Python main Examples

Example #1

def test_generate_test_reflections(tmpdir):
    tmpdir.chdir()
    from libtbx.phil import command_line

    from dials.algorithms.simulation.generate_test_reflections import main, master_phil

    cmd = command_line.argument_interpreter(master_phil=master_phil)
    working_phil = cmd.process_and_fetch(
        args=[
            """nrefl = 10
shoebox_size {
  x = 20
  y = 20
  z = 20
}
spot_size {
  x = 1
  y = 3
  z = 1
}
spot_offset {
  x = -0.5
  y = -0.5
  z = -0.5
}
mask_nsigma = 3.0
counts = 10000
background = 0
background_a = 10
background_b = 0.1
background_c = -0.1
background_d = 0
pixel_mask = *all static precise
background_method = *xds mosflm
integration_methpd = *xds mosflm
output {
  over = None
  under = None
  all = all_refl.refl
}
rotation {
  axis {
    x = 0
    y = 0
    z = 1
  }
  angle = 45
}
"""
        ]
    )
    main(working_phil.extract())
    assert (tmpdir / "all_refl.refl").check()

Example #2

File: tst_background_subtraction.py Project: kek-pf-mx/dials

    def generate_profiles(self, num, counts):
        from dials.algorithms.simulation.generate_test_reflections import main
        from dials.algorithms.simulation.generate_test_reflections import \
          master_phil
        from libtbx.phil import command_line
        cmd = command_line.argument_interpreter(master_params=master_phil)
        working_phil = cmd.process_and_fetch(args=[
            """
      nrefl = %d
      shoebox_size {
        x = 10
        y = 10
        z = 10
      }
      spot_size {
        x = 1
        y = 1
        z = 1
      }
      spot_offset {
        x = -0.5
        y = -0.5
        z = -0.5
      }
      mask_nsigma = 3.0
      counts = %d
      background = 10
      pixel_mask = all *static precise
      background_method = *xds mosflm
      integration_methpd = *xds mosflm
      output {
        over = None
        under = None
        all = all_refl.pickle
      }
      rotation {
        axis {
          x = 0
          y = 0
          z = 1
        }
        angle = 0
      }

      """ % (num, counts)
        ])
        main(working_phil.extract())
        import six.moves.cPickle as pickle
        with open("all_refl.pickle", "rb") as fh:
            return pickle.load(fh)

Example #3

File: tst_generate_test_refl.py Project: biochem-fan/dials

def tst_generate_test_reflections():
  from dials.algorithms.simulation.generate_test_reflections import main
  from dials.algorithms.simulation.generate_test_reflections import \
    master_phil
  from libtbx.phil import command_line
  cmd = command_line.argument_interpreter(master_params = master_phil)
  working_phil = cmd.process_and_fetch(args = ["""nrefl = 10
shoebox_size {
  x = 20
  y = 20
  z = 20
}
spot_size {
  x = 1
  y = 3
  z = 1
}
spot_offset {
  x = -0.5
  y = -0.5
  z = -0.5
}
mask_nsigma = 3.0
counts = 10000
background = 0
background_a = 10
background_b = 0.1
background_c = -0.1
background_d = 0
pixel_mask = *all static precise
background_method = *xds mosflm
integration_methpd = *xds mosflm
output {
  over = None
  under = None
  all = all_refl.pickle
}
rotation {
  axis {
    x = 0
    y = 0
    z = 1
  }
  angle = 45
}

"""])
  main(working_phil.extract())
  print 'OK'

Example #4

File: tst_background_subtraction.py Project: biochem-fan/dials

  def generate_profiles(self, num, counts):
    from dials.algorithms.simulation.generate_test_reflections import main
    from dials.algorithms.simulation.generate_test_reflections import \
      master_phil
    from libtbx.phil import command_line
    cmd = command_line.argument_interpreter(master_params = master_phil)
    working_phil = cmd.process_and_fetch(args = ["""
      nrefl = %d
      shoebox_size {
        x = 10
        y = 10
        z = 10
      }
      spot_size {
        x = 1
        y = 1
        z = 1
      }
      spot_offset {
        x = -0.5
        y = -0.5
        z = -0.5
      }
      mask_nsigma = 3.0
      counts = %d
      background = 10
      pixel_mask = all *static precise
      background_method = *xds mosflm
      integration_methpd = *xds mosflm
      output {
        over = None
        under = None
        all = all_refl.pickle
      }
      rotation {
        axis {
          x = 0
          y = 0
          z = 1
        }
        angle = 0
      }

      """ % (num, counts)])
    main(working_phil.extract())
    import cPickle as pickle
    return pickle.load(open("all_refl.pickle", "rb"))