Released versions of NeXpy are available on PyPI and as a Conda installation.
If you have the Python Setup Tools installed, then you can install using either:
$ pip install nexpy
or:
$ easy_install nexpy
If you have an Anaconda installation, use:
$ conda install -c https://conda.anaconda.org/nexpy nexpy
If you have trouble with the pip or easy_install installations, you can install the package from the source code either by downloading one of the Github releases or by cloning the latest development version in the NeXpy Git repository:
$ git clone https://github.com/nexpy/nexpy.git
You can then install NeXpy by changing to the source directory and typing:
$ python setup.py install
To install in an alternate location:
$ python setup.py install --prefix=/path/to/installation/dir
As of v0.6.0, the Python API for reading and writing NeXus files is in a separate package, nexusformat, which is also available on PyPI and will be automatically installed as a NeXpy dependency if you use pip.
If the NeXpy GUI is not required, the package may be used in a regular Python shell. It may be installed using:
$ pip install nexusformat
or:
$ easy_install nexusformat
or:
$ conda install -c https://conda.anaconda.org/nexpy nexusformat
The package can also be installed from the source code using the setup commands described above. The source code is available either by downloading one of the Github releases or by cloning the latest development version in the NeXpy Git repository:
$ git clone https://github.com/nexpy/nexusformat.git
The current version of NeXpy uses h5py to read and write NeXus files because of its ability to handle large data files. There is therefore no dependency on the NeXus C API. This also means that the current version cannot read and write HDF4 or XML NeXus files.
If you only intend to utilize the Python API from the command-line, the only other required library is Numpy.
| Library | URL |
|---|---|
| nexusformat | https://github.com/nexpy/nexusformat |
| h5py | http://www.h5py.org |
| numpy | http://numpy.scipy.org/ |
Note
If you need to read HDF4 or XML files now, please clone the old-master branch (https://github.com/nexpy/nexpy/tree/old-master).
The GUI is built using the PyQt. The latest version supports PyQt4, PySide, and with v0.10.0, PyQt5, and should load whichever library it finds. None are listed as a dependency but one or other must be installed. PyQt5 is included in the Anaconda default distribution while PySide is included in the Enthought Python Distribution or within Enthought's Canopy Application.
The GUI includes an IPython shell and a Matplotlib plotting pane. The IPython shell is embedded in the Qt GUI using an implementation based on the newly-released Jupyter QtConsole, which has replaced the old IPython QtConsole.
| Library | URL |
|---|---|
| jupyter | http://jupyter.org/ |
| IPython v4.0.0 | http://ipython.org/ |
| matplotlib v1.4.0 | http://matplotlib.sourceforge.net/ |
| ansi2html | https://pypi.python.org/pypi/ansi2html/ |
Warning
Some people have reported that NeXpy crashes on launch on some Linux systems. We believe that this may be due to both PyQt4 and PyQt5 being installed, although that doesn't cause a problem on all systems. If NeXpy crashes on launch, please try setting the environment variable QT_API to either 'pyqt', for the PyQt4 library, 'pyqt5' for the PyQt5 library, or 'pyside', for the PySide library, depending on what you have installed, e.g., in BASH, type
export QT_API=pyqt
Note
As of v0.10.3, ansi2html has been added as a dependency, since colorized tracebacks are now produced by uncaught GUI exceptions and displayed in dialog boxes and stored in the log files.
.. seealso:: If you are having problems linking to the PySide library, you may
need to run the PySide post-installation script after installing
PySide, *i.e.*, ``python pyside_postinstall.py -install``. See
`this issue <https://github.com/nexpy/nexpy/issues/29>`_.
Additional functionality is provided by other external Python packages. Least-squares fitting requires Matt Newville's least-squares fitting package, lmfit-py. Importers may also require libraries to read the imported files in their native format, e.g., spec2nexus for reading SPEC files.
Warning
As of v0.7.1, NeXpy no longer includes the tifffile module. This can now be
installed with pip install tifffile.
From v0.1.5, we now have an importer for Crystallographic Binary Files, using PyCBF, which must be separately installed.
From v0.9.1, a new 2D smoothing option is available in the list of
interpolations in the signal tab if astropy
is installed. It is labelled 'convolve' and provides, by default, a
2-pixel Gaussian smoothing of the data. The number of pixels can be
changed in the shell by setting plotview.smooth.
| Library | URL |
|---|---|
| lmfit | http://newville.github.io/lmfit-py/ |
| tifffile | https://pypi.python.org/pypi/tifffile |
| pycbf | http://sourceforge.net/projects/cbflib/files/cbflib/pycbf/ |
| spec2nexus | http://spec2nexus.readthedocs.org/ |
| astropy | http://www.astropy.org |
Note
NeXpy should still run without these additional packages, but invoking the relevant menu items may trigger an exception.
With the release of v0.1.0, NeXpy is using Semantic Versioning.
Consult the NeXpy documentation for details of both the Python command-line API and how to use the NeXpy GUI. If you have any general questions concerning the use of NeXpy, please address them to the NeXus Mailing List. If you discover any bugs, please submit a Github issue, preferably with relevant tracebacks.
The NeXus format for neutron, x-ray and muon data is developed by an international collaboration under the supervision of the NeXus International Advisory Committee. The Python tree API used in NeXpy was originally developed by Paul Kienzle, who also wrote the standard Python interface to the NeXus C-API. The original version of NeXpy was initially developed by Boyana Norris, Jason Sarich, and Daniel Lowell, and Ray Osborn using wxPython, and formed the inspiration for the current PyQt version.