Example #1
0
def exercise_mosflm_integrater(dials_regression, tmp_dir, nproc):
  from xia2.Handlers.Phil import PhilIndex
  PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc

  xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
  template = os.path.join(xia2_demo_data, "insulin_1_###.img")

  # otherwise if this test is running multiple times simultaneously two mosflm
  # processes try to write to the same genfile
  os.environ['CCP4_SCR'] = tmp_dir

  from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
  from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
  from dxtbx.datablock import DataBlockTemplateImporter
  indexer = MosflmIndexer()
  indexer.set_working_directory(tmp_dir)
  importer = DataBlockTemplateImporter([template])
  datablocks = importer.datablocks
  imageset = datablocks[0].extract_imagesets()[0]
  indexer.add_indexer_imageset(imageset)

  from xia2.Schema.XCrystal import XCrystal
  from xia2.Schema.XWavelength import XWavelength
  from xia2.Schema.XSweep import XSweep
  from xia2.Schema.XSample import XSample
  cryst = XCrystal("CRYST1", None)
  wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
  samp = XSample("X1", cryst)
  directory, image = os.path.split(imageset.get_path(1))
  sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
  indexer.set_indexer_sweep(sweep)

  from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
  refiner = MosflmRefiner()
  refiner.set_working_directory(tmp_dir)
  refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)

  nref_error = 500

  integrater = MosflmIntegrater()
  integrater.set_working_directory(tmp_dir)
  integrater.setup_from_image(imageset.get_path(1))
  integrater.set_integrater_refiner(refiner)
  #integrater.set_integrater_indexer(indexer)
  integrater.set_integrater_sweep(sweep)
  integrater.integrate()

  integrater_intensities = integrater.get_integrater_intensities()
  assert os.path.exists(integrater_intensities)
  from iotbx.reflection_file_reader import any_reflection_file
  reader = any_reflection_file(integrater_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()
  assert mtz_object.column_labels() == [
    'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'IPR', 'SIGIPR',
    'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
    'BGPKRATIOS']

  assert integrater.get_integrater_wedge() == (1, 45)
  assert approx_equal(integrater.get_integrater_cell(),
                      (78.014, 78.014, 78.014, 90.0, 90.0, 90.0), eps=1e-2)

  # test serialization of integrater
  json_str = integrater.as_json()
  #print json_str
  integrater2 = MosflmIntegrater.from_json(string=json_str)
  integrater2.set_integrater_sweep(sweep, reset=False)
  integrater2_intensities = integrater.get_integrater_intensities()
  assert integrater2_intensities == integrater_intensities

  integrater2.set_integrater_finish_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()

  integrater2.set_integrater_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()

  integrater2.set_integrater_prepare_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
         mtz_object.n_reflections()
Example #2
0
def exercise_mosflm_integrater(nproc=None):
  if not have_dials_regression:
    print "Skipping exercise_mosflm_integrater(): dials_regression not configured"
    return

  if nproc is not None:
    from xia2.Handlers.Phil import PhilIndex
    PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc

  xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
  template = os.path.join(xia2_demo_data, "insulin_1_###.img")

  cwd = os.path.abspath(os.curdir)
  tmp_dir = os.path.abspath(open_tmp_directory())
  os.chdir(tmp_dir)
  # otherwise if this test is running multiple times simultaneously two mosflm
  # processes try to write to the same genfile
  os.environ['CCP4_SCR'] = tmp_dir

  from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
  from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
  from dxtbx.datablock import DataBlockTemplateImporter
  indexer = MosflmIndexer()
  indexer.set_working_directory(tmp_dir)
  importer = DataBlockTemplateImporter([template])
  datablocks = importer.datablocks
  imageset = datablocks[0].extract_imagesets()[0]
  indexer.add_indexer_imageset(imageset)

  from xia2.Schema.XCrystal import XCrystal
  from xia2.Schema.XWavelength import XWavelength
  from xia2.Schema.XSweep import XSweep
  from xia2.Schema.XSample import XSample
  cryst = XCrystal("CRYST1", None)
  wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
  samp = XSample("X1", cryst)
  directory, image = os.path.split(imageset.get_path(1))
  sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
  indexer.set_indexer_sweep(sweep)

  from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
  refiner = MosflmRefiner()
  refiner.set_working_directory(tmp_dir)
  refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)

  nref_error = 500

  integrater = MosflmIntegrater()
  integrater.set_working_directory(tmp_dir)
  integrater.setup_from_image(imageset.get_path(1))
  integrater.set_integrater_refiner(refiner)
  #integrater.set_integrater_indexer(indexer)
  integrater.set_integrater_sweep(sweep)
  integrater.integrate()

  integrater_intensities = integrater.get_integrater_intensities()
  assert os.path.exists(integrater_intensities)
  from iotbx.reflection_file_reader import any_reflection_file
  reader = any_reflection_file(integrater_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()
  assert mtz_object.column_labels() == [
    'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'IPR', 'SIGIPR',
    'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
    'BGPKRATIOS']

  assert integrater.get_integrater_wedge() == (1, 45)
  assert approx_equal(integrater.get_integrater_cell(),
                      (78.014, 78.014, 78.014, 90.0, 90.0, 90.0), eps=1e-2)

