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GNU Astronomy Utilities GNU Astronomy Utilities Astronomical data manipulation and analysis programs and libraries for version 0.15.58-2b10e, 23 September 2021 Mohammad Akhlaghi Gnuastro (source code, book and web page) authors (sorted by number of commits): Mohammad Akhlaghi ([email protected], 1812) Pedram Ashofteh Ardakani ([email protected], 54) Raul Infante-Sainz ([email protected], 34) Mos`eGiordano ([email protected], 29) Vladimir Markelov ([email protected], 18) Sachin Kumar Singh ([email protected], 13) Zahra Sharbaf ([email protected], 12) Nat´aliD. Anzanello ([email protected], 8) Boud Roukema ([email protected], 7) Carlos Morales-Socorro ([email protected], 3) Th´er`eseGodefroy ([email protected], 3) Joseph Putko ([email protected], 2) Samane Raji ([email protected], 2) Alexey Dokuchaev ([email protected], 1) Andreas Stieger ([email protected], 1) Fran¸coisOchsenbein ([email protected], 1) Kartik Ohri ([email protected], 1) Leindert Boogaard ([email protected], 1) Lucas MacQuarrie ([email protected], 1) Madhav Bansal ([email protected], 1) Miguel de Val-Borro ([email protected], 1) Sepideh Eskandarlou ([email protected], 1) This book documents version 0.15.58-2b10e of the GNU Astronomy Utilities (Gnuastro). Gnuastro provides various programs and libraries for astronomical data manipulation and analysis. Copyright c 2015-2021, Free Software Foundation, Inc. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled \GNU Free Documentation License". For myself, I am interested in science and in philosophy only because I want to learn something about the riddle of the world in which we live, and the riddle of man's knowledge of that world. And I believe that only a revival of interest in these riddles can save the sciences and philosophy from narrow specialization and from an obscurantist faith in the expert's special skill, and in his personal knowledge and authority; a faith that so well fits our `post-rationalist' and `post- critical' age, proudly dedicated to the destruction of the tradition of rational philosophy, and of rational thought itself. |Karl Popper. The logic of scientific discovery. 1959. i Short Contents 1 Introduction :::::::::::::::::::::::::::::::::::::::::: 1 2 Tutorials:::::::::::::::::::::::::::::::::::::::::::: 16 3 Installation:::::::::::::::::::::::::::::::::::::::::: 86 4 Common program behavior:::::::::::::::::::::::::::: 118 5 Data containers ::::::::::::::::::::::::::::::::::::: 160 6 Data manipulation::::::::::::::::::::::::::::::::::: 222 7 Data analysis ::::::::::::::::::::::::::::::::::::::: 293 8 Modeling and fitting ::::::::::::::::::::::::::::::::: 389 9 High-level calculations :::::::::::::::::::::::::::::::: 415 10 Installed scripts ::::::::::::::::::::::::::::::::::::: 428 11 Library :::::::::::::::::::::::::::::::::::::::::::: 441 12 Developing ::::::::::::::::::::::::::::::::::::::::: 595 A Gnuastro programs list ::::::::::::::::::::::::::::::: 624 B Other useful software::::::::::::::::::::::::::::::::: 626 C GNU Free Doc. License::::::::::::::::::::::::::::::: 631 D GNU Gen. Pub. License v3 ::::::::::::::::::::::::::: 639 Index: Macros, structures and functions ::::::::::::::::::::: 650 Index ::::::::::::::::::::::::::::::::::::::::::::::::: 657 ii Table of Contents 1 Introduction ::::::::::::::::::::::::::::::::::::: 1 1.1 Quick start ::::::::::::::::::::::::::::::::::::::::::::::::::::: 1 1.2 Gnuastro manifesto: Science and its tools ::::::::::::::::::::::: 2 1.3 Your rights ::::::::::::::::::::::::::::::::::::::::::::::::::::: 6 1.4 Naming convention ::::::::::::::::::::::::::::::::::::::::::::: 7 1.5 Version numbering:::::::::::::::::::::::::::::::::::::::::::::: 7 1.5.1 GNU Astronomy Utilities 1.0 :::::::::::::::::::::::::::::: 8 1.6 New to GNU/Linux? ::::::::::::::::::::::::::::::::::::::::::: 8 1.6.1 Command-line interface :::::::::::::::::::::::::::::::::::: 9 1.7 Report a bug :::::::::::::::::::::::::::::::::::::::::::::::::: 11 1.8 Suggest new feature ::::::::::::::::::::::::::::::::::::::::::: 12 1.9 Announcements ::::::::::::::::::::::::::::::::::::::::::::::: 13 1.10 Conventions :::::::::::::::::::::::::::::::::::::::::::::::::: 13 1.11 Acknowledgments :::::::::::::::::::::::::::::::::::::::::::: 14 2 Tutorials :::::::::::::::::::::::::::::::::::::::: 16 2.1 Sufi simulates a detection :::::::::::::::::::::::::::::::::::::: 17 2.2 General program usage tutorial :::::::::::::::::::::::::::::::: 24 2.2.1 Calling Gnuastro's programs :::::::::::::::::::::::::::::: 25 2.2.2 Accessing documentation ::::::::::::::::::::::::::::::::: 25 2.2.3 Setup and data download ::::::::::::::::::::::::::::::::: 27 2.2.4 Dataset inspection and cropping :::::::::::::::::::::::::: 28 2.2.5 Angular coverage on the sky :::::::::::::::::::::::::::::: 29 2.2.6 Cosmological coverage :::::::::::::::::::::::::::::::::::: 32 2.2.7 Building custom programs with the library :::::::::::::::: 34 2.2.8 Option management and configuration files:::::::::::::::: 36 2.2.9 Warping to a new pixel grid :::::::::::::::::::::::::::::: 38 2.2.10 NoiseChisel and Multiextension FITS files ::::::::::::::: 39 2.2.11 NoiseChisel optimization for detection ::::::::::::::::::: 41 2.2.12 NoiseChisel optimization for storage ::::::::::::::::::::: 46 2.2.13 Segmentation and making a catalog :::::::::::::::::::::: 47 2.2.14 Working with catalogs (estimating colors) :::::::::::::::: 50 2.2.15 Column statistics (color-magnitude diagram)::::::::::::: 54 2.2.16 Aperture photometry :::::::::::::::::::::::::::::::::::: 57 2.2.17 Matching catalogs ::::::::::::::::::::::::::::::::::::::: 58 2.2.18 Finding reddest clumps and visual inspection :::::::::::: 59 2.2.19 Writing scripts to automate the steps :::::::::::::::::::: 61 2.2.20 Citing and acknowledging Gnuastro :::::::::::::::::::::: 67 2.3 Detecting large extended targets ::::::::::::::::::::::::::::::: 67 2.3.1 Downloading and validating input data ::::::::::::::::::: 68 2.3.2 NoiseChisel optimization:::::::::::::::::::::::::::::::::: 69 2.3.3 Image surface brightness limit::::::::::::::::::::::::::::: 75 2.3.4 Achieved surface brightness level :::::::::::::::::::::::::: 80 iii 2.3.5 Extract clumps and objects (Segmentation) ::::::::::::::: 82 3 Installation ::::::::::::::::::::::::::::::::::::: 86 3.1 Dependencies:::::::::::::::::::::::::::::::::::::::::::::::::: 86 3.1.1 Mandatory dependencies:::::::::::::::::::::::::::::::::: 87 3.1.1.1 GNU Scientific library ::::::::::::::::::::::::::::::: 87 3.1.1.2 CFITSIO :::::::::::::::::::::::::::::::::::::::::::: 87 3.1.1.3 WCSLIB :::::::::::::::::::::::::::::::::::::::::::: 88 3.1.2 Optional dependencies :::::::::::::::::::::::::::::::::::: 89 3.1.3 Bootstrapping dependencies :::::::::::::::::::::::::::::: 91 3.1.4 Dependencies from package managers ::::::::::::::::::::: 93 3.2 Downloading the source ::::::::::::::::::::::::::::::::::::::: 97 3.2.1 Release tarball:::::::::::::::::::::::::::::::::::::::::::: 97 3.2.2 Version controlled source:::::::::::::::::::::::::::::::::: 98 3.2.2.1 Bootstrapping ::::::::::::::::::::::::::::::::::::::: 99 3.2.2.2 Synchronizing :::::::::::::::::::::::::::::::::::::: 100 3.3 Build and install ::::::::::::::::::::::::::::::::::::::::::::: 102 3.3.1 Configuring ::::::::::::::::::::::::::::::::::::::::::::: 102 3.3.1.1 Gnuastro configure options:::::::::::::::::::::::::: 102 3.3.1.2 Installation directory ::::::::::::::::::::::::::::::: 105 3.3.1.3 Executable names :::::::::::::::::::::::::::::::::: 109 3.3.1.4 Configure and build in RAM :::::::::::::::::::::::: 110 3.3.2 Separate build and source directories::::::::::::::::::::: 111 3.3.3 Tests :::::::::::::::::::::::::::::::::::::::::::::::::::: 114 3.3.4 A4 print book ::::::::::::::::::::::::::::::::::::::::::: 114 3.3.5 Known issues :::::::::::::::::::::::::::::::::::::::::::: 115 4 Common program behavior :::::::::::::::::: 118 4.1 Command-line ::::::::::::::::::::::::::::::::::::::::::::::: 118 4.1.1 Arguments and options :::::::::::::::::::::::::::::::::: 119 4.1.1.1 Arguments ::::::::::::::::::::::::::::::::::::::::: 120 4.1.1.2 Options :::::::::::::::::::::::::::::::::::::::::::: 120 4.1.2 Common options :::::::::::::::::::::::::::::::::::::::: 122 4.1.2.1 Input/Output options :::::::::::::::::::::::::::::: 123 4.1.2.2 Processing options :::::::::::::::::::::::::::::::::: 125 4.1.2.3 Operating mode options :::::::::::::::::::::::::::: 128 4.1.3 Shell TAB completion (highly customized) ::::::::::::::: 132 4.1.4 Standard input :::::::::::::::::::::::::::::::::::::::::: 133 4.2 Configuration files :::::::::::::::::::::::::::::::::::::::::::: 135 4.2.1 Configuration file format::::::::::::::::::::::::::::::::: 135 4.2.2 Configuration file precedence :::::::::::::::::::::::::::: 136 4.2.3 Current directory and User wide ::::::::::::::::::::::::: 137 4.2.4 System wide::::::::::::::::::::::::::::::::::::::::::::: 137 4.3 Getting help ::::::::::::::::::::::::::::::::::::::::::::::::: 138 4.3.1 --usage ::::::::::::::::::::::::::::::::::::::::::::::::: 138 4.3.2 --help :::::::::::::::::::::::::::::::::::::::::::::::::: 139 4.3.3 Man pages :::::::::::::::::::::::::::::::::::::::::::::: 140 iv 4.3.4 Info ::::::::::::::::::::::::::::::::::::::::::::::::::::: 140 4.3.5 help-gnuastro
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