Loading and saving data

Loading files: the load function

HyperSpy can read and write to multiple formats (see Supported formats). To load data use the load() command. For example, to load the image spam.jpg you can type:

>>> s = hs.load("spam.jpg")

If loading was successful, the variable s contains a HyperSpy signal or any type of signal defined in on of the HyperSpy extensions - see available signal subclasses for more information. To list the signal types available on your local installation use:

>>> hs.print_known_signal_types()

HyperSpy will try to guess the most likely data type for the corresponding file. However, you can force it to read the data as a particular data type by providing the signal_type keyword, which has to correspond to one of the available subclasses of signal, e.g.:

>>> s = hs.load("filename", signal_type="EELS")

If the loaded file contains several datasets, the load() functions will return a list of the corresponding signals:

>>> s = hs.load("spameggsandham.hspy")
>>> s
[<Signal1D, title: spam, dimensions: (32,32|1024)>,
<Signal1D, title: eggs, dimensions: (32,32|1024)>,
<Signal1D, title: ham, dimensions: (32,32|1024)>]

Note

Note for python programmers: the data is stored in a numpy array in the data attribute, but you will not normally need to access it there.

HyperSpy will attempt to infer the appropriate file reader to use based on the file extension (for example. .hspy, .emd and so on). You can override this using the reader keyword:

# Load a .hspy file with an unknown extension
>>> s = hs.load("filename.some_extension", reader="hspy")

Some file formats store some extra information about the data (metadata) and HyperSpy reads most of them and stores them in the original_metadata attribute. Also, depending on the file format, a part of this information will be mapped by HyperSpy to the metadata attribute, where it can be used by e.g. routines operating on the signal. See metadata structure for details.

Note

Extensive metadata can slow down loading and processing, and loading the original_metadata can be disabled using the load_original_metadata argument of the load() function; in this case, the metadata will still be populated.

To print the content of the attributes simply use:

>>> s.original_metadata
>>> s.metadata

The original_metadata and metadata can be exported to text files using the export() method, e.g.:

>>> s.original_metadata.export('parameters')

Deprecated since version 1.2: memmap_dir and load_to_memory load() keyword arguments. Use lazy instead of load_to_memory. lazy makes memmap_dir unnecessary.

Almost all file readers support lazy loading, which means accessing the data without loading it to memory (see Supported formats for a list). This feature can be useful when analysing large files. To use this feature set lazy to True e.g.:

>>> s = hs.load("filename.hspy", lazy=True)

More details on lazy evaluation support in Working with big data.

The units of the navigation and signal axes can be converted automatically during loading using the convert_units parameter. If True, the convert_to_units method of the axes_manager will be used for the conversion and if set to False, the units will not be converted (default).

Loading multiple files

Rather than loading files individually, several files can be loaded with a single command. This can be done by passing a list of filenames to the load functions, e.g.:

>>> s = hs.load(["file1.hspy", "file2.hspy"])

or by using shell-style wildcards:

>>> s = hs.load("file*.hspy")

Alternatively, regular expression type character classes can be used such as [a-z] for lowercase letters or [0-9] for one digit integers:

>>> s = hs.load('file[0-9].hspy')

Note

Wildcards are implemented using glob.glob(), which treats *, [ and ] as special characters for pattern matching. If your filename or path contains square brackets, you may want to set escape_square_brackets=True:

>>> # Say there are two files like this:
>>> # /home/data/afile[1x1].hspy
>>> # /home/data/afile[1x2].hspy

>>> s = hs.load("/home/data/afile[*].hspy", escape_square_brackets=True)

HyperSpy also supports `pathlib.Path <https://docs.python.org/3/library/pathlib.html>`_ objects, for example:

>>> import hyperspy.api as hs
>>> from pathlib import Path

>>> # Use pathlib.Path
>>> p = Path("/path/to/a/file.hspy")
>>> s = hs.load(p)

>>> # Use pathlib.Path.glob
>>> p = Path("/path/to/some/files/").glob("*.hspy")
>>> s = hs.load(p)

By default HyperSpy will return a list of all the files loaded. Alternatively, by setting stack=True, HyperSpy can be instructed to stack the data - given that the files contain data with exactly the same dimensions. If this is not the case, an error is raised. If each file contains multiple (N) signals, N stacks will be created. Here, the number of signals per file must also match, or an error will be raised.

>>> ls
CL1.raw  CL1.rpl  CL2.raw  CL2.rpl  CL3.raw  CL3.rpl  CL4.raw  CL4.rpl
LL3.raw  LL3.rpl  shift_map-SI3.npy  hdf5/
>>> s = hs.load('*.rpl')
>>> s
[<EELSSpectrum, title: CL1, dimensions: (64, 64, 1024)>,
<EELSSpectrum, title: CL2, dimensions: (64, 64, 1024)>,
<EELSSpectrum, title: CL3, dimensions: (64, 64, 1024)>,
<EELSSpectrum, title: CL4, dimensions: (64, 64, 1024)>,
<EELSSpectrum, title: LL3, dimensions: (64, 64, 1024)>]
>>> s = hs.load('*.rpl', stack=True)
>>> s
<EELSSpectrum, title: mva, dimensions: (5, 64, 64, 1024)>

Saving data to files

To save data to a file use the save() method. The first argument is the filename and the format is defined by the filename extension. If the filename does not contain the extension, the default format (HSpy - HyperSpy’s HDF5 Specification) is used. For example, if the s variable contains the BaseSignal that you want to write to a file, the following will write the data to a file called spectrum.hspy in the default HSpy - HyperSpy’s HDF5 Specification format:

>>> s.save('spectrum')

If you want to save to the ripple format instead, write:

>>> s.save('spectrum.rpl')

Some formats take extra arguments. See the relevant subsections of Supported formats for more information.

Supported formats

Here is a summary of the different formats that are currently supported by HyperSpy. The “lazy” column specifies if lazy evaluation is supported.

Supported file formats

Format	Read	Write	lazy
Gatan’s dm3	Yes	No	Yes
Gatan’s dm4	Yes	No	Yes
FEI’s emi and ser	Yes	No	Yes
hspy	Yes	Yes	Yes
zspy	Yes	Yes	Yes
Image: e.g. jpg, png, tif, …	Yes	Yes	Yes
TIFF	Yes	Yes	Yes
MRC	Yes	No	Yes
MRCZ	Yes	Yes	Yes
EMSA/MSA	Yes	Yes	No
NetCDF	Yes	No	No
Ripple	Yes	Yes	Yes
SEMPER unf	Yes	Yes	Yes
Blockfile	Yes	Yes	Yes
DENSsolutions’ Impulse log	Yes	No	No
DENSsolutions’ Digiheater log	Yes	No	No
Bruker’s bcf	Yes	No	Yes
Bruker’s spx	Yes	No	No
EMD (NCEM)	Yes	Yes	Yes
EMD (Velox)	Yes	No	Yes
Protochips log	Yes	No	No
EDAX spc and spd	Yes	No	Yes
h5USID h5	Yes	Yes	Yes
Phenom elid	Yes	No	No
DigitalSurf’s sur and pro	Yes	No	No
Nexus nxs	Yes	Yes	Yes
EMPAD xml	Yes	No	Yes
JEOL asw, map, img, pts, eds	Yes	No	No
TVIPS .tvips	Yes	Yes	Yes

HSpy - HyperSpy’s HDF5 Specification

This is the default format and it is the only one that guarantees that no information will be lost in the writing process and that supports saving data of arbitrary dimensions. It is based on the HDF5 open standard. The HDF5 file format is supported by many applications. Part of the specification is documented in Metadata structure.

New in version 1.2: Enable saving HSpy files with the .hspy extension. Previously only the .hdf5 extension was recognised.

Changed in version 1.3: The default extension for the HyperSpy HDF5 specification is now .hspy. The option to change the default is no longer present in preferences.

Only loading of HDF5 files following the HyperSpy specification are supported. Usually their extension is .hspy extension, but older versions of HyperSpy would save them with the .hdf5 extension. Both extensions are recognised by HyperSpy since version 1.2. However, HyperSpy versions older than 1.2 won’t recognise the .hspy extension. To workaround the issue when using old HyperSpy installations simply change the extension manually to .hdf5 or save directly the file using this extension by explicitly adding it to the filename e.g.:

>>> s = hs.signals.BaseSignal([0])
>>> s.save('test.hdf5')

When saving to hspy, all supported objects in the signal’s metadata is stored. This includes lists, tuples and signals. Please note that in order to increase saving efficiency and speed, if possible, the inner-most structures are converted to numpy arrays when saved. This procedure homogenizes any types of the objects inside, most notably casting numbers as strings if any other strings are present:

>>> # before saving:
>>> somelist
[1, 2.0, 'a name']
>>> # after saving:
['1', '2.0', 'a name']

The change of type is done using numpy “safe” rules, so no information is lost, as numbers are represented to full machine precision.

This feature is particularly useful when using get_lines_intensity():

>>> s = hs.datasets.example_signals.EDS_SEM_Spectrum()
>>> s.metadata.Sample.intensities = s.get_lines_intensity()
>>> s.save('EDS_spectrum.hspy')

>>> s_new = hs.load('EDS_spectrum.hspy')
>>> s_new.metadata.Sample.intensities
[<BaseSignal, title: X-ray line intensity of EDS SEM Signal1D: Al_Ka at 1.49 keV, dimensions: (|)>,
 <BaseSignal, title: X-ray line intensity of EDS SEM Signal1D: C_Ka at 0.28 keV, dimensions: (|)>,
 <BaseSignal, title: X-ray line intensity of EDS SEM Signal1D: Cu_La at 0.93 keV, dimensions: (|)>,
 <BaseSignal, title: X-ray line intensity of EDS SEM Signal1D: Mn_La at 0.63 keV, dimensions: (|)>,
 <BaseSignal, title: X-ray line intensity of EDS SEM Signal1D: Zr_La at 2.04 keV, dimensions: (|)>]

New in version 1.3.1: chunks keyword argument

The hyperspy HDF5 format supports chunking the data into smaller pieces to make it possible to load only part of a dataset at a time. By default, the data is saved in chunks that are optimised to contain at least one full signal. It is possible to customise the chunk shape using the chunks keyword. For example, to save the data with (20, 20, 256) chunks instead of the default (7, 7, 2048) chunks for this signal:

>>> s = hs.signals.Signal1D(np.random.random((100, 100, 2048)))
>>> s.save("test_chunks", chunks=(20, 20, 256))

Note that currently it is not possible to pass different customised chunk shapes to all signals and arrays contained in a signal and its metadata. Therefore, the value of chunks provided on saving will be applied to all arrays contained in the signal.

By passing True to chunks the chunk shape is guessed using h5py’s guess_chunk function what, for large signal spaces usually leads to smaller chunks as guess_chunk does not impose the constrain of storing at least one signal per chunks. For example, for the signal in the example above passing chunks=True results in (7, 7, 256) chunks.

Choosing the correct chunk-size can significantly affect the speed of reading, writing and performance of many HyperSpy algorithms. See the chunking section for more information.

Extra saving arguments

• compression: One of None, 'gzip', 'szip', 'lzf' (default is 'gzip'). 'szip' may be unavailable as it depends on the HDF5 installation including it.

  Note

  HyperSpy uses h5py for reading and writing HDF5 files and, therefore, it supports all compression filters supported by h5py. The default is 'gzip'. It is possible to enable other compression filters such as blosc by installing e.g. hdf5plugin. However, be aware that loading those files will require installing the package providing the compression filter. If not available an error will be raised.

  Compression can significantly increase the saving speed. If file size is not an issue, it can be disabled by setting compression=None. Notice that only compression=None and compression='gzip' are available in all platforms, see the h5py documentation for more details. Therefore, if you choose any other compression filter for saving a file, be aware that it may not be possible to load it in some platforms.

• chunks: tuple of integer or None. Define the chunking used for saving the dataset. If None, calculates chunks for the signal, with preferably at least one chunk per signal space.

• close_file: if False, doesn’t close the file after writing. The file should not be closed if the data need to be accessed lazily after saving. Default is True.

• write_dataset: if False, doesn’t write the dataset when writing the file. This can be useful to overwrite signal attributes only (for example axes_manager) without having to write the whole dataset, which can take time. Default is True.

ZSpy - HyperSpy’s Zarr Specification

Similarly to the hspy format, the zspy format guarantees that no information will be lost in the writing process and that supports saving data of arbitrary dimensions. It is based on the Zarr project. Which exists as a drop in replacement for hdf5 with the intention to fix some of the speed and scaling issues with the hdf5 format and is therefore suitable for saving big data.

>>> s = hs.signals.BaseSignal([0])
>>> s.save('test.zspy') # will save in nested directory
>>> hs.load('test.zspy') # loads the directory

When saving to zspy, all supported objects in the signal’s metadata is stored. This includes lists, tuples and signals. Please note that in order to increase saving efficiency and speed, if possible, the inner-most structures are converted to numpy arrays when saved. This procedure homogenizes any types of the objects inside, most notably casting numbers as strings if any other strings are present:

By default, a zarr.storage.NestedDirectoryStore is used, but other zarr store can be used by providing a zarr store instead as argument to the save() or the load() function. If a zspy file has been saved with a different store, it would need to be loaded by passing a store of the same type:

>>> import zarr
>>> filename = 'test.zspy'
>>> store = zarr.LMDBStore(filename)
>>> signal.save(store) # saved to LMDB

To load this file again

>>> import zarr
>>> filename = 'test.zspy'
>>> store = zarr.LMDBStore(filename)
>>> s = hs.load(store) # load from LMDB

Extra saving arguments

• compressor: Numcodecs codec, a compressor can be passed to the save function to compress the data efficiently. The default is to call a Blosc compressor object.

  >>> from numcodecs import Blosc
  >>> compressor=Blosc(cname='zstd', clevel=1, shuffle=Blosc.SHUFFLE) # Used by default
  >>> s.save('test.zspy', compressor = compressor) # will save with Blosc compression
  

  Note

  Lazy operations are often i-o bound, reading and writing the data creates a bottle neck in processes due to the slow read write speed of many hard disks. In these cases, compressing your data is often beneficial to the speed of some operations. Compression speeds up the process as there is less to read/write with the trade off of slightly more computational work on the CPU.

• chunks: tuple of integer or None. Define the chunking used for saving the dataset. If None, calculates chunks for the signal, with preferably at least one chunk per signal space.

• close_file: only relevant for some zarr store (ZipStore, DBMStore) requiring store to flush data to disk. If False, doesn’t close the file after writing. The file should not be closed if the data need to be accessed lazily after saving. Default is True.

• write_dataset: if False, doesn’t write the dataset when writing the file. This can be useful to overwrite signal attributes only (for example axes_manager) without having to write the whole dataset, which can take time. Default is True.

NetCDF

This was the default format in HyperSpy’s predecessor, EELSLab, but it has been superseded by HSpy - HyperSpy’s HDF5 Specification in HyperSpy. We provide only reading capabilities but we do not support writing to this format.

Note that only NetCDF files written by EELSLab are supported.

To use this format a python netcdf interface must be installed manually because it is not installed by default when using the automatic installers.

MRC

This is a format widely used for tomographic data. Our implementation is based on this specification. We also partly support FEI’s custom header. We do not provide writing features for this format, but, as it is an open format, we may implement this feature in the future on demand.

For mrc files load takes the mmap_mode keyword argument enabling loading the file using a different mode (default is copy-on-write) . However, note that lazy loading does not support in-place writing (i.e lazy loading and the “r+” mode are incompatible).

MRCZ

MRCZ is an extension of the CCP-EM MRC2014 file format. CCP-EM MRC2014 file format. It uses the blosc meta-compression library to bitshuffle and compress files in a blocked, multi-threaded environment. The supported data types are:

[float32,`int8`,`uint16`,`int16`,`complex64`]

It supports arbitrary meta-data, which is serialized into JSON.

MRCZ also supports asynchronous reads and writes.

Repository: https://github.com/em-MRCZ PyPI: https://pypi.python.org/pypi/mrcz Citation: Submitted. Preprint: http://www.biorxiv.org/content/early/2017/03/13/116533

Support for this format is not enabled by default. In order to enable it install the mrcz and optionally the blosc Python packages.

