magni.imaging.measurements._spiral module

Module providing public functions for the magni.imaging.measurements subpackage.

Routine listings

spiral_sample_image(h, w, scan_length, num_points, rect_area=False)

Function for spiral sampling an image.

spiral_sample_surface(l, w, speed, sample_rate, time, rect_area=False)

Function for spiral sampling a surface.

magni.imaging.measurements._spiral.spiral_sample_image(h, w, scan_length, num_points, rect_area=False)

Sample an image using an archimedean spiral pattern.

The coordinates (in units of pixels) resulting from sampling an image of size h times w using an archimedean spiral pattern are determined. The scan_length determines the length of the path scanned whereas num_points indicates the number of samples taken on that path.

Parameters:

• h (int) – The height of the area to scan in units of pixels.
• w (int) – The width of the area to scan in units of pixels.
• scan_length (float) – The length of the path to scan in units of pixels.
• num_points (int) – The number of samples to take on the scanned path.
• rect_area (bool) – A flag indicating whether or not the full rectangular area is sampled (the default value is False which implies that the “corners” of the rectangular area are not sampled).

Returns:

coords (ndarray) – The coordinates of the samples arranged into a 2D array, such that each row is a coordinate pair (x, y).

Notes

The orientation of the coordinate system is such that the width w is measured along the x-axis whereas the height h is measured along the y-axis. The width must equal the height for an archimedian spiral to make sense.

If the rect_area flag is True, then it is assumed that the sampling continues outside of the rectangular area specified by h and w such that the “corners” of the rectangular area are also sampled. The sample points outside of the rectangular area are discarded and, hence, not returned.

Examples

For example,

>>> import numpy as np
>>> from magni.imaging.measurements import spiral_sample_image
>>> h = 10
>>> w = 10
>>> scan_length = 50.0
>>> num_points = 12
>>> np.set_printoptions(suppress=True)
>>> spiral_sample_image(h, w, scan_length, num_points)
array([[ 6.28776846,  5.17074073],
       [ 3.13304898,  5.24133767],
       [ 6.07293751,  2.93873701],
       [ 6.99638041,  6.80851189],
       [ 2.89868434,  7.16724999],
       [ 2.35773914,  3.00320067],
       [ 6.41495385,  1.71018152],
       [ 8.82168896,  5.27557847],
       [ 6.34932919,  8.83624957],
       [ 2.04885699,  8.11199373],
       [ 0.6196052 ,  3.96939755]])

magni.imaging.measurements._spiral.spiral_sample_surface(l, w, speed, sample_rate, time, rect_area=False)

Sample a surface area using an archimedean spiral pattern.

The coordinates (in units of meters) resulting from sampling an area of size l times w using an archimedean spiral pattern are determined. The scanned path is determined from the probe speed and the scan time.

Parameters:

• l (float) – The length of the area to scan in units of meters.
• w (float) – The width of the area to scan in units of meters.
• speed (float) – The probe speed in units of meters/second.
• sample_rate (float) – The sample rate in units of Hertz.
• time (float) – The scan time in units of seconds.
• rect_area (bool) – A flag indicating whether or not the full rectangular area is sampled (the default value is False which implies that the “corners” of the rectangular area are not sampled).

Returns:

coords (ndarray) – The coordinates of the samples arranged into a 2D array, such that each row is a coordinate pair (x, y).

Notes

The orientation of the coordinate system is such that the width w is measured along the x-axis whereas the length l is measured along the y-axis. The width must equal the length for an archimedian sprial to make sense.

If the rect_area flag is True, then it is assumed that the sampling continues outside of the rectangular area specified by l and w such that the “corners” of the rectangular area are also sampled. The sample points outside of the rectangular area are discarded and, hence, not returned.

Examples

For example,

>>> import numpy as np
>>> from magni.imaging.measurements import spiral_sample_surface
>>> l = 1e-6
>>> w = 1e-6
>>> speed = 7e-7
>>> sample_rate = 1.0
>>> time = 12.0
>>> np.set_printoptions(suppress=True)
>>> spiral_sample_surface(l, w, speed, sample_rate, time)
array([[ 0.00000036,  0.00000046],
       [ 0.00000052,  0.00000071],
       [ 0.00000052,  0.00000024],
       [ 0.00000059,  0.00000079],
       [ 0.00000021,  0.00000033],
       [ 0.00000084,  0.00000036],
       [ 0.00000049,  0.0000009 ],
       [ 0.0000001 ,  0.00000036],
       [ 0.00000072,  0.00000011],
       [ 0.00000089,  0.00000077],
       [ 0.00000021,  0.00000091]])