Getting started

Starting Python in Windows

If you used the bundle installation you should be able to use the context menus to get started. Right-click on the folder containing the data you wish to analyse and select “Jupyter notebook here” or “Jupyter qtconsole here”. We recommend the former, since notebooks have many advantages over conventional consoles, as will be illustrated in later sections. The examples in some later sections assume Notebook operation. A new tab should appear in your default browser listing the files in the selected folder. To start a python notebook choose “Python 3” in the “New” drop-down menu at the top right of the page. Another new tab will open which is your Notebook.

Starting Python in Linux and MacOS

You can start IPython by opening a system terminal and executing ipython, (optionally followed by the “frontend”: “qtconsole” for example). However, in most cases, the most agreeable way to work with HyperSpy interactively is using the Jupyter Notebook (previously known as the IPython Notebook), which can be started as follows:

$ jupyter notebook

Linux users may find it more convenient to start Jupyter/IPython from the file manager context menu. In either OS you can also start by double-clicking a notebook file if one already exists.

Starting HyperSpy in the notebook (or terminal)

Typically you will need to set up IPython for interactive plotting with matplotlib using %matplotlib (which is known as a ‘Jupyter magic’) before executing any plotting command. So, typically, after starting IPython, you can import HyperSpy and set up interactive matplotlib plotting by executing the following two lines in the IPython terminal (In these docs we normally use the general Python prompt symbol >>> but you will probably see In [1]: etc.):

>>> %matplotlib qt
>>> import hyperspy.api as hs

Note that to execute lines of code in the notebook you must press Shift+Return. (For details about notebooks and their functionality try the help menu in the notebook). Next, import two useful modules: numpy and matplotlib.pyplot, as follows:

>>> import numpy as np
>>> import matplotlib.pyplot as plt

The rest of the documentation will assume you have done this. It also assumes that you have installed at least one of HyperSpy’s GUI packages: jupyter widgets GUI and the traitsui GUI.

Possible warnings when importing HyperSpy?

HyperSpy supports different GUIs and matplotlib backends which in specific cases can lead to warnings when importing HyperSpy. Most of the time there is nothing to worry about — the warnings simply inform you of several choices you have. There may be several causes for a warning, for example:

• not all the GUIs packages are installed. If none is installed, we reccomend you to install at least the hyperspy-gui-ipywidgets package is your are planning to perform interactive data analysis in the Jupyter Notebook. Otherwise, you can simply disable the warning in preferences as explained below.

• the hyperspy-gui-traitsui package is installed and you are using an incompatible matplotlib backend (e.g. notebook, nbagg or widget).

  • If you want to use the traitsui GUI, use the qt matplotlib backend instead.

  • Alternatively, if you prefer to use the notebook or widget matplotlib backend, and if you don’t want to see the (harmless) warning, make sure that you have the hyperspy-gui-ipywidgets installed and disable the traitsui GUI in the preferences.

By default, HyperSpy warns the user if one of the GUI packages is not installed. These warnings can be turned off using the preferences GUI or programmatically as follows:

>>> import hyperspy.api as hs
>>> hs.preferences.GUIs.warn_if_guis_are_missing = False
>>> hs.preferences.save()

Changed in version v1.3: HyperSpy works with all matplotlib backends, including the notebook (also called nbAgg) backend that enables interactive plotting embedded in the jupyter notebook.

Warning

When using the qt4 backend in Python 2 the matplotlib magic must be executed after importing HyperSpy and qt must be the default HyperSpy backend.

Note

When running in a headless system it is necessary to set the matplotlib backend appropiately to avoid a cannot connect to X server error, for example as follows:

>>> import matplotlib
>>> matplotlib.rcParams["backend"] = "Agg"
>>> import hyperspy.api as hs

Getting help

When using IPython, the documentation (docstring in Python jargon) can be accessed by adding a question mark to the name of a function. e.g.:

>>> hs?
>>> hs.load?
>>> hs.signals?

This syntax is a shortcut to the standard way one of displaying the help associated to a given functions (docstring in Python jargon) and it is one of the many features of IPython, which is the interactive python shell that HyperSpy uses under the hood.

Please note that the documentation of the code is a work in progress, so not all the objects are documented yet.

Up-to-date documentation is always available in the HyperSpy website.

Autocompletion

Another useful IPython feature is the autocompletion of commands and filenames using the tab and arrow keys. It is highly recommended to read the Ipython documentation (specially their Getting started section) for many more useful features that will boost your efficiency when working with HyperSpy/Python interactively.

Loading data

Once HyperSpy is running, to load from a supported file format (see Supported formats) simply type:

>>> s = hs.load("filename")

Hint

The load function returns an object that contains data read from the file. We assign this object to the variable s but you can choose any (valid) variable name you like. for the filename, don’t forget to include the quotation marks and the file extension.

If no argument is passed to the load function, a window will be raised that allows to select a single file through your OS file manager, e.g.:

>>> # This raises the load user interface
>>> s = hs.load()

It is also possible to load multiple files at once or even stack multiple files. For more details read Loading files: the load function

“Loading” data from a numpy array

HyperSpy can operate on any numpy array by assigning it to a BaseSignal class. This is useful e.g. for loading data stored in a format that is not yet supported by HyperSpy—supposing that they can be read with another Python library—or to explore numpy arrays generated by other Python libraries. Simply select the most appropriate signal from the signals module and create a new instance by passing a numpy array to the constructor e.g.

>>> my_np_array = np.random.random((10,20,100))
>>> s = hs.signals.Signal1D(my_np_array)
>>> s
<Signal1D, title: , dimensions: (20, 10|100)>

The numpy array is stored in the data attribute of the signal class.

Loading example data and data from online databases

HyperSpy is distributed with some example data that can be found in hs.datasets.example_signals. The following example plots one of the example signals:

>>> hs.datasets.example_signals.EDS_TEM_Spectrum().plot()

New in version 1.4: artificial_data

There are also artificial datasets, which are made to resemble real experimental data.

>>> s = hs.datasets.artificial_data.get_core_loss_eels_signal()
>>> s.plot()

The eelsdb() function in hs.datasets can directly load spectra from The EELS Database. For example, the following loads all the boron trioxide spectra currently available in the database:

>>> hs.datasets.eelsdb(formula="B2O3")
[<EELSSpectrum, title: Boron oxide, dimensions: (|520)>,
 <EELSSpectrum, title: Boron oxide, dimensions: (|520)>]

The navigation and signal dimensions

In HyperSpy the data is interpreted as a signal array and, therefore, the data axes are not equivalent. HyperSpy distinguishes between signal and navigation axes and most functions operate on the signal axes and iterate on the navigation axes. For example, an EELS spectrum image (i.e. a 2D array of spectra) has three dimensions X, Y and energy-loss. In HyperSpy, X and Y are the navigation dimensions and the energy-loss is the signal dimension. To make this distinction more explicit the representation of the object includes a separator | between the navigation and signal dimensions e.g.

In HyperSpy a spectrum image has signal dimension 1 and navigation dimension 2 and is stored in the Signal1D subclass.

>>> s = hs.signals.Signal1D(np.zeros((10, 20, 30)))
>>> s
<Signal1D, title: , dimensions: (20, 10|30)>

An image stack has signal dimension 2 and navigation dimension 1 and is stored in the Signal2D subclass.

>>> im = hs.signals.Signal2D(np.zeros((30, 10, 20)))
>>> im
<Signal2D, title: , dimensions: (30|20, 10)>

Note that HyperSpy rearranges the axes when compared to the array order. The following few paragraphs explain how and why it does it.

Depending how the array is arranged, some axes are faster to iterate than others. Consider an example of a book as the dataset in question. It is trivially simple to look at letters in a line, and then lines down the page, and finally pages in the whole book. However if your words are written vertically, it can be inconvenient to read top-down (the lines are still horizontal, it’s just the meaning that’s vertical!). It’s very time-consuming if every letter is on a different page, and for every word you have to turn 5-6 pages. Exactly the same idea applies here - in order to iterate through the data (most often for plotting, but applies for any other operation too), you want to keep it ordered for “fast access”.

In Python (more explicitly numpy) the “fast axes order” is C order (also called row-major order). This means that the last axis of a numpy array is fastest to iterate over (i.e. the lines in the book). An alternative ordering convention is F order (column-major), where it is the reverse - the first axis of an array is the fastest to iterate over. In both cases, the further an axis is from the fast axis the slower it is to iterate over it. In the book analogy you could think, for example, think about reading the first lines of all pages, then the second and so on.

When data is acquired sequentially it is usually stored in acquisition order. When a dataset is loaded, HyperSpy generally stores it in memory in the same order, which is good for the computer. However, HyperSpy will reorder and classify the axes to make it easier for humans. Let’s imagine a single numpy array that contains pictures of a scene acquired with different exposure times on different days. In numpy the array dimensions are (D, E, Y, X). This order makes it fast to iterate over the images in the order in which they were acquired. From a human point of view, this dataset is just a collection of images, so HyperSpy first classifies the image axes (X and Y) as signal axes and the remaining axes the navigation axes. Then it reverses the order of each sets of axes because many humans are used to get the X axis first and, more generally the axes in acquisition order from left to right. So, the same axes in HyperSpy are displayed like this: (E, D | X, Y).

Extending this to arbitrary dimensions, by default, we reverse the numpy axes, chop it into two chunks (signal and navigation), and then swap those chunks, at least when printing. As an example:

In the background, HyperSpy also takes care of storing the data in memory in a “machine-friendly” way, so that iterating over the navigation axes is always fast.

Setting axis properties

The axes are managed and stored by the AxesManager class that is stored in the axes_manager attribute of the signal class. The individual axes can be accessed by indexing the AxesManager. e.g.

>>> s = hs.signals.Signal1D(np.random.random((10, 20 , 100)))
>>> s
<Signal1D, title: , dimensions: (20, 10|100)>
>>> s.axes_manager
<Axes manager, axes: (<Unnamed 0th axis, size: 20, index: 0>, <Unnamed 1st
axis, size: 10, index: 0>|<Unnamed 2nd axis, size: 100>)>
>>> s.axes_manager[0]
<Unnamed 0th axis, size: 20, index: 0>

The axis properties can be set by setting the DataAxis attributes e.g.

>>> s.axes_manager[0].name = "X"
>>> s.axes_manager[0]
<X axis, size: 20, index: 0>

Once the name of an axis has been defined it is possible to request it by its name e.g.:

>>> s.axes_manager["X"]
<X axis, size: 20, index: 0>
>>> s.axes_manager["X"].scale = 0.2
>>> s.axes_manager["X"].units = "nm"
>>> s.axes_manager["X"].offset = 100

It is also possible to set the axes properties using a GUI by calling the gui() method of the AxesManager

>>> s.axes_manager.gui()

AxesManager ipywidgets GUI.

or the DataAxis, e.g:

>>> s.axes_manager["X"].gui()

DataAxis ipywidgets GUI.

To simply change the “current position” (i.e. the indices of the navigation axes) you could use the navigation sliders:

>>> s.axes_manager.gui_navigation_sliders()

Navigation sliders ipywidgets GUI.

Alternatively, the “current position” can be changed programmatically by directly accessing indices attribute of a Signal’s AxesManager. This is particularly useful if trying to set a specific location with which to initialize a model’s parameters to sensible values before preforming a fit over an entire spectrum image. The indices must be provided as a tuple, with the same length as the number of navigation dimensions:

>>> s.axes_manager.indices = (5, 4)

Using quantity and converting units

The scale and the offset of each axis can be set and retrieved as quantity.

>>> s = hs.signals.Signal1D(np.arange(10))
>>> s.axes_manager[0].scale_as_quantity
1.0 dimensionless
>>> s.axes_manager[0].scale_as_quantity = '2.5 µm'
>>> s.axes_manager
<Axes manager, axes: (|10)>
            Name |   size |  index |  offset |   scale |  units
================ | ====== | ====== | ======= | ======= | ======
---------------- | ------ | ------ | ------- | ------- | ------
     <undefined> |     10 |        |       0 |     2.5 |     µm
>>> s.axes_manager[0].offset_as_quantity = '2.5 nm'
<Axes manager, axes: (|10)>
            Name |   size |  index |  offset |   scale |  units
================ | ====== | ====== | ======= | ======= | ======
---------------- | ------ | ------ | ------- | ------- | ------
     <undefined> |     10 |        |     2.5 | 2.5e+03 |     nm

Internally, HyperSpy uses the pint library to manage the scale and offset quantities. The scale_as_quantity and offset_as_quantity attributes return pint object:

>>> q = s.axes_manager[0].offset_as_quantity
>>> type(q) # q is a pint quantity object
pint.quantity.build_quantity_class.<locals>.Quantity
>>> q
2.5 nanometer

The convert_units method of the AxesManager converts units, which by default (no parameters provided) converts all axis units to an optimal units to avoid using too large or small number.

