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Getting started on a mac

A minimal set of data processing tools could include

  • Fabian : to look at diffraction images and median calculations
  • ImageD11: script for peak search, experimental parameters refinement, peak assignment, can do grain indexing, and many others
  • GrainSpotter: grain indexing
  • Specific TIMEleSS tools: a collection of scripts from the TIMEleSS projects, for both pre- and post-processing

Those are themselves built against a suite of libraries and could be hard to get working.

Step 1: Anaconda

From the Anaconda website,

Conda is an open-source package and environment management system that runs on Windows, macOS, and Linux. Conda quickly installs, runs, and updates packages and their dependencies. It also easily creates, saves, loads, and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language.

In fact, Anaconda is the easiest route to get multigrain data processing working on a mac. You first step is hence to install Anaconda on your mac.

Once Anaconda is installed,

  • Open the MacOS Terminal and type: python
  • You should see something like Python 3.6.3 | Anaconda Inc. |
  • At the Python REPL (the Python »> prompt), exit out of the Python REPL using the command exit().

The following packages should be installed from anaconda to avoid compatibility issues

  • numpy: conda install -c anaconda numpy
  • scipy: conda install -c anaconda scipy
  • matplotlib: conda install -c anaconda matplotlib
  • pyqt: conda install -c anaconda pyqt
  • Pmw: conda install -c conda-forge pmw
  • OpenPG: conda install pyopenGL

Then there are two packages with ended up conflicting when trying to install using conda. Resorting to pip instead:

  • fabio: python -m pip install fabio
  • pyopengltk: python -m pip install pyopengltk

Step 2: Fable-3XRD packages with pip or automated install

Python packages can be installed from source, downloading the source code from the original website, or through pip. Source download will always get you the latest version, with the latest developments. Installation with pip is much easier, but may not be the most up-to-date.

If you are super comfortable with python, anaconda, and such, jump to the next section and install everything from the source files at github. If not, stay here and do part of the work with pip.

Some of the Fable-3XRD packages are easy to install

  • ImageD11, simply type the following command in your anaconda terminal python -m pip install ImageD11
  • TIMEleSS-tools: python -m pip install timeless-tools
  • silx: python -m pip install silx (not a Fable-3XRD but could become useful in the future)

GrainSpotter, also, is available automatically on Anaconda if you are using linux (GrainSpotter is a C program, hence the difference procedure)

  • In a terminal: conda install -c fable grainspotter
  • This does not seem to work with a mac, see below (installing from source)

Those few lines will install the packages, but also thousands of various libraries that they depend on.

Step 3: Fable-3XRD packages from source

Other packages are required but need to be installed from the Fable-3DXRD source at github:

For both, procedure is identical

  • enter the corresponding repository (polyxsim or fabian)
  • at the top right of the page, click on the green Code button, and download a zip archive,
  • on your machine, unzip the archive,
  • from the terminal, move into the folder that was created,
  • type python build,
  • type python install

GrainSpotter is a C program which, on a mac, is not readily available in anaconda

It should work out of the box.

By now, you should be done and have a minimal working installation on your mac.

software/gettingstartedmax.txt · Last modified: 2023/12/09 21:26 by smerkel