Corral Framework: Trustworthy and Fully Functional Data Intensive Parallel Astronomical Pipelines
Total Page：16
File Type：pdf, Size：1020Kb
Corral Framework: Trustworthy and Fully Functional Data Intensive Parallel Astronomical Pipelines J. B. Cabrala,b,∗, B. Sanchez´ a, M. Beroizc,d, M. Dom´ıngueza, M. Laresa, S. Gurovicha, P. Granittoe a Instituto De Astronom´ıaTe´oricay Experimental - Observatorio Astron´omicoC´ordoba (IATE–OAC–UNC–CONICET), Laprida 854, X5000BGR, C´ordoba, Argentina. b Facultad de Ciencias Exactas, Ingenier´ıay Agrimensura, UNR, Pellegrini 250 - S2000BTP, Rosario, Argentina. c University of Texas Rio Grande Valley (UTRGV), One West University Blvd. Brownsville, Texas 78520, USA. d University of Texas at San Antonio (UTSA), 1 UTSA Circle, San Antonio, TX 78249, USA. e Centro Internacional Franco Argentino de Ciencias de la Informaci´ony de Sistemas (CIFASIS, CONICET–UNR), Ocampo y Esmeralda, S2000EZP, Rosario, Argentina. Abstract Data processing pipelines represent an important slice of the astronomical software library that include chains of processes that transform raw data into valuable information via data reduction and analysis. In this work we present Corral, a Python framework for astronomical pipeline generation. Corral features a Model-View-Controller design pattern on top of an SQL Relational Database capable of handling: custom data models; processing stages; and communication alerts, and also provides automatic quality and structural metrics based on unit testing. The Model-View-Controller provides concept separation between the user logic and the data models, delivering at the same time multi-processing and distributed computing capabilities. Corral represents an improve- ment over commonly found data processing pipelines in Astronomy since the design pattern eases the programmer from dealing with processing flow and parallelization issues, allowing them to focus on the specific algorithms needed for the successive data transformations and at the same time provides a broad measure of quality over the created pipeline. Corral and working examples of pipelines that use it are available to the community at https://github.com/toros-astro. Keywords: Astroinformatics, Astronomical Pipeline, Software and its engineering: Multiprocessing; Design Patterns 1. Introduction discovery engine for the intermediate Palomar Transient Fac- tory (iPTF Kulkarni, 2013); and the Pan-STARRS PS1 Image The development of modern ground–based and space–born Processing Pipeline (Magnier et al., 2006), performing the im- telescopes, covering all observable windows in the electro- age processing and analysis for the Pan-STARRS PS1 proto- magnetic spectrum, and an ever increasing variability interest type telescope data and making the results available to other via time–domain astronomy have raised the necessity for large systems within Pan-STARRS and Vista survey pipeline that in- databases of astronomical observations. The amount of data cludes VIRCAM, a 16 CCD nearIR camera for the VISTA Data to be processed has been steadily increasing, imposing higher flow system Emerson et al. (2004) . In fact, the implementation demands over: quality; storage needs and analysis tools. This of pipelines in Astronomy is a common task to the construction phenomenon is a manifestation of the deep transformation that of surveys (e.g. Marx and Reyes, 2015; Hughes et al., 2016; Astronomy is going through, along with the development of Hadjiyska et al., 2013), and it is even used to operate telescopes new technologies in the Big Data era. In this context, new au- remotely, as described in Kubanek´ et al. (2010). Standard tools for pipeline generation have already been developed and can tomatic data analysis techniques have emerged as the preferred 1 solution to the so-called “data tsunami” (Cavuoti, 2013). be found in the literature. Some examples are Luigi , which implements a method for the creation of distributive pipelines; arXiv:1701.05566v2 [astro-ph.IM] 7 Aug 2017 The development of an information processing pipeline is a OPUS (Rose et al., 1995), conceived by the Space Telescope natural consequence of science projects involving the acquisi- Science Institute; and more recently Kira (Zhang et al., 2016), a tion of data and its posterior analysis. Some examples of these distributed tool focused on astronomical image analysis. In the data intensive projects include The Dark Energy Survey Data experimental sciences, collecting, pre-processing and storing Management System (Mohr et al., 2008), designed to exploit a data are common recurring patterns regardless of the science camera with 74 CCDs at the Blanco telescope to study the na- field or the nature of the experiment. This means that pipelines ture of cosmic acceleration; the Infrared Processing and Analy- are in some sense re-written repeatedly. A