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[gnuastro-commits] master 54864806 1/2: Adding the color-faint-gray arXi
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From: |
Mohammad Akhlaghi |
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Subject: |
[gnuastro-commits] master 54864806 1/2: Adding the color-faint-gray arXiv references |
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Date: |
Tue, 16 Jan 2024 16:36:49 -0500 (EST) |
branch: master
commit 54864806562b85bae92865844ad28f9eb8d0bf49
Author: Raul Infante-Sainz <infantesainz@gmail.com>
Commit: Raul Infante-Sainz <infantesainz@gmail.com>
Adding the color-faint-gray arXiv references
Until this commit, we did not have a formal reference for the paper
presenting the 'astscript-color-faint-gray' script. However, this paper
has been accepted in the RNAAS and submitted to arXiv.
With this commit, I have included this reference into the script, as well
as its arXiv URL into the Book. In addition to this, I modified a bit the
BibTeX text appearing on the 'astscript-zeropoint' script to follow the
same standards.
---
bin/script/color-faint-gray.sh | 72 +++++++++++++++++++++++++++++++++++++++++-
bin/script/zeropoint.sh | 50 +++++++++++++----------------
doc/gnuastro.texi | 13 ++++----
3 files changed, 99 insertions(+), 36 deletions(-)
diff --git a/bin/script/color-faint-gray.sh b/bin/script/color-faint-gray.sh
index 7235d00a..d80c01d7 100644
--- a/bin/script/color-faint-gray.sh
+++ b/bin/script/color-faint-gray.sh
@@ -186,6 +186,76 @@ EOF
}
+print_citation() {
+ empty="" # needed for the ascii art!
+ cat <<EOF
+
+Thank you for using $scriptname (GNU Astronomy Utilities) $version
+
+Citations and acknowledgement are vital for the continued work on Gnuastro.
+
+Please cite the following record(s) and add the acknowledgement statement
below in your work to support us. Please note that different Gnuastro programs
may have different corresponding papers. Hence, please check all the programs
you used. Don't forget to also include the version as shown above for
reproducibility.
+
+Paper introducing this script
+-----------------------------
+ @ARTICLE{astscript-color-faint-gray,
+ author = {{Infante-Sainz}, Ra{\'u}l and {Akhlaghi}, Mohammad},
+ title = "{Gnuastro: Visualizing the Full Dynamic Range in Color
Images}",
+ journal = {Research Notes of the American Astronomical Society},
+ keywords = {Astronomy software, Astronomy data visualization, Open
source software, Low surface brightness galaxies, 1855, 1968, 1866, 940,
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics -
Astrophysics of Galaxies, Computer Science - Computer Vision and Pattern
Recognition},
+ year = 2024,
+ month = jan,
+ volume = {8},
+ number = {1},
+ eid = {10},
+ pages = {10},
+ doi = {10.3847/2515-5172/ad1aae},
+ archivePrefix = {arXiv},
+ eprint = {2401.03814},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2024RNAAS...8...10I},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ }
+
+Paper introducing Gnuastro (currently main citation)
+----------------------------------------------------
+ @ARTICLE{gnuastro,
+ author = {{Akhlaghi}, M. and {Ichikawa}, T.},
+ title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
+ journal = {ApJS},
+ archivePrefix = "arXiv",
+ eprint = {1505.01664},
+ primaryClass = "astro-ph.IM",
+ year = 2015,
+ month = sep,
+ volume = 220,
+ eid = {1},
+ pages = {1},
+ doi = {10.1088/0067-0049/220/1/1},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ }
+
+Acknowledgement
+---------------
+This work was partly done using GNU Astronomy Utilities (Gnuastro,
ascl.net/1801.009) version $version. Work on Gnuastro has been funded by the
Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
scholarship and its Grant-in-Aid for Scientific Research (21244012, 24253003),
the European Research Council (ERC) advanced grant 339659-MUSICOS, the Spanish
Ministry of Economy and Competitiveness (MINECO, grant number AYA2016-76219-P)
and the NextGenerationEU grant [...]
+ ,
+ {|'--.
+ {{\ \ $empty
+ Many thanks from all |/\`'--./=.
+ Gnuastro developers! \`\.---' \`\\
+ |\ ||
+ | |//
+ \//_/|
+ //\__/
+ //
+ (http://www.chris.com/ascii/) |/
+
+EOF
+}
+
+
+
@@ -305,7 +375,7 @@ do
-'?'*|--help=*) on_off_option_error --help -?;;
-V|--version) print_version; exit 0;;
-V*|--version=*) on_off_option_error --version -V;;
- --cite) astfits --cite; exit 0;;
+ --cite) print_citation; exit 0;;
--cite=*) on_off_option_error --cite;;
# Unrecognized option:
diff --git a/bin/script/zeropoint.sh b/bin/script/zeropoint.sh
index a61ca08d..88b9d766 100644
--- a/bin/script/zeropoint.sh
+++ b/bin/script/zeropoint.sh
@@ -158,9 +158,6 @@ Written/developed by Sepideh Eskandarlou et al.
