Loading README.md +6 −24 Original line number Diff line number Diff line # AGILE: AGNs In the LSST Era # [](https://lincc-ppt.readthedocs.io/en/latest/) [](https://pypi.org/project/lsst_agile/) Loading @@ -18,35 +18,17 @@ refer to the links below. ## Links - Documentation - User guide - Introduction - Installation - Usage - Notebooks - Using AGILE - Create a truth catalog - Create lightcurves - Simulate images - Analyze simulated images - Using AGILE data products - Analyzing catalogs - Analyzing SEDs - Analyzing lightcurves - Analyzing images - Comparing to DP1 - API reference - Development - AGILE webpage: https://www.oa-roma.inaf.it/lsst-agn/ ## Literature Viitanen+2026, A&A submitted - Viitanen+2026, A&A submitted ## Credits - Akke Viitanen, development lead - Angela Bongiorno, project lead, - Ivano Saccheo, AGN SEDs - Daniel Roberts, MBH module - Vincenzo Petrecca, AGN lightcurve module - Ivano Saccheo, AGN SED module, - Daniel Roberts, MBH module, - Vincenzo Petrecca, AGN lightcurve module, - Giulia De Somma, Cepheid lightcurve module docs/conf.py +11 −1 Original line number Diff line number Diff line Loading @@ -24,7 +24,7 @@ version = ".".join(release.split(".")[:2]) # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration extensions = ["sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.viewcode"] extensions = ["sphinx.ext.autodoc", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.viewcode"] extensions.append("autoapi.extension") extensions.append("nbsphinx") Loading Loading @@ -58,3 +58,13 @@ autoapi_member_order = "bysource" autoapi_keep_files = True html_theme = "sphinx_rtd_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 4, } autoclass_content = "class" autoapi_python_class_content = "class" napoleon_include_init_with_doc = False napoleon_include_special_with_doc = False docs/index.rst +53 −10 Original line number Diff line number Diff line ========================== AGILE: AGN In the LSST Era ========================== .. lsst_inaf_agile documentation main file. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. AGILE is an end-to-end simulation pipeline designed to simulate truth catalogs as well as realistic LSST-like images, and photometric catalogs of AGNs, galaxies, and stars. AGILE is developed by INAF-OAR and in close collaboration with the Rubin-LSST AGN Science Collaboration. AGILE: AGN In the LSST Era documentation =============================================================================== The AGILE software and its first data release are both described in the science publication Viitanen+2026 (A&A submitted). This documentation aims to cover the installation, usage, and how to contribute to the development. The source code of AGILE is hosted in the INAF GitLab: https://www.ict.inaf.it/gitlab/akke.viitanen/inaf_lsst_agile AGILE adheres to the software development guidelines for Rubin-LSST in-kind contributors as detailed in RDO-41: https://docushare.lsst.org/docushare/dsweb/Get/RDO-041 Contact: akke.viitanen@iki.fi AGILE in a nutshell ------------------- AGILE is designed to allow for the characterization and investigation of the AGN population from Rubin-LSST optical/NIR photometric data, including variability. In its essence, AGILE is a forward model of an underlying truth catalog, and the LSST survey. The main features of AGILE are: 1. Simulating an underlying truth catalog of AGNs, galaxies, and stars 2. Simulating optical/near-IR variability of AGNs and stars 3. Simulating synthetic LSST images 4. Analyzing simulated LSST images In addition, AGILE DR1 is the first production-scale simulation using the AGILE pipeline. It consists of a 24deg2 truth catalog centered around the COSMOS field, and simulated images and photometric catalogs of the central 1deg2 for up to three years of LSST operations. Useful resources ---------------- - EGG: https://cschreib.github.io/egg/ - LSST DP0.2: https://dp0-2.lsst.io/ - LSST DP1: https://dp1.lsst.io/ - Opsim runs: https://usdf-maf.slac.stanford.edu/ - Key numbers: https://rubinobservatory.org/for-scientists/rubin-101/key-numbers - DESC imSim: https://lsstdesc.org/imSim/ - LSST Science Pipelines: https://pipelines.lsst.io/ .. toctree:: :maxdepth: 2 :hidden: Introduction <self> Installation <installation/index> User guide <userguide/index> Notebooks <notebooks> API reference <autoapi/index> self install userguide notebooks autoapi docs/install.rst 0 → 100644 +99 −0 Original line number Diff line number Diff line Install ======= Due to the modular nature, installation of AGILE is done in a few distinct steps that are detailed here. An installation script is provided, which could very well work on a typical UNIX-based system. The install script is located in ``install.sh`` (see below). The script attempts to simply automatize the steps that are detailed here. It is recommended to read through the following sections in order to gain an understanding of what is being installed and why. Installing the AGILE repository ------------------------------- The main AGILE repository contains the actual pipeline as well as necessary data files for running the software. First, enter a directory to install AGILE in e.g. ``/home/user/lsst_inaf_agile``. :: cd /home/user git clone