Extra saving arguments

• do_async: currently supported within HyperSpy for writing only, this will save the file in a background thread and return immediately. Defaults to False.

Warning

There is no method currently implemented within Hyperspy to tell if an asychronous write has finished.

• compressor: The compression codec, one of [None,`’zlib`’,`’zstd’, `’lz4’]. Defaults to None.

• clevel: The compression level, an int from 1 to 9. Defaults to 1.

• n_threads: The number of threads to use for ‘blosc’ compression. Defaults to the maximum number of virtual cores (including Intel Hyperthreading) on your system, which is recommended for best performance. If do_async = True you may wish to leave one thread free for the Python GIL.

The recommended compression codec is ‘zstd’ (zStandard) with clevel=1 for general use. If speed is critical, use ‘lz4’ (LZ4) with clevel=9. Integer data compresses more redably than floating-point data, and in general the histogram of values in the data reflects how compressible it is.

To save files that are compatible with other programs that can use MRC such as GMS, IMOD, Relion, MotionCorr, etc. save with compressor=None, extension .mrc. JSON metadata will not be recognized by other MRC-supporting software but should not cause crashes.

Example Usage

>>> s.save('file.mrcz', do_async=True, compressor='zstd', clevel=1)

>>> new_signal = hs.load('file.mrcz')

EMSA/MSA

This open standard format is widely used to exchange single spectrum data, but it does not support multidimensional data. It can be used to exchange single spectra with Gatan’s Digital Micrograph.

Warning

If several spectra are loaded and stacked (hs.load('pattern', stack_signals=True) the calibration read from the first spectrum and applied to all other spectra.

Extra saving arguments

For the MSA format the format argument is used to specify whether the energy axis should also be saved with the data. The default, ‘Y’ omits the energy axis in the file. The alternative, ‘XY’, saves a second column with the calibrated energy data. It is possible to personalise the separator with the separator keyword.

Warning

However, if a different separator is chosen the resulting file will not comply with the MSA/EMSA standard and HyperSpy and other software may not be able to read it.

The default encoding is latin-1. It is possible to set a different encoding using the encoding argument, e.g.:

>>> s.save('file.msa', encoding = 'utf8')

Ripple

This open standard format developed at NIST as native format for Lispix is widely used to exchange multidimensional data. However, it only supports data of up to three dimensions. It can also be used to exchange data with Bruker and used in combination with the ImportRPL Digital Micrograph plugin it is very useful for exporting data to Gatan’s Digital Micrograph.

The default encoding is latin-1. It is possible to set a different encoding using the encoding argument, e.g.:

>>> s.save('file.rpl', encoding = 'utf8')

For mrc files load takes the mmap_mode keyword argument enabling loading the file using a different mode (default is copy-on-write) . However, note that lazy loading does not support in-place writing (i.e lazy loading and the “r+” mode are incompatible).

Images

HyperSpy can read and write data to all the image formats supported by imageio, which uses the Python Image Library (PIL/pillow). This includes png, pdf, gif, etc. It is important to note that these image formats only support 8-bit files, and therefore have an insufficient dynamic range for most scientific applications. It is therefore highly discouraged to use any general image format (with the exception of TIFF which uses another library) to store data for analysis purposes.

Extra saving arguments

• scalebar (bool, optional): Export the image with a scalebar. Default is False.

• scalebar_kwds (dict, optional): dictionary of keyword arguments for the scalebar. Useful to set formattiong, location, etc. of the scalebar. See the matplotlib-scalebar documentation for more information.

• output_size : (int, tuple of length 2 or None, optional): the output size of the image in pixels:

  • if int, defines the width of the image, the height is determined from the aspect ratio of the image.

  • if tuple of length 2, defines the width and height of the image. Padding with white pixels is used to maintain the aspect ratio of the image.

  • if None, the size of the data is used.

  For output sizes larger than the data size, “nearest” interpolation is used by default and this behaviour can be changed through the imshow_kwds dictionary.

• imshow_kwds (dict, optional): Keyword arguments dictionary for imshow().

• **kwds : keyword arguments supported by the individual file writers as documented at https://imageio.readthedocs.io/en/stable/formats.html when exporting an image without scalebar. When exporting with a scalebar, the keyword arguments are passed to the pil_kwargs dictionary of matplotlib.pyplot.savefig()

When saving an image, a scalebar can be added to the image and the formatting, location, etc. of the scalebar can be set using the scalebar_kwds arguments:

>>> s.save('file.jpg', scalebar=True)
>>> s.save('file.jpg', scalebar=True, scalebar_kwds={'location':'lower right'})

In the example above, the image is created using imshow(), and additional keyword arguments can be passed to this function using imshow_kwds. For example, this can be used to save an image displayed using a matplotlib colormap:

>>> s.save('file.jpg', imshow_kwds=dict(cmap='viridis'))

The resolution of the exported image can be adjusted:

>>> s.save('file.jpg', output_size=512)

TIFF

HyperSpy can read and write 2D and 3D TIFF files using using Christoph Gohlke’s tifffile library. In particular, it supports reading and writing of TIFF, BigTIFF, OME-TIFF, STK, LSM, NIH, and FluoView files. Most of these are uncompressed or losslessly compressed 2**(0 to 6) bit integer, 16, 32 and 64-bit float, grayscale and RGB(A) images, which are commonly used in bio-scientific imaging. See the library webpage for more details.

Currently HyperSpy has limited support for reading and saving the TIFF tags. However, the way that HyperSpy reads and saves the scale and the units of TIFF files is compatible with ImageJ/Fiji and Gatan Digital Micrograph software. HyperSpy can also import the scale and the units from TIFF files saved using FEI, Zeiss SEM, Olympus SIS, Jeol SightX and Hamamatsu HPD-TA (streak camera) software.

Extra loading arguments

• force_read_resolution (bool, optional): Force read image resolution using the x_resolution, y_resolution and resolution_unit tags of the TIFF. Beware: most software don’t (properly) use these tags when saving TIFF files. Default is False.

• hamamatsu_streak_axis_type (str, optional): decide the type of the time axis for hamamatsu streak files:

  • if uniform, the best-fit linear axis is used, inducing a (small) linearisation error. Initialise a UniformDataAxis.

  • if data, the raw time axis parsed from the metadata is used. Initialise a DataAxis.

  • if functional, the best-fit 3rd-order polynomial axis is used, avoiding linearisation error. Initialise a FunctionalDataAxis.

By default, uniform is used but a warning of the linearisation error is issued. Explicitly passing hamamatsu_streak_axis_type='uniform' suppresses the warning. In all cases, the original axis values are stored in the original_metadata of the signal object.

>>> # Force read image resolution using the x_resolution, y_resolution and
>>> # the resolution_unit of the TIFF tags.
>>> s = hs.load('file.tif', force_read_resolution=True)
>>> # Load a non-uniform axis from a hamamatsu streak file:
>>> s = hs.load('file.tif', hamamatsu_streak_axis_type='data')

Extra saving arguments

• extratags (tuple, optional): save custom tags through the

  tifffile library. Must conform to a specific convention (see tifffile documentation and example below).

>>> # Saving the string 'Random metadata' in a custom tag (ID 65000)
>>> extratag = [(65000, 's', 1, "Random metadata", False)]
>>> s.save('file.tif', extratags=extratag)

>>> # Saving the string 'Random metadata' from a custom tag (ID 65000)
>>> s2 = hs.load('file.tif')
>>> s2.original_metadata['Number_65000']
b'Random metadata'

Warning

The file will be saved with the same bit depth as the signal. Since most processing operations in HyperSpy and numpy will result in 64-bit floats, this can result in 64-bit .tiff files, which are not always compatible with other imaging software.

You can first change the dtype of the signal before saving:

>>> s.data.dtype
dtype('float64')
>>> s.change_dtype('float32')
>>> s.data.dtype
dtype('float32')
>>> s.save('file.tif')

Gatan Digital Micrograph

HyperSpy can read both dm3 and dm4 files but the reading features are not complete (and probably they will remain so unless Gatan releases the specifications of the format). That said, we understand that this is an important feature and if loading a particular Digital Micrograph file fails for you, please report it as an issue in the issues tracker to make us aware of the problem.

Some of the tags in the DM-files are added to the metadata of the signal object. This includes, microscope information and certain parameters for EELS, EDS and CL signals.

Extra loading arguments

• optimize: bool, default is True. During loading, the data is replaced by its optimized copy to speed up operations, e. g. iteration over navigation axes. The cost of this speed improvement is to double the memory requirement during data loading.

Warning

It has been reported that in some versions of Gatan Digital Micrograph, any binned data stores the _averages_ of the binned channels or pixels, rather than the _sum_, which would be required for proper statistical analysis. We therefore strongly recommend that all binning is performed using Hyperspy where possible.

See the original bug report here.

EDAX TEAM/Genesis SPD and SPC

HyperSpy can read both .spd (spectrum image) and .spc (single spectra) files from the EDAX TEAM software and its predecessor EDAX Genesis. If reading an .spd file, the calibration of the spectrum image is loaded from the corresponding .ipr and .spc files stored in the same directory, or from specific files indicated by the user. If these calibration files are not available, the data from the .spd file will still be loaded, but with no spatial or energy calibration. If elemental information has been defined in the spectrum image, those elements will automatically be added to the signal loaded by HyperSpy.

Currently, loading an EDAX TEAM spectrum or spectrum image will load an EDSSEMSpectrum Signal. If support for TEM EDS data is needed, please open an issue in the issues tracker to alert the developers of the need.

For further reference, file specifications for the formats are available publicly available from EDAX and are on Github (.spc, .spd, and .ipr).

Extra loading arguments for SPD file

• spc_fname: {None, str}, name of file from which to read the spectral calibration. If data was exported fully from EDAX TEAM software, an .spc file with the same name as the .spd should be present. If None, the default filename will be searched for. Otherwise, the name of the .spc file to use for calibration can be explicitly given as a string.

• ipr_fname: {None, str}, name of file from which to read the spatial calibration. If data was exported fully from EDAX TEAM software, an .ipr file with the same name as the .spd (plus a “_Img” suffix) should be present. If None, the default filename will be searched for. Otherwise, the name of the .ipr file to use for spatial calibration can be explicitly given as a string.

• **kwargs: remaining arguments are passed to the Numpy memmap function.

Extra loading arguments for SPD and SPC files

• load_all_spc : bool, switch to control if all of the .spc header is read, or just the important parts for import into HyperSpy.

FEI TIA SER and EMI

HyperSpy can read ser and emi files but the reading features are not complete (and probably they will be unless FEI releases the specifications of the format). That said we know that this is an important feature and if loading a particular ser or emi file fails for you, please report it as an issue in the issues tracker to make us aware of the problem.

HyperSpy (unlike TIA) can read data directly from the .ser files. However, by doing so, the information that is stored in the emi file is lost. Therefore strongly recommend to load using the .emi file instead.

When reading an .emi file if there are several .ser files associated with it, all of them will be read and returned as a list.

Extra loading arguments

• only_valid_data : bool, in case of series or linescan data with the acquisition stopped before the end: if True, load only the acquired data. If False, the empty data are filled with zeros. The default is False and this default value will change to True in version 2.0.

SEMPER UNF binary format

SEMPER is a fully portable system of programs for image processing, particularly suitable for applications in electron microscopy developed by Owen Saxton (see DOI: 10.1016/S0304-3991(79)80044-3 for more information). The unf format is a binary format with an extensive header for up to 3 dimensional data. HyperSpy can read and write unf-files and will try to convert the data into a fitting BaseSignal subclass, based on the information stored in the label. Currently version 7 of the format should be fully supported.

Blockfile

HyperSpy can read and write the blockfile format from NanoMegas ASTAR software. It is used to store a series of diffraction patterns from scanning precession electron diffraction (SPED) measurements, with a limited set of metadata. The header of the blockfile contains information about centering and distortions of the diffraction patterns, but is not applied to the signal during reading. Blockfiles only support data values of type np.uint8 (integers in range 0-255).

Warning

While Blockfiles are supported, it is a proprietary format, and future versions of the format might therefore not be readable. Complete interoperability with the official software can neither be guaranteed.

Blockfiles are by default loaded in a “copy-on-write” manner using numpy.memmap . For blockfiles load takes the mmap_mode keyword argument enabling loading the file using a different mode. However, note that lazy loading does not support in-place writing (i.e lazy loading and the “r+” mode are incompatible).

Extra saving arguments

• intensity_scaling : in case the dataset that needs to be saved does not have the np.uint8 data type, casting to this datatype without intensity rescaling results in overflow errors (default behavior). This option allows you to perform linear intensity scaling of the images prior to saving the data. The options are:

  • ‘dtype’: the limits of the datatype of the dataset, e.g. 0-65535 for np.uint16, are mapped onto 0-255 respectively. Does not work for float data types.

  • ‘minmax’: the minimum and maximum in the dataset are mapped to 0-255.

  • ‘crop’: everything below 0 and above 255 is set to 0 and 255 respectively

  • 2-tuple of floats or ints: the intensities between these values are scaled between 0-255, everything below is 0 and everything above is 255.

• navigator_signal: the BLO file also stores a virtual bright field (VBF) image which behaves like a navigation signal in the ASTAR software. By default this is set to ‘navigator’, which results in the default navigator signal to be used. If this signal was not calculated before (e.g. by calling plot()), it is calculated when save() is called, which can be time consuming. Alternatively, setting the argument to None will result in a correctly sized zero array to be used. Finally, a custom Signal2D object can be passed, but the shape must match the navigation dimensions.

DENSsolutions formats

HyperSpy can read any logfile from DENSsolutions’ new Impulse software as well as the legacy heating software DigiHeater.

DENSsolutions Impulse logfile

Impulse logfiles are stored in csv format. All metadata linked to the experiment is stored in a separate metadata.log file. This metadata file contains crucial information about the experiment and should be included in the same folder with the csv file when reading data into Hyperspy.

To read Impulse logfiles, use the reader argument to define the correct file reader:

>>> hs.load("filename.csv", reader="impulse")

DENSsolutions DigiHeater logfile

HyperSpy can read the heater log format from the DENSsolutions’ DigiHeater software. The format stores all the captured data for each timestamp, together with a small header in a plain-text format. The reader extracts the measured temperature along the time axis, as well as the date and calibration constants stored in the header.

Bruker’s formats

Bruker’s Esprit(TM) software and hardware allows to acquire and save the data in different kind of formats. Hyperspy can read two main basic formats: bcf and spx.

Bruker composite file

HyperSpy can read “hypermaps” saved with Bruker’s Esprit v1.x or v2.x in bcf hybrid (virtual file system/container with xml and binary data, optionally compressed) format. Most bcf import functionality is implemented. Both high-resolution 16-bit SEM images and hyperspectral EDX data can be retrieved simultaneously.

BCF can look as all inclusive format, however it does not save some key EDX parameters: any of dead/live/real times, FWHM at Mn_Ka line. However, real time for whole map is calculated from pixelAverage, lineAverage, pixelTime, lineCounter and map height parameters.

Note that Bruker Esprit uses a similar format for EBSD data, but it is not currently supported by HyperSpy.

Extra loading arguments

• select_type : one of (None, ‘spectrum’, ‘image’). If specified, only the corresponding type of data, either spectrum or image, is returned. By default (None), all data are loaded.

• index : one of (None, int, “all”). Allow to select the index of the dataset in the bcf file, which can contains several datasets. Default None value result in loading the first dataset. When set to ‘all’, all available datasets will be loaded and returned as separate signals.

• downsample : the downsample ratio of hyperspectral array (height and width only), can be integer >=1, where ‘1’ results in no downsampling (default 1). The underlying method of downsampling is unchangeable: sum. Differently than block_reduce from skimage.measure it is memory efficient (does not creates intermediate arrays, works inplace).