more efficient ap- sis Center (Masci et al., 2016), a near real-time transient-source proach would exploit existing resources to build new tools and perform new tasks, taking advantage of established procedures ∗Corresponding author Email address: [email protected] (J. B. Cabral) 1Luigi: https://luigi.readthedocs.io/ Preprint submitted to Astronomy and Computing June 24, 2021 that have been widely tested by the community. Some success- 2. Astronomical Pipelines ful examples of this are the BLAS library for Linear Algebra, the package NumPy for Python (Van Der Walt et al., 2011) and Typical pipeline architecture involve chains of processes that the random number generators. Modern Astronomy presents consume a data flow, such that every processing stage is depen- plenty of examples where pipeline development is crucial. In dent output of a previous stage. According to Bowman-Amuah this work, we present a python framework for astronomical (2004), any pipeline formalism must include the following en- pipeline generation developed in the context of the TOROS tities: collaboration (“Transient Optical Robotic Observatory of the Stream: The data stream usually means a continuous flow South”, Diaz et al., 2014). The TOROS project is dedicated of data produced by an experiment that needs to be trans- to the search of electromagnetic counterparts to gravitational formed and stored. wave (GW) events, as a response to the dawn of Gravitational Wave Astronomy. TOROS participated in the first observation Filters: a point where an atomic action is being executed on run O1 of the Advanced LIGO GW interferometer (Abramovici the data and can be summarized as stages of the pipeline et al., 1992; Abbott et al., 2016) from September 2015 through where the data stream undergoes transformations. January 2016 with promising results (Beroiz et al., 2016) and Connectors is currently attempting to deploy a wide-field optical telescope : the bridges between two filters. Several connec- in Cordon´ Macon,´ in the Atacama Plateau, northwestern Ar- tors can converge to a single filter, linking one stage of gentina (Renzi et al., 2009; Tremblin et al., 2012). The collab- processing with one or more previous stages. oration faced the challenge of starting a robotic observatory in Branches: data in the stream may be of a different nature and the extreme environment of the Cordon´ Macon.´ Given the iso- serve different purposes, meaning that pipelines can host lation of this geographic location (the site is at 4,600 m AMSL groups of filters on which every kind of data must pass, as and the closest city is 300 km away), human interaction and well as a disjoint set of filters specific to different kinds of that Internet connectivity is not readily available, this imposes data. This concept allows pipelines the ability to process strong demands for in-situ pipeline data processing and storage data in parallel whenever data is independent. requirements along with failure tolerance issues. To assess this, we provide the formalization of a pipeline framework based on This architecture is commonly used on experimental projects the well known design pattern Model–View–Controller (MVC), that need to handle massive amounts of data. We argue that it and an Open Source BSD-3 License2 pure Python package ca- is suitable for managing the data flow from telescopes immedi- pable of creating a high performance abstraction layer over a ately after data ingestion through to the data analysis. data warehouse, with multiprocessing data manipulation and In general, most dedicated telescopes or observatories have quality assurance reporting. This provides simple Object Ori- at least one pipeline in charge of capturing, transforming and ented structures that seizes the power of modern multi-core storing data to be analyzed in the future, manually or automat- computer hardware. On the assurance reporting given the mas- ically (Klaus et al., 2010; Tucker et al., 2006; Emerson et al., sive amount of data expected to be processed, Corral extracts 2004). This is also important because many of the upcoming quality assurance metrics for the pipeline run, useful for error large astronomical surveys (e.g. LSST, Ivezic et al., 2008), debugging. are expected to be in the PetaByte scale in terms of raw data,3, 4, meaning that a faster and more reliable type of pipeline en- This work is organized as follows. In section 2 the pipeline gine is needed. LSST is currently maintaining their own foun- formalism and the relevance of this architecture is discussed, in dation for pipelines and data management software (Axelrod section 3 the framework and the design choices made are ex- et al., 2010). plained. The theoretical ideas are implemented into code as an Open Source Python software tool, as shown in section 4. In section 5 a short introductory code case for