Glossary
- ADS
TODO
- Algorithm
A set of instructions that can be executed to produce a result. In the context of SNAP, this mostly refers to Mantid Algorithms or collections of Mantid Algorithms triggered by a Recipe. Base Mantid Algorithm Index: https://docs.mantidproject.org/nightly/algorithms/categories/AlgorithmIndex.html There are also a collection of custom algorithms that are used to perform SNAP specific tasks in this repo.
- API Layer
The architectural layer that provides the single point of interaction between the backend and frontend. Agnostic of frontend implementation, it recieves requests from the frontend and forwards them to the corresponding Service. In addition it is also responsible for catching errors, and returning a human readable error message to the frontend.
- Background Run Number
The identifier for a background run, which is a measurement taken under the same conditions as a primary experimental run but without the sample present. This data is used to subtract background noise and artifacts from the experimental data, enabling more accurate analysis. In the context of SNAP, the Background Run ID refers to the unique ID associated with such a run, used in processes like Normalization to correct the primary data set.
- Calibrant Samples
A json configuration representing various phyiscal properties of known samples that are used to calibrate the instrument. Most notably, the cif file that contains the known crystallographic properties of the sample.
- Calibration
The process by which the instrument state configuration is calibrated to account for the effects of the instrument on the diffraction data. This is done by comparing the diffraction data to a known standard or previous Calibration, and adjusting the instrument to match. This is done by a series of algorithms that are triggered by a Recipe.
- Calibration Folder
TODO
- Calibration Index
The data/file that contains a ledger of which Calibration applies to which Run in a given Instrument State.
- Calibration Mask
The outcome of various systematic effects can lead to failures in pixel event detection. This may cause the calibration process to fail for individual or groups of pixels. These are handled by creating a mask indicating which faulty pixels will not be used in any reduction employing the related calibration.
- Calibration Record
This is a file written to the :term: state <State> calibration folder that contains a record of information related to the calibration. This includes all of the parameters that govern the calibration, the location of all the files generated during the calibration (e.g. calibration mask) and also some statistical information capturing the “quality” of the calibration.
- CIS
Computational Instrument Scientist (CIS). A domain expert, usually responsible for all aspects of data collection and reduction using a given instrument.
- Config
A configuration mapping used to control many configurable aspects of the SNAPRed application. This is implemented as a mapping between multiple-key sequences, represented as “<key-1>.<key-2>. … <key-n>”, and string and number values, such as paths or default-parameter values. At the start of the application, this configuration is initialized from the YAML-format file
application.yml(, which may be overridden using thedev.ymlfile).- Component
Architectural term for a single unit of abstraction that fulfills a mid level Developer Requirement. This includes concepts like Data State Management, Persistence, and Data Calculation
- Data Objects
The architectural layer that represents concepts and contracts as easily validated and serializable objects. It consists entirely of Pydantic models with minimal to no buisness logic. These objects represent things like Requests, Focus Groups, Instrument State, etc.
- Data Component
The architectural Component that provides an abstraction for data aquisition and storage. It provides a means for the rest of the backend to interact with data without having to worry about the underlying implementation. It handles serialization and deserialization of data to terms the backend is familiar with. Example: A user may request a Calibration for a specific run, regardless of whether the data is stored on a remote server or locally, it will be retrieved, deserialized, and returned.
- Data State Management
The process by which the backend manages the state of the data it is working with. This includes things like Caching, Serialization, Deserialization, Calculation, and Transformation. If given the proper interface, consumers should recieve consistently populated Data Access Objects regardless of current state.
- Diagnostic Mode
TODO
- Detector
A physical component of the instrument used for for particle-flux measurement, usually comprised of multiple pixels.
- Detector ID
A unique integer associated with each pixel in the instrument. Apart from uniqueness, detector-id integer values are arbitrary. For example, they are not required to be consecutive, and negative values may be used to indicate pixels with a special function, such as monitor pixels.
- Diffraction Focussing
TODO
- Focus Group
A predetermined set of parameters used to split diffraction data into useful formations, i.e. like slices vs. squares of pizza This may include predetermined data such as dimensions and tolerances, or derived values such as Pixel Grouping Parameters.
