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These catalogs may be used as inputs to image simulation (originally +only for the Rubin Observatory; since also used in simulations for the +Roman Observatory) and as truth catalogs. + +This documentation covers installation and usage instructions for the package. + +The source code of *skyCatalogs* is hosted at +https://github.com/LSSTDESC/skyCatalogs. + + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + installation + usage_read + usage_create + ops-rehearsals-3-4/galaxies + ops-rehearsals-3-4/UW_stars + ops-rehearsals-3-4/SSO + roman-rubin-1.1.2/diffsky_galaxy + roman-rubin-1.1.2/UW_stars + roman-rubin-1.1.2/snana + +.. toctree:: + :maxdepth: 2 + :caption: Reference: + :hidden: + + reference_python + +.. toctree:: + :maxdepth: 2 + :caption: Contact: + :hidden: + + contact + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt new file mode 100644 index 0000000..25f74f4 --- /dev/null +++ b/_sources/installation.rst.txt @@ -0,0 +1,107 @@ +Installation Instructions +========================= + +.. note:: + + **Prerequisites**: + + To use **skyCatalogs 1.7.x** + + all that is required is a reasonably current version of the `LSST science pipelines `_ . See installation instructions below. + +.. note:: + + **Use with imSim**: + + If you intend to use skyCatalogs with imSim, you should follow the `imSim installation instructions `_ . In that case, you need proceed no further with the instructions here; you're all set. The remainder of these notes is largely extracted from the imSim instructions, omitting anything not required for skyCatalogs. + +Installing LSST science pipelines +--------------------------------- + +There are several methods of installation. Only the simplest (using a prebuilt cvmfs version) is described here. For other methods, see the imSim installation instructions. + +If you are working at the USDF (Rubin Project computing) or at NERSC (DESC computing), perhaps the easiest way to setup and use *skyCatalogs* is to rely on the prebuilt versions of the pipelines contained in the cvmfs distribution which is installed there. This solution is also appropriate for personal laptops and university/lab based computing systems if you are able to install the *cvmfs* system. + +The `CernVM file system `_ (cvmfs) is a distributed read-only file system developed at CERN for reliable low-maintenance world-wide software distribution. LSST-France distributes weekly builds of the Rubin science pipelines for both Linux and MacOS. Details and installation instructions can be found at `sw.lsst.eu `_ . The distribution includes conda and skyCatalogs dependencies from conda-forge along with the science pipelines. + +Load and setup the science pipelines +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +First you need to setup the science pipelines. This involves sourcing a setup file and then using the Rubin *eups* commands to set them up. + +.. note:: + + Version ``w_2024_20`` or later of the science pipelines is recommended. This will guarantee other dependencies of skyCatalogs, such as GalSim, are new enough. + + Also note: the cvmfs distribution is a read-only distribution. This means you cannot add packages to the included conda environment and packages you install via *pip* will be installed in the user area. If you need a *conda* environment you will need to use a different installation method. + +Source the appropriate setup script (note the -ext in the name) and then setup the distribution (if you are on MacOS use darwin-x86_64 instead of linux-x86_64). + +.. code-block:: sh + + source /cvmfs/sw.lsst.eu/linux-x86_64/lsst_distrib/w_2024_20/loadLSST-ext.bash + setup lsst_distrib + + +Install needed data files +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Now go to where you would like to install *skyCatalogs* and download some needed data files (you will only need to do this once). + +.. code-block:: sh + + mkdir -p rubin_sim_data/sims_sed_library + curl https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/rubin_sim_data/throughputs_2023_09_07.tgz | tar -C rubin_sim_data -xz + curl https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/sed_library/seds_170124.tar.gz | tar -C rubin_sim_data/sims_sed_library -xz + +Set up skyCatalogs itself +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Clone the skyCatalogs package from GitHub: + +.. code-block:: sh + + git clone https://github.com/LSSTDESC/skyCatalogs + +at this point if you would only like to use *skyCatalogs* you can ``pip install skyCatalog/`` however we instead suggest using the *eups* tool to simply setup the package for use without installing it. This will allow you to edit the package in place, use multiple versions, change branches etc. You should definitely do this if you plan to do any *skyCatalogs* development. