Пример #1
0
  def DialsSpotfinder(self):
    from xia2.Wrappers.Dials.Spotfinder import Spotfinder
    spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
    spotfinder.set_working_directory(self.get_working_directory())
    spotfinder.setup_from_imageset(self.get_imageset())

    auto_logfiler(spotfinder, 'SPOTFINDER')

    return spotfinder
Пример #2
0
    def DialsSpotfinder(self):
        spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
        spotfinder.set_working_directory(self.get_working_directory())
        spotfinder.setup_from_imageset(self.get_imageset())

        auto_logfiler(spotfinder, "SPOTFINDER")

        return spotfinder
Пример #3
0
    def DialsSpotfinder(self):
        from xia2.Wrappers.Dials.Spotfinder import Spotfinder
        spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
        spotfinder.set_working_directory(self.get_working_directory())
        spotfinder.setup_from_imageset(self.get_imageset())

        auto_logfiler(spotfinder, 'SPOTFINDER')

        return spotfinder
Пример #4
0
def exercise_dials_wrappers(template, nproc=None):
    if nproc is not None:
        PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc

    scan_ranges = [(1, 45)]
    image_range = (1, 45)

    print("Begin importing")
    importer = Import()
    importer.setup_from_image(template % 1)
    importer.set_image_range(image_range)
    importer.run()
    print("".join(importer.get_all_output()))
    print("Done importing")

    print("Begin spotfinding")
    spotfinder = Spotfinder()
    spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
    spotfinder.set_scan_ranges(scan_ranges)
    spotfinder.run()
    print("".join(spotfinder.get_all_output()))
    print("Done spotfinding")

    print("Begin indexing")
    indexer = Index()
    indexer.add_spot_filename(spotfinder.get_spot_filename())
    indexer.add_sweep_filename(importer.get_sweep_filename())
    indexer.run("fft3d")
    print("".join(indexer.get_all_output()))
    print("Done indexing")

    print("Begin refining")
    rbs = RefineBravaisSettings()
    rbs.set_experiments_filename(indexer.get_experiments_filename())
    rbs.set_indexed_filename(indexer.get_indexed_filename())
    rbs.run()
    print("".join(rbs.get_all_output()))
    print("Done refining")
    bravais_setting_22 = rbs.get_bravais_summary()[22]
    assert bravais_setting_22["bravais"] == "cI"
    assert bravais_setting_22["cb_op"] == "b+c,a+c,a+b"
    assert bravais_setting_22["unit_cell"] == pytest.approx(
        (78.14, 78.14, 78.14, 90, 90, 90), abs=1e-1
    )
    bravais_setting_22_json = bravais_setting_22["experiments_file"]
    assert os.path.exists(bravais_setting_22_json)

    print("Begin reindexing")
    reindexer = Reindex()
    reindexer.set_experiments_filename(indexer.get_experiments_filename())
    reindexer.set_indexed_filename(indexer.get_indexed_filename())
    reindexer.set_cb_op(bravais_setting_22["cb_op"])
    reindexer.run()
    assert os.path.exists(reindexer.get_reindexed_experiments_filename())
    assert os.path.exists(reindexer.get_reindexed_reflections_filename())
    print("".join(reindexer.get_all_output()))
    print("Done reindexing")

    print("Begin refining")
    refiner = Refine()
    refiner.set_experiments_filename(bravais_setting_22_json)
    refiner.set_indexed_filename(reindexer.get_reindexed_reflections_filename())
    refiner.set_scan_varying(True)
    refiner.run()
    assert os.path.exists(refiner.get_refined_experiments_filename())
    print("".join(refiner.get_all_output()))
    print("Done refining")

    print("Begin integrating")
    integrater = Integrate()
    integrater.set_experiments_filename(refiner.get_refined_experiments_filename())
    integrater.set_reflections_filename(reindexer.get_reindexed_reflections_filename())
    integrater.run()
    print("".join(integrater.get_all_output()))
    print("Done integrating")

    print("Begin exporting")
    exporter = ExportMtz()
    exporter.set_experiments_filename(integrater.get_integrated_experiments())
    exporter.set_reflections_filename(integrater.get_integrated_reflections())
    exporter.run()
    print("".join(exporter.get_all_output()))
    print("Done exporting")
    assert os.path.exists(exporter.get_mtz_filename())

    print("Begin exporting xds_ascii")
    exporter = ExportXDSASCII()
    exporter.set_experiments_filename(integrater.get_integrated_experiments())
    exporter.set_reflections_filename(integrater.get_integrated_reflections())
    exporter.run()
    print("".join(exporter.get_all_output()))
    print("Done exporting")
    assert os.path.exists(exporter.get_hkl_filename())

    # Test combine experiments wrapper. Duplicate the file and adjust the
    # identifier to allow combination.
    shutil.copy(indexer.get_experiments_filename(), "copy.expt")
    shutil.copy(indexer.get_indexed_filename(), "copy.refl")

    expts = load.experiment_list("copy.expt")
    expts[0].identifier = "0"
    expts.as_file("copy.expt")
    refls = flex.reflection_table.from_file("copy.refl")
    refls.experiment_identifiers()[0] = "0"
    refls.as_file("copy.refl")

    exporter = CombineExperiments()
    exporter.add_experiments(indexer.get_experiments_filename())
    exporter.add_experiments("copy.expt")
    exporter.add_reflections(indexer.get_indexed_filename())
    exporter.add_reflections("copy.refl")
    exporter.run()
    print("".join(exporter.get_all_output()))
    print("Done combining")
    assert os.path.exists(exporter.get_combined_experiments_filename())
    assert os.path.exists(exporter.get_combined_reflections_filename())
Пример #5
0
def exercise_dials_wrappers(nproc=None):
  if not have_dials_regression:
    print "Skipping exercise_dials_wrappers(): dials_regression not configured"
    return

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

  from xia2.Wrappers.Dials.Import import Import
  from xia2.Wrappers.Dials.Spotfinder import Spotfinder
  from xia2.Wrappers.Dials.Index import Index
  from xia2.Wrappers.Dials.Integrate import Integrate
  from xia2.Wrappers.Dials.RefineBravaisSettings import RefineBravaisSettings
  from xia2.Wrappers.Dials.Refine import Refine
  from xia2.Wrappers.Dials.Reindex import Reindex
  from xia2.Wrappers.Dials.ExportMtz import ExportMtz
  from xia2.Wrappers.Dials.ExportXDSASCII import ExportXDSASCII

  xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
  template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
  scan_ranges = [(1, 45)]
  image_range = (1, 45)

  cwd = os.path.abspath(os.curdir)
  tmp_dir = os.path.abspath(open_tmp_directory())
  os.chdir(tmp_dir)

  print "Begin importing"
  importer = Import()
  importer.setup_from_image(template %1)
  importer.set_image_range(image_range)
  importer.run()
  print ''.join(importer.get_all_output())
  print "Done importing"

  print "Begin spotfinding"
  spotfinder = Spotfinder()
  spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
  spotfinder.set_scan_ranges(scan_ranges)
  spotfinder.run()
  print ''.join(spotfinder.get_all_output())
  print "Done spotfinding"

  print "Begin indexing"
  indexer = Index()
  indexer.add_spot_filename(spotfinder.get_spot_filename())
  indexer.add_sweep_filename(importer.get_sweep_filename())
  indexer.run('fft3d')
  print ''.join(indexer.get_all_output())
  print "Done indexing"

  print "Begin refining"
  rbs = RefineBravaisSettings()
  rbs.set_experiments_filename(indexer.get_experiments_filename())
  rbs.set_indexed_filename(indexer.get_indexed_filename())
  rbs.run()
  print ''.join(rbs.get_all_output())
  print "Done refining"
  bravais_setting_22 = rbs.get_bravais_summary()[22]
  assert bravais_setting_22['bravais'] == 'cI'
  assert bravais_setting_22['cb_op'] == 'b+c,a+c,a+b'
  assert approx_equal(bravais_setting_22['unit_cell'],
                      (78.14,78.14,78.14,90,90,90), eps=1e-1)
  bravais_setting_22_json = bravais_setting_22['experiments_file']
  assert os.path.exists(bravais_setting_22_json)

  print "Begin reindexing"
  reindexer = Reindex()
  reindexer.set_experiments_filename(indexer.get_experiments_filename())
  reindexer.set_indexed_filename(indexer.get_indexed_filename())
  reindexer.set_cb_op(bravais_setting_22['cb_op'])
  reindexer.run()
  assert os.path.exists(reindexer.get_reindexed_experiments_filename())
  assert os.path.exists(reindexer.get_reindexed_reflections_filename())
  print ''.join(reindexer.get_all_output())
  print "Done reindexing"

  print "Begin refining"
  refiner = Refine()
  refiner.set_experiments_filename(bravais_setting_22_json)
  refiner.set_indexed_filename(reindexer.get_reindexed_reflections_filename())
  refiner.set_scan_varying(True)
  refiner.run()
  assert os.path.exists(refiner.get_refined_experiments_filename())
  print ''.join(refiner.get_all_output())
  print "Done refining"

  print "Begin integrating"
  integrater = Integrate()
  integrater.set_experiments_filename(refiner.get_refined_experiments_filename())
  integrater.set_reflections_filename(reindexer.get_reindexed_reflections_filename())
  integrater.run()
  print ''.join(integrater.get_all_output())
  print "Done integrating"

  print "Begin exporting"
  exporter = ExportMtz()
  exporter.set_experiments_filename(integrater.get_integrated_experiments())
  exporter.set_reflections_filename(integrater.get_integrated_reflections())
  exporter.run()
  print ''.join(exporter.get_all_output())
  print "Done exporting"
  assert os.path.exists(exporter.get_mtz_filename())

  print "Begin exporting xds_ascii"
  exporter = ExportXDSASCII()
  exporter.set_experiments_filename(integrater.get_integrated_experiments())
  exporter.set_reflections_filename(integrater.get_integrated_reflections())
  exporter.run()
  print ''.join(exporter.get_all_output())
  print "Done exporting"
  assert os.path.exists(exporter.get_hkl_filename())

  import shutil
  shutil.copy(indexer.get_experiments_filename(), "copy.json")
  shutil.copy(indexer.get_indexed_filename(), "copy.pickle")
  print "Begin combining"
  from xia2.Wrappers.Dials.CombineExperiments import CombineExperiments
  exporter = CombineExperiments()
  exporter.add_experiments(indexer.get_experiments_filename())
  exporter.add_experiments("copy.json")
  exporter.add_reflections(indexer.get_indexed_filename())
  exporter.add_reflections("copy.pickle")
  exporter.run()
  print ''.join(exporter.get_all_output())
  print "Done combining"
  assert os.path.exists(exporter.get_combined_experiments_filename())
  assert os.path.exists(exporter.get_combined_reflections_filename())
Пример #6
0
def exercise_dials_wrappers(dials_regression, nproc=None):
    if nproc is not None:
        from xia2.Handlers.Phil import PhilIndex
        PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc

    from xia2.Wrappers.Dials.Import import Import
    from xia2.Wrappers.Dials.Spotfinder import Spotfinder
    from xia2.Wrappers.Dials.Index import Index
    from xia2.Wrappers.Dials.Integrate import Integrate
    from xia2.Wrappers.Dials.RefineBravaisSettings import RefineBravaisSettings
    from xia2.Wrappers.Dials.Refine import Refine
    from xia2.Wrappers.Dials.Reindex import Reindex
    from xia2.Wrappers.Dials.ExportMtz import ExportMtz
    from xia2.Wrappers.Dials.ExportXDSASCII import ExportXDSASCII

    xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
    template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
    scan_ranges = [(1, 45)]
    image_range = (1, 45)

    print("Begin importing")
    importer = Import()
    importer.setup_from_image(template % 1)
    importer.set_image_range(image_range)
    importer.run()
    print(''.join(importer.get_all_output()))
    print("Done importing")

    print("Begin spotfinding")
    spotfinder = Spotfinder()
    spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
    spotfinder.set_scan_ranges(scan_ranges)
    spotfinder.run()
    print(''.join(spotfinder.get_all_output()))
    print("Done spotfinding")

    print("Begin indexing")
    indexer = Index()
    indexer.add_spot_filename(spotfinder.get_spot_filename())
    indexer.add_sweep_filename(importer.get_sweep_filename())
    indexer.run('fft3d')
    print(''.join(indexer.get_all_output()))
    print("Done indexing")

    print("Begin refining")
    rbs = RefineBravaisSettings()
    rbs.set_experiments_filename(indexer.get_experiments_filename())
    rbs.set_indexed_filename(indexer.get_indexed_filename())
    rbs.run()
    print(''.join(rbs.get_all_output()))
    print("Done refining")
    bravais_setting_22 = rbs.get_bravais_summary()[22]
    assert bravais_setting_22['bravais'] == 'cI'
    assert bravais_setting_22['cb_op'] == 'b+c,a+c,a+b'
    assert approx_equal(bravais_setting_22['unit_cell'],
                        (78.14, 78.14, 78.14, 90, 90, 90),
                        eps=1e-1)
    bravais_setting_22_json = bravais_setting_22['experiments_file']
    assert os.path.exists(bravais_setting_22_json)

    print("Begin reindexing")
    reindexer = Reindex()
    reindexer.set_experiments_filename(indexer.get_experiments_filename())
    reindexer.set_indexed_filename(indexer.get_indexed_filename())
    reindexer.set_cb_op(bravais_setting_22['cb_op'])
    reindexer.run()
    assert os.path.exists(reindexer.get_reindexed_experiments_filename())
    assert os.path.exists(reindexer.get_reindexed_reflections_filename())
    print(''.join(reindexer.get_all_output()))
    print("Done reindexing")

    print("Begin refining")
    refiner = Refine()
    refiner.set_experiments_filename(bravais_setting_22_json)
    refiner.set_indexed_filename(
        reindexer.get_reindexed_reflections_filename())
    refiner.set_scan_varying(True)
    refiner.run()
    assert os.path.exists(refiner.get_refined_experiments_filename())
    print(''.join(refiner.get_all_output()))
    print("Done refining")

    print("Begin integrating")
    integrater = Integrate()
    integrater.set_experiments_filename(
        refiner.get_refined_experiments_filename())
    integrater.set_reflections_filename(
        reindexer.get_reindexed_reflections_filename())
    integrater.run()
    print(''.join(integrater.get_all_output()))
    print("Done integrating")

    print("Begin exporting")
    exporter = ExportMtz()
    exporter.set_experiments_filename(integrater.get_integrated_experiments())
    exporter.set_reflections_filename(integrater.get_integrated_reflections())
    exporter.run()
    print(''.join(exporter.get_all_output()))
    print("Done exporting")
    assert os.path.exists(exporter.get_mtz_filename())

    print("Begin exporting xds_ascii")
    exporter = ExportXDSASCII()
    exporter.set_experiments_filename(integrater.get_integrated_experiments())
    exporter.set_reflections_filename(integrater.get_integrated_reflections())
    exporter.run()
    print(''.join(exporter.get_all_output()))
    print("Done exporting")
    assert os.path.exists(exporter.get_hkl_filename())

    import shutil
    shutil.copy(indexer.get_experiments_filename(), "copy.json")
    shutil.copy(indexer.get_indexed_filename(), "copy.pickle")
    print("Begin combining")
    from xia2.Wrappers.Dials.CombineExperiments import CombineExperiments
    exporter = CombineExperiments()
    exporter.add_experiments(indexer.get_experiments_filename())
    exporter.add_experiments("copy.json")
    exporter.add_reflections(indexer.get_indexed_filename())
    exporter.add_reflections("copy.pickle")
    exporter.run()
    print(''.join(exporter.get_all_output()))
    print("Done combining")
    assert os.path.exists(exporter.get_combined_experiments_filename())
    assert os.path.exists(exporter.get_combined_reflections_filename())