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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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  <identifier identifierType="DOI">10.5281/zenodo.1164774</identifier>
  <creators>
    <creator>
      <creatorName>Akhlaghi, Mohammad</creatorName>
      <givenName>Mohammad</givenName>
      <familyName>Akhlaghi</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1710-6613</nameIdentifier>
      <affiliation>Univ Lyon, Univ Lyon1, Ens de Lyon, CNRS, Centre de Recherche Astrophysique de  Lyon UMR5574, F-69230 Saint-Genis-Laval France</affiliation>
    </creator>
    <creator>
      <creatorName>Bacon, Roland</creatorName>
      <givenName>Roland</givenName>
      <familyName>Bacon</familyName>
      <affiliation>Univ Lyon, Univ Lyon1, Ens de Lyon, CNRS, Centre de Recherche Astrophysique de  Lyon UMR5574, F-69230 Saint-Genis-Laval France</affiliation>
    </creator>
    <creator>
      <creatorName>Inami, Hanae</creatorName>
      <givenName>Hanae</givenName>
      <familyName>Inami</familyName>
      <affiliation>Univ Lyon, Univ Lyon1, Ens de Lyon, CNRS, Centre de Recherche Astrophysique de  Lyon UMR5574, F-69230 Saint-Genis-Laval France</affiliation>
    </creator>
  </creators>
  <titles>
    <title>MUSE HUDF survey I &amp; II, Sections 7.3 &amp; 3.4: photometry for objects with no prior broad-band segmentation map</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>astronomy, astrophysics, galaxies, detection, catalog, reproduction pipeline</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-02-02</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1164774</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1051/0004-6361/201730833</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsSupplementTo">10.1051/0004-6361/201731195</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1164773</relatedIdentifier>
  </relatedIdentifiers>
  <version>4-2-gf97e</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by-nc/4.0/legalcode">Creative Commons Attribution Non Commercial 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;a href="http://akhlaghi.org/reproducible-science.html"&gt;Reproduction pipeline&lt;/a&gt;&amp;nbsp;and necessary data&amp;nbsp;for Sections 7.3 and 3.4 of Bacon et al., (&lt;a href="https://www.aanda.org/articles/aa/full_html/2017/12/aa30833-17/aa30833-17.html"&gt;2017&lt;/a&gt;) and Inami et al., (&lt;a href="https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html"&gt;2017&lt;/a&gt;)&amp;nbsp;respectively (papers I and II&amp;nbsp;of the &lt;a href="https://www.aanda.org/component/toc/?task=topic&amp;amp;id=868"&gt;series of papers&lt;/a&gt;&amp;nbsp;on &amp;quot;&lt;em&gt;The MUSE Hubble Ultra Deep Field Survey&lt;/em&gt;&amp;quot;, published in Astronomy &amp;amp; Astrophysics, 608, &lt;a href="https://www.aanda.org/articles/aa/abs/2017/12/aa30833-17/aa30833-17.html"&gt;A1&lt;/a&gt; and &lt;a href="https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html"&gt;A2&lt;/a&gt;). This pipeline will&amp;nbsp;estimate&amp;nbsp;the&amp;nbsp;Hubble Space Telescope (HST)&amp;nbsp;segmentation maps (for paper 1) and make&amp;nbsp;the necessary measurements (for paper 2) for objects that were detected in the &lt;a href="http://muse-vlt.eu/science/"&gt;MUSE&lt;/a&gt; 3D cubes, but didn&amp;#39;t&amp;nbsp;correspond to&amp;nbsp;any detection in the&amp;nbsp;Rafelski et al. (&lt;a href="http://adsabs.harvard.edu/abs/2015AJ....150...31R"&gt;2015&lt;/a&gt;) catalog.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;This repository on Zenodo contains all the necessary input data, software and&amp;nbsp;&lt;a href="http://akhlaghi.org/reproducible-science.html"&gt;reproduction pipeline&lt;/a&gt;&amp;nbsp;(containing the scripts, configuration files and settings to exactly reproduce the results in&amp;nbsp;Sections 7.3 and 3.4 of the papers above). Below is a description of the contents:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;
	&lt;p&gt;&lt;a href="https://zenodo.org/record/1164774/files/gnuastro-0.2.51-bc56-bugfix.tar.gz"&gt;&lt;code&gt;gnuastro-0.2.51-bc64-bugfix.tar.gz&lt;/code&gt;&lt;/a&gt;: 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&amp;nbsp;&lt;a href="https://doi.org/10.5281/zenodo.1163746"&gt;zenodo.1163746&lt;/a&gt;. However,&amp;nbsp;a bug relating to estimation of upper-limit magnitudes was later found.&amp;nbsp;This bug was&amp;nbsp;fixed, but along with many other changes that made&amp;nbsp;the whole Gnuastro package&amp;nbsp;incompatible with this pipeline. Hence, this&amp;nbsp;bug-fixed&amp;nbsp;copy of Gnuastro 0.2.51 was used in the catalog of Inami et al. (&lt;a href="https://www.aanda.org/articles/aa/abs/2017/12/aa31195-17/aa31195-17.html"&gt;2017&lt;/a&gt;).&lt;/p&gt;

	&lt;p&gt;The reproduction pipeline below contains the fixed&amp;nbsp;file and instructions on how to make this version from version 0.2.51 that is available in the&amp;nbsp;official Gnuastro version controlled history. The library dependencies of this version of Gnuastro can be downloaded from&amp;nbsp;&lt;a href="https://doi.org/10.5281/zenodo.1163746"&gt;zenodo.1163746&lt;/a&gt; (&lt;a href="https://zenodo.org/record/1163746/files/gnuastro-dependencies.tar.gz"&gt;&lt;code&gt;gnuastro-dependencies.tar.gz&lt;/code&gt;&lt;/a&gt;).&lt;/p&gt;

	&lt;p&gt;IMPORTANT NOTE: Since version 0.2.51 of Gnuastro was released, CFITSIO (one of Gnuastro&amp;#39;s dependencies) has added a dependency for the cURL library (to read https URLs). Therefore, to install Gnuastro 0.2.51, please install &lt;a href="https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz"&gt;CFITSIO version 3.41&lt;/a&gt; or earlier.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;&lt;a href="https://zenodo.org/record/1164774/files/hst-uvudf.tar.gz"&gt;&lt;code&gt;hst-uvudf.tar.gz&lt;/code&gt;&lt;/a&gt;: images and weight maps in 0.06 arcsec/pixel resolution from the HST-&lt;a href="https://asd.gsfc.nasa.gov/UVUDF/"&gt;UVUDF survey&lt;/a&gt;. These images are not necessary to run the reproduction pipeline (they will be downloaded from the &lt;a href="https://archive.stsci.edu/pub/hlsp/uvudf/v2.0/"&gt;HST archives&lt;/a&gt; if not present). They are stored here for the self-sufficiency of this repository&amp;nbsp;and faster download: in this lossless compressed format, they are roughly 1/4th&amp;nbsp;the volume of the same files in&amp;nbsp;HST archives.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;&lt;a href="https://zenodo.org/record/1164774/files/hst-xdf.tar.gz"&gt;&lt;code&gt;hst-xdf.tar.gz&lt;/code&gt;&lt;/a&gt;: images and weight maps in 0.06 arcsec/pixel resolution from the HST-&lt;a href="https://archive.stsci.edu/prepds/xdf/"&gt;XDF survey&lt;/a&gt;.&amp;nbsp;These are also available from the&amp;nbsp;&lt;a href="https://archive.stsci.edu/pub/hlsp/xdf/"&gt;HST archives&lt;/a&gt;&amp;nbsp;and are kept here with similar reasons to above (with a compression ratio of almost 1/3rd).&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;&lt;a href="https://zenodo.org/record/1164774/files/output-v4-2-gf97e.tar.gz"&gt;&lt;code&gt;output-v4-2-gf97e.tar.gz&lt;/code&gt;&lt;/a&gt;: output of the reproduction pipeline.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;&lt;a href="https://zenodo.org/record/1164774/files/reproduce-v4-2-gf97e.tar.gz"&gt;&lt;code&gt;reproduce-v4-2-gf97e.tar.gz&lt;/code&gt;&lt;/a&gt;:&amp;nbsp;The&amp;nbsp;&lt;a href="http://akhlaghi.org/reproducible-science.html"&gt;reproduction pipeline&lt;/a&gt;&amp;nbsp;(version 4-2-gf97e) that produces the results (tables) plotted in the paper. The full&amp;nbsp;Git version controlled&amp;nbsp;history of this repository is available on&amp;nbsp;&lt;a href="https://git-cral.univ-lyon1.fr/mohammad.akhlaghi/muse-udf-origin-only-hst-magnitudes"&gt;git-cral.univ-lyon1.fr&lt;/a&gt;&amp;nbsp;or&amp;nbsp;&lt;a href="https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes"&gt;gitlab.com&lt;/a&gt;. We recommend cloning from the Git repository&amp;nbsp;if it is available. This tarball is&amp;nbsp;kept here in case those servers don&amp;#39;t work or Git is no longer in common use.&amp;nbsp;Please see the&amp;nbsp;&lt;code&gt;README&lt;/code&gt;&amp;nbsp;file in this repository for instructions on how to run the reproduction pipeline&amp;nbsp;and exactly reproduce the results. This pipeline will download all the necessary data if they aren&amp;#39;t already present on the&amp;nbsp;system (it is&amp;nbsp;probably just necessary&amp;nbsp;to install the required&amp;nbsp;version of Gnuastro).&lt;/p&gt;
	&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;The Creative Commons Attribution-NonCommercial 4.0&amp;nbsp;copyright mentioned in the Zenodo webpage is only applicable to files that don&amp;#39;t have an explicit copyright within them. The copyright of other files (mainly scripts and software) is mentioned within them (all are &lt;a href="https://www.gnu.org/licenses/licenses.en.html"&gt;free&amp;nbsp;licenses&lt;/a&gt;).&lt;/p&gt;

&lt;p&gt;For any issues with the pipeline/processing, please contact&amp;nbsp;&lt;a href="http://akhlaghi.org/"&gt;Mohammad Akhlaghi&lt;/a&gt;.&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["Illingworth et al. (2013), Astrophysical Journal Supplement, Volume 209, Issue 1, article id. 6", "Rafelski et al. (2015), Astronomical Journal, Volume 150, Issue 1, article id. 31"]}</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/339659/">339659</awardNumber>
      <awardTitle>MUSE Imaging of the Cosmic Web – Ultra-Deep Observations of  Intergalactic and Circumgalactic Gas</awardTitle>
    </fundingReference>
  </fundingReferences>
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