snpl.afm module

I/O interface utilities for AFM (atomic force microscope) images.

class snpl.afm.GwyddionSimpleField(fp=None)

Bases: object

Read/write interface for Gwyddion Simple Field format.

See http://gwyddion.net/documentation/user-guide-en/gsf.html for specifications.

Parameters:

fp – Source file (path or file-like object). If None, create an empty object.

h

header.

• “XRes”: pixel number along the x axis.

• “YRes”: pixel number along the y axis.

• “XReal”: real length of the image along the x axis (in meter).

• “YReal”: real length of the image along the y axis (in meter).

• “XOffset”: offset to the x coordinates.

• “YOffset”: offset to the y coordinates.

• “Title”: title string.

• “XYUnits”: string describing the unit. (usually m (meter)).

• “ZUnits”: string describing the unit. (usually m (meter)).

Type:

dict

x

1-d array of the x-coordinates along x axis.

Type:

numpy.ndarray

y

1-d array of the y-coordinates along y axis.

Type:

numpy.ndarray

zmat

2-d array of the z data (height, phase angle, etc)

Type:

numpy.ndarray

xmat

2-d array of the x coordinates.

Type:

numpy.ndarray

ymat

2-d array of the y coordinates.

Type:

numpy.ndarray

path

path to the source file, if any.

Type:

str

Example

>>> d = afm.GwyddionSimpleField("test.gsf")
>>> pyplot.pcolormesh(d.xmat, d.ymat, d.zmat, shading="nearest")
>>> pyplot.show()
>>> d.save("save_test.gsf")

load_from_binary(bindata)

save(fp)

Saves the image in GSF format.

The saved file can be opened by Gwyddion (hopefully)

Parameters:

fp (str or file-like) – destination

snpl.afm.load_xq(fp, ztype='auto')

Loads a .xqdx or .xqpx files from Hitachi AFM.

Parameters:

• fp – file path or file-like object. The object must be in the binary read mode.

• ztype – type of the z axis. if “auto”, it is inferred from the extension. .xqdx = height, .xqpx = phase. Or it can be either of “topography” or “phase”.

Returns:

a GwyddionSimpleField object.

Examples

>>> d = afm.load_xq("test_afm_raw_data_file.xqdx")
>>> pyplot.pcolormesh(d.xmat, d.ymat, d.zmat, shading="nearest")
>>> pyplot.show()
>>> d.save("test_afm_saved_data.gjf") # save it as a Gwyddion Simple Field format

snpl.afm.row_background_polynomial(xmat, zmat, polydeg=1, mask=None)

Calculates polynomial background for each scan row.

Performs polynomial fitting to each row in zmat. This is one of the basic method to correct for the mismatch between scan lines and the curving of each scan line.

Parameters:

• xmat (numpy.ndarray) – 2-d array of x coordinates.

• zmat (numpy.ndarray) – 2-d array of z coordinates (e.g., height)

• polydeg (int) – Degree of polynomial used in the fitting. Must be a non-negative integer. Defaults to 1.

• mask (numpy.ndarray or None) – A 2-d truth array specifying which points to use in the fitting. If None, all points will be used. Defaults to None.

Returns:

A 2-d numpy.ndarray with the same size as zmat.

Examples

>>> d = afm.load_xq("test_data.xqdx")
>>> xmat = d.xmat*1e6
>>> ymat = d.ymat*1e6
>>> zmat = d.zmat*1e6
>>>
>>> mask = np.logical_or(xmat < 2.5, 16.0 < xmat) # mask a part of the image
>>> zbmat = afm.row_background_polynomial(xmat, zmat, polydeg=1, mask=mask)
>>>
>>> pyplot.gca().set_aspect("equal")
>>> pyplot.pcolormesh(xmat, ymat, zmat - zbmat)
>>> pyplot.colorbar()
>>> pyplot.show()