Software

The XSD Scientific Software Engineering & Data Management group develops and maintains a number of software products for the APS and its users. Below is a list of some of the group's larger products. In addition, the group provides ad hoc services and efforts for smaller projects and tasks.

Data Management

APS Data Management System

The APS Data Management system consists of tools to help automate the transfer of data between acquisition devices, computing resources, and data storage systems, and distribute data to users.

Data Reduction & Analysis

	Bragg Coherent Diffraction Imaging (BCDI) Tools A new development effort to create an HPC-enabled implementation of the genetic CDI phase retrieval approach. This work is under active development and is not yet deployed for regular use.
	Hadoop XPCS Analysis Extracts length scale dependent dynamical information probed sample by computing the time autocorrelation function using a series of 2D area detector images in near real-time on a Hadoop HPC environment. It can be used to process data irrespective of the geometry of the measurement such as small angle in transmission, grazing incidence or under diffraction conditions.
	RSMap3D Process diffraction data collected at APS and represents the result as a 3D Reciprocal Space Map. Provides the means to look at various cuts through the map. The input for processing of this data consists of a series of images collected over a range of diffractometer angles and or input energy.
	Laue GPU Depth Reconstruction Laue diffraction microscopy uses the polychromatic Laue micro-diffraction technique to examine the structure of materials with sub-micron spatial resolution in all three dimensions. This GPU-based implementation of a depth reconstruction algorithm for Laue diffraction patterns provides up to a 10 - 15 times speed-up as compared to a CPU-implementation.
	MapsPy The next generation HPC-enabled x-ray fluorescence mapping tool for the APS. It provides implementations of five core mapping algorithms: region-of-interest (ROI), nonnegative least squares (NNLS), singular value decomposition (SVD), Matrix-lmfit, and Matrix-mpfit.
	XRF Mapper The next generation HPC-enabled x-ray fluorescence mapping tool for the APS. It provides implementations of five core mapping algorithms: region-of-interest (ROI), nonnegative least squares (NNLS), singular value decomposition (SVD), Matrix-lmfit, and Matrix-mpfit.

Experiment Control & Planning

Data Quality Verification Tools

Beamline data integrity and quality assessment toolbox for ensuring data is good enough for analysis and interpretation.

uProbeX

A tool for the accurate and easy coordination of visible light microscopy scans performed on a commodity microscope with fluorescence scans performed at the APS. Allows users to acquire a fast overview of a sample on a visible light microscope, and then select a region-of-interest on the visible light image over which to acquire an elemental map without the need to first acquire a fluorescence overview image.

TXM Experiment Control Software

Experiment control system for tomography beamlines that interfaces with EPICS for beamline control and provides configurable scanning via Python scripts or a GUI-based scan builder, live and offline data viewing, basic image manipulation features, and scan sequencing that coordinates EPICS-enabled apparatus.

Area Detector Plug-ins Originally Developed by SDM Group Members

	QImaging areaDetector 2.x Plug-in An EPICS areaDetector 2.x driver for detectors from QImaging Technology using the QCam SDK. https://github.com/areaDetector/ADQImaging
	PICAM areaDetector 2.x Plug-in An EPICS areaDetector 2.x driver for Cameras from Princeton Instruments that support the PICAM library. https://github.com/areaDetector/ADPICam
	X-Spectrum LAMBDA areaDetector 2.x Plug-in An EPICS areaDetector 2.x driver for the X-Spectrum Lambda detector. https://github.com/areaDetector/ADLambda
	HDF5 Writer Plug-in for areaDetector 2.x A new HDF5 writer plug-in for the EPICS Area Detector framework has been developed by the Scientific Software Engineering & Data Management group in collaboration with GSECARS, and software engineers at Diamond Light Source. This plug-in provides the ability to configure custom HDF5 data layouts via XML configuration files enabling users to add custom experiment metadata tailored to particular experiments and beamlines. Configurable chunking and data compression parameters allow optimization of data reading and writing to be able to keep up with high data rate experiments. https://github.com/areaDetector/ADCore/tree/master/ADApp/pluginSrc

APS Upgrade Funded Work

Component Database (CDB)

The Component Database (CDB) is a tool to assist in documenting, organizing, and tracking the components for the accelerator and beamlines. It assists in capturing the documentation of components, provides a repository for inspection and measurement data (e.g. travelers), and supports the logging of component history through the component’s life cycle. The CDB also provides links and interfaces to other commonly used administrative tools, such as PDMLink, ICMS, PARIS, etc.

Real-time Feedback / DAQ

The Real-time Feedback Data Acquisition (RTFB/DAQ) system represents software framework and tools that enable fast data collection for controls, statistics and diagnostics associated with the state-of-the-art embedded controllers utilized by the APS Upgrade multi-bend achromat accelerator (MBA).

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