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Programs used to detect Island Mass Effects (IMEs) in the tropical Pacific, accompanying the paper "Basin-scale biogeochemical and ecological impacts of islands in the tropical Pacific Ocean" (Messié et al., 2022). This code runs the IME detection method on tropical Pacific islands on a climatological basis, and reproduces results presented in Fig. 1, Extended Fig. 1, and Table 1 of the paper. The method was developed within the SAPPHIRE project funded by Horizon 2020 (Marie Skłodowska-Curie grant agreement No. 746530). The programs are written for Matlab and require the Image Processing toolbox. The main .zip file (messiem/toolbox_IME_detection-v1.0.0.zip) contains the toolbox architecture and code, as well as output figures. Files with .mat extensions are not correctly represented in the main .zip file because of using Git LFS on GitHub. They are provided within the additional zip file toolbox_IME_detection_mat_files.zip. Tu use the toolbox, replace the .mat files from the main zip by the corresponding files within toolbox_IME_detection_mat_files.zip.

Reproduction pipeline and necessary data for Sections 7.3 and 3.4 of Bacon et al., (2017) and Inami et al., (2017) respectively (papers I and II of the series of papers on "The MUSE Hubble Ultra Deep Field Survey", published in Astronomy & Astrophysics, 608, A1 and A2). This pipeline will estimate the Hubble Space Telescope (HST) segmentation maps (for paper 1) and make the necessary measurements (for paper 2) for objects that were detected in the MUSE 3D cubes, but didn't correspond to any detection in the Rafelski et al. (2015) catalog. This repository on Zenodo contains all the necessary input data, software and reproduction pipeline (containing the scripts, configuration files and settings to exactly reproduce the results in Sections 7.3 and 3.4 of the papers above). Below is a description of the contents: gnuastro-0.2.51-bc64-bugfix.tar.gz: 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 zenodo.1163746. However, a bug relating to estimation of upper-limit magnitudes was later found. This bug was fixed, but along with many other changes that made the whole Gnuastro package incompatible with this pipeline. Hence, this bug-fixed copy of Gnuastro 0.2.51 was used in the catalog of Inami et al. (2017). The reproduction pipeline below contains the fixed file and instructions on how to make this version from version 0.2.51 that is available in the official Gnuastro version controlled history. The library dependencies of this version of Gnuastro can be downloaded from zenodo.1163746 (gnuastro-dependencies.tar.gz). IMPORTANT NOTE: Since version 0.2.51 of Gnuastro was released, CFITSIO (one of Gnuastro's dependencies) has added a dependency for the cURL library (to read https URLs). Therefore, to install Gnuastro 0.2.51, please install CFITSIO version 3.41 or earlier. hst-uvudf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-UVUDF survey. These images are not necessary to run the reproduction pipeline (they will be downloaded from the HST archives if not present). They are stored here for the self-sufficiency of this repository and faster download: in this lossless compressed format, they are roughly 1/4th the volume of the same files in HST archives. hst-xdf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-XDF survey. These are also available from the HST archives and are kept here with similar reasons to above (with a compression ratio of almost 1/3rd). output-v4-2-gf97e.tar.gz: output of the reproduction pipeline. reproduce-v4-2-gf97e.tar.gz: The reproduction pipeline (version 4-2-gf97e) that produces the results (tables) plotted in the paper. The full Git version controlled history of this repository is available on git-cral.univ-lyon1.fr or gitlab.com. We recommend cloning from the Git repository if it is available. This tarball is kept here in case those servers don't work or Git is no longer in common use. Please see the README file in this repository for instructions on how to run the reproduction pipeline and exactly reproduce the results. This pipeline will download all the necessary data if they aren't already present on the system (it is probably just necessary to install the required version of Gnuastro). The Creative Commons Attribution-NonCommercial 4.0 copyright mentioned in the Zenodo webpage is only applicable to files that don't have an explicit copyright within them. The copyright of other files (mainly scripts and software) is mentioned within them (all are free licenses). For any issues with the pipeline/processing, please contact Mohammad Akhlaghi. {"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"]}

Implementation in C++ of state-of-the-art algorithms for computing the k shortest simple paths from a source to a destination in a weighted directed graph.

autoSSA algorithm which allows an unsupervised usage of the singular spectrum analysis (SSA).