- Grouping-schema Map
A mapping between grouping-schema common names, and their file locations on disk. File locations may be specified either as relative paths, with respect to <instrument.calibration.powder.grouping.home>, or as absolute paths.
- Grocery
Within SNAPRed code, this refers to workspace data (as opposed to ingredient data) which are needed for an operation. They are requested by handing the Grocery Service a grocery list of workspaces to fetch.
- Group Calibration
TODO
- Grouping Schema
A relationship, usually a mapping, between each detector-id in the instrument and an integer group number.
- HDF5
The most recent variant of Hierarchical Data Format (HDF). A binary file format designed to scalably store and access large scientific data sets.
- Histogram
A graphical representation of the distribution of numerical data. It is an estimate of the probability distribution of a continuous variable and is used to visualize the distribution of data points. A histogram is constructed by dividing the range of the data into bins (also called intervals or buckets) and counting the number of data points that fall into each bin.
- Ingredients
The data required to perform a unit of calculations and produce a well cooked result. These are typically the configuration input to a Recipe. They are also typically passed through a Recipe to the various algorithms it triggers.
- Instrument
The physical apparatus used to collect diffraction data. In the case of SNAP, it consists of a sample to shoot neutrons at, a source that provides said neutrons, and several detectors with variable physical positions, the specifics of depending on the requirements of a given experiment. The configuration of these components define what is referred to as an Instrument State.
- Instrument State
The configuration of an instrument at a given point in time. This includes the positions of the detectors, the sample, and the source. It is also dependant on a number of other configurations relating to the instrument.
- Interface Controller
The central controller within the SNAPRed application responsible for managing the lifecycle of SNAPRequests and producing corresponding SNAPResponses. It acts as the primary entry point for processing requests, utilizing a ServiceFactory to delegate tasks to specific services and handling both standard and recoverable exceptions.
- Interface Layer
The architectural layer that provides the single point of interaction between the backend and frontend. Agnostic of frontend implementation, it recieves requests from the frontend and forwards them to the Orchestration Layer.
- IPTS
TODO
- JSON
Javascript Object Notation (JSON). An text-based data representation, used by many applications where a human-editable representation is required.
- Layer
A collection of Components that work together to provide a single unit of high level Developer Requirements Examples include: API, Orchestration, Data Processing, etc.
- Lite Mode
The SNAP instrument uses detectors comprised of many more pixels than are actually required to achieve the target d-spacing resolution. In Lite mode, all of the event data will be used, but it will be grouped into effective pixels, one for each 8x8 block of native pixels. (See Native Mode)
- Mantid
Neutron scattering data reduction code maintained by the Mantid Project.
- Mantid Snapper
A thin wrapper around the Mantid Algorithm API that allows for meta processes to be performed around a queue of algorithms. Examples may include: Progress reporting, Quality of Life improvements, multi-threading, etc.
- MTD
Analysis Data Service (ADS, aka Mantid Data (MTD)), the internal database held by Mantid of all named workspaces. Any workspace referenced “by name”, usually by a Mantid algorithm, needs to be registered in this database.
- Native Mode
The SNAP instrument uses detectors comprised of many more pixels than are actually required to achieve the target d-spacing resolution. In Native mode, both event data, and physical specifics, from all of these pixels will be used during processing. (See Lite Mode)
- Normalization
The process of adjusting diffraction data to correct for variations in instrumental performance and experimental conditions. Normalization ensures that data from different runs or different instrument states can be directly compared or combined without bias due to instrument efficiency, sample positioning, or other systemic factors. This is typically achieved by dividing the raw data by a normalization standard, such as a vanadium run, which represents the instrument response. The process involves a series of algorithms, often encapsulated within a Recipe, to apply these corrections and produce normalized data suitable for further analysis or interpretation.
- Orchestration Layer
The architectural layer that handles the stitching together of the various Service Components, Data Components, and Recipe Components to achieve and abstract goal. This may include handling User Requests, or performing Data State Management.