EOF
}
-
-
-
# Output of `--cite':
print_citation() {
empty="" # needed for the ascii art!
@@ -172,29 +169,29 @@ Citations and acknowledgement are vital for the continued
work on Gnuastro.
Please cite the following record(s) and add the acknowledgement statement
below in your work to support us. Please note that different Gnuastro programs
may have different corresponding papers. Hence, please check all the programs
you used. Don't forget to also include the version as shown above for
reproducibility.
-Paper introducing the zero point script
----------------------------------------
-@ARTICLE{astscrip-zeropoint,
- author = {{Eskandarlou}, Sepideh and {Akhlaghi}, Mohammad and
{Infante-Sainz}, Ra{\'u}l and {Saremi}, Elham and {Raji}, Samane and {Sharbaf},
Zahra and {Golini}, Giulia and {Ghaffari}, Zohreh and {Knapen}, Johan H.},
- title = "{Gnuastro: Estimating the Zero-point Magnitude in
Astronomical Imaging}",
- journal = {Research Notes of the American Astronomical Society},
- keywords = {Flux calibration, Astronomy software, Open source software,
Astronomical techniques, 544, 1855, 1866, 1684, Astrophysics - Instrumentation
and Methods for Astrophysics},
- year = 2023,
- month = dec,
- volume = {7},
- number = {12},
- eid = {269},
- pages = {269},
- doi = {10.3847/2515-5172/ad14f4},
-archivePrefix = {arXiv},
- eprint = {2312.04263},
- primaryClass = {astro-ph.IM},
- adsurl = {https://ui.adsabs.harvard.edu/abs/2023RNAAS...7..269E},
- adsnote = {Provided by the SAO/NASA Astrophysics Data System}
-}
+Paper introducing this script
+-----------------------------
+ @ARTICLE{astscrip-zeropoint,
+ author = {{Eskandarlou}, Sepideh and {Akhlaghi}, Mohammad and
{Infante-Sainz}, Ra{\'u}l and {Saremi}, Elham and {Raji}, Samane and {Sharbaf},
Zahra and {Golini}, Giulia and {Ghaffari}, Zohreh and {Knapen}, Johan H.},
+ title = "{Gnuastro: Estimating the Zero-point Magnitude in
Astronomical Imaging}",
+ journal = {Research Notes of the American Astronomical Society},
+ keywords = {Flux calibration, Astronomy software, Open source software,
Astronomical techniques, 544, 1855, 1866, 1684, Astrophysics - Instrumentation
and Methods for Astrophysics},
+ year = 2023,
+ month = dec,
+ volume = {7},
+ number = {12},
+ eid = {269},
+ pages = {269},
+ doi = {10.3847/2515-5172/ad14f4},
+ archivePrefix = {arXiv},
+ eprint = {2312.04263},
+ primaryClass = {astro-ph.IM},
+ adsurl = {https://ui.adsabs.harvard.edu/abs/2023RNAAS...7..269E},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+ }
-Paper introducing Gnuastro
---------------------------
+Paper introducing Gnuastro (currently main citation)
+----------------------------------------------------
@ARTICLE{gnuastro,
author = {{Akhlaghi}, M. and {Ichikawa}, T.},
title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
@@ -212,9 +209,6 @@ Paper introducing Gnuastro
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
-
-
-
Acknowledgement
---------------
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index cd433039..da16f7d8 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -8765,7 +8765,6 @@ In this tutorial, we review how to prepare your images
and create informative RG
We start with aligning the images to the same pixel grid (which is usually
necessary!) and using the low-level engine (Gnuastro's @ref{ConvertType}
program) directly to create an RGB image.
Afterwards, we will use a higher-level installed script (@ref{Color images
with gray faint regions}).
This is a high-level wrapper over ConvertType that does some pre-processing
and stretches the pixel values to enhance their 8-bit representation before
calling ConvertType.
-@c This installed script was first described in Infante-Sainz et al. (2023,
@url{TBD}).
@menu
* Color channels in same pixel grid:: Warping all inputs to the same pixel
grid.
@@ -8973,7 +8972,7 @@ But we saw that showing the brighter and fainter parts of
the galaxy in a single
In this section, we will use Gnuastro's @command{astscript-color-faint-gray}
installed script to address this problem and create images which visualize a
major fraction of the contents of our astronomical data.
