-- Loops through .pack files that have 6 images in and saves all 6 images to nifti files.


local folder = [[D:\data\MPhys2019\PETCT-HN\26-11\Rigid\BigDoseCropRigid\]]; --This folder contains .pack files
local folder_nifti= [[D:\data\MPhys2019\PETCT-HN\26-11\Rigid\BigDoseCropRigid\nifti\]]; --Save .nifti files to this folder

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 t = scandir(folder);

--t = {'688912716.pack'} --This overwrites t, use if only want to save one pack

for k,patientpack in ipairs(t) do

  loadpack( folder .. patientpack )
  patientpack_new= patientpack:gsub(".pack","")

    skip= false

  --Don't want to look at the patients with missing scans
    for i = 1,6 do
        if wm.Scan[i].Data.empty then skip = true

    end
  end

  if not skip then

      for p = 1,6 do --goes through 6 images

        scan_name= ("%s_scan%d"):format(patientpack_new,p) --"patientpack_new_scanp"


        --file_name= ([[D:/data/MPhys2019/PETCT-HN/Test/%s.nii]]):format(scan_name)
        wm.Scan[p]:write_nifty(folder_nifti .. scan_name .. ".nii") --Writes to nifti
    end

  end
end