DOCSLIB.ORG

Getting Started with Astropy

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Getting Started with Astropy Astropy Documentation Release 0.2.5 The Astropy Developers October 28, 2013 CONTENTS i ii Astropy Documentation, Release 0.2.5 Astropy is a community-driven package intended to contain much of the core functionality and some common tools needed for performing astronomy and astrophysics with Python. CONTENTS 1 Astropy Documentation, Release 0.2.5 2 CONTENTS Part I User Documentation 3 Astropy Documentation, Release 0.2.5 Astropy at a glance 5 Astropy Documentation, Release 0.2.5 6 CHAPTER ONE OVERVIEW Here we describe a broad overview of the Astropy project and its parts. 1.1 Astropy Project Concept The “Astropy Project” is distinct from the astropy package. The Astropy Project is a process intended to facilitate communication and interoperability of python packages/codes in astronomy and astrophysics. The project thus en- compasses the astropy core package (which provides a common framework), all “affiliated packages” (described below in Affiliated Packages), and a general community aimed at bringing resources together and not duplicating efforts. 1.2 astropy Core Package The astropy package (alternatively known as the “core” package) contains various classes, utilities, and a packaging framework intended to provide commonly-used astronomy tools. It is divided into a variety of sub-packages, which are documented in the remainder of this documentation (see User Documentation for documentation of these components). The core also provides this documentation, and a variety of utilities that simplify starting other python astron- omy/astrophysics packages. As described in the following section, these simplify the process of creating affiliated packages. 1.3 Affiliated Packages The Astropy project includes the concept of “affiliated packages.” An affiliated package is an astronomy-related python package that is not part of the astropy core source code, but has requested to be included in the Astropy project. Such a package may be a candidate for eventual inclusion in the main astropy package (although this is not required). There is a registry of affiliated packages at http://affiliated.astropy.org, and in the near future, the astropy core will include a tool to install affiliated packages by name. See the config module documentation for details about the affiliated package registry and install tool. Note that affiliated packages do not use the astropy namespace, which is reserved for the core. Instead, they either use their package name directly, or awastropy.packagename (“affiliated with astropy”). If you are interested in starting an affiliated package, or have a package you are interested in making more compatible with astropy, the astropy core package includes a variety of features that simplify and homogenize package man- agement. Astropy provides a package template that provides a common way to organize packages, to make your life 7 Astropy Documentation, Release 0.2.5 simpler. You can use this template either with a new package you are starting or an existing package to make it more compatible with Astropy and the affiliated package installer. See the usage instructions in the template for further details. 1.4 Community Aside from the actual code, Astropy is also a community of astronomy-associated users and developers that agree that sharing utilities is healthy for the community and the science it produces. This community is of course central to accomplishing anything with the code itself. 8 Chapter 1. Overview CHAPTER TWO INSTALLATION 2.1 Requirements Astropy has the following strict requirements: • Python 2.6, 2.7, 3.1 or 3.2 • Numpy 1.4 or later Astropy also depends on other packages for optional features: • h5py: To read/write Table objects from/to HDF5 files • scipy: To power a variety of features (currently mainly cosmology-related functionality) • xmllint: To validate VOTABLE XML files. However, note that these only need to be installed if those particular features are needed. Astropy will import even if these dependencies are not installed. 2.2 Installing Astropy 2.2.1 Using pip To install Astropy with pip, simply run: pip install --no-deps astropy Note: You will need a C compiler (e.g. gcc or clang) to be installed (see Building from source below) for the installation to succeed. Note: The --no-deps flag is optional, but highly recommended if you already have Numpy installed, since otherwise pip will sometimes try to “help” you by upgrading your Numpy installation, which may not always be desired. Note: If you get a PermissionError this means that you do not have the required administrative access to install new packages to your Python installation. In this case you may consider using the --user option to install the package into your home directory. You can read more about how to do this in the pip documentation. Alternatively, if you intend to do development on other software that uses Astropy, such as an affiliated package, consider installing Astropy into a virtualenv. 9 Astropy Documentation, Release 0.2.5 Do not install Astropy or other third-party packages using sudo unless you are fully aware of the risks. 2.2.2 Binary installers Binary installers are available on Windows for Python 2.6, 2.7, 3.1, and 3.2 at PyPI. 2.2.3 Testing an installed Astropy The easiest way to test your installed version of astropy is running correctly is to use the astropy.test() function: import astropy astropy.test() The tests should run and print out any failures, which you can report at the Astropy issue tracker. Note: This way of running the tests may not work if you do it in the astropy source distribution. See Testing a source code build of Astropy for how to run the tests from the source code directory, or Running Tests for more details. 2.3 Building from source 2.3.1 Prerequisites You will need a compiler suite and the development headers for Python and Numpy in order to build Astropy. On Linux, using the package manager for your distribution will usually be the easiest route, while on MacOS X you will need the XCode command line tools. The instructions for building Numpy from source are also a good resource for setting up your environment to build Python packages. You will also need Cython installed to build from source, unless you are installing a numbered release. (The releases packages have the necessary C files packaged with them, and hence do not require Cython.) Note: If you are using MacOS X, you will need to the XCode command line tools. One way to get them is to install XCode. If you are using OS X 10.7 (Lion) or later, you must also explicitly install the command line tools. You can do this by opening the XCode application, going to Preferences, then Downloads, and then under Components, click on the Install button to the right of Command Line Tools. Alternatively, on 10.7 (Lion) or later, you do not need to in- stall XCode, you can download just the command line tools from https://developer.apple.com/downloads/index.action (requires an Apple developer account). 2.3.2 Obtaining the source packages Source packages The latest stable source package for Astropy can be downloaded here. 10 Chapter 2. Installation Astropy Documentation, Release 0.2.5 Development repository The latest development version of Astropy can be cloned from github using this command: git clone git://github.com/astropy/astropy.git Note: If you wish to participate in the development of Astropy, see Developer Documentation. This document covers only the basics necessary to install Astropy. 2.3.3 Building and Installing Astropy uses the Python distutils framework for building and installing and requires the distribute extension–the later is automatically downloaded when running python setup.py if it is not already provided by your system. To build Astropy (from the root of the source tree): python setup.py build To install Astropy (from the root of the source tree): python setup.py install 2.3.4 Troubleshooting If you get an error mentioning that you do not have the correct permissions to install Astropy into the default site-packages directory, you can try installing with: python setup.py install --user which will install into a default directory in your home directory. External C libraries The Astropy source ships with the C source code of a number of libraries. By default, these internal copies are used to build Astropy. However, if you wish to use the system-wide installation of one of those libraries, you can pass one or more of the --use-system-X flags to the setup.py build command. For example, to build Astropy using the system libexpat, use: python setup.py build --use-system-expat To build using all of the system libraries, use: python setup.py build --use-system-libraries To see which system libraries Astropy knows how to build against, use: python setup.py build --help As with all distutils commandline options, they may also be provided in a setup.cfg in the same directory as setup.py. For example, to use the system libexpat, add the following to the setup.cfg file: [build] use_system_expat=1 2.3. Building from source 11 Astropy Documentation, Release 0.2.5 The required version of setuptools is not available If upon running the setup.py script you get a message like The required version of setuptools (>=0.9.8) is not available, and can’t be installed while this script is running. Please install a more recent version first, using ‘easy_install -U setuptools’. (Currently using setuptools 0.6c11 (/path/to/setuptools-0.6c11-py2.7.egg)) this is because you have a very outdated version of the setuptools package which is used to install Python packages.
