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formats.md

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Formats

This package includes some functions to read and write data.

To import:

from instamatic.formats import *

The following readers are available:

  • read_image(fname)
  • read_tiff(fname)
  • read_mrc(fname)
  • read_hdf5(fname)
  • read_adsc(fname)
  • read_cbf(fname)

These functions return a tuple containing the data and header as a dictionary.

The following writers are available:

  • write_image(fname, data, header=None)
    This function figures out the data type from the filename.

  • write_tiff(fname, data, header=None)
    Writes tiff files using the tifffile library, which has support for TVIPS headers. If a header is specified, it is stored in the description tag in yaml format.

  • write_mrc(fname, data, header=None)
    Uses the mrc implementation from the arachnid project.

  • write_hdf5(fname, data, header=None)
    HDF5 files are written using h5py.

  • write_adsc(fname, data, header=None)
    SMV files (adsc) are written using the implementation in fabio.

  • write_cbf(fname, data, header=None)
    Not implemented yet.

Where fname should be a string or a pathlib.Path instance. Data is a numpy array, and the header is a python dictionary.

Example usage:

from instamatic.formats import read_tiff, write_tiff
import numpy as np

fn = "important_data.tiff"
img = (np.random.random((512, 512)) * 1000).astype(np.uint16)

header = {}
header['xres'] = img.shape[0]
header['yres'] = img.shape[1]
header['comment'] = "This is a tiff file"

# save the data
write_tiff(fn, img, header=header)

# read the data
arr, h = read_tiff(fn)

# make sure they are equal
print(arr.shape)
print("allclose:", np.allclose(img, arr))