--Define input folder
local folder = [[D:\data\MPhys2019\PETCT-HN\SEM2\Nonrigid_inversewarp\]];  --Nonrigid registration scans are the input
local output_folder = [[D:\data\MPhys2019\PETCT-HN\SEM2\Sensitivity\maximum_entity\]]; --Output folder

--local file = io.open(output_folder.."print.txt","w")
local function scandir(directory)
  local i, t, popen = 0, {}, io.popen
  for filename in popen('dir "'..directory..'" /o:n /b'):lines() do
      i = i + 1
      t[i] = filename
  end
  return t
end
local function has_item(tab, val) --Check is val in tab
  for index, value in ipairs(tab) do
    if value == val then
      return true
    end
  end
  return false
end

local t = scandir(folder);
--Comment following line to cycle through packs - paste desired pack name otherwise:
--t = {'263538649.pack'}

local skip_these =  {[[empty]]}
fraction=1
for k,patientpack in ipairs(t) do
  if string.find(patientpack, ".pack") then
    patientpack_new= patientpack:gsub(".pack","")

    skip_scan= false
    if has_item(skip_these, patientpack) then skip_scan= true end
    if skip_scan == false then

      loadpack( folder .. patientpack )


        skip= false
        if wm.Delineation.CTV1 == nil then
          skip = true
          --CTV_missing:write(patientpack_new.."\n")
        end
        if skip == false then

        mask= wm.Scan[1]:burn(wm.Delineation.CTV1)
        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"mask")
        mask:write_nifty(output_folder .. name ..".nii")

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"original")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")



        --wm.Scan[9]=mask
        cb = Clipbox:new()
        cb:fit(wm.Scan[9])
        local minx = cb.Coordinates:getvalue(0)
        local maxx = cb.Coordinates:getvalue(1)
        local miny = cb.Coordinates:getvalue(2)
        local maxy = cb.Coordinates:getvalue(3)
        local minz = cb.Coordinates:getvalue(4)
        local maxz = cb.Coordinates:getvalue(5)

       -- file.write(minx)
        --io.close(file)

        local deltax= 0.1*(maxx-minx) --Want to translate CTV by 10% of the diameter in x,y,z directions respectively
        local deltay= 0.1*(maxy-miny)
        local deltaz= 0.1*(maxz-minz)
        a=1

        --- First do x ---
        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        --wm.Scan[8].Adjust:setvalue(3,0,-a)
        wm.Scan[9].Adjust:setvalue(3,0,-fraction*deltax)
        wm.Scan[9]=wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"x_minus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        wm.Scan[9].Adjust:setvalue(3,0,fraction*deltax)
        wm.Scan[9]= wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"x_plus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

        --- Now do y ---
        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        wm.Scan[9].Adjust:setvalue(3,1,-fraction*deltay)
        wm.Scan[9]= wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"y_minus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        wm.Scan[9].Adjust:setvalue(3,1,fraction*deltay)
        wm.Scan[9]= wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"y_plus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

        -- Now do z ---
        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        wm.Scan[9].Adjust:setvalue(3,2,-fraction*deltaz)
        wm.Scan[9]= wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"z_minus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

        wm.Scan[9]= Scan:new()
        wm.Scan[9]= wm.Scan[1]
        wm.Scan[9].Adjust:setvalue(3,2,fraction*deltaz)
        wm.Scan[9]= wm.Scan[9]:as(wm.Scan[1])
        wm.Scan[9]:mask(mask)

        name= ("%s_scan%d_CTV_%s"):format(patientpack_new,1,"z_plus")
        wm.Scan[9]:write_nifty(output_folder .. name ..".nii")

       end
      end
  end
end