hyperspy.axes module

class hyperspy.axes.AxesManager(axes_list)

Bases: traits.has_traits.HasTraits

Contains and manages the data axes.

It supports indexing, slicing, subscripting and iteration. As an iterator, iterate over the navigation coordinates returning the current indices. It can only be indexed and sliced to access the DataAxis objects that it contains. Standard indexing and slicing follows the “natural order” as in Signal, i.e. [nX, nY, …,sX, sY,…] where n indicates a navigation axis and s a signal axis. In addition AxesManager support indexing using complex numbers a + bj, where b can be one of 0, 1, 2 and 3 and a a valid index. If b is 3 AxesManager is indexed using the order of the axes in the array. If b is 1(2), indexes only the navigation(signal) axes in the natural order. In addition AxesManager supports subscription using axis name.

coordinates

Get and set the current coordinates if the navigation dimension is not 0. If the navigation dimension is 0 it raises AttributeError when attempting to set its value.

Type: tuple

indices

Get and set the current indices if the navigation dimension is not 0. If the navigation dimension is 0 it raises AttributeError when attempting to set its value.

Type: tuple

signal_axes, navigation_axes

Contain the corresponding DataAxis objects

Type: list

Examples

Create a spectrum with random data

>>> s = hs.signals.Signal1D(np.random.random((2,3,4,5)))
>>> s.axes_manager
<Axes manager, axes: (4, 3, 2|5)>
            Name |   size |  index |  offset |   scale |  units
================ | ====== | ====== | ======= | ======= | ======
     <undefined> |      4 |      0 |       0 |       1 | <undefined>
     <undefined> |      3 |      0 |       0 |       1 | <undefined>
     <undefined> |      2 |      0 |       0 |       1 | <undefined>
---------------- | ------ | ------ | ------- | ------- | ------
     <undefined> |      5 |        |       0 |       1 | <undefined>
>>> s.axes_manager[0]
<Unnamed 0th axis, size: 4, index: 0>
>>> s.axes_manager[3j]
<Unnamed 2nd axis, size: 2, index: 0>
>>> s.axes_manager[1j]
<Unnamed 0th axis, size: 4, index: 0>
>>> s.axes_manager[2j]
<Unnamed 3rd axis, size: 5>
>>> s.axes_manager[1].name = "y"
>>> s.axes_manager["y"]
<y axis, size: 3, index: 0>
>>> for i in s.axes_manager:
...     print(i, s.axes_manager.indices)
...
(0, 0, 0) (0, 0, 0)
(1, 0, 0) (1, 0, 0)
(2, 0, 0) (2, 0, 0)
(3, 0, 0) (3, 0, 0)
(0, 1, 0) (0, 1, 0)
(1, 1, 0) (1, 1, 0)
(2, 1, 0) (2, 1, 0)
(3, 1, 0) (3, 1, 0)
(0, 2, 0) (0, 2, 0)
(1, 2, 0) (1, 2, 0)
(2, 2, 0) (2, 2, 0)
(3, 2, 0) (3, 2, 0)
(0, 0, 1) (0, 0, 1)
(1, 0, 1) (1, 0, 1)
(2, 0, 1) (2, 0, 1)
(3, 0, 1) (3, 0, 1)
(0, 1, 1) (0, 1, 1)
(1, 1, 1) (1, 1, 1)
(2, 1, 1) (2, 1, 1)
(3, 1, 1) (3, 1, 1)
(0, 2, 1) (0, 2, 1)
(1, 2, 1) (1, 2, 1)
(2, 2, 1) (2, 2, 1)
(3, 2, 1) (3, 2, 1)

_get_data_slice(fill=None)

Return a tuple of slice objects to slice the data.

Parameters: fill (None or iterable of (int, slice)) – If not None, fill the tuple of index int with the given slice.

_remove_one_axis(axis)

Remove the given Axis.

Raises: ValueError – If the Axis is not present.

_set_axis_attribute_values(attr, values)

Set the given attribute of all the axes to the given value(s)

Parameters

attr (string) – The DataAxis attribute to set.
values (any) – If iterable, it must have the same number of items as axes are in this AxesManager instance. If not iterable, the attribute of all the axes are set to the given value.

_sort_axes()

Sort _axes to align them.

When the data are aligned with the axes the axes order in self._axes is [nav_n, nav_n-1, …, nav_0, sig_m, sig_m-1 …, sig_0]. This method sort the axes in this way. Warning: this doesn’t sort the data axes.

property axes_are_aligned_with_data

Verify if the data axes are aligned with the signal axes.

When the data are aligned with the axes the axes order in self._axes is [nav_n, nav_n-1, …, nav_0, sig_m, sig_m-1 …, sig_0].

Returns: aligned
Return type: bool

convert_units(axes=None, units=None, same_units=True, factor=0.25)

Convert the scale and the units of the selected axes. If the unit of measure is not supported by the pint library, the scale and units are not changed.

Parameters

axes ({int | string | iterable of DataAxis | None}) – Default = None Convert to a convenient scale and units on the specified axis. If int, the axis can be specified using the index of the axis in axes_manager. If string, argument can be navigation or signal to select the navigation or signal axes. The axis name can also be provided. If None, convert all axes.
units ({list of string of the same length than axes | str | None}) – Default = None If list, the selected axes will be converted to the provided units. If str, the navigation or signal axes will be converted to the provided units. If None, the scale and the units are converted to the appropriate scale and units to avoid displaying scalebar with >3 digits or too small number. This can be tweaked by the factor argument.
same_units (bool) – If True, force to keep the same units if the units of the axes differs. It only applies for the same kind of axis, navigation or signal. By default the converted units of the first axis is used for all axes. If False, convert all axes individually.
factor (float (default: 0.25)) – ‘factor’ is an adjustable value used to determine the prefix of the units. The product factor * scale * size is passed to the pint to_compact method to determine the prefix.

create_axes(axes_list)

Given a list of dictionaries defining the axes properties create the DataAxis instances and add them to the AxesManager.

The index of the axis in the array and in the _axes lists can be defined by the index_in_array keyword if given for all axes. Otherwise it is defined by their index in the list.