Installation

Software requirements

PDFgetX3 has been written in Python programming language, therefore to use the software, you must have Python 3.6, 3.5, 3.4, 2.7 or 2.6 installed. In addition, the following third-party Python libraries are also required:

  • setuptools - tools for installing Python packages
  • six - Python 2 and 3 compatibility library
  • NumPy - library for scientific computing with Python
  • matplotlib - Python plotting library
  • IPython - enhanced interactive Python shell

Standard Python releases can be obtained from https://www.python.org/downloads. The third-party libraries can be found at the Python Package Index or using any Internet search engine.

Another more convenient option is to obtain one of the science-oriented Python distributions such as Anaconda Python, Enthought Canopy or PythonXY, These distributions already include all the necessary libraries, so the required Python software can be all installed in one step.

On Linux operating systems the third-party libraries are usually included in a system software package repository. For example on an Ubuntu Linux computer the software dependencies can be all installed with a single shell command

sudo apt-get install \
  python3-six python3-setuptools python3-numpy python3-matplotlib ipython3

This may be, of course, just as well accomplished using the GUI driven Synaptic package manager. Other Linux distributions may use different software management tools, but the names of the necessary packages should be very similar to those above.

On Windows operating system, it may be necessary to add the C:\Python35 directory and the scripts directory C:\Python35\Scripts to the system PATH. Some Python distributions may already do that as a part of their installation process. The easiest way to check is to start the Command Prompt, type there python and see if this starts the Python interpreter.

PDFgetX3 installation

PDFgetX3 is distributed as a Python egg package, which can be obtained from the Columbia Technology Ventures. Once all the required software is in place, start the command prompt on Windows or a Unix terminal on Linux or Mac, navigate to the directory that contains the egg file and execute the following command:

python -m easy_install ./diffpy.pdfgetx-VERSION.egg

Here VERSION needs to be replaced to match the actual filename. It is critical to use one of the supported Python versions otherwise the program would not work. On Linux and Mac operating systems the installation may need to run with root user privileges, for example, by prepending sudo to the command line above. If root access is not available, use the easy_install options --user, --prefix or --install-dir to install PDFgetX3 to a user-writable directory.

To verify if pdfgetx3 has been correctly installed, type the following command:

pdfgetx3 --version

This should display the software version, which should be the same as the VERSION string in the egg file name. The installation also includes a plotdata command for an easy plotting of text data files. To verify if plotdata works, run the plotdata --version command.

IPython magic command

These instructions are intended for IPython users who would like to integrate PDFgetX3 into their IPython environment. If you don’t plan to use IPython in such way, you can safely skip this section.

When pdfgetx3 is run in an interactive mode, it starts IPython interactive shell and defines an extra %pdfgetx3 magic command within the IPython session. The IPython magic commands are not valid Python code, but work in a similar fashion as standard shell commands. The %pdfgetx3 magic can be thus used with the same options and arguments as if run from the shell. This is useful for processing more files, while preserving all plots or variables that were already created within the IPython session.

The %pdfgetx3 magic command can be defined permanently so it is available in all IPython sessions. To make the %pdfgetx3 command permanent

  1. find the profile_default/ipython_config.py file and open it in a text editor. If that file does not exists, create it first by executing

    ipython profile create

  2. navigate to the paragraph that contains the c.InteractiveShellApp.extensions and add there the following line:

    c.InteractiveShellApp.extensions = ['diffpy.pdfgetx.ipy_pdfgetx3']

    There must be no leading indent, i.e., the text must start at the very first column.

Note

This setup works for the latest IPython 5.0 and for the older versions going back to 0.13. For IPython 0.11 or 0.12 use ipy012_pdfgetx3 in the extension module name instead of ipy_pdfgetx3.