coarse_align_reconstruct.lua

#!/usr/bin/env talua
--[[
  Copyright (c) 2015 Dustin Reed Morado

  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:

  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.

  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.
--]]

local tomoauto = require('tomoauto')
local yalgo = require('yalgo')
local io, os, string, table = io, os, string, table
local assert, ipairs, pairs = assert, ipairs, pairs
local print = print

_ENV = nil

local parser = yalgo:new_parser('Coarse align and reconstruct a tilt-series.')

parser:add_argument({
  name = 'input',
  description = 'Input tilt-series for processing.',
  meta_value = 'INPUT.st',
  is_positional = true,
  is_required = true
})

parser:add_argument({
  name = 'local_configuration',
  description = 'Use local configuration file.',
  meta_value = 'CONFIG_FILE',
  long_option = '--local-configuration',
  short_option = '-L',
  has_argument = true
})

parser:add_argument({
  name = 'mdoc',
  long_option = '--mdoc',
  short_option = '-M',
  has_argument = true,
  description = 'Use provided mdoc file as opposed to default.',
  meta_value = 'MDOC_FILE'
})

parser:add_argument({
  name = 'tilt_axis_angle',
  long_option = '--tilt-axis',
  short_option = '-t',
  description = 'Tilt axis angle as opposed to default in the MRC header.',
  has_argument = true,
  meta_value = 'TILT_ANGLE'
})

local options = parser:get_arguments()

assert(tomoauto.utils.is_file(options.input))
local MRC = assert(tomoauto.mrcio.new_MRC(options.input))
local config_path = options.local_configuration
local sandbox = tomoauto.config.load_local_configuration(config_path)

-- Run ccderaser as in pre-processing step
local ccderaser = tomoauto.settings.ccderaser
ccderaser = ccderaser:apply_local_configuration(sandbox)
ccderaser = ccderaser:setup(MRC)
ccderaser:write()
ccderaser:run()
local ccderaser_log = ccderaser:get_log()
ccderaser:cleanup()
assert(tomoauto.utils.is_file(ccderaser.OutputFile.value))
assert(tomoauto.utils.run('mv ' .. MRC.filename .. ' ' .. 
                          MRC.basename ..  '_orig.st')) 

assert(tomoauto.utils.run('mv ' .. ccderaser.OutputFile.value .. ' ' ..
                          MRC.filename))

-- Run tiltxcorr as in the coarse alignment step
assert(tomoauto.utils.run('get_tilt_angles ' .. MRC.filename .. ' ' ..
                          MRC.basename .. '.rawtlt'))

local tiltxcorr = tomoauto.settings.tiltxcorr
tiltxcorr = tiltxcorr:apply_local_configuration(sandbox)
tiltxcorr = tiltxcorr:setup(MRC)
tiltxcorr:write()
tiltxcorr:run()
local tiltxcorr_log = tiltxcorr:get_log()
tiltxcorr:cleanup()
assert(tomoauto.utils.is_file(tiltxcorr.OutputFile.value))

-- Run xftoxg as in the coarse alignment step
local xftoxg = tomoauto.settings.xftoxg
xftoxg = xftoxg:apply_local_configuration(sandbox)
xftoxg = xftoxg:setup(MRC)
xftoxg:write()
xftoxg:run()
local xftoxg_log = xftoxg:get_log()
xftoxg:cleanup()
assert(tomoauto.utils.is_file(xftoxg.GOutputFile.value))
assert(os.remove(tiltxcorr.OutputFile.value))

-- Run newstack as in the coarse alignment step but with binning to 1K x 1K and
-- rotate the tilt-series by the tilt-axis angle.
local prenewstack = tomoauto.settings.prenewstack
local angle = options.tilt_axis_angle or MRC.tilt_axis_angle

local _prenewstack = {
  BinByFactor = { use = true, value = 4 },
  RotateByAngle = { use = true, value = angle },
}

prenewstack = prenewstack:update(_prenewstack)
prenewstack = prenewstack:apply_local_configuration(sandbox)
prenewstack = prenewstack:setup(MRC)
prenewstack:write()
prenewstack:run()
local prenewstack_log = prenewstack:get_log()
prenewstack:cleanup()
assert(tomoauto.utils.is_file(prenewstack.OutputFile.value))
assert(os.remove(xftoxg.GOutputFile.value))

-- Run tomo3d to generate the reconstruction
local tomo3d = tomoauto.settings.tomo3d
local _tomo3d = {
  TiltFile = { use = true, value = '-a TOMOAUTO{basename}.rawtlt \\' },
  InputFile = { use = true, value = '-i TOMOAUTO{basename}.preali \\' },
  SIRT = { use = true, value = '-S \\' },
  Height = { use = true, value = '-z 800 \\' }
}

tomo3d = tomo3d:update(_tomo3d)
tomo3d = tomo3d:apply_local_configuration(sandbox)
tomo3d = tomo3d:setup(MRC)
tomo3d:write()
tomo3d:run()
local tomo3d_log = tomo3d:get_log()
tomo3d:cleanup()

assert(os.remove(MRC.basename .. '.rawtlt'))
assert(tomoauto.utils.run('mv ' .. MRC.basename .. '_orig.st ' .. MRC.filename))