• cutoff_at_kV : if set (can be None, int, float (kV), one of ‘zealous’ or ‘auto’) can be used either to crop or enlarge energy (or number of channels) range at max values. It can be used to conserve memory or enlarge the range if needed to mach the size of other file. Default value is None (which does not influence size). Numerical values should be in kV. ‘zealous’ truncates to the last non zero channel (this option should not be used for stacks, as low beam current EDS can have different last non zero channel per slice). ‘auto’ truncates channels to SEM/TEM acceleration voltage or energy at last channel, depending which is smaller. In case the hv info is not there or hv is off (0 kV) then it fallbacks to full channel range.

Example of loading reduced (downsampled, and with energy range cropped) “spectrum only” data from bcf (original shape: 80keV EDS range (4096 channels), 100x75 pixels; SEM acceleration voltage: 20kV):

>>> hs.load("sample80kv.bcf", select_type='spectrum', downsample=2, cutoff_at_kV=10)
<EDSSEMSpectrum, title: EDX, dimensions: (50, 38|595)>

load the same file with limiting array size to SEM acceleration voltage:

>>> hs.load("sample80kv.bcf", cutoff_at_kV='auto')
[<Signal2D, title: BSE, dimensions: (|100, 75)>,
<Signal2D, title: SE, dimensions: (|100, 75)>,
<EDSSEMSpectrum, title: EDX, dimensions: (100, 75|1024)>]

The loaded array energy dimension can by forced to be larger than the data recorded by setting the ‘cutoff_at_kV’ kwarg to higher value:

>>> hs.load("sample80kv.bcf", cutoff_at_kV=60)
[<Signal2D, title: BSE, dimensions: (|100, 75)>,
<Signal2D, title: SE, dimensions: (|100, 75)>,
<EDSSEMSpectrum, title: EDX, dimensions: (100, 75|3072)>]

loading without setting cutoff_at_kV value would return data with all 4096 channels. Note that setting downsample to >1 currently locks out using SEM images for navigation in the plotting.

SPX format

Hyperspy can read Bruker’s spx format (single spectra format based on XML). The format contains extensive list of details and parameters of EDS analyses which are mapped in hyperspy to metadata and original_metadata dictionaries.

EMD

EMD stands for “Electron Microscopy Dataset.” It is a subset of the open source HDF5 wrapper format. N-dimensional data arrays of any standard type can be stored in an HDF5 file, as well as tags and other metadata.

EMD (NCEM)

This EMD format was developed by Colin Ophus at the National Center for Electron Microscopy (NCEM). This format is used by the prismatic software to save the simulation outputs.

Extra loading arguments

• dataset_path : None, str or list of str. Path of the dataset. If None, load all supported datasets, otherwise the specified dataset(s).

• stack_group : bool, default is True. Stack datasets of groups with common path. Relevant for emd file version >= 0.5 where groups can be named ‘group0000’, ‘group0001’, etc.

• chunks : None, True or tuple. Determine the chunking of the dataset to save. See the chunks arguments of the hspy file format for more details.

For files containing several datasets, the dataset_name argument can be used to select a specific one:

>>> s = hs.load("adatafile.emd", dataset_name="/experimental/science_data_1/data")

Or several by using a list:

>>> s = hs.load("adatafile.emd",
...             dataset_name=[
...                 "/experimental/science_data_1/data",
...                 "/experimental/science_data_2/data"])

EMD (Velox)

This is a non-compliant variant of the standard EMD format developed by Thermo-Fisher (former FEI). HyperSpy supports importing images, EDS spectrum and EDS spectrum streams (spectrum images stored in a sparse format). For spectrum streams, there are several loading options (described below) to control the frames and detectors to load and if to sum them on loading. The default is to import the sum over all frames and over all detectors in order to decrease the data size in memory.

Note

Pruned Velox EMD files only contain the spectrum image in a proprietary format that HyperSpy cannot read. Therefore, don’t prune Velox EMD files if you intend to read them with HyperSpy.

>>> hs.load("sample.emd")
[<Signal2D, title: HAADF, dimensions: (|179, 161)>,
<EDSSEMSpectrum, title: EDS, dimensions: (179, 161|4096)>]

Note

FFTs made in Velox are loaded in as-is as a HyperSpy ComplexSignal2D object. The FFT is not centered and only positive frequencies are stored in the file. Making FFTs with HyperSpy from the respective image datasets is recommended.

Note

DPC data is loaded in as a HyperSpy ComplexSignal2D object.

Note

Currently only lazy uncompression rather than lazy loading is implemented. This means that it is not currently possible to read EDS SI Velox EMD files with size bigger than the available memory.

Warning

This format is still not stable and files generated with the most recent version of Velox may not be supported. If you experience issues loading a file, please report it to the HyperSpy developers so that they can add support for newer versions of the format.

Extra loading arguments

• select_type : one of {None, ‘image’, ‘single_spectrum’, ‘spectrum_image’} (default is None).

• first_frame : integer (default is 0).

• last_frame : integer (default is None)

• sum_frames : boolean (default is True)

• sum_EDS_detectors : boolean (default is True)

• rebin_energy : integer (default is 1)

• SI_dtype : numpy dtype (default is None)

• load_SI_image_stack : boolean (default is False)

The select_type parameter specifies the type of data to load: if image is selected, only images (including EDS maps) are loaded, if single_spectrum is selected, only single spectra are loaded and if spectrum_image is selected, only the spectrum image will be loaded. The first_frame and last_frame parameters can be used to select the frame range of the EDS spectrum image to load. To load each individual EDS frame, use sum_frames=False and the EDS spectrum image will be loaded with an extra navigation dimension corresponding to the frame index (time axis). Use the sum_EDS_detectors=True parameter to load the signal of each individual EDS detector. In such a case, a corresponding number of distinct EDS signal is returned. The default is sum_EDS_detectors=True, which loads the EDS signal as a sum over the signals from each EDS detectors. The rebin_energy and SI_dtype parameters are particularly useful in combination with sum_frames=False to reduce the data size when one want to read the individual frames of the spectrum image. If SI_dtype=None (default), the dtype of the data in the emd file is used. The load_SI_image_stack parameter allows loading the stack of STEM images acquired simultaneously as the EDS spectrum image. This can be useful to monitor any specimen changes during the acquisition or to correct the spatial drift in the spectrum image by using the STEM images.

>>> hs.load("sample.emd", sum_EDS_detectors=False)
[<Signal2D, title: HAADF, dimensions: (|179, 161)>,
<EDSSEMSpectrum, title: EDS - SuperXG21, dimensions: (179, 161|4096)>,
<EDSSEMSpectrum, title: EDS - SuperXG22, dimensions: (179, 161|4096)>,
<EDSSEMSpectrum, title: EDS - SuperXG23, dimensions: (179, 161|4096)>,
<EDSSEMSpectrum, title: EDS - SuperXG24, dimensions: (179, 161|4096)>]

>>> hs.load("sample.emd", sum_frames=False, load_SI_image_stack=True, SI_dtype=np.int8, rebin_energy=4)
[<Signal2D, title: HAADF, dimensions: (50|179, 161)>,
<EDSSEMSpectrum, title: EDS, dimensions: (50, 179, 161|1024)>]

Protochips log

HyperSpy can read heater, biasing and gas cell log files for Protochips holder. The format stores all the captured data together with a small header in a csv file. The reader extracts the measured quantity (e. g. temperature, pressure, current, voltage) along the time axis, as well as the notes saved during the experiment. The reader returns a list of signal with each signal corresponding to a quantity. Since there is a small fluctuation in the step of the time axis, the reader assumes that the step is constant and takes its mean, which is a good approximation. Further release of HyperSpy will read the time axis more precisely by supporting non-uniform axis.

To read Protochips logfiles, use the reader argument to define the correct file reader:

>>> hs.load("filename.csv", reader="protochips")

USID

Background

Universal Spectroscopy and Imaging Data (USID) is an open, community-driven, self-describing, and standardized schema for representing imaging and spectroscopy data of any size, dimensionality, precision, instrument of origin, or modality. USID data is typically stored in Hierarchical Data Format Files (HDF5) and the combination of USID within HDF5 files is referred to as h5USID.

pyUSID provides a convenient interface to I/O operations on such h5USID files. USID (via pyUSID) forms the foundation for other materials microscopy scientific python package called pycroscopy. If you have any questions regarding this module, please consider contacting the developers of pyUSID.

