ img >= window[2] ] = window[2]    
  		orthographic(img)
    }
	})

  output$dlimg <- downloadHandler(
    filename = function() {
      stopifnot(input$niifname!="")
      print(input$niifname)
      f = paste0(input$niifname, ".nii.gz")
      return(f)
    },
    content = function(file) {
      # print(file)
      writeNIfTI(makenii()$nii, filename = file, 
        gzipped= TRUE)
      file.rename(paste0(file, ".nii.gz"), file)
    }
  )
})

ui.R

library(shinyIncubator)
shinyUI(pageWithSidebar(
  headerPanel("DICOM TO NIfTI Converter"),
  sidebarPanel(
    fileInput("files", "File data", multiple=TRUE),
    uiOutput("sld_window"),
    checkboxInput("gzipped", "gzip nii?", TRUE),
    textInput("niifname", "Filename of nii (no .nii on it)"),
    downloadButton('dlimg', 'Download NIfTI')
  ),
  mainPanel(
    progressInit(),
    plotOutput("ortho"),

    p("Code on ", 
      a("GitHub", "https://github.com/muschellij2/dcm2nii_shiny"))
  )
))