3. Larch: Motivation and Overview

Larch brings together data processing routines for synchrotron X-ray techniques and provides high-level scripting tools for data manipulation, visualization, and analysis. The initial goal was to replace the Ifeffit package for XAFS analysis in order to better deal with larger datasets, make it easier to modify and improve XAFS analysis algorithms, and to provide more modern data manipulation and visualization tools. Visualization and analysis of X-ray fluorescence spatial maps and spectra from X-ray microprobe beamlines was is a key requirement, and incorporating tools for related techniques like X-ray standing waves and X-ray diffraction is a high priority. Larch also makes it easy to bring visualization, processing, and analysis routines with data collection processes to give a more seamless workflow that spans data collection and analysis, using core functionality that can be scripted and GUIs built on top of these core functions. While Larch is a work in progress, it has already met most of these initial goals.

Larch is written in Python, a free, general-purpose interpreted language known for its clear syntax and readability. Python has become quite popular in a range of scientific disciplines due to many well-designed an supported libraries, including numpy, scipy, h5py, and matplotlib, and is being adopted by many groups in the synchrotron X-ray community. Being able to build on existing tools and tap into a large pool of scientists who are able and willing to work in Python was seen as a huge benefit in the development of Larch.

The key design decision for Larch is to build a domain-specific language or macro language as the framework to tie together the various functionality. In the synchrotron community, many scientists are familiar with the Spec program for data collection, which is implemented as an interactive macro language - a language that is fairly general purpose, but also has many built in functions for interactively collecting diffraction data. Ifeffit was built with a similar approach, though with a much worse macro language than Spec, though one that was complete and flexible enough for writing complex analysis scripts, and for GUIs to be built upon this macro language. In some sense, Larch is an attempt to make something akin to Spec for Data Analysis, in which high-level analysis and visualization routines are readily available in a coherent scripting environment.

Thus, Larch provides a macro language that gives a simple command-line interface (a Read-Eval-Print Loop). Scripts can be written and be run “batch mode”. GUIs can be built upon Larch by simply generating the commands, which makes it easy to separate the GUI controls layout from the actual processing steps, so that the processing steps might be recorded and used to make a script to reproduce or refine the steps defined from the GUI. In addition you can use Larch with remote-procedure calls, so that it can be run as a service, and called from a variety of languages and from different machines. Finally, Larch can be used as a Python library, nearly completely side-stepping the Larch macro language.

The Larch macro language is implemented in Python with Python’s own language tools, and is very closely related to Python. It is designed have a slightly shallower learching curve and less formal approach. To be clear, it is a worse general purpose programming language than Python, but better suited to the tasks needed for manipulating and analyzing X-ray data. Since its syntax is so closely related to Python, it is possible to write code that is both valid Python and Larch.

In fact, the Larch language is so closely related to Python that a few key points should be made:

  1. All data items in Larch are really Python objects.
  2. All Larch code is translated into Python and then run using builtin Python tools.

In a sense, Larch is a dialect of Python. Thus an understanding Larch and Python are close to one another. This in itself can be seen as an advantage – Python is a popular, open-source, language that any programmer can easily learn. Books and web documentation about Python are plentiful. If you known Python, Larch will be very easy to use, and vice versa.

3.1. Key Concepts of Larch

Since Larch is intended for processing scientific data, the organization of data is a key consideration. There also needs to be some organization of functions and routines. The main concept that Larch uses to help the user with organizing data is Group. This is simply a container into which any sort of data or function can be placed, including other Groups. The data in a Group can be accessed using a syntax of <Group>.<Member>, as with:

larch> my_group = group(x = range(11), scale=10.2, title='group 1')
larch> my_group.y = my_group.scale * sin(my_group.x)
larch> plot(my_group.x, my_group.y, title=my_group.title)

The Group my_group holds data for x, y, and title. Here, the range() function gives an array of 11 elements ([0, 1, 2, …, 10]) that will be held by my_group.x. You can see the contents of a group with the show() function:

larch> show(my_group)
== Group 0x6e15970: 4 symbols ==
  scale: 10.2
  t: 'group 1'
  x: array<shape=(11,), type=dtype('int32')>
  y: array<shape=(11,), type=dtype('float64')>

which shows that this group has 4 components, and lists the components. As the x and y members hold array, the size and datatype of the array is shown. Doing:

larch> print my_group.y
[  0.           8.58300405   9.27483375   1.43942408  -7.71938545
  -9.7810276   -2.85003808   6.70126331  10.09145412   4.20360855
  -5.54901533]

will show the array elements. The plot() function will show a graph of y(x).

Since much of what Larch is used for is modeling or fitting small data sets, another key organizing principle is the Parameter. This holds a value that you might want to be optimized in a least-squares fit. Thus, a Parameter can be flagged as a variable, or fixed to not be varied. In addition, it can be given a mathematical expression in terms of other Parameters to determine its value as a constrained value.

3.2. Capabilities

At this writing, Larch has the following general capabilities:

  • a full suite of mathematical functionality, with array handling builtin (so that functions work on full arrays).
  • a general purpose language with flow-control (for and while loops), and conditional evaluation (if-then-else).
  • some built-in I/O functionality for ASCII files and HDF5.
  • simple line plots, with customizable line properties.
  • simple 2-D image dispays, with some rudimentary customization.
  • general-purpose minimization and curve-fitting.

For XAFS analysis in particular, Larch is able to do essentially all the data processing and analysis steps that Ifeffit can do, including:

  • pre-edge background subtraction and normalization
  • background subtraction for isolating chi(k)
  • XAFS Fourier transforms
  • reading and manipulating Feff Path files
  • fitting Feff Paths to XAFS data
  • general-purpose minimization and curve-fitting.