Requirements

1. Reading and writing h5USID files require the installation of pyUSID.

2. Files must use the .h5 file extension in order to use this io plugin. Using the .hdf5 extension will default to HyperSpy’s own plugin.

Reading

h5USID files can contain multiple USID datasets within the same file. HyperSpy supports reading in one or more USID datasets.

Extra loading arguments

• dataset_path: str. Absolute path of USID Main HDF5 dataset. (default is None - all USID Main Datasets will be read)

• ignore_non_linear_dims: bool, default is True. If True, parameters that were varied non-linearly in the desired dataset will result in Exceptions. Else, all such non-linearly varied parameters will be treated as linearly varied parameters and a Signal object will be generated.

Reading the sole dataset within a h5USID file:

>>> hs.load("sample.h5")
<Signal2D, title: HAADF, dimensions: (|128, 128)>

If multiple datasets are present within the h5USID file and you try the same command again, all available datasets will be loaded.

Note

Given that HDF5 files can accommodate very large datasets, setting lazy=True is strongly recommended if the contents of the HDF5 file are not known apriori. This prevents issues with regard to loading datasets far larger than memory.

Also note that setting lazy=True leaves the file handle to the HDF5 file open. If it is important that the files be closed after reading, set lazy=False.

>>> hs.load("sample.h5")
[<Signal2D, title: HAADF, dimensions: (|128, 128)>,
<Signal1D, title: EELS, dimensions: (|64, 64, 1024)>]

We can load a specific dataset using the dataset_path keyword argument. Setting it to the absolute path of the desired dataset will cause the single dataset to be loaded.

>>> # Loading a specific dataset
>>> hs.load("sample.h5", dataset_path='/Measurement_004/Channel_003/Main_Data')
<Signal2D, title: HAADF, dimensions: (|128, 128)>

h5USID files support the storage of HDF5 dataset with compound data types. As an (oversimplified) example, one could store a color image using a compound data type that allows each color channel to be accessed by name rather than an index. Naturally, reading in such a compound dataset into HyperSpy will result in a separate signal for each named component in the dataset:

>>> hs.load("file_with_a_compound_dataset.h5")
[<Signal2D, title: red, dimensions: (|128, 128)>,
Signal2D, title: blue, dimensions: (|128, 128)>,
Signal2D, title: green, dimensions: (|128, 128)>]

h5USID files also support parameters or dimensions that have been varied non-uniformly. This capability is important in several spectroscopy techniques where the bias is varied as a bi-polar triangular waveform rather than uniformly from the minimum value to the maximum value. Since HyperSpy Signals expect uniform variation of parameters / axes, such non-uniform information would be lost in the axes manager. The USID plugin will default to a warning when it encounters a parameter that has been varied non-uniformly:

>>> hs.load("sample.h5")
UserWarning: Ignoring non-uniformity of dimension: Bias
<BaseSignal, title: , dimensions: (|7, 3, 5, 2)>

Obviously, the In order to prevent accidental misinterpretation of information downstream, the keyword argument ignore_non_uniform_dims can be set to False which will result in a ValueError instead.

>>> hs.load("sample.h5")
ValueError: Cannot load provided dataset. Parameter: Bias was varied non-uniformly.
Supply keyword argument "ignore_non_uniform_dims=True" to ignore this error

Writing

Signals can be written to new h5USID files using the standard save() function. Setting the overwrite keyword argument to True will append to the specified HDF5 file. All other keyword arguments will be passed to pyUSID.hdf_utils.write_main_dataset()

>>> sig.save("USID.h5")

Note that the model and other secondary data artifacts linked to the signal are not written to the file but these can be implemented at a later stage.

Nexus

Background

NeXus is a common data format originally developed by the neutron and x-ray science x-ray communities. It is still being developed as an international standard by scientists and programmers representing major scientific facilities in order to facilitate greater cooperation in the analysis and visualization of data. Nexus uses a variety of classes to record data, values, units and other experimental metadata associated with an experiment. For specific types of experiments an Application Definition may exist, which defines an agreed common layout that facilities can adhere to.

Nexus metadata and data are stored in Hierarchical Data Format Files (HDF5) with a .nxs extension although standards HDF5 extensions are sometimes used. Files must use the .nxs file extension in order to use this io plugin. Using the .nxs extension will default to the Nexus loader. If your file has an HDF5 extension, you can also explicitly set the Nexus file reader:

# Load a NeXus file with a .h5 extension
>>> s = hs.load("filename.h5", reader="nxs")

The loader will follow version 3 of the Nexus data rules. The signal type, Signal1D or Signal2D, will be inferred by the interpretation attribute, if this is set to spectrum or image, in the NXdata description. If the interpretation attribute is not set, the loader will return a BaseSignal, which must then be converted to the appropriate signal type. Following the Nexus data rules, if a default dataset is not defined, the loader will load NXdata and HDF datasets according to the keyword options in the reader. A number of the Nexus examples from large facilties do not use NXdata or use older versions of the Nexus implementation. Data can still be loaded from these files but information or associations may be missing. However, this missing information can be recovered from within the original_metadata which contains the overall structure of the entry.

As the Nexus format uses the HDF5 format and needs to read both data and metadata structured in different ways, the loader is written to be quite flexible and can also be used to inspect any hdf5 based file.

Differences with respect to hspy

HyperSpy metadata structure stores arrays as hdf datasets without attributes and stores floats, ints and strings as attributes. Nexus formats typically use hdf datasets attributes to store additional information such as an indication of the units for an axis or the NX_class which the dataset structure follows. The metadata, hyperspy or original_metadata, therefore needs to be able to indicate the values and attributes of a dataset. To implement this structure the value and attrs of a dataset can also be defined. The value of a dataset is set using a value key. The attributes of a dataset are defined by an attrs key.

For example, to store an array called axis_x, with a units attribute within original_metadata, the following structure would be used:

├──original_metadata
│   ├── axis_x
│   │   ├── value : array([1.0,2.0,3.0,4.0,5.0])
│   │   ├── attrs
│   │   │   ├── units : mm

>>> original_metadata.set_item(axis_x.value,[1.0,2.0,3.0,4.0,5.0])
>>> original_metadata.set_item(axis_x.attrs.units,"mm")

To access the axis information:

>>> original_metadata.axis_x.value
>>> original_metadata.axis_x.attrs.units

To modify the axis information:

>>> original_metadata.axis_x.value = [2.0,3.0,4.0,5.0,6.0]
>>> original_metadata.axis_x.attrs.units = "um"

To store data in a Nexus monochromator format, value and attrs keys can define additional attributes:

├── monochromator
│   ├── energy
│   │   ├── value : 12.0
│   │   ├── attrs
│   │   │   ├── units : keV
│   │   │   ├── NXclass : NXmonochromator

The attrs key can also be used to define Nexus structures for the definition of structures and relationships between data:

├── mydata
│   ├── attrs
│   │   ├── NX_class : "NXdata"
│   │   ├── axes : ["x","."]
│   ├── data
│   │   ├──value : [[30,23...110]
│   ├── x
│   │   ├──value : [1,2.....100]
│   │   ├── attrs
│   │   │   ├── unit : "mm"

The use of attrs or value to set values within the metadata is optional and metadata values can also be set, read or modified in the normal way.

>>> original_metadata.monochromator.energy = 12.5

HyperSpy metadata is stored within the Nexus file and should be automatically restored when a signal is loaded from a previously saved Nexus file.

Note

Altering the standard metadata structure of a signal using attrs or value keywords is not recommended.

Reading

Nexus files can contain multiple datasets within the same file, but the ordering of datasets can vary depending on the setup of an experiment or processing step when the data was collected. For example, in one experiment Fe, Ca, P, Pb were collected but in the next experiment Ca, P, K, Fe, Pb were collected. HyperSpy supports reading in one or more datasets and returns a list of signals but in this example case the indexing is different. To control which data or metadata is loaded and in what order some additional loading arguments are provided.

Extra loading arguments

• dataset_key: None, str or list of strings - Default is None . String(s) to search for in the path to find one or more datasets.

• dataset_path: None, str or list of strings - Default is None . Absolute path(s) to search for in the path to find one or more datasets.

