NSLS-II Software Documentation

The NSLS-II software toolchain is a set of cooperative software components for scientific data acquisition, management, and analysis. It aims to address the entire process, from experiment specification to the composition of publication-quality plots.

Design Goals

  • Integrated data collection and analysis.
  • Rich Metadata is automatically captured and organized for rich search and reproducibility.
  • Live, Streaming Data: Available for inline visualization and processing.
  • Pluggable I/O: Export data (live) into any desired format or database; standardized in-memory format for retrieval.
  • Experiment Generality: Seamlessly reuse a procedure on completely different hardware.
  • Use same tools for prompt and offline analysis
  • Capture provenance and result of intermediate computation.
  • Use existing, open-source technologies and languages.

Overview of Software Components

This diagram illustrates the scope of each library in the NSLS-II software stack and the libraries’ interfaces. Bluesky orchestrates the execution of an experiment, communicating with hardware only via a high-level abstraction provided by ophyd. Bluesky collates measurements and metadata into documents which are stored in a database and, concurrently, used in any live visualization or processing. These documents can then be accessed later via the databroker. Detectors with high acquisition rates may write files directly (in any format). Records for locating and interpreting these files are also stored in the database.

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Bluesky is agnostic to the underlying control system and has been co-developed with ophyd, a hardware abstraction library. Ophyd currently interfaces with EPICS, but is designed to be generalized to support other control systems.

The Documents organize measurements and metadata in an event-based model. The model is formally specified but minimalist. It is flexible, able to capture the wide range of scientific domains studied at NSLS-II. Nothing in the model is specific to NSLS-II or even to synchrotron science.

Project Status & Roadmap

The acquisition software (ophyd & bluesky) have stabilized and are used in production at twelve NSLS-II beamlines. We have been able to handle all of the expected use cases and several unforeseen applications, validating the architecture of ophyd/bluesky and the document model. Recently, most of the development effort has been going into documentation and community-building. (The bluesky documentation is particularly polished and comprehensive.) In addition, the software has been installed at several other facilities for testing and evaluation.

Simple prompt analysis (plots, data tables, curve fitting) is widely used at NSLS-II. Some beamlines are taking full advantage of the event-based data model and live access to data, and there are some early examples of feeding prompt analysis back into the experiment control logic.

Going into the Spring 2017 cycle, the focus will shift to data access and analysis. This includes streamlining the user interface to saved data (databroker) and optimizing the data storage backends with performance and portability in mind. Additionally, work is ongoing to capture intermediate analysis results with associated provenance.

Building on top of this data retrieval software, we will write cross-beamline multimodal analysis tools.

Detailed plans for each project are managed and discussed in the open on GitHub, where the user community is invited to observe, comment, and contribute.

Software Packages

Each package has its own documentation, linked below.

  • Specify experiment procedures and acquire data using bluesky.
  • Set up hardware to communicate with bluesky using ophyd.
  • Access saved data (and metadata) using databroker.

The following projects are in use but in a less mature stage of development.

  • For high-throughput applications, make a database of samples using amostra.
  • Align (“de-multiplex”) asynchronously collected data streams, based on time stamps, using datamuxer.
  • Export data from the databroker to common formats using suitcase.
  • Write analysis code using scikit-beam, in conjunction with widely-used scientific Python libraries.
  • Utilize beamline-specific libraries in the Github organizations maintained by individual NSLS-II beamlines at github.com/NSLS-II-XXX where XXX is the three-letter beamline acronym (e.g., HXN, ISS, CHX, etc.).