  # test serialization of integrater
  json_str = integrater.as_json()
  #print json_str
  integrater2 = MosflmIntegrater.from_json(string=json_str)
  integrater2.set_integrater_sweep(sweep, reset=False)
  integrater2_intensities = integrater.get_integrater_intensities()
  assert integrater2_intensities == integrater_intensities

  integrater2.set_integrater_finish_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()

  integrater2.set_integrater_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
      mtz_object.n_reflections()

  integrater2.set_integrater_prepare_done(False)
  integrater2_intensities = integrater2.get_integrater_intensities()
  assert os.path.exists(integrater2_intensities)
  reader = any_reflection_file(integrater2_intensities)
  assert reader.file_type() == "ccp4_mtz"
  mtz_object = reader.file_content()
  assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
         mtz_object.n_reflections()
def exercise_mosflm_integrater(dials_data, tmp_dir, nproc):
    from xia2.Handlers.Phil import PhilIndex

    PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc

    template = dials_data("insulin").join("insulin_1_###.img").strpath

    # otherwise if this test is running multiple times simultaneously two mosflm
    # processes try to write to the same genfile
    os.environ["CCP4_SCR"] = tmp_dir

    from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
    from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
    from dxtbx.model.experiment_list import ExperimentListTemplateImporter

    indexer = MosflmIndexer()
    indexer.set_working_directory(tmp_dir)
    importer = ExperimentListTemplateImporter([template])
    experiments = importer.experiments
    imageset = experiments.imagesets()[0]
    indexer.add_indexer_imageset(imageset)

    from xia2.Schema.XCrystal import XCrystal
    from xia2.Schema.XWavelength import XWavelength
    from xia2.Schema.XSweep import XSweep
    from xia2.Schema.XSample import XSample

    cryst = XCrystal("CRYST1", None)
    wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
    samp = XSample("X1", cryst)
    directory, image = os.path.split(imageset.get_path(1))
    sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
    indexer.set_indexer_sweep(sweep)

    from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner

    refiner = MosflmRefiner()
    refiner.set_working_directory(tmp_dir)
    refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)

    nref_error = 500

    integrater = MosflmIntegrater()
    integrater.set_working_directory(tmp_dir)
    integrater.setup_from_image(imageset.get_path(1))
    integrater.set_integrater_refiner(refiner)
    # integrater.set_integrater_indexer(indexer)
    integrater.set_integrater_sweep(sweep)
    integrater.integrate()

    integrater_intensities = integrater.get_integrater_intensities()
    assert os.path.exists(integrater_intensities)
    from iotbx.reflection_file_reader import any_reflection_file

    reader = any_reflection_file(integrater_intensities)
    assert reader.file_type() == "ccp4_mtz"
    mtz_object = reader.file_content()
    assert (abs(mtz_object.n_reflections() - 81116) <
            nref_error), mtz_object.n_reflections()
    assert mtz_object.column_labels() == [
        "H",
        "K",
        "L",
        "M_ISYM",
        "BATCH",
        "I",
        "SIGI",
        "IPR",
        "SIGIPR",
        "FRACTIONCALC",
        "XDET",
        "YDET",
        "ROT",
        "WIDTH",
        "LP",
        "MPART",
        "FLAG",
        "BGPKRATIOS",
    ]

    assert integrater.get_integrater_wedge() == (1, 45)
    assert approx_equal(
        integrater.get_integrater_cell(),
        (78.014, 78.014, 78.014, 90.0, 90.0, 90.0),
        eps=1e-2,
    )

    # test serialization of integrater
    json_str = integrater.as_json()
    # print json_str
    integrater2 = MosflmIntegrater.from_json(string=json_str)
    integrater2.set_integrater_sweep(sweep, reset=False)
    integrater2_intensities = integrater.get_integrater_intensities()
    assert integrater2_intensities == integrater_intensities

    integrater2.set_integrater_finish_done(False)
    integrater2_intensities = integrater2.get_integrater_intensities()
    assert os.path.exists(integrater2_intensities)
    reader = any_reflection_file(integrater2_intensities)
    assert reader.file_type() == "ccp4_mtz"
    mtz_object = reader.file_content()
    assert (abs(mtz_object.n_reflections() - 81116) <
            nref_error), mtz_object.n_reflections()

    integrater2.set_integrater_done(False)
    integrater2_intensities = integrater2.get_integrater_intensities()
    assert os.path.exists(integrater2_intensities)
    reader = any_reflection_file(integrater2_intensities)
    assert reader.file_type() == "ccp4_mtz"
    mtz_object = reader.file_content()
    assert (abs(mtz_object.n_reflections() - 81116) <
            nref_error), mtz_object.n_reflections()

    integrater2.set_integrater_prepare_done(False)
    integrater2_intensities = integrater2.get_integrater_intensities()
    assert os.path.exists(integrater2_intensities)
    reader = any_reflection_file(integrater2_intensities)
    assert reader.file_type() == "ccp4_mtz"
    mtz_object = reader.file_content()
    assert (abs(mtz_object.n_reflections() - 81116) <
            nref_error), mtz_object.n_reflections()