https://www.ict.inaf.it/gitlab/akke.viitanen/lsst_inaf_agile.git cd /home/user/lsst_inaf_agile Then, a virtual environment is created by using the python module ``venv`` :: python -m venv ./venv Finally, this environment is activate by using :: . venv/bin/activate pip install -e . The virtual environment should be activated each time a new terminal session is activated. Installing EGG -------------- AGILE uses ``EGG`` (Empirical Galaxy Generator) for the creation of the truth galaxy catalog. In addition, EGG requires the ``vif`` library to be installed. The installation of both of these components is described in the ``EGG`` documentation https://cschreib.github.io/egg/files/EGG.pdf The only AGILE consideration is that we recommend to install ``EGG`` and ``vif`` under ``opt/`` e.g. to use the following paths: :: lsst_inaf_agile/opt/egg lsst_inaf_agile/opt/vif Note that AGILE uses a custom stellar mass function for ``EGG`` based on the COSMOS2020 galaxies. In addition, the filter bandpasses are provided in the EGG format. These are described in the ``EGG`` documentation. The stellar mass function as well as the filter bandpasses are shipped with the AGILE repository and are located in :: data/egg/share Installing imSim ---------------- AGILE uses ``imSim`` (https://lsstdesc.org/imSim/) to simulate synthetic LSST-like images. The installation instructions for ``imSim`` are provided online (https://lsstdesc.org/imSim/install.html). While any of the provided installation methods may work, the ``conda`` method has been tried and tested by the AGILE team. The details are provided here: https://lsstdesc.org/imSim/install.html#method-2-conda-and-the-stackvana-package Installing the LSST Science Pipelines ------------------------------------- AGILE uses the LSST Science Pipelines (https://pipelines.lsst.io/) to both reduce and analyze the simulated images. The installation of the LSST Science Pipelines is described here: https://pipelines.lsst.io/#installation. The ``lsstinstall`` method has been tried and tested. To use the LSST Science Pipelines with AGILE, an additional set of calibration-level data should be downloaded. Instructions on downloading these ``repo_assets`` follow: :: # Create repo_assets directory mkdir /home/user/lsst_inaf_agile/opt/repo_assets # Extract the files from https://portal.nersc.gov/cfs/descssim/imSim/repo_assets/ # to the created directory # Point REPO_ASSET_DIR environment variable to the location export REPO_ASSET_DIR=/home/user/lsst_inaf_agile/opt/repo_assets docs/installation/index.rstdeleted 100644 → 0 +0 −2 Original line number Diff line number Diff line Installation ============ Loading
README.md +6 −24 Original line number Diff line number Diff line # AGILE: AGNs In the LSST Era # [](https://lincc-ppt.readthedocs.io/en/latest/) [](https://pypi.org/project/lsst_agile/) Loading @@ -18,35 +18,17 @@ refer to the links below. ## Links - Documentation - User guide - Introduction - Installation - Usage - Notebooks - Using AGILE - Create a truth catalog - Create lightcurves - Simulate images - Analyze simulated images - Using AGILE data products - Analyzing catalogs - Analyzing SEDs - Analyzing lightcurves - Analyzing images - Comparing to DP1 - API reference - Development - AGILE webpage: https://www.oa-roma.inaf.it/lsst-agn/ ## Literature Viitanen+2026, A&A submitted - Viitanen+2026, A&A submitted ## Credits - Akke Viitanen, development lead - Angela Bongiorno, project lead, - Ivano Saccheo, AGN SEDs - Daniel Roberts, MBH module - Vincenzo Petrecca, AGN lightcurve module - Ivano Saccheo, AGN SED module, - Daniel Roberts, MBH module, - Vincenzo Petrecca, AGN lightcurve module, - Giulia De Somma, Cepheid lightcurve module
docs/conf.py +11 −1 Original line number Diff line number Diff line Loading @@ -24,7 +24,7 @@ version = ".".join(release.split(".")[:2]) # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration extensions = ["sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.viewcode"] extensions = ["sphinx.ext.autodoc", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.viewcode"] extensions.append("autoapi.extension") extensions.append("nbsphinx") Loading Loading @@ -58,3 +58,13 @@ autoapi_member_order = "bysource" autoapi_keep_files = True html_theme = "sphinx_rtd_theme" html_theme_options = { "collapse_navigation": False, "navigation_depth": 4, } autoclass_content = "class" autoapi_python_class_content = "class" napoleon_include_init_with_doc = False napoleon_include_special_with_doc = False
docs/index.rst +53 −10 Original line number Diff line number Diff line ========================== AGILE: AGN In the LSST Era ========================== .. lsst_inaf_agile documentation main file. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. AGILE is an end-to-end simulation pipeline designed to simulate truth catalogs as well as realistic LSST-like images, and photometric catalogs of AGNs, galaxies, and stars. AGILE is developed by INAF-OAR and in close collaboration with the Rubin-LSST AGN Science Collaboration. AGILE: AGN In the LSST Era documentation =============================================================================== The AGILE software and its first data release are both described in the science publication Viitanen+2026 (A&A submitted). This documentation aims to cover the installation, usage, and how to contribute to the development. The source code of AGILE is hosted in the INAF GitLab: https://www.ict.inaf.it/gitlab/akke.viitanen/inaf_lsst_agile AGILE adheres to the software development guidelines for Rubin-LSST in-kind contributors as detailed in RDO-41: https://docushare.lsst.org/docushare/dsweb/Get/RDO-041 Contact: akke.viitanen@iki.fi AGILE in a nutshell ------------------- AGILE is designed to allow for the characterization and investigation of the AGN population from Rubin-LSST optical/NIR photometric data, including variability. In its essence, AGILE is a forward model of an underlying truth catalog, and the LSST survey. The main features of AGILE are: 1. Simulating an underlying truth catalog of AGNs, galaxies, and stars 2. Simulating optical/near-IR variability of AGNs and stars 3. Simulating synthetic LSST images 4. Analyzing simulated LSST images In addition, AGILE DR1 is the first production-scale simulation using the AGILE pipeline. It consists of a 24deg2 truth catalog centered around the COSMOS field, and simulated images and photometric catalogs of the central 1deg2 for up to three years of LSST operations. Useful resources ---------------- - EGG: https://cschreib.github.io/egg/ - LSST DP0.2: https://dp0-2.lsst.io/ - LSST DP1: https://dp1.lsst.io/ - Opsim runs: https://usdf-maf.slac.stanford.edu/ - Key numbers: https://rubinobservatory.org/for-scientists/rubin-101/key-numbers - DESC imSim: https://lsstdesc.org/imSim/ - LSST Science Pipelines: https://pipelines.lsst.io/ .. toctree:: :maxdepth: 2 :hidden: Introduction <self> Installation <installation/index> User guide <userguide/index> Notebooks <notebooks> API reference <autoapi/index> self install userguide notebooks autoapi
docs/install.rst 0 → 100644 +99 −0 Original line number Diff line number Diff line Install ======= Due to the modular nature, installation of AGILE is done in a few distinct steps that are detailed here. An installation script is provided, which could very well work on a typical UNIX-based system. The install script is located in ``install.sh`` (see below). The script attempts to simply automatize the steps that are detailed here. It is recommended to read through the following sections in order to gain an understanding of what is being installed and why. Installing the AGILE repository ------------------------------- The main AGILE repository contains the actual pipeline as well as necessary data files for running the software. First, enter a directory to install AGILE in e.g. ``/home/user/lsst_inaf_agile``. :: cd /home/user git clone https://www.ict.inaf.it/gitlab/akke.viitanen/lsst_inaf_agile.git cd /home/user/lsst_inaf_agile Then, a virtual environment is created by using the python module ``venv`` :: python -m venv ./venv Finally, this environment is activate by using :: . venv/bin/activate pip install -e . The virtual environment should be activated each time a new terminal session is activated. Installing EGG -------------- AGILE uses ``EGG`` (Empirical Galaxy Generator) for the creation of the truth galaxy catalog. In addition, EGG requires the ``vif`` library to be installed. The installation of both of these components is described in the ``EGG`` documentation https://cschreib.github.io/egg/files/EGG.pdf The only AGILE consideration is that we recommend to install ``EGG`` and ``vif`` under ``opt/`` e.g. to use the following paths: :: lsst_inaf_agile/opt/egg lsst_inaf_agile/opt/vif Note that AGILE uses a custom stellar mass function for ``EGG`` based on the COSMOS2020 galaxies. In addition, the filter bandpasses are provided in the EGG format. These are described in the ``EGG`` documentation. The stellar mass function as well as the filter bandpasses are shipped with the AGILE repository and are located in :: data/egg/share Installing imSim ---------------- AGILE uses ``imSim`` (https://lsstdesc.org/imSim/) to simulate synthetic LSST-like images. The installation instructions for ``imSim`` are provided online (https://lsstdesc.org/imSim/install.html). While any of the provided installation methods may work, the ``conda`` method has been tried and tested by the AGILE team. The details are provided here: https://lsstdesc.org/imSim/install.html#method-2-conda-and-the-stackvana-package Installing the LSST Science Pipelines ------------------------------------- AGILE uses the LSST Science Pipelines (https://pipelines.lsst.io/) to both reduce and analyze the simulated images. The installation of the LSST Science Pipelines is described here: https://pipelines.lsst.io/#installation. The ``lsstinstall`` method has been tried and tested. To use the LSST Science Pipelines with AGILE, an additional set of calibration-level data should be downloaded. Instructions on downloading these ``repo_assets`` follow: :: # Create repo_assets directory mkdir /home/user/lsst_inaf_agile/opt/repo_assets # Extract the files from https://portal.nersc.gov/cfs/descssim/imSim/repo_assets/ # to the created directory # Point REPO_ASSET_DIR environment variable to the location export REPO_ASSET_DIR=/home/user/lsst_inaf_agile/opt/repo_assets
docs/installation/index.rstdeleted 100644 → 0 +0 −2 Original line number Diff line number Diff line Installation ============