This script aims to solve the problems mentioned in the previous section.
-See Infante-Sainz et al. (2023, which first introduced this script) for
examples of the final images we will be producing in this tutorial.
+See Infante-Sainz et al. (2024, @url{https://arxiv.org/abs/2401.03814}), which
first introduced this script, for examples of the final images we will be
producing in this tutorial.
This script uses a non-linear transformation to modify the bright input values
before combining them to produce the color image.
Furthermore, for the faint regions of the image, it will use grayscale and
avoid color over all (as we saw, colored noised is not too nice to look at!).
The faint regions are also inverted: so the brightest pixel in the faint
(black-and-white or grayscale) region is black and the faintest pixels will be
white.
@@ -9304,7 +9303,7 @@ In certain situations, the combination of channels may
not have a traditional co
For instance, combining an X-ray channel with an optical filter and a
far-infrared image can complicate the interpretation in terms of human
understanding of color.
But the physical interpretation remains valid as the different channels
(colors in the output) represent different physical phenomena of astronomical
sources.
Another easier example is the use of narrow-band filters such as the H-alpha
of J-PLUS survey.
-This is shown in the Bottom-right panel of Figure 1 by Infante-Sainz et al.
(2023, @url{TBD}), in this case the G channel has been substituted by the image
corresponding to the H-alpha filter to show the star formation regions.
+This is shown in the Bottom-right panel of Figure 1 by Infante-Sainz et al.
(2024, @url{https://arxiv.org/abs/2401.03814}), in this case the G channel has
been substituted by the image corresponding to the H-alpha filter to show the
star formation regions.
Therefore, please use the weights with caution, as it can significantly affect
the output and misinform your readers/viewers.
If you do apply weights be sure to report the weights in the caption of the
image (beside the filters that were used for each channel).
@@ -9345,15 +9344,15 @@ Two additional options are available to smooth
different regions by convolving w
The value specified for these options represents the full width at half
maximum of the Gaussian kernel.
Congratulations!
-By following the tutorial up to this point, we have been able to reproduce
three images of Infante-Sainz et al. (2023, @url{TBD}).
-You can see the commands that were used to generate them within the
reproducible source of that paper at @url{TBD}.
+By following the tutorial up to this point, we have been able to reproduce
three images of Infante-Sainz et al. (2024,
@url{https://arxiv.org/abs/2401.03814}).
+You can see the commands that were used to generate them within the
reproducible source of that paper at
@url{https://codeberg.org/gnuastro/papers/src/branch/color-faint-gray}.
Remember that this paper is reproducible throught Maneage, so you can explore
and build the entire paper by yourself.
For more on Maneage, see Akhlaghi et al.
@url{https://ui.adsabs.harvard.edu/abs/2021CSE....23c..82A, 2021}.
This tutorial provided a general overview of the various options to construct
a color image from three different FITS images using the
@command{astscript-color-faint-gray} script.
Keep in mind that the optimal parameters for generating the best color image
depend on your specific goals and the quality of your input images.
We encourage you to follow this tutorial with the provided J-PLUS images and
later with your own dataset.
-See @ref{Color images with gray faint regions} for more information, and
please consider citing Infante-Sainz et al. (2023, @url{TBD}) if you use this
script in your work (the full Bib@TeX{} entry of this paper will be given to
you with the @option{--cite} option).
+See @ref{Color images with gray faint regions} for more information, and
please consider citing Infante-Sainz et al. (2024,
@url{https://arxiv.org/abs/2401.03814}) if you use this script in your work
(the full Bib@TeX{} entry of this paper will be given to you with the
@option{--cite} option).
@node Zero point of an image, Pointing pattern design, Color images with full
dynamic range, Tutorials
@section Zero point of an image
@@ -34592,7 +34591,7 @@ To solve this issue, it is possible to perform some
transformations of the image
This is actually what the current script does: it makes some non-linear
transformations and then uses Gnuastro's ConvertType to generate the color
image.
There are several parameters and options in order to change the final output
that are described in @ref{Invoking astscript-color-faint-gray}.
A full tutorial describing this script with actual data is available in
@ref{Color images with full dynamic range}.
-A general overview of this script will be published in Infante-Sainz et al.
@url{TBD, 2023}; please cite it if this script proves useful in your research.
+A general overview of this script is published in Infante-Sainz et al.
@url{https://arxiv.org/abs/2401.03814, 2024}; please cite it if this script
proves useful in your research.
@menu
* Invoking astscript-color-faint-gray:: Details of options and arguments.