hollowfoot 0.5.0

Companion workflow engine for xraylarch.

Hollowfoot

A work-flow engine for performing analysis of experimental X-ray data using xraylarch and other domain-specific frameworks.

A hollowfoot analysis is:

Declarative: A typical analysis workflow in hollowfoot is best thought of as a series of steps to be performed on some underlying data. The analysis engine is responsible for executing the steps for you when needed.

Jupyter-first: Many analysis frameworks, like xraylarch, provide tools that are used as part of some larger analysis application. Hollowfoot aims to extend these tools so that they can be used as first-class objects in a jupyter notebook environment.

Documentation

Sphinx-generated documentation for this project can be found here: https://spc-group.github.io/hollowfoot/

Usage

An example workflow for XAFS analysis might look like:

import hollowfoot as hf

analysis = (
    XAFSAnalysis  # What kind of analysis are we doing?
        .from_aps_20bmb("my_data_folder/")  # Load data from disk
        .to_mu("mono-energy", "It", "I0", is_transmission=True)  # Apply reference correction
        .plot_mu()  # Plot all data sets together
        .merge()  # Merge data sets into a single group
        .fit_edge_jump()  # Do some normalization, etc
        .subtract_background()  # Convert from µ(E) to χ(E)
        .plot_mu()  # Plot the single, corrected dataset
    	.summarize()  # Print out a summary of the steps that have been taken
)

Notice how each line of the previous code snippet describes a concise step of analysis. These steps can be re-ordered or commented out, making for easy comparisons between analysis strategies.

Installation

The following will download the package and load it into the python environment.

$ pip install hollowfoot

Running the Tests

$ uv run --dev pytest

File Format Support

XAS Data Interchange Format (XDI)

Hollowfoot includes an Xarray backend for loading .xdi files.l

The easiest way to import XDI files is with xarray.open_dataset():

import xarray as xr

dataset = xr.open_dataset("example.xdi")

It is also possible to load XDI data from a string using hollowfoot.xdi.load():

import hollowfoot as hf

with open("tests/example.xdi") as fp:
    dataset = hf.xdi.load(fp.read())

It is also possible to convert a dataset back to XDI:

# This example overwrites existing files, be careful!
with open("new_file.xdi", mode='w') as fp:
    fp.write(hf.xdi.dump(dataset))