anntzer / gwyfile

A pure Python interface to reading and writing Gwyddion files.

gwyfile

A pure Python interface to reading and writing Gwyddion files.

Installation

$ pip install gwyfile

Usage

At the heart of this module is the GwyObject class, derived from collections.OrderedDict. Gwyddion files are just serialized copies of GwyObjects and its subclasses (GwyContainer, GwyDataField, ...).

Here is a simple example that shows how to load a file and display a data channel:

import gwyfile

# Load a Gwyddion file into memory
obj = gwyfile.load('test.gwy')
# Return a dictionary with the datafield titles as keys and the
# datafield objects as values.
channels = gwyfile.util.get_datafields(obj)
channel = channels['Test']
# Datafield objects have a `data` property to access their
# two-dimensional data as numpy arrays.
data = channel.data

# Plot the data using matplotlib.
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.imshow(data, interpolation='none', origin='upper',
        extent=(0, channel.xreal, 0, channel.yreal))
plt.show()

It is also possible to manipulate and save objects:

import numpy as np
from gwyfile.objects import GwyContainer, GwyDataField
obj = GwyContainer()
obj['/0/data/title'] = 'Noise'
data = np.random.normal(size=(256, 256))
obj['/0/data'] = GwyDataField(data)
obj.tofile('noise.gwy')

The Gwyddion manual has a nice description of the file format. See there for further information on object properties.

Status

GwyObject serialization and deserialization should be complete. There are specialized subclasses for GwyDataField and GwySIUnit, but other convenience wrappers e.g. for GwyBrick are missing.

License

This project is licensed under the MIT license. See LICENSE.rst for details.

© 2014-17 Tino Wagner