hyperspy.api.roi

hyperspy.api.roi.CircleROI([cx, cy, r, r_inner])	Selects a circular or annular region in a 2D space.
hyperspy.api.roi.Line2DROI([x1, y1, x2, y2, ...])	Selects a line of a given width in 2D space.
hyperspy.api.roi.Point1DROI([value])	Selects a single point in a 1D space.
hyperspy.api.roi.Point2DROI([x, y])	Selects a single point in a 2D space.
hyperspy.api.roi.RectangularROI([left, top, ...])	Selects a range in a 2D space.
hyperspy.api.roi.SpanROI([left, right])	Selects a range in a 1D space.

Region of interests (ROIs) operate on BaseSignal instances and include widgets for interactive operation.

The following 1D ROIs are available:

1D ROIs

Point1DROI	Single element ROI of a 1D signal
SpanROI	Interval ROI of a 1D signal

The following 2D ROIs are available:

2D ROIs

Point2DROI	Single element ROI of a 2D signal
RectangularROI	Rectagular ROI of a 2D signal
CircleROI	(Hollow) circular ROI of a 2D signal
Line2DROI	Line profile of a 2D signal with customisable width

class hyperspy.api.roi.CircleROI(cx=None, cy=None, r=None, r_inner=0)

Bases: BaseInteractiveROI

Selects a circular or annular region in a 2D space. The coordinates of the center of the circle are stored in the ‘cx’ and ‘cy’ attributes. The radious in the r attribute. If an internal radius is defined using the r_inner attribute, then an annular region is selected instead. CircleROI can be used in place of a tuple containing (cx, cy, r), (cx, cy, r, r_inner) when r_inner is not None.

Sets up events.changed event, and inits HasTraits.

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

is_valid()

Determine if the ROI is in a valid state.

This is typically determined by all the coordinates being defined, and that the values makes sense relative to each other.

class hyperspy.api.roi.Line2DROI(x1=None, y1=None, x2=None, y2=None, linewidth=0)

Bases: BaseInteractiveROI

Selects a line of a given width in 2D space. The coordinates of the end points of the line are stored in the x1, y1, x2, y2 parameters. The length is available in the length parameter and the method angle computes the angle of the line with the axes.

Line2DROI can be used in place of a tuple containing the coordinates of the two end-points of the line and the linewdith (x1, y1, x2, y2, linewidth).

Sets up events.changed event, and inits HasTraits.

angle(axis='horizontal', units='degrees')

“Angle between ROI line and selected axis

Parameters:

axisstr, {‘horizontal’, ‘vertical’}, optional

Select axis against which the angle of the ROI line is measured. ‘x’ is alias to ‘horizontal’ and ‘y’ is ‘vertical’ (Default: ‘horizontal’)

unitsstr, {‘degrees’, ‘radians’}

The angle units of the output (Default: ‘degrees’)

Returns:

anglefloat

Examples

>>> r = hs.roi.Line2DROI(0., 0., 1., 2.)
>>> print(r.angle())
63.43494882292201

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

static profile_line(img, src, dst, axes, linewidth=1, order=1, mode='constant', cval=0.0)

Return the intensity profile of an image measured along a scan line.

Parameters:

imgnumpy.ndarray

The image, either grayscale (2D array) or multichannel (3D array, where the final axis contains the channel information).

srctuple of float, tuple of int

The start point of the scan line. Length of tuple is 2.

dsttuple of float, tuple of int

The end point of the scan line. Length of tuple is 2.

linewidthint, optional

Width of the scan, perpendicular to the line

order{0, 1, 2, 3, 4, 5}, optional

The order of the spline interpolation to compute image values at non-integer coordinates. 0 means nearest-neighbor interpolation.

mode{‘constant’, ‘nearest’, ‘reflect’, ‘wrap’}, optional

How to compute any values falling outside of the image.

cvalfloat, optional

If mode='constant', what constant value to use outside the image.

Returns:

numpy.ndarray

The intensity profile along the scan line. The length of the profile is the ceil of the computed length of the scan line.

Notes

The destination point is included in the profile, in contrast to standard numpy indexing. Requires uniform navigation axes.

class hyperspy.api.roi.Point1DROI(value=None)

Bases: BasePointROI

Selects a single point in a 1D space. The coordinate of the point in the 1D space is stored in the ‘value’ trait.

Point1DROI can be used in place of a tuple containing the value of value.

Examples

>>> roi = hs.roi.Point1DROI(0.5)
>>> value, = roi
>>> print(value)
0.5

Sets up events.changed event, and inits HasTraits.

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

class hyperspy.api.roi.Point2DROI(x=None, y=None)

Bases: BasePointROI

Selects a single point in a 2D space. The coordinates of the point in the 2D space are stored in the traits 'x' and 'y'.

Point2DROI can be used in place of a tuple containing the coordinates of the point (x, y).

Examples

>>> roi = hs.roi.Point2DROI(3, 5)
>>> x, y = roi
>>> print(x, y)
3.0 5.0

Sets up events.changed event, and inits HasTraits.

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

class hyperspy.api.roi.RectangularROI(left=None, top=None, right=None, bottom=None)

Bases: BaseInteractiveROI

Selects a range in a 2D space. The coordinates of the range in the 2D space are stored in the traits 'left', 'right', 'top' and 'bottom'. Convenience properties 'x', 'y', 'width' and 'height' are also available, but cannot be used for initialization.

RectangularROI can be used in place of a tuple containing (left, right, top, bottom).

Examples

>>> roi = hs.roi.RectangularROI(left=0, right=10, top=20, bottom=20.5)
>>> left, right, top, bottom = roi
>>> print(left, right, top, bottom)
0.0 10.0 20.0 20.5

Sets up events.changed event, and inits HasTraits.

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

property height

Returns / sets the height of the ROI

is_valid()

Determine if the ROI is in a valid state.

This is typically determined by all the coordinates being defined, and that the values makes sense relative to each other.

property width

Returns / sets the width of the ROI

property x

Returns / sets the x coordinate of the ROI without changing its width

property y

Returns / sets the y coordinate of the ROI without changing its height

class hyperspy.api.roi.SpanROI(left=None, right=None)

Bases: BaseInteractiveROI

Selects a range in a 1D space. The coordinates of the range in the 1D space are stored in the traits 'left' and 'right'.

SpanROI can be used in place of a tuple containing the left and right values.

Examples

>>> roi = hs.roi.SpanROI(-3, 5)
>>> left, right = roi
>>> print(left, right)
-3.0 5.0

Sets up events.changed event, and inits HasTraits.

gui(display=True, toolkit=None, **kwargs)

Display or return interactive GUI element if available.

Parameters:

displaybool

If True, display the user interface widgets. If False, return the widgets container in a dictionary, usually for customisation or testing.

toolkitstr, iterable of str or None

If None (default), all available widgets are displayed or returned. If string, only the widgets of the selected toolkit are displayed if available. If an interable of toolkit strings, the widgets of all listed toolkits are displayed or returned.

is_valid()

Determine if the ROI is in a valid state.

This is typically determined by all the coordinates being defined, and that the values makes sense relative to each other.