• metadata_key: None, str or list of strings - Default is None . Absolute path(s) or string(s) to search for in the path to find metadata.

• skip_array_metadata: bool - Default is False. Option to skip loading metadata that are arrays to avoid duplicating loading of data.

• nxdata_only: bool - Default is False. Option to only convert NXdata formatted data to signals.

• hardlinks_only: bool - Default is False. Option to ignore soft or External links in the file.

• use_default: bool - Default is False. Only load the default dataset, if defined, from the file. Otherwise load according to the other keyword options.

Note

Given that HDF5 files can accommodate very large datasets, setting lazy=True is strongly recommended if the content of the HDF5 file is not known apriori. This prevents issues with regard to loading datasets far larger than memory.

Also note that setting lazy=True leaves the file handle to the HDF5 file open and it can be closed with close_file() or when using compute() with close_file=True.

Reading a Nexus file (a single Nexus dataset):

>>> sig = hs.load("sample.nxs")

By default, the loader will look for stored NXdata objects. If there are hdf datasets which are not stored as NXdata, but which should be loaded as signals, set the nxdata_only keyword to False and all hdf datasets will be returned as signals:

>>> sig = hs.load("sample.nxs", nxdata_only=False)

We can load a specific dataset using the dataset_path keyword argument. Setting it to the absolute path of the desired dataset will cause the single dataset to be loaded:

>>> # Loading a specific dataset
>>> hs.load("sample.nxs", dataset_path="/entry/experiment/EDS/data")

We can also choose to load datasets based on a search key using the dataset_key keyword argument. This can also be used to load NXdata not outside of the default version 3 rules. Instead of providing an absolute path, a string can be provided as well, and datasets with this key will be returned. The previous example could also be written as:

>>> # Loading datasets containing the string "EDS"
>>> hs.load("sample.nxs", dataset_key="EDS")

The difference between dataset_path and dataset_key is illustrated here:

>>> # Only the dataset /entry/experiment/EDS/data will be loaded
>>> hs.load("sample.nxs", dataset_path="/entry/experiment/EDS/data")
>>> # All datasets contain the entire string "/entry/experiment/EDS/data" will be loaded
>>> hs.load("sample.nxs", dataset_key="/entry/experiment/EDS/data")

Multiple datasets can be loaded by providing a number of keys:

>>> # Loading a specific dataset
>>> hs.load("sample.nxs", dataset_key=["EDS", "Fe", "Ca"])

Metadata can also be filtered in the same way using metadata_key:

>>> # Load data with metadata matching metadata_key
>>> hs.load("sample.nxs", metadata_key="entry/instrument")

Note

The Nexus loader removes any NXdata blocks from the metadata.

Metadata that are arrays can be skipped by using skip_array_metadata:

>>> # Load data while skipping metadata that are arrays
>>> hs.load("sample.nxs", skip_array_metadata=True)

Nexus files also support parameters or dimensions that have been varied non-linearly. Since HyperSpy Signals expect linear variation of parameters / axes, such non-linear information would be lost in the axes manager and replaced with indices. Nexus and HDF can result in large metadata structures with large datasets within the loaded original_metadata. If lazy loading is used this may not be a concern but care must be taken when saving the data. To control whether large datasets are loaded or saved, use the metadata_key to load only the most relevant information. Alternatively, set skip_array_metadata to True to avoid loading those large datasets in original_metadata.

Writing

Signals can be written to new Nexus files using the standard save() function.

Extra saving arguments

• save_original_metadata: bool - Default is True, option to save the original_metadata when storing to file.

• skip_metadata_key: bool - None, str or list of strings - Default is None. Option to skip certain metadata keys when storing to file.

• use_default: bool - Default is False. Set the default attribute for the Nexus file.

>>> sig.save("output.nxs")

Using the save method will store the nexus file with the following structure:

├── entry1
│   ├── signal_name
│   │   ├── auxiliary
│   │   │   ├── original_metadata
│   │   │   ├── hyperspy_metadata
│   │   │   ├── learning_results
│   │   ├── signal_data
│   │   │   ├── data and axes (NXdata format)

The original_metadata can include hdf datasets which you may not wish to store. The original_metadata can be omitted using save_original_metadata.

>>> sig.save("output.nxs", save_original_metadata=False)

If only certain metadata are to be ignored, use skip_metadata_key:

>>> sig.save("output.nxs", skip_metadata_key=['xsp3', 'solstice_scan'])

To save multiple signals, the file_writer method can be called directly.

>>> from hyperspy.io_plugins.nexus import file_writer
>>> file_writer("test.nxs",[signal1,signal2])

When saving multiple signals, a default signal can be defined. This can be used when storing associated data or processing steps along with a final result. All signals can be saved but a single signal can be marked as the default for easier loading in HyperSpy or plotting with Nexus tools. The default signal is selected as the first signal in the list:

>>> from hyperspy.io_plugins.nexus import file_writer
>>> import hyperspy.api as hs
>>> file_writer("test.nxs", [signal1, signal2], use_default = True)
>>> hs.load("test.nxs", use_default = True)

The output will be arranged by signal name:

├── entry1 (NXentry)
│   ├── signal_name (NXentry)
│   │   ├── auxiliary (NXentry)
│   │   │   ├── original_metadata (NXcollection)
│   │   │   ├── hyperspy_metadata (NXcollection)
│   │   │   ├── learning_results  (NXcollection)
│   │   ├── signal_data (NXdata format)
│   │   │   ├── data and axes
├── entry2 (NXentry)
│   ├── signal_name (NXentry)
│   │   ├── auxiliary (NXentry)
│   │   │   ├── original_metadata (NXcollection)
│   │   │   ├── hyperspy_metadata (NXcollection)
│   │   │   ├── learning_results (NXcollection)
│   │   ├── signal_data (NXdata)
│   │   │   ├── data and axes

Note

Signals saved as nxs by this plugin can be loaded normally and the original_metadata, signal data, axes, metadata and learning_results will be restored. Model information is not currently stored. Nexus does not store how the data should be displayed. To preserve the signal details an additional navigation attribute is added to each axis to indicate if it is a navigation axis.

Inspecting

Looking in a Nexus or HDF file for specific metadata is often useful - e.g. to find what position a specific stage was at. The methods read_metadata_from_file and list_datasets_in_file can be used to load the file contents or list the hdf datasets contained in a file. The inspection methods use the same metadata_key or dataset_key as when loading. For example to search for metadata in a file:

>>> from hyperspy.io_plugins.nexus import read_metadata_from_file
>>> read_metadata_from_file("sample.hdf5",metadata_key=["stage1_z"])
{'entry': {'instrument': {'scannables': {'stage1': {'stage1_z': {'value': -9.871700000000002,
'attrs': {'gda_field_name': 'stage1_z',
'local_name': 'stage1.stage1_z',
'target': '/entry/instrument/scannables/stage1/stage1_z',
'units': 'mm'}}}}}}}

To list the datasets stored in the file:

>>> from hyperspy.io_plugins.nexus import read_datasets_from_file
>>> list_datasets_in_file("sample.nxs")
NXdata found
/entry/xsp3_addetector
/entry/xsp3_addetector_total
HDF datasets found
/entry/solstice_scan/keys/uniqueKeys
/entry/solstice_scan/scan_shape
Out[3]:
(['/entry/xsp3_addetector', '/entry/xsp3_addetector_total'],
 ['/entry/solstice_scan/keys/uniqueKeys', '/entry/solstice_scan/scan_shape'])

SUR and PRO format

This is a format developed by the digitalsurf company to handle various types of scientific measurements data such as profilometer, SEM, AFM, RGB(A) images, multilayer surfaces and profiles. Even though it is essentially a surfaces format, 1D signals are supported for spectra and spectral maps. Specifically, this file format is used by Attolight SA for its scanning electron microscope cathodoluminescence (SEM-CL) hyperspectral maps. Metadata parsing is supported, including user-specific metadata, as well as the loading of files containing multiple objects packed together.

The plugin was developed based on the MountainsMap software documentation, which contains a description of the binary format.