- Particle Bounds
These parameters within SNAPRed define the acceptable ranges for particle parameters such as wavelength and time-of-flight (TOF).
- Pixel
The smallest physical sensing element for particle-flux measurement. Detector panels are comprised of pixels.
- Pixel Calibration
TODO
- Pixel Group
This is the a pixel grouping scheme that is used within the reduction process.
- Pixel Grouping Parameters
The expectation value of selected pixel physical-location and d-spacing parameters, taken over a specified grouping schema. For each specific parameter, there is one entry for each integer pixel group.
- Pydantic
A data object serialization and validation framework, implemented in Python.
- Processing Layer
The architectural layer responsible for implementation level details of the backend. This includes things like the Data Component, and the Recipe Component.
- Reduction
The process by which raw diffraction data is filtered, distilled into more compact and meaningful data that a scientist may draw conclusions from.
- Recipe
A collection of algorithms or calculations that are triggered by a request to perform a specific task. Examples include: Reduction, Calculate Pixel Grouping Parameters, Purge Overlapping Peaks etc.
Recipe Component The architectural Component that provides an abstraction for the execution of data Calculation and Transformation. It is responsible for executing Buisness Logic provided by the Product Owner, and returning the results to the caller. Examples include: Reduction, Calculate Pixel Grouping Parameters, Purge Overlapping Peaks etc.
- Recipe Component
TODO
- Resource
Small, static configuration data stored within the codebase that may easily be looked up via relative path or key.
- Run
A single collection of diffraction data that was collected at a specific point in time. It is identified by a unique ID, and is associated with a specific Instrument State and Calibration.
- Run ID
TODO
- Run Number
The unique integer identifier of a Run. Note that certain facilities (e.g. ISIS SANS) may allow the addition of non-integer suffixes to the run number string.
- Service Component
The architectural Component that provides the individual units of backend fuctionality that a user may interact with. Examples include: Data Reduction, Calibration Quality Assessment, Instrument State Initialization, etc. It provides this functionality by orchestrating Data and Recipes Components to produce the expected results.
- Smoothing Parameter
A numerical value used to control the degree of smoothing applied to diffraction data during processing. Smoothing is a technique used to reduce noise and enhance signal clarity, making it easier to identify and analyze peaks in the data. The smoothing parameter determines the extent of this smoothing effect, with higher values leading to a smoother signal. It is often adjusted as part of the Normalization or Reduction processes and is applied via algorithms within a Recipe.
- SNAPRequest
An object containing a Recipe to be executed
- SNAPResponse
The resulting object after executing a SNAPRequest that contains a response code, and may contain a message and other data.
- Software Metadata
This refers data about how SNAPRed operates. A prime example of this is the current mappings the InterfaceController has to the various services. Another example may be the current version of SNAPRed or its various configurations stored in the application.yml.
- Spectrum
A vector of either histogram or event data, consisting of both location (e.g. “x”) and counts (or fluence, e.g. “y”) values. For special applications such as grouping and masking, spectra may be single valued.
- State
The static positions of the detectors and any other distict configurable characteristics of the Instrument recorded as part of a Run.
- State Folder
The folder that contains all configurable data unique to a specific State. It is named after the hash of the State it represents.
- State ID
A secure-hash algorithm (SHA) generated ID associated with a specific instrument state. This ID is usually represented by its 16-character hexadecimal digest.
- Vanadium
A reference material commonly used in neutron diffraction experiments for calibration and normalization purposes due to its well-understood scattering properties. Vanadium calibration is essential for instrument performance verification and for correcting systematic errors in diffraction data. It plays a crucial role in the Calibration and Normalization processes within SNAP, ensuring accurate and reliable data analysis.
- User
TODO
- User Request
A request made by the backend consumer to perform a specific task given sufficent input data.
- Workspace
A data object used by mantid to store most data, including neutron scattering data and grouping maps.
- Workspace List
TODO
- XML
Extensible Markup Language (XML). A fully generalizable text-based markup language, allowing the representation of any type of data.