Each axis can also be converted individually using the convert_to_units method of the DataAxis:

>>> axis = hs.hyperspy.axes.DataAxis(size=10, scale=0.1, offset=10, units='mm')
>>> axis.scale_as_quantity
0.1 millimeter
>>> axis.convert_to_units('µm')
>>> axis.scale_as_quantity
100.0 micrometer

Saving Files

The data can be saved to several file formats. The format is specified by the extension of the filename.

>>> # load the data
>>> d = hs.load("example.tif")
>>> # save the data as a tiff
>>> d.save("example_processed.tif")
>>> # save the data as a png
>>> d.save("example_processed.png")
>>> # save the data as an hspy file
>>> d.save("example_processed.hspy")

Some file formats are much better at maintaining the information about how you processed your data. The preferred format in HyperSpy is hspy, which is based on the HDF5 format. This format keeps the most information possible.

There are optional flags that may be passed to the save function. See Saving data to files for more details.

Accessing and setting the metadata

When loading a file HyperSpy stores all metadata in the BaseSignal original_metadata attribute. In addition, some of those metadata and any new metadata generated by HyperSpy are stored in metadata attribute.

>>> s = hs.load("NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217.msa")
>>> s.metadata
├── original_filename = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217.msa
├── record_by = spectrum
├── signal_type = EELS
└── title = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217

>>> s.original_metadata
├── DATATYPE = XY
├── DATE =
├── FORMAT = EMSA/MAS Spectral Data File
├── NCOLUMNS = 1.0
├── NPOINTS = 1340.0
├── OFFSET = 120.0003
├── OWNER = eelsdatabase.net
├── SIGNALTYPE = ELS
├── TIME =
├── TITLE = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217
├── VERSION = 1.0
├── XPERCHAN = 0.5
├── XUNITS = eV
└── YUNITS =

>>> s.set_microscope_parameters(100, 10, 20)
>>> s.metadata
├── TEM
│   ├── EELS
│   │   └── collection_angle = 20
│   ├── beam_energy = 100
│   └── convergence_angle = 10
├── original_filename = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217.msa
├── record_by = spectrum
├── signal_type = EELS
└── title = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217

>>> s.metadata.TEM.microscope = "STEM VG"
>>> s.metadata
├── TEM
│   ├── EELS
│   │   └── collection_angle = 20
│   ├── beam_energy = 100
│   ├── convergence_angle = 10
│   └── microscope = STEM VG
├── original_filename = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217.msa
├── record_by = spectrum
├── signal_type = EELS
└── title = NbO2_Nb_M_David_Bach,_Wilfried_Sigle_217

Configuring HyperSpy

The behaviour of HyperSpy can be customised using the Preferences class. The easiest way to do it is by calling the gui() method:

>>> hs.preferences.gui()

This command should raise the Preferences user interface if one of the hyperspy gui packages are installed and enabled:

Preferences user interface.

New in version 1.3: Possibility to enable/disable GUIs in the preferences.

It is also possible to set the preferences programmatically. For example, to disable the traitsui GUI elements and save the changes to disk:

>>> hs.preferences.GUIs.enable_traitsui_gui = False
>>> hs.preferences.save()
>>> # if not saved, this setting will be used until the next jupyter kernel shutdown

Changed in version 1.3: The following items were removed from preferences: General.default_export_format, General.lazy, Model.default_fitter, Machine_learning.multiple_files, Machine_learning.same_window, Plot.default_style_to_compare_spectra, Plot.plot_on_load, Plot.pylab_inline, EELS.fine_structure_width, EELS.fine_structure_active, EELS.fine_structure_smoothing, EELS.synchronize_cl_with_ll, EELS.preedge_safe_window_width, EELS.min_distance_between_edges_for_fine_structure.

Messages log

HyperSpy writes messages to the Python logger. The default log level is “WARNING”, meaning that only warnings and more severe event messages will be displayed. The default can be set in the preferences. Alternatively, it can be set using set_log_level() e.g.:

>>> import hyperspy.api as hs
>>> hs.set_log_level('INFO')
>>> hs.load(r'my_file.dm3')
INFO:hyperspy.io_plugins.digital_micrograph:DM version: 3
INFO:hyperspy.io_plugins.digital_micrograph:size 4796607 B
INFO:hyperspy.io_plugins.digital_micrograph:Is file Little endian? True
INFO:hyperspy.io_plugins.digital_micrograph:Total tags in root group: 15
<Signal2D, title: My file, dimensions: (|1024, 1024)