convert_rotx_pos_to_slab.lua

#!/usr/bin/env talua

local tomoauto = require('tomoauto')
local yalgo = require('yalgo')
local io = io

local parser = yalgo:new_parser('Convert pos file from rotx tomogram to slab.')
parser:add_argument({
  name = 'tomogram',
  description = 'Slab style tomogram to change pos file onto.',
  meta_value = 'TOMOGRAM.mrc',
  is_positional = true,
  is_required = true,
})

parser:add_argument({
  name = 'posfile',
  description = 'Original posfile to transform; 3 coordinates per line X, Y, Z',
  meta_value = 'POSFILE.pos',
  is_positional = true,
  is_required = true,
})

parser:add_argument({
  name = 'output',
  description = 'New posfile name',
  meta_value = 'NEW_POSFILE.pos',
  is_positional = true,
  is_required = true,
})

local options = parser:get_arguments()

assert(tomoauto.utils.is_file(options.tomogram), 'Tomogram file not found.')
assert(tomoauto.utils.is_file(options.posfile), 'Position file not found.')

local MRC = assert(tomoauto.mrcio.new_MRC(options.tomogram))
local posfile = assert(io.open(options.posfile, 'r'))
local newpos  = assert(io.open(options.output,  'w'))
local ny = MRC.header.ny

for line in posfile:lines() do
  local old_x, old_y, old_z = line:match('(%d+)%s+(%d+)%s+(%d+)')
  local new_x, new_y, new_z = old_x, ny - old_z, old_y
  local new_line = string.format('%d\t%d\t%d\n', new_x, new_y, new_z)
  newpos:write(new_line)
end

assert(posfile:close())
assert(newpos:close())