EMPAD format

This is the file format used by the Electron Microscope Pixel Array Detector (EMPAD). It is used to store a series of diffraction patterns from scanning transmission electron diffraction measurements, with a limited set of metadata. Similarly, to the ripple format, the raw data and metadata are saved in two different files and for the EMPAD reader, these are saved in the raw and xml files, respectively. To read EMPAD data, use the xml file:

>>> sig = hs.load("file.xml")

which will automatically read the raw data from the raw file too. The filename of the raw file is defined in the xml file, which implies changing the file name of the raw file will break reading the file.

Phenom ELID format

This is the file format used by the software package Element Identification for the Thermo Fisher Scientific Phenom desktop SEM. It is a proprietary binary format which can contain images, single EDS spectra, 1D line scan EDS spectra and 2D EDS spectrum maps. The reader will convert all signals and its metadata into hyperspy signals.

The current implementation supports ELID files created with Element Identification version 3.8.0 and later. You can convert older ELID files by loading the file into a recent Element Identification release and then save the ELID file into the newer file format.

JEOL ASW format

This is the file format used by the JEOL Analysist Station software for which hyperspy can read the asw, pts, map and eds format. To read the calibration, it is required to load the asw file, which will load all others files automatically.

Extra loading arguments

• rebin_energy : int, default 1. Factor used to rebin the energy dimension. It must be a factor of the number of channels, typically 4096.

• sum_frames : bool, default True. If False, each individual frame (sweep in JEOL software jargon) is loaded. Be aware that loading each individual will use a lot of memory, however, it can be used in combination with rebin_energy, cutoff_at_kV and downsample to reduce memory usage.

• SI_dtype : dtype, default np.uint8. set dtype of the eds dataset. Useful to adjust memory usage and maximum number of X-rays per channel.

• cutoff_at_kV : int, float, or None, default None. if set (>= 0), use to crop the energy range up the specified energy. If None, the whole energy range is loaded. Useful to reduce memory usage.

• downsample : int, default 1. the downsample ratio of the navigation dimension of EDS dataset, it can be integer or a tuple of length 2 to define x and y separetely and it must be a mutiple of the size of the navigation dimension.

• only_valid_data : bool, default True. for pts file only, ignore incomplete and partly acquired last frame, which typically occurs when the acquisition was interrupted. When loading incomplete data (only_valid_data=False), the missing data are filled with zeros. If sum_frames=True, this argument will be ignored to enforce consistent sum over the mapped area.

• read_em_image : bool, default False. for pts file only, If read_em_image=True, read SEM/STEM image from pts file if available. In this case, both spectrum Image and SEM/STEM Image will be returned as list.

• frame_list : list of integer or None, default None for pts file only, frames in frame_list will be loaded. for example, frame_list=[1,3] means second and forth frame will be loaded. If None, all frames are loaded.

• frame_shifts : list of [int, int], list of [int, int, int], or None, default None for pts file only, each frame will be loaded with offset of [dy, dx (, and optionary dEnergy)]. Units are pixels/channels. The result of estimate_shift2D() can be used as a parameter of frame_shifts. This is useful for express drift correction. Not suitable for accurate analysis.

• lazy : bool, default False for pts file only, spectrum image is loaded as a dask.array if lazy == true. This is useful to reduce memory usage, with cost of cpu time for calculation.

Example of loading data downsampled, and with energy range cropped with the original navigation dimension 512 x 512 and the EDS range 40 keV over 4096 channels:

>>> hs.load("sample40kv.asw", downsample=8, cutoff_at_kV=10)
[<Signal2D, title: IMG1, dimensions: (|512, 512)>,
 <Signal2D, title: C K, dimensions: (|512, 512)>,
 <Signal2D, title: O K, dimensions: (|512, 512)>,
 <EDSTEMSpectrum, title: EDX, dimensions: (64, 64|1096)>]

load the same file without extra arguments:

>>> hs.load("sample40kv.asw")
[<Signal2D, title: IMG1, dimensions: (|512, 512)>,
 <Signal2D, title: C K, dimensions: (|512, 512)>,
 <Signal2D, title: O K, dimensions: (|512, 512)>,
 <EDSTEMSpectrum, title: EDX, dimensions: (512, 512|4096)>]

TVIPS format

The TVIPS format is the default format for image series collected by pixelated cameras from the TVIPS company. Typically individual images captured by these cameras are stored in the TIFF format which can also be loaded by Hyperspy. This format instead serves to store image streams from in-situ and 4D-STEM experiments. During collection, the maximum file size is typically capped meaning the dataset is typically split over multiple files ending in _xyz.tvips. The _000.tvips will contain the main header and it is essential for loading the data. If a filename is provided for loading or saving without a _000 suffix, this will automatically be added. Loading will not work if no such file is found.

Warning

While TVIPS files are supported, it is a proprietary format, and future versions of the format might therefore not be readable. Complete interoperability with the official software can neither be guaranteed.

Warning

The TVIPS format currently stores very limited amount of metadata about scanning experiments. To reconstruct scan data, e.g. 4D-STEM datasets, parameters like the shape and scales of the scan dimensions should be manually recorded.

Extra loading arguments

• scan_shape: a tuple of integers to indicate the shape of the navigation axes. For example, (3, 4) will have 3 scan points in the y direction and 4 in the x direction. If this argument is not provided, the data will be loaded as a 1D stack of images. auto is also an option which aims to reconstruct the scan based on the rotidx indices in frame headers. Since this only works for square scan grids and is prone to failure, this option is not recommended.

• scan_start_frame: index of the first frame of the dataset to consider, mainly relevant for 4D-STEM datasets. If scan_shape=”auto” this parameter is ignored.

• winding_scan_axis: if the acquisition software collected data without beam flyback but with a winding “snake” scan, then every second scan row or column needs to be reversed to make sense of the data. This can be indicated with values “x” or “y”, depending on whether winding happened along the primary or secondary axis. By default, flyback scan without winding is assumed with x the fast scan and y the slow scan direction.

• hysteresis: if winding scan was active it is likely there is an overshoot of a few pixels (2-5) every second scan row. This parameter shifts every second row by the indicated number of scan points to align even and odd scan rows. Default is 0, no hysteresis.

• rechunking: only relevant when using lazy loading. If set to False each TVIPS file is loaded as a single chunk. For a better experience, with the default setting of auto rechunking is performed such that the navigation axes are optimally chunked and the signal axes are not chunked. If set to anything else, the value will be passed to the chunks argument in dask.array.rechunk.

Extra saving arguments

• max_file_size: approximate maximum size of individual files in bytes. In this way a dataset can be split into multiple files. A file needs to be at least the size of the main header in the first file plus one frame and its frame header. By default there is no maximum and the entire dataset is saved to one file.

• version: TVIPS file format version, defaults to version 2. Only version 1 and 2 are currently supported.

• frame_header_extra_bytes: the number of bytes to pad the frame headers with. By default this is 0.

• mode: 1 for imaging, 2 for diffraction. By default the mode is guessed from the signal type and signal unites.

Reading data generated by HyperSpy using other software packages

The following scripts may help reading data generated by HyperSpy using other software packages.

ImportRPL Digital Micrograph plugin

This Digital Micrograph plugin is designed to import Ripple files into Digital Micrograph. It is used to ease data transit between DigitalMicrograph and HyperSpy without losing the calibration using the extra keywords that HyperSpy adds to the standard format.

When executed it will ask for 2 files:

1. The riple file with the data format and calibrations

2. The data itself in raw format.

If a file with the same name and path as the riple file exits with raw or bin extension it is opened directly without prompting. ImportRPL was written by Luiz Fernando Zagonel.

Download ImportRPL

HDF5 reader plugin for Digital Micrograph

This Digital Micrograph plugin is designed to import HDF5 files and like the ImportRPL script above, it can be used to easily transfer data from HyperSpy to Digital Micrograph by using the HDF5 hyperspy format (hspy extension).

Download gms_plugin_hdf5 from its Github repository.

readHyperSpyH5 MATLAB Plugin

This MATLAB script is designed to import HyperSpy’s saved HDF5 files (.hspy extension). Like the Digital Micrograph script above, it is used to easily transfer data from HyperSpy to MATLAB, while retaining spatial calibration information.

Download readHyperSpyH5 from its Github repository.