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MUSE HUDF survey I & II, Sections 7.3 & 3.4: photometry for objects with no prior broad-band segmentation map

Akhlaghi, Mohammad; Bacon, Roland; Inami, Hanae


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        "affiliation": "Univ Lyon, Univ Lyon1, Ens de Lyon, CNRS, Centre de Recherche Astrophysique de  Lyon UMR5574, F-69230 Saint-Genis-Laval France", 
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    "description": "<p><a href=\"http://akhlaghi.org/reproducible-science.html\">Reproduction pipeline</a>&nbsp;and necessary data&nbsp;for Sections 7.3 and 3.4 of Bacon et al., (<a href=\"https://www.aanda.org/articles/aa/full_html/2017/12/aa30833-17/aa30833-17.html\">2017</a>) and Inami et al., (<a href=\"https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html\">2017</a>)&nbsp;respectively (papers I and II&nbsp;of the <a href=\"https://www.aanda.org/component/toc/?task=topic&amp;id=868\">series of papers</a>&nbsp;on &quot;<em>The MUSE Hubble Ultra Deep Field Survey</em>&quot;, published in Astronomy &amp; Astrophysics, 608, <a href=\"https://www.aanda.org/articles/aa/abs/2017/12/aa30833-17/aa30833-17.html\">A1</a> and <a href=\"https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html\">A2</a>). This pipeline will&nbsp;estimate&nbsp;the&nbsp;Hubble Space Telescope (HST)&nbsp;segmentation maps (for paper 1) and make&nbsp;the necessary measurements (for paper 2) for objects that were detected in the <a href=\"http://muse-vlt.eu/science/\">MUSE</a> 3D cubes, but didn&#39;t&nbsp;correspond to&nbsp;any detection in the&nbsp;Rafelski et al. (<a href=\"http://adsabs.harvard.edu/abs/2015AJ....150...31R\">2015</a>) catalog.&nbsp;</p>\n\n<p>This repository on Zenodo contains all the necessary input data, software and&nbsp;<a href=\"http://akhlaghi.org/reproducible-science.html\">reproduction pipeline</a>&nbsp;(containing the scripts, configuration files and settings to exactly reproduce the results in&nbsp;Sections 7.3 and 3.4 of the papers above). Below is a description of the contents:</p>\n\n<ul>\n\t<li>\n\t<p><a href=\"https://zenodo.org/record/1164774/files/gnuastro-0.2.51-bc56-bugfix.tar.gz\"><code>gnuastro-0.2.51-bc64-bugfix.tar.gz</code></a>: Gnuastro version 0.2.51 with a small bug fix only relevant to this analysis. The base Gnuastro 0.2.51 was used for this pipeline when it was written, similar to&nbsp;<a href=\"https://doi.org/10.5281/zenodo.1163746\">zenodo.1163746</a>. However,&nbsp;a bug relating to estimation of upper-limit magnitudes was later found.&nbsp;This bug was&nbsp;fixed, but along with many other changes that made&nbsp;the whole Gnuastro package&nbsp;incompatible with this pipeline. Hence, this&nbsp;bug-fixed&nbsp;copy of Gnuastro 0.2.51 was used in the catalog of Inami et al. (<a href=\"https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html\">2017</a>).</p>\n\n\t<p>The reproduction pipeline below contains the fixed&nbsp;file and instructions on how to make this version from version 0.2.51 that is available in the&nbsp;official Gnuastro version controlled history. The library dependencies of this version of Gnuastro can be downloaded from&nbsp;<a href=\"https://doi.org/10.5281/zenodo.1163746\">zenodo.1163746</a> (<a href=\"https://zenodo.org/record/1163746/files/gnuastro-dependencies.tar.gz\"><code>gnuastro-dependencies.tar.gz</code></a>).</p>\n\n\t<p>IMPORTANT NOTE: Since version 0.2.51 of Gnuastro was released, CFITSIO (one of Gnuastro&#39;s dependencies) has added a dependency for the cURL library (to read https URLs). Therefore, to install Gnuastro 0.2.51, please install <a href=\"https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz\">CFITSIO version 3.41</a> or earlier.</p>\n\t</li>\n\t<li>\n\t<p><a href=\"https://zenodo.org/record/1164774/files/hst-uvudf.tar.gz\"><code>hst-uvudf.tar.gz</code></a>: images and weight maps in 0.06 arcsec/pixel resolution from the HST-<a href=\"https://asd.gsfc.nasa.gov/UVUDF/\">UVUDF survey</a>. These images are not necessary to run the reproduction pipeline (they will be downloaded from the <a href=\"https://archive.stsci.edu/pub/hlsp/uvudf/v2.0/\">HST archives</a> if not present). They are stored here for the self-sufficiency of this repository&nbsp;and faster download: in this lossless compressed format, they are roughly 1/4th&nbsp;the volume of the same files in&nbsp;HST archives.</p>\n\t</li>\n\t<li>\n\t<p><a href=\"https://zenodo.org/record/1164774/files/hst-xdf.tar.gz\"><code>hst-xdf.tar.gz</code></a>: images and weight maps in 0.06 arcsec/pixel resolution from the HST-<a href=\"https://archive.stsci.edu/prepds/xdf/\">XDF survey</a>.&nbsp;These are also available from the&nbsp;<a href=\"https://archive.stsci.edu/pub/hlsp/xdf/\">HST archives</a>&nbsp;and are kept here with similar reasons to above (with a compression ratio of almost 1/3rd).</p>\n\t</li>\n\t<li>\n\t<p><a href=\"https://zenodo.org/record/1164774/files/output-v4-2-gf97e.tar.gz\"><code>output-v4-2-gf97e.tar.gz</code></a>: output of the reproduction pipeline.</p>\n\t</li>\n\t<li>\n\t<p><a href=\"https://zenodo.org/record/1164774/files/reproduce-v4-2-gf97e.tar.gz\"><code>reproduce-v4-2-gf97e.tar.gz</code></a>:&nbsp;The&nbsp;<a href=\"http://akhlaghi.org/reproducible-science.html\">reproduction pipeline</a>&nbsp;(version 4-2-gf97e) that produces the results (tables) plotted in the paper. The full&nbsp;Git version controlled&nbsp;history of this repository is available on&nbsp;<a href=\"https://git-cral.univ-lyon1.fr/mohammad.akhlaghi/muse-udf-origin-only-hst-magnitudes\">git-cral.univ-lyon1.fr</a>&nbsp;or&nbsp;<a href=\"https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes\">gitlab.com</a>. We recommend cloning from the Git repository&nbsp;if it is available. This tarball is&nbsp;kept here in case those servers don&#39;t work or Git is no longer in common use.&nbsp;Please see the&nbsp;<code>README</code>&nbsp;file in this repository for instructions on how to run the reproduction pipeline&nbsp;and exactly reproduce the results. This pipeline will download all the necessary data if they aren&#39;t already present on the&nbsp;system (it is&nbsp;probably just necessary&nbsp;to install the required&nbsp;version of Gnuastro).</p>\n\t</li>\n</ul>\n\n<p>The Creative Commons Attribution-NonCommercial 4.0&nbsp;copyright mentioned in the Zenodo webpage is only applicable to files that don&#39;t have an explicit copyright within them. The copyright of other files (mainly scripts and software) is mentioned within them (all are <a href=\"https://www.gnu.org/licenses/licenses.en.html\">free&nbsp;licenses</a>).</p>\n\n<p>For any issues with the pipeline/processing, please contact&nbsp;<a href=\"http://akhlaghi.org/\">Mohammad Akhlaghi</a>.</p>"
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