#!/usr/bin/env python
# rebatch.py
#
#   Copyright (C) 2011 Diamond Light Source, Graeme Winter
#
#   This code is distributed under the BSD license, a copy of which is
#   included in the root directory of this package.
#
# Replacement for CCP4 program rebatch, using cctbx Python.
#

import sys

from iotbx import mtz
from cctbx.array_family import flex

def rebatch(hklin, hklout, first_batch):
  '''Need to implement: include batch range, exclude batches, add N to
  batches, start batches at N.'''

  mtz_obj = mtz.object(file_name = hklin)

  batch_column = None
  batch_dataset = None

  for crystal in mtz_obj.crystals():
    for dataset in crystal.datasets():
      for column in dataset.columns():
        if column.label() == 'BATCH':
          batch_column = column
          batch_dataset = dataset

  if not batch_column:
    raise RuntimeError, 'no BATCH column found in %s' % hklin

  batch_column_values = batch_column.extract_values(
      not_a_number_substitute = -1)

  valid = flex.bool()

  # modify batch columns, and also the batch headers

  if first_batch != None:
    offset = first_batch - min(batch_column_values)
    batch_column_values = batch_column_values + offset

    for batch in mtz_obj.batches():
      batch.set_num(int(batch.num() + offset))

  # done modifying

  batch_column.set_values(values = batch_column_values,
                          selection_valid = valid)

  # and write this lot out as hklout

  mtz_obj.write(file_name = hklout)

def copy_r_file(hklin, hklout):

  mtz_obj = mtz.object(file_name = hklin)

  mtz_out = mtz.object()

  mtz_out.set_space_group(mtz_obj.space_group())

  for batch in mtz_obj.batches():
    if batch.num() % 2 == 0:
      batch_out = mtz_out.add_batch()
      batch_out.set_num(batch.num())
      batch_out.set_title(batch.title())
      batch_out.set_gonlab(batch.gonlab())
      batch_out.set_ndet(batch.ndet())
      batch_out.set_phixyz(batch.phixyz())
      batch_out.set_detlm(batch.detlm())

  batch_column = None

  for crystal in mtz_obj.crystals():

    crystal_out = mtz_out.add_crystal(
        crystal.name(), crystal.project_name(), crystal.unit_cell())

    for dataset in crystal.datasets():

      dataset_out = crystal_out.add_dataset(dataset.name(),
                                            dataset.wavelength())

      for column in dataset.columns():

        dataset_out.add_column(column.label(), column.type())

        if column.label() == 'BATCH':
          batch_column = column

  if not batch_column:
    raise RuntimeError, 'no BATCH column found in %s' % hklin

  batch_column_values = batch_column.extract_values(
      not_a_number_substitute = -1)

  valid = flex.bool()

  remove = []

  for j, b in enumerate(batch_column_values):
    if b % 2 != 0:
      remove.append(j)

  remove.reverse()

  for crystal in mtz_obj.crystals():
    for dataset in crystal.datasets():
      for column in dataset.columns():
        print column.label()
        values = column.extract_values(
            not_a_number_substitute = -999999)
        for r in remove:
          del(values[r])
        mtz_out.get_column(column.label()).set_values(
            values = values, selection_valid = valid)

  mtz_out.write(file_name = hklout)

  return

if __name__ == '__main__':

  import sys

  hklin = sys.argv[1]
  hklout = 'arse.mtz'

  copy_r_file(hklin, hklout)