Basic Usage#

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.

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.

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.:

In [1]: import hyperspy.api as hs

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.

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 introduction for many more useful features that will boost your efficiency when working with HyperSpy/Python interactively.

Creating signal 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:

>>> s.data

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:

(a1, a2, a3, a4, a5, a6) # original (numpy)
(a6, a5, a4, a3, a2, a1) # reverse
(a6, a5) (a4, a3, a2, a1) # chop
(a4, a3, a2, a1) (a6, a5) # swap (HyperSpy)

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.

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 formats are hspy and zspy, because they are open formats and keep most information possible.

There are optional flags that may be passed to the save function. See Saving 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.

>>> import exspy  
>>> s = exspy.data.eelsdb(formula="NbO2", edge="M2,3")[0] 
>>> s.metadata  
├── Acquisition_instrument
│   └── TEM
│       ├── Detector
│       │   └── EELS
│       │       └── collection_angle = 6.5
│       ├── beam_energy = 100.0
│       ├── convergence_angle = 10.0
│       └── microscope = VG HB501UX
├── General
│   ├── author = Wilfried Sigle
│   └── title = Niobium oxide NbO2
├── Sample
│   ├── chemical_formula = NbO2
│   ├── description =  Analyst: David Bach, Wilfried Sigle. Temperature: Room.
│   └── elements = ['Nb', 'O']
└── Signal
    ├── quantity = Electrons ()
    └── signal_type = EELS

>>> s.original_metadata  
├── emsa
│   ├── 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 =
└── json
    ├── api_permalink = https://api.eelsdb.eu/spectra/niobium-oxide-nbo2-2/
    ├── associated_spectra = [{'name': 'Niobium oxide NbO2', 'link': 'https://eelsdb.eu/spectra/niobium-oxide-nbo2/', 'type': 'Low Loss'}]
    ├── author
    │   ├── name = Wilfried Sigle
    │   ├── profile_api_url = https://api.eelsdb.eu/author/wsigle/
    │   └── profile_url = https://eelsdb.eu/author/wsigle/
    ├── beamenergy = 100 kV
    ├── collection = 6.5 mrad
    ├── comment_count = 0
    ├── convergence = 10 mrad
    ├── darkcurrent = Yes
    ├── description =  Analyst: David Bach, Wilfried Sigle. Temperature: Room.
    ├── detector = Parallel: Gatan ENFINA
    ├── download_link = https://eelsdb.eu/wp-content/uploads/2015/09/DspecYB7EbW.msa
    ├── edges = ['Nb_M2,3', 'Nb_M4,5', 'O_K']
    ├── elements = ['Nb', 'O']
    ├── formula = NbO2
    ├── gainvariation = Yes
    ├── guntype = cold field emission
    ├── id = 21727
    ├── integratetime = 5 secs
    ├── keywords = ['imported from old site']
    ├── max_energy = 789.5 eV
    ├── microscope = VG HB501UX
    ├── min_energy = 120 eV
    ├── monochromated = No
    ├── other_links = [{'url': 'http://pc-web.cemes.fr/eelsdb/index.php?page=displayspec.php&id=217', 'title': 'Old EELS DB'}]
    ├── permalink = https://eelsdb.eu/spectra/niobium-oxide-nbo2-2/
    ├── published = 2008-02-15 00:00:00
    ├── readouts = 10
    ├── resolution = 1.3 eV
    ├── stepSize = 0.5 eV/pixel
    ├── thickness = 0.58 t/&lambda;
    ├── title = Niobium oxide NbO2
    └── type = Core Loss

>>> s.metadata.General.title = "NbO2 Nb_M edge"  
>>> s.metadata  
├── Acquisition_instrument
│   └── TEM
│       ├── Detector
│       │   └── EELS
│       │       └── collection_angle = 6.5
│       ├── beam_energy = 100.0
│       ├── convergence_angle = 10.0
│       └── microscope = VG HB501UX
├── General
│   ├── author = Wilfried Sigle
│   └── title = NbO2 Nb_M edge
├── Sample
│   ├── chemical_formula = NbO2
│   ├── description =  Analyst: David Bach, Wilfried Sigle. Temperature: Room.
│   └── elements = ['Nb', 'O']
└── Signal
    ├── quantity = Electrons ()
    └── signal_type = EELS

Configuring HyperSpy#

The behaviour of HyperSpy can be customised using the preferences. 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:

../_images/preferences.png

Preferences user interface.#

Added 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('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)