Load more

Recommended publications
  • The Astropy Project: Building an Open-Science Project and Status of the V2.0 Core Package*
    The Astronomical Journal, 156:123 (19pp), 2018 September https://doi.org/10.3847/1538-3881/aabc4f © 2018. The American Astronomical Society. The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package* The Astropy Collaboration, A. M. Price-Whelan1 , B. M. Sipőcz44, H. M. Günther2,P.L.Lim3, S. M. Crawford4 , S. Conseil5, D. L. Shupe6, M. W. Craig7, N. Dencheva3, A. Ginsburg8 , J. T. VanderPlas9 , L. D. Bradley3 , D. Pérez-Suárez10, M. de Val-Borro11 (Primary Paper Contributors), T. L. Aldcroft12, K. L. Cruz13,14,15,16 , T. P. Robitaille17 , E. J. Tollerud3 (Astropy Coordination Committee), and C. Ardelean18, T. Babej19, Y. P. Bach20, M. Bachetti21 , A. V. Bakanov98, S. P. Bamford22, G. Barentsen23, P. Barmby18 , A. Baumbach24, K. L. Berry98, F. Biscani25, M. Boquien26, K. A. Bostroem27, L. G. Bouma1, G. B. Brammer3 , E. M. Bray98, H. Breytenbach4,28, H. Buddelmeijer29, D. J. Burke12, G. Calderone30, J. L. Cano Rodríguez98, M. Cara3, J. V. M. Cardoso23,31,32, S. Cheedella33, Y. Copin34,35, L. Corrales36,99, D. Crichton37,D.D’Avella3, C. Deil38, É. Depagne4, J. P. Dietrich39,40, A. Donath38, M. Droettboom3, N. Earl3, T. Erben41, S. Fabbro42, L. A. Ferreira43, T. Finethy98, R. T. Fox98, L. H. Garrison12 , S. L. J. Gibbons44, D. A. Goldstein45,46, R. Gommers47, J. P. Greco1, P. Greenfield3, A. M. Groener48, F. Grollier98, A. Hagen49,50, P. Hirst51, D. Homeier52 , A. J. Horton53, G. Hosseinzadeh54,55 ,L.Hu56, J. S. Hunkeler3, Ž. Ivezić57, A. Jain58, T. Jenness59 , G. Kanarek3, S. Kendrew60 , N. S. Kern45 , W. E.
    [Show full text]
  • Data Analysis Tools for the HST Community
    EXPANDING THE FRONTIERS OF SPACE ASTRONOMY Data Analysis Tools for the HST Community STUC 2019 Erik Tollerud Data Analysis Tools Branch Project Scientist What Are Data Analysis Tools? The Things After the Pipeline • DATs: Post-Pipeline Tools Spectral visualization tools Specutils Image visualization tools io models training & documentation modeling fitting - Analysis Tools astropy-helpers gwcs: generalized wcs wcs asdf: advanced data format JWST Tools tutorials ‣ Astropy software distribution astroquery MAST JWST data structures nddata ‣ Photutils models & fitting Astronomy Python Tool coordination photutils + others Development at STScI ‣ Specutils STAK: Jupyter notebooks - Visualization Tools IRAF Add to existing python lib cosmology External replacement Build replacement pkg ‣ Python Imexam (+ds9) constants astropy dev IRAF switchers guide affiliated packages no replacement ‣ Ginga ‣ SpecViz ‣ (MOSViz) ‣ (CubeViz) Data Analysis Software at STScI is for the Community Software that is meant to be used by the astronomy community to do their science. This talk is about some newer developments of interest to the HST user community. 2. 3. 1. IRAF • IRAF was amazing for its time, and the DAT for generations of astronomers What is the long-term replacement strategy? Python’s Scientific Ecosystem Has what Astro Needs Python is now the single most- used programming language in astronomy. Momcheva & Tollerud 2015 And 3rd-most in industry… Largely because of the vibrant scientific and numerical ecosystem (=Data Science): (Which HST’s pipelines helped start!) IRAF<->Python is not 1-to-1. Hence STAK Lead: Sara Ogaz Supporting both STScI’s internal scientists and the astronomy community at large (viewers like you) requires that the community be able to transition from IRAF to the Python-world.
