Fix import of reflection file reader

import h5py

import iotbx 

from iotbx.reflection_file_reader import any_reflection_file

import numpy as np

import scipy.linalg

instrument_mask = '/HFIR/CG4D/shared/instrument/data/instrument_coverage.nxs'

mtz_file = '/HFIR/CG4D/shared/instrument/data/t4-mtz-files/5VNQ.0.mtz'

instrument_mask = 'instrument_coverage.nxs'

mtz_file = '5VNQ.0.mtz'

# load instrument mapping

f = h5py.File(instrument_mask, 'r')

coverage = data['signal'][()].T

f.close()

# transform bin edges to centers and create dense mesh

# transform bin edges to centers and create dense mesh #kb 3d volume of what?

Qx, Qy, Qz = [0.5*(comp[1:]+comp[:-1]) for comp in [Qx, Qy, Qz]] # bin edges to centers

Qx, Qy, Qz = np.meshgrid(Qx, Qy, Qz, indexing='ij')

# mask only regions that are in laboratory coverage space

# mask only regions that are in laboratory coverage space #kb detector_coverage?

mask = coverage > 0

Qx, Qy, Qz = Qx[mask], Qy[mask], Qz[mask]

# read reflection file

hkl_file = iotbx.reflection_file_reader.any_reflection_file(mtz_file)

hkl_file = any_reflection_file(mtz_file)

miller = hkl_file.as_miller_arrays()

cryst_symm = miller[0].crystal_symmetry()