bruceravel / xraylarch Goto Github PK

• Documentation: http://xraypy.github.io/xraylarch
• Code: http://github.com/xraypy/xraylarch

Larch is an open-source analysis and visualization toolkit and library for processing scientific data. The primary emphasis is on X-ray spectroscopic and scattering data, especially that collected at modern synchrotrons and X-ray sources. But, Larch also provides many general-purpose processing, analysis, and visualization tools for dealing with arrays of scientific data.

Larch is written in Python, making heavy use of the wonderful numpy, scipy, h5py, and matplotlib libraries. For interactive and batch processing, Larch provides a Python-like and Python-derived language (a macro language, or domain specific language) that is intended to be very easy to use for novices while also being complete enough for advanced data processing and analysis. In addition, Larch can be used as a Python library, used within Python scripts, and extended using Python. Finally, Larch can be run as a service, interacting with other processes via XML-RPC.

Larch has several related target application areas, including:

• XAFS analysis, becoming version 2 of the Ifeffit Package.
• Visualizing and analyzing micro-X-ray fluorescence maps.
• Quantitative X-ray fluorescence analysis.
• X-ray standing waves and surface scattering analysis.
• Data collection software for synchrotron data.

The initial goal was to rewrite the older Ifeffit XAFS Analysis package, and this is largely complete. Other application areas are nearly complete or in early stages of development.

All the scientific domain-specific code is exposed through a plugin mechanism. Plugins are written in Python (which can use compiled code and 3rd party Python libraries), and are loaded from Python source at runtime, making development very easy. Plugins do not need to know much about the internals of Larch. Adding a small amount of Larch-awareness to a Plugin can make functions defined in Plugins work very easily with Larch's interactive macro language.

Larch provides a dialect of Python for interactive use. The intention is to provide a very easy and complete macro language for data processing. By building Larch with Python, Larch has many important similarities to Python:

1. All variables in Larch are real Python objects.
2. Existing Python libraries can be imported and used from Larch.
3. Syntax for lists, dictionaries, array slicing, and so on are identical to python.
4. Control flow syntax (if, while, for, try) are nearly identical to Python (see below).

The Larch macro language differs from Python in a few significant ways:

1. Larch does not use indentation level to define blocks of code. Rather, a block is ended with one of:

    if X:
       do_something()
    endif
    if Y:
       do_another_thing()
   #endif
   

and similarly for/endfor, while/endwhile, def/enddef, and try/endtry.

Properly indenting and using the '#end' version allows code to be both valid larch and python, and is strongly encouraged.

2. "Command" syntax -- not requiring parentheses for function calls -- is supported in many cases. If the first word of an expression typed at the command prompt is a word that is a valid symbol name (and not a reserved word) and the second word that is either a valid name or a number, and if the line does not end with a ')', the first word is taken as a function name and parentheses are added, so that:

command arg1, arg2

is converted to command(arg1, arg2) and so on.

3. Larch has a nested namespace and a deeper level of name resolution. This is more complex than Python's simple and elegant model, but allows more functionality and data to be readily available at an interactive prompt.

4. While the Larch macro language is a com a Larch does not support many important Python constructs. These include

• class -- creating a new object class
• lambda -- anonymous functions.
• generators, yield -- deferred generation of sequences.
• decorators -- function modifiers

For the sensitive Python-lovers, please note that I am not saying that I think these changes from Python are in anyway shortcomings of Python that are being fixed by Larch. Rather, the changes (and omissions) are to make Larch a simple scientific macro language. The fact that the macro language is close to Python is a strong benefit, but it is still a domain-specific language.

The implementation of the Larch macro language turns out to be rather simple. The input Larch program text is converted to valid python code, and then parsed into Python's own Abstract Syntax Tree (AST). This AST representation is then interpreted directly, using a custom symbol table for name lookup and resolution. This implementation gives several benefits:

1. the intermediate python code can be saved so that code validation and translation of larch to python are now trivial
2. the parsed AST tree is guaranteed (at least as far as python itself is) to be correct.
3. Interpreting the AST tree is very simple, including all loop and control-flow code, and the resulting compiler is very simpler and powerful.

In addition, the symbol table is simplified so that a symbolTable contains python objects and Groups (simple containers for other objects and Groups). Namespaces are built simply using attributes of the Group class. That is, attribute lookup is heavily used, and symbols just python objects.