HyperSpy Documentation Release 1.0 The HyperSpy Developers Mar 04, 2017 Contents 1 HyperSpy User Guide (DRAFT)1 1.1 Introduction...............................................1 1.1.1 What is HyperSpy........................................1 1.1.2 Our vision............................................1 1.1.3 HyperSpy’s character......................................1 1.2 What’s new................................................2 1.2.1 v1.0...............................................2 1.2.2 v0.8.5..............................................4 1.2.3 v0.8.4..............................................4 1.2.4 v0.8.3..............................................4 1.2.5 v0.8.2..............................................4 1.2.6 v0.8.1..............................................4 1.2.7 v0.8...............................................5 1.2.8 v0.7.3..............................................6 1.2.9 v0.7.2..............................................6 1.2.10 v0.7.1..............................................7 1.2.11 v0.7...............................................7 1.2.12 v0.6...............................................9 1.2.13 v0.5.1.............................................. 10 1.2.14 v0.5............................................... 11 1.2.15 v0.4.1.............................................. 12 1.2.16 v0.4............................................... 13 1.3 Installing HyperSpy........................................... 16 1.3.1 HyperSpy Bundle for Microsoft Windows........................... 16 1.3.2 Quick instructions to install HyperSpy using Anaconda (Linux, MacOs, Windows)..... 16 1.3.3 Install using Python installers.................................. 17 1.3.4 Creating Conda environment for HyperSpy.......................... 17 1.3.5 Install from a binary...................................... 17 1.3.6 Install from source....................................... 17 1.3.7 Installing the required libraries................................. 18 1.3.8 Known issues.......................................... 19 1.4 Getting started.............................................. 19 1.4.1 Starting Python in Windows.................................. 19 1.4.2 Starting Python in Linux and MacOS............................. 19 1.4.3 Starting HyperSpy in the notebook (or terminal)........................ 20 1.4.4 Getting help........................................... 20 i 1.4.5 Autocompletion......................................... 21 1.4.6 Loading data.......................................... 21 1.4.7 “Loading” data from a numpy array.............................. 21 1.4.8 Loading example data and data from online databases..................... 21 1.4.9 The navigation and signal dimensions............................. 22 1.4.10 Setting axis properties..................................... 22 1.4.11 Saving Files........................................... 23 1.4.12 Accessing and setting the metadata............................... 23 1.4.13 Configuring HyperSpy..................................... 24 1.4.14 Messages log.......................................... 24 1.5 Tools: the Signal class.......................................... 24 1.5.1 The Signal class and its subclasses............................... 24 1.5.2 The navigation and signal dimensions............................. 26 1.5.3 Binned and unbinned signals.................................. 28 1.5.4 Generic tools.......................................... 29 1.5.5 Basic statistical analysis.................................... 39 1.5.6 Setting the noise properties................................... 41 1.5.7 Speeding up operations..................................... 43 1.5.8 Interactive operations...................................... 43 1.5.9 Region Of Interest (ROI).................................... 44 1.5.10 Calculate the angle / phase / argument............................. 49 1.5.11 Phase unwrapping........................................ 49 1.5.12 Add a linear phase ramp.................................... 49 1.6 Signal1D Tools.............................................. 50 1.6.1 Cropping............................................ 50 1.6.2 Background removal...................................... 50 1.6.3 Calibration........................................... 50 1.6.4 Alignment............................................ 50 1.6.5 Integration............................................ 50 1.6.6 Data smoothing......................................... 50 1.6.7 Spike removal.......................................... 51 1.6.8 Peak finding........................................... 51 1.6.9 Other methods......................................... 51 1.7 Signal2D Tools.............................................. 51 1.7.1 Two dimensional signal registration (alignment)........................ 52 1.7.2 Cropping an image....................................... 52 1.7.3 Add a linear ramp........................................ 52 1.8 Data visualization............................................ 52 1.8.1 Multidimensional spectral data................................. 52 1.8.2 Multidimensional image data.................................. 54 1.8.3 Customising image plot..................................... 54 1.8.4 Customizing the “navigator”.................................. 55 1.8.5 Using Mayavi to visualize 3D data............................... 60 1.8.6 Plotting multiple signals.................................... 62 1.8.7 Markers............................................. 74 1.9 Machine learning............................................. 76 1.9.1 Introduction........................................... 76 1.9.2 Nomenclature.......................................... 76 1.9.3 Decomposition......................................... 76 1.9.4 Blind Source Separation.................................... 81 1.9.5 Visualizing results....................................... 82 1.9.6 Obtaining the results as BaseSignal instances......................... 82 1.9.7 Saving and loading results................................... 82 1.10 Model fitting............................................... 83 ii 1.10.1 Creating a model........................................ 83 1.10.2 Adding components to the model................................ 84 1.10.3 Indexing model......................................... 88 1.10.4 Getting and setting parameter values and attributes...................... 89 1.10.5 Fitting the model to the data.................................. 91 1.10.6 Storing models......................................... 97 1.10.7 Batch setting of parameter attributes.............................. 98 1.10.8 Smart Adaptive Multi-dimensional Fitting (SAMFire)..................... 98 1.11 Electron Energy Loss Spectroscopy................................... 100 1.11.1 Tools for EELS data analysis.................................. 100 1.11.2 EELS curve fitting....................................... 102 1.12 Energy-Dispersive X-ray Spectrometry (EDS)............................. 104 1.12.1 Signal1D loading and parameters................................ 104 1.12.2 Describing the sample..................................... 108 1.12.3 Plotting............................................. 110 1.12.4 Geting the intensity of an X-ray line.............................. 111 1.12.5 EDS Quantification....................................... 115 1.12.6 EDS curve fitting........................................ 116 1.13 Dielectric function tools......................................... 119 1.13.1 Number of effective electrons................................. 119 1.13.2 Compute the electron energy-loss signal............................ 119 1.14 Loading and saving data......................................... 119 1.14.1 Loading files: the load function................................. 120 1.14.2 Saving data to files....................................... 121 1.14.3 Supported formats....................................... 122 1.15 Events.................................................. 127 1.15.1 Connecting to events...................................... 127 1.15.2 Suppressing events....................................... 128 1.15.3 Triggering events........................................ 128 1.16 Metadata structure............................................ 129 1.16.1 General............................................. 130 1.16.2 Acquisition_instrument..................................... 130 1.16.3 Sample............................................. 132 1.16.4 Signal.............................................. 132 1.16.5 _Internal_parameters...................................... 133 1.17 Bibliography............................................... 133 1.17.1 Bibliography.......................................... 133 1.17.2 Peer-review articles with results obtained using HyperSpy.................. 133 2 hyperspy 135 2.1 hyperspy package............................................ 135 2.1.1 Subpackages.......................................... 135 2.1.2 Submodules........................................... 207 2.1.3 hyperspy.Release module.................................... 207 2.1.4 hyperspy.api module...................................... 207 2.1.5 hyperspy.axes module...................................... 207 2.1.6 hyperspy.component module.................................. 207 2.1.7 hyperspy.components1d module................................ 207 2.1.8 hyperspy.components2d module................................ 207 2.1.9 hyperspy.decorators module.................................. 207