--Performs nonrigid registration

local rigid_folder = [[D:\data\MPhys2019\PETCT-HN\RIGIDCODE5 RESULTS\]]; --Folder that contains rigidly registered images

local nonrigid_folder = [[D:\data\MPhys2019\PETCT-HN\RIGIDCODE5 RESULTS\nonrigid\]]; --Folder you want to save nonrigid scans to


local oldmethod_file = io.open (nonrigid_folder .. "Niftyregf3d_old2.txt", "w") --Contains list of packs registered with old niftyreg
local newmethod_file = io.open (nonrigid_folder .. "Niftyregf3d_new2.txt", "w") --List of packs registered with new niftyreg

local function scandir(directory)
  local i, t, popen = 0, {}, io.popen
  for filename in popen('dir "'..directory..'" /o:n /b'):lines() do
    if string.find(filename, ".pack") then
      i = i + 1
      t[i] = filename
    end
  end
  return t
end

local t = scandir(rigid_folder);

--t = {'401227364.pack'}

numpacks_done= 0
t1 = os.time()
for k,patientpack in ipairs(t) do
  patientpack_new= patientpack:gsub(".pack","")

  loadpack( rigid_folder .. patientpack )

  for i=3,5,2 do --Want to register scan3 and scan5 to scan 1

--Perform non-rigid registration
  t2= os.time()
  wm.Scan[i]:niftyreg_f3d(wm.Scan[1], nil, [[-ln 5 -be 0.05 -jl 0.0001 -maxit 800 ]]) --old niftyregf3d
  --newmethod_file:write(patientpack_new.."\n")

  if( wm.Scan[i].InverseWarp==nil ) then --if the old one doesn't work, it sets the InverseWarp to empty
    t2= os.time()
    wm.Scan[i]:niftyreg_f3d(wm.Scan[1], nil, [[-ln 5 -be 0.05 -jl 0.0001 -maxit 800 -new]]) -- New niftyireg algorithm
    newmethod_file:write(patientpack_new.."\n")
  else
    oldmethod_file:write(patientpack_new.."\n")
  end

  t3= os.time()
  print(('%s'):format(patientpack).. ',' ..os.difftime(t3, t2) .."\n") --Time taken for nonrigid registration



  --wm.Scan[i]:niftyreg_f3d(wm.Scan[1])
--Apply the result of the registration to the PET signal
  wm.Scan[i+1].InverseWarp = wm.Scan[i].InverseWarp

-- Puts scan[i] in grid of scan 1
  wm.Scan[i]= wm.Scan[i]:as(wm.Scan[1])
-- Puts scan[i+1] in grid of scan 1
  wm.Scan[i+1]= wm.Scan[i+1]:as(wm.Scan[1])

end
numpacks_done= numpacks_done+1

savepack(nonrigid_folder .. patientpack) --Saves pack

end

--time_file:write(os.difftime(os.time(), t1)) --Writes to time_file the time in seconds the code took to run

io.close(oldmethod_file)
io.close(newmethod_file)