    [Show full text]
  • Python for Astronomers an Introduction to Scientific Computing
    Python for Astronomers An Introduction to Scientific Computing Imad Pasha Christopher Agostino Copyright c 2014 Imad Pasha & Christopher Agostino DEPARTMENT OF ASTRONOMY,UNIVERSITY OF CALIFORNIA,BERKELEY Aknowledgements: We would like to aknowledge Pauline Arriage and Baylee Bordwell for their work in assembling much of the base topics covered in this class, and for creating many of the resources which influenced the production of this textbook. First Edition, January, 2015 Contents 1 Essential Unix Skills ..............................................7 1.1 What is UNIX, and why is it Important?7 1.2 The Interface7 1.3 Using a Terminal8 1.4 SSH 8 1.5 UNIX Commands9 1.5.1 Changing Directories.............................................. 10 1.5.2 Viewing Files and Directories........................................ 11 1.5.3 Making Directories................................................ 11 1.5.4 Deleting Files and Directories....................................... 11 1.5.5 Moving/Copying Files and Directories................................. 12 1.5.6 The Wildcard.................................................... 12 2 Basic Python .................................................. 15 2.1 Data-types 15 2.2 Basic Math 16 2.3 Variables 17 2.4 String Concatenation 18 2.5 Array, String, and List Indexing 19 2.5.1 Two Dimensional Slicing............................................ 20 2.6 Modifying Lists and Arrays 21 3 Libraries and Basic Script Writing ............................... 23 3.1 Importing Libraries 23 3.2 Writing Basic Programs 24 3.2.1 Writing Functions................................................. 25 3.3 Working with Arrays 26 3.3.1 Creating a Numpy Array........................................... 26 3.3.2 Basic Array Manipulation........................................... 26 4 Conditionals and Loops ........................................ 29 4.1 Conditional Statements 29 4.1.1 Combining Conditionals........................................... 30 4.2 Loops 31 4.2.1 While-Loops....................................................
    [Show full text]
  • Investigating Interoperability of the LSST Data Management Software Stack with Astropy
    Investigating interoperability of the LSST Data Management software stack with Astropy Tim Jennessa, James Boschb, Russell Owenc, John Parejkoc, Jonathan Sicka, John Swinbankb, Miguel de Val-Borrob, Gregory Dubois-Felsmannd, K-T Lime, Robert H. Luptonb, Pim Schellartb, K. Simon Krughoffc, and Erik J. Tollerudf aLSST Project Management Office, Tucson, AZ, U.S.A. bPrinceton University, Princeton, NJ, U.S.A. cUniversity of Washington, Seattle, WA, U.S.A dInfrared Processing and Analysis Center, California Institute of Technology, Pasadena, CA, U.S.A. eSLAC National Laboratory, Menlo Park, CA, U.S.A. fSpace Telescope Science Institute, 3700 San Martin Dr, Baltimore, MD, 21218, USA ABSTRACT The Large Synoptic Survey Telescope (LSST) will be an 8.4 m optical survey telescope sited in Chile and capable of imaging the entire sky twice a week. The data rate of approximately 15 TB per night and the requirements to both issue alerts on transient sources within 60 seconds of observing and create annual data releases means that automated data management systems and data processing pipelines are a key deliverable of the LSST construction project. The LSST data management software has been in development since 2004 and is based on a C++ core with a Python control layer. The software consists of nearly a quarter of a million lines of code covering the system from fundamental WCS and table libraries to pipeline environments and distributed process execution. The Astropy project began in 2011 as an attempt to bring together disparate open source Python projects and build a core standard infrastructure that can be used and built upon by the astronomy community.
