Metadata-Version: 2.0
Name: SPIEPy
Version: 0.2.0
Summary: SPIEPy (Scanning Probe Image Enchanter using Python) is a Python library to improve automatic processing of SPM images.
Home-page: https://pypi.org/project/SPIEPy/
Author: Stephan Zevenhuizen
Author-email: S.J.M.Zevenhuizen@uu.nl
License: The license file is in the package.
Description-Content-Type: UNKNOWN
Keywords: SPM scanning probe microscopy image analysis flattening nano nanotechnology
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=2.6, !=3.0.*, !=3.1.*, !=3.2.*, <4
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: scipy

Python is a great language to use for automatic processing of scientific data.
Scanning probe microscopes (SPM) produce scientific data in the form of images,
images of surfaces that can have atomic or molecular resolutions. The microscope
produces surfaces that are not level. Before you can analyse the surface, the
surface must first be levelled (flattened). This Python library provides
routines to flatten the surface and to generate statistical data on surface
structures. Surfaces with contaminations, step edges and atomic or molecular
resolution can be handled.

SPIEPy and SPIW - MATLAB Toolbox [`source`_] are related projects. SPIEPy uses
many algorithms originally designed by the SPIW project. The performance of
these algorithms is discussed in REVIEW OF SCIENTIFIC INSTRUMENTS **84**, 113701
(2013) [`DOI`_].

.. _source: http://sourceforge.net/projects/spiw/
.. _DOI: http://dx.doi.org/10.1063/1.4827076

The library SPIEPy has the packages spiepy with the modules for the tasks
described above and spiepy.demo to generate sample data. With this sample data,
you can familiarize yourself with SPIEPy.

Dependencies
------------
SPIEPy requires the NumPy library (http://www.numpy.org), SciPy library
(http://scipy.org) and the Matplotlib library (http://matplotlib.org).

Installation
------------
Using pip::

    > pip install SPIEPy

CLASSES
-------
Im
    SPIEPy_image_structure, set attribute ``data`` with a 2D ndarray of image
    data, set all other attributes with the metadata of the image.

FUNCTIONS
---------
Flattening functions:

- flatten_by_iterate_mask
- flatten_by_peaks
- flatten_poly_xy
- flatten_xy

Locating functions:

- locate_masked_points_and_remove
- locate_regions
- locate_steps
- locate_troughs_and_peaks

Masking functions:

- mask_by_mean
- mask_by_troughs_and_peaks
- mask_tidy

Measuring functions:

- measure_feature_properties

Demo functions:

- list_demo_files
- load_demo_file

DATA
----
NANOMAP
    Colormap which is the standard orange colormap used my most SPM software.

Help
----
On the interpreter console use the built-in help function to get the help page
of the module, function, ...

.. code-block:: pycon

    >>> import spiepy, spiepy.demo
    >>> help(spiepy)
    ...
    >>> help(spiepy.demo)
    ...
    >>> help(spiepy.flatten_by_iterate_mask)
    ...

**Documentation:** http://www.staff.science.uu.nl/~zeven101/SPIEPy/

Example usage
-------------
.. code-block:: python

    # -*- coding: utf-8 -*-
    #
    #   Copyright © 2014 - 2017 Stephan Zevenhuizen
    #   Flattening terrace image, (09-10-2017).
    #

    import spiepy, spiepy.demo
    import matplotlib.pyplot as plt
    import numpy as np

    im = spiepy.Im()
    demos = spiepy.demo.list_demo_files()
    print(demos)
    im.data = spiepy.demo.load_demo_file(demos[1])

    plt.imshow(im.data, cmap = spiepy.NANOMAP, origin = 'lower')
    print('Original image.')
    plt.show()

    im_out, _ = spiepy.flatten_xy(im)
    plt.imshow(im_out.data, cmap = spiepy.NANOMAP, origin = 'lower')
    print('Preflattened image.')
    plt.show()

    mask = spiepy.locate_steps(im_out, 4)
    plot_image = np.ma.array(im_out.data, mask = mask)
    palette = spiepy.NANOMAP
    palette.set_bad('#00ff00', 1.0)
    plt.imshow(plot_image, cmap = palette, origin = 'lower')
    print('Preflattened image, mask.')
    plt.show()

    im_final, _ = spiepy.flatten_xy(im, mask)
    plt.imshow(im_final.data, cmap = spiepy.NANOMAP, origin = 'lower')
    print('Flattened image.')
    plt.show()

    y, x = np.histogram(im_out.data, bins = 200)
    ys, xs = np.histogram(im_final.data, bins = 200)
    fig, ax = plt.subplots()
    ax.plot(x[:-1], y, '-b', label = 'Standard plane flattening')
    ax.plot(xs[:-1], ys, '-r', label = 'SPIEPy stepped plane flattening')
    ax.legend(loc = 2, fancybox = True, framealpha = 0.2)
    ax.set_xlabel('z (nm)')
    ax.set_ylabel('count')
    plt.show()

Authors & affiliations
----------------------
Stephan J. M. Zevenhuizen [#]_

..  [#] Condensed Matter and Interfaces, Debye Institute for Nanomaterials
    Science, Utrecht University, Utrecht, The Netherlands.


