Reading CXI files

1) File structure

CXI files are really HDF5 files with a defined structure and naming convention. The files follow the standards of CXI-DB files (www.cxidb.org).

The CXI files that are produced by Condor have the following structure:

Path	Content	Shape
/entry_1/data_1/	Image data group
/entry_1/data_1/data	Intensity patterns	(N,X,Y)
/entry_1/data_1/data_fourier	Diffraction amplitudes (complex valued)	(N,X,Y)
/entry_1/data_1/mask	Pixel masks (see condor.utils.pixelmask.PixelMask)	(N,X,Y)
/source/	Source data group
/source/pulse_energy	pulse_energy	N
/source/. . .	. . .	. . .
/particles/particle_0i	Particle #i data group
/particles/particle_00/extrinsic_quaternion	Quaternions defining particle orientation	(N,4)
/particles/particle_00/. . .	. . .	. . .
/detector	Detector data group
/detector/cx	X-coord. for center of the diffraction patterns	N
/detector/. . .	. . .	. . .

CXI files can be opened with any HDF5 file reader. For browsing and inspecting diffraction patterns produced with Condor the viewer Owl can come handy (github.com/FilipeMaia/owl/wiki/Owl-wiki).

2) Examples

Here are examples for Python and Matlab demonstrating how to access the data stored in a CXI file.

a) Python

import h5py, numpy

with h5py.File('condor.cxi', 'r') as f:
  intensity_pattern0 = numpy.asarray(f["entry_1/data_1/data"])

print("Maximum intensity value in first pattern: %f photons" % intensity_pattern[0].max())

b) Matlab

fid = H5F.open('condor.cxi');
dset_id = H5D.open(fid,'/entry_1/data_1/data');

intensity_patterns = H5D.read(dset_id);

H5D.close(dset_id);
H5F.close(fid);