    [Show full text]
  • Research and Technical Resource Guide
    Research and Technical Resources Princeton Astrophysics This guide is meant to provide an overview of essential tools used in astronomy and astrophysics research. They are primarily aimed at the undergraduates beginning to learn the ins and outs of research. 1 General Information about the Department Here are some general things to be aware of as students in Peyton Hall. • The undergraduate portion of the website: www.princeton.edu/astro/undergraduate. This is the best place to look for requirements. • Peyton Hall documentation wiki: www.astro.princeton.edu/docs/Main Page. Lots of information on technical matters, ranging from ssh-ing into workstations to setting up printers on your computer. • See www.astro.princeton.edu/docs/Requesting assistance for the email to contact for any IT assistance you need. • Spring colloquium series: During the Spring semester, we host a speaker every Tuesday afternoon (at 4:30), followed by a reception. Speakers are invited at least partially based on their ability to give good talks. The schedule can be found at www.princeton.edu/astro/news-events/public-events. • Wunch (Wednesday Lunch): www.astro.princeton.edu/∼wunch. Slightly less formal talks are given throughout the academic year, Wednesdays, 12:30. The speakers are often postdocs or grad students. Feel free to bring (or order|see the website) lunch. • Institute for Advanced Study colloquium: www.sns.ias.edu/∼seminar/colloquia.shtml. Though not often frequented by undergrads, you are welcome to attend the Tuesday morning (11:00) talks they host. These are often given by well-known and established astrophysicists, so if one comes up on a topic you are interested in, you should check it out.
    [Show full text]
  • Python Data Analysis and Reduction Tools for Large-Scale Spectroscopy
    Community Python Data Analysis and Reduction Tools for Large-Scale Spectroscopy Erik Tollerud @eteq Astropy Coordination Data Analysis Tools Branch Committee Member Project Scientist (Also: lover of large-scale spectroscopy of local galaxies… talk to me about an Astro2020 White Paper w/ K. Gilbert about M31 & the outer LG!) Python is now the dominant Language in Astro Research Momcheva & Tollerud 2015 Python (esp. in Science) Embraces an Open Ecosystem Openness leads to sharing the load Although: Open Source ≠ Open Development (More on this later) Astropy Mirrors this “Community ecosystem” (Professional) Astronomers help write it with This means both by engineers’ guidance and for the community, It should be useful pooling our for them as part of resources their day-to-day work Specutils https://specutils.readthedocs.io An Astropy-coordinated package with data structures and standard analysis functions for spectroscopy. • Pythonic data structures for spectra ^ • MOS support specifically built-in! • Analysis functions -> • Flux, Centroids, FWHM • Continuum fitting/subtraction • Spectral arithmetic, respecting units • Line modeling Specreduce https://github.com/astropy/specreduce An in-planning (read: mostly not yet implemented) package for reducing OIR spectra (think IRAF twodspec/ onedspec’s calib parts, or IDL spec2d) Needs more contributors! Too many instruments have decided to “roll their own.” (sometimes for good reasons, sometimes not…) This could be a great place for the MSE community to start… JWST DATs are Leveraging the above Spectral
    [Show full text]
  • The Astropy Project: Building an Inclusive, Open-Science Project and Status of the V2.0 Core Package
    This is a repository copy of The Astropy Project: Building an inclusive, open-science project and status of the v2.0 core package. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/130174/ Version: Published Version Article: Collaboration, T.A., Price-Whelan, A.M., Sipőcz, B.M. et al. (134 more authors) (2018) The Astropy Project: Building an inclusive, open-science project and status of the v2.0 core package. The Astronomical Journal , 156 (3). 123. ISSN 0004-6256 https://doi.org/10.3847/1538-3881/aabc4f Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ The Astronomical Journal, 156:123 (19pp), 2018 September https://doi.org/10.3847/1538-3881/aabc4f © 2018. The American Astronomical Society. The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package* The Astropy Collaboration, A. M. Price-Whelan1 , B. M. Sipőcz44, H. M. Günther2,P.L.Lim3, S. M. Crawford4 , S. Conseil5, D. L. Shupe6, M. W. Craig7, N.
    [Show full text]
  • Matt's Astro Python Toolbox Documentation
    Matt’s astro python toolbox Documentation Release 0.1 Matt Craig February 24, 2017 Contents 1 Contents 1 1.1 Overview.................................................1 1.2 Installation................................................2 1.3 Automated header processing......................................4 1.4 Manual header processing........................................ 15 1.5 Image Management........................................... 16 1.6 Header processing............................................ 20 1.7 Index................................................... 34 Python Module Index 35 i ii CHAPTER 1 Contents Overview This package provides two types of functionality; only the first is likely to be of general interest. Classes for managing a collection of FITS files The class ImageFileCollection provides a table summarizing the values of FITS keywords in the files in a directory and provides easy ways to iterate over the HDUs, headers or data in those files. As a quick example: >>> from msumastro import ImageFileCollection >>> ic= ImageFileCollection('.', keywords=['imagetyp','filter']) >>> for hdu in ic.hdus(imagetype='LIGHT', filter='I'): ... print hdu.header, hdu.data.mean() does what you would expect: it loops over all of the images in the collection whose image type is ‘LIGHT’ and filter is ‘I’. For more details see Image Management. The TableTree constructs, from the summary table of an ImageFileCollection, a tree organized by values in the FITS headers of the collection. See Image Management for more details and examples. Header processing of images from the Feder Observatory Semi-automatic image processing Command line scripts for automated updating of FITS header keywords. The intent with these is that they will rarely need to be used manually once a data preparation pipeline is set up. The simplest option here is to use run_standard_header_process which will chain together all of the steps in data preparation for you.
    [Show full text]
  • Fink , a New Generation of Broker for the LSST Community Anais Möller, Julien Peloton, Emille E
    Fink , a new generation of broker for the LSST community Anais Möller, Julien Peloton, Emille E. O. Ishida, Chris Arnault, Etienne Bachelet, Tristan Blaineau, Dominique Boutigny, Abhishek Chauhan, Emmanuel Gangler, Fabio Hernandez, et al. To cite this version: Anais Möller, Julien Peloton, Emille E. O. Ishida, Chris Arnault, Etienne Bachelet, et al.. Fink , a new generation of broker for the LSST community. Monthly Notices of the Royal Astronomical Society, Oxford University Press (OUP): Policy P - Oxford Open Option A, 2021, 501 (3), pp.3272-3288. 10.1093/mnras/staa3602. hal-03045627 HAL Id: hal-03045627 https://hal-cnrs.archives-ouvertes.fr/hal-03045627 Submitted on 8 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Version 24 November 2020 Fink, a new generation of broker for the LSST community Anais Möller1¢, Julien Peloton2y, Emille E. O. Ishida1z, Chris Arnault2, Etienne Bachelet 3, Tristan Blaineau2, Dominique Boutigny4, Abhishek Chauhan5, Emmanuel Gangler1, Fabio Hernandez6, Julius Hrivnac2, Marco Leoni2,7, Nicolas Leroy2, Marc Moniez2, Sacha Pateyron2, Adrien Ramparison2, Damien Turpin8, Réza Ansari2, Tarek Allam Jr.9,10, Armelle Bajat 11, Biswajit Biswas1,12, Alexandre Boucaud13, Johan Bregeon14, Jean-Eric Campagne2, Johann Cohen-Tanugi15,1, Alexis Coleiro13, Damien Dornic17, Dominique Fouchez16, Olivier Godet18, Philippe Gris1, Sergey Karpov 11, Ada Nebot Gomez-Moran 18, Jérémy Neveu2, Stephane Plaszczynski2, Volodymyr Savchenko19, Natalie Webb17 1LPC, Université Clermont Auvergne, CNRS/IN2P3, F-63000 Clermont-Ferrand, France.
    [Show full text]
  • Astroquery Documentation Release 0.3.7
    astroquery Documentation Release 0.3.7 Adam Ginsburg Mar 29, 2018 Contents I Introduction3 II Installation7 III Requirements 17 IV Using astroquery 21 V Available Services 25 VI Catalog, Archive, and Other 393 i ii astroquery Documentation, Release 0.3.7 This is the documentation for the Astroquery affiliated package of astropy. Code and issue tracker are on GitHub. Contents 1 astroquery Documentation, Release 0.3.7 2 Contents Part I Introduction 3 astroquery Documentation, Release 0.3.7 Astroquery is a set of tools for querying astronomical web forms and databases. There are two other packages with complimentary functionality as Astroquery: astropy.vo is in the Astropy core and pyvo is an Astropy affiliated package. They are more oriented to general virtual observatory discovery and queries, whereas Astroquery has web service specific interfaces. Check out the A Gallery of Queries for some nice examples. 5 astroquery Documentation, Release 0.3.7 6 Part II Installation 7 astroquery Documentation, Release 0.3.7 The latest version of astroquery can be conda installed while the latest and development versions can be pip installed or be downloaded directly from GitHub. 9 astroquery Documentation, Release 0.3.7 10 CHAPTER 1 Using pip $ pip install astroquery and the ‘bleeding edge’ master version: $ pip install https://github.com/astropy/astroquery/archive/master.zip 11 astroquery Documentation, Release 0.3.7 12 Chapter 1. Using pip CHAPTER 2 Using conda It is also possible to install the latest astroquery with anaconda from the astropy channel: $ conda install -c astropy astroquery 13 astroquery Documentation, Release 0.3.7 14 Chapter 2.
    [Show full text]
  • Automated Workflow to Measure Arabidopsis Thaliana Root Tip Angle Dynamic
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452462; this version posted July 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Title ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamic Authors Nelson BC Serre and Matyas Fendrych Affiliation Cell Growth Laboratory, Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Prague, Czech Republic. Corresponding author [email protected] Key Words Root gravitropism - Image segmentation - Deep Machine Learning - Python - UNET Summary Plants respond to the surrounding environment in countless ways. One of these responses is their ability to sense and orient their root growth toward the gravity vector. Root gravitropism is studied in many laboratories as a hallmark of auxin-related phenotypes. However, manual analysis of images and microscopy data is known to be subjected to human bias. This is particularly the case for manual measurements of root bending as the selection lines to calculate the angle are set subjectively. Therefore, it is essential to develop and use automated or semi-automated image analysis to produce reproducible and unbiased data. Moreover, the increasing usage of vertical-stage microscopy in plant root biology yields gravitropic experiments with an unprecedented spatiotemporal resolution. To this day, there is no available solution to measure root bending angle over time for vertical-stage microscopy. To address these problems, we developed ACORBA (Automatic Calculation Of Root Bending Angles), a fully automated software to measure root bending angle over time from vertical- stage microscope and flatbed scanner images.
    [Show full text]
  • Astronomical Imaging in Python 2D Arrays
    Week 5 Astronomical Imaging in Python 2D arrays • The astronomical images we deal with, at a basic level, are 2D arrays with each pixel representing a “photon bin.” • Once you have extracted this 2D array from a FITS file, you can work with it in the way we talked about last week. Indexing a 2D array • When indexing a 2D array, we have a broader set of options for what we may want to index • For example, we may want to pull an individual value, a whole row or column, a group of rows and columns, or select a small area of image. Syntax • The syntax for pulling a single element is the double bracket: pull = image_name[456][345] #In row then column format • To pull a range of elements, we use comma notation: pull = image_name[456:500,323:350] • We specify the row range with a colon, then the column range (separated by a comma). The above would pull a sub-array (2D) that was a rectangle on the original image Syntax • We can use our colon shortcuts to index whole rows/columns: pull_col = image_name[ : , 350] #pulls the 350th column pull_row = image_name[40 , : ] #pulls 40th row • We can do the same to specify a range of columns or rows • Exercise: create a 10x10 array using arange.reshape (length 100), and then pull the second, third, and forth columns. Then pull the 5th, 6th, and 7th row. Image Transformations • Sometimes we need to flip our images vertically, horizontally, or both. • To flip an image vertically we can use either: image = image[: : -1] #or image = image[: : -1, :] • The reasoning here is that you are setting the image equal to itself indexed in reversed order along the axis specified (the first version is just a short hand version of the second) Image Transformations • Similarly, if we want to reverse an image horizontally (left/right): image = image[ : , : : -1] • To do both, we can simply apply these transformations in one ([::-1,::-1]).
    [Show full text]