BornAgain ≻ 24 ≻ Documentation ≻ Reference ≻ Data import ≻ Detector images

Formats

Area detectors save binary image formats: TIFF, EDF, CBF, HDF5, MAR, Pilatus, and many more. The Python package Fabio decodes some 35 such formats, including their metadata conventions. It is not installed with BornAgain; install it once with

pip install fabio

Import

import fabio
import numpy as np

img = fabio.open("detector_image.tif.gz")
image = np.asarray(img.data, dtype=float)

or, equivalently:

import fabio

img = fabio.open("detector_image.tif.gz")
image = img.data.astype(float)

fabio.open handles compression (.gz, .bz2) transparently and returns an image object:

  • img.data — the pixel matrix as a 2D NumPy array of shape (rows, columns), with the dtype stored in the file (often integer counts — hence the conversion to float);
  • img.header — a dict with the file’s metadata.

The array shape must match the detector pixel layout used by the simulation, namely (n_alpha, n_phi) for SphericalDetector intensities, with row 0 at the smallest alpha_f. Verify the row orientation once per instrument against a known feature — for instance, the specular peak must sit at alpha_f = alpha_i; if it does not, flip the image:

image = np.flipud(image)

For a worked example, see expfit_galaxi.py, which fits a GISAS pattern to a TIFF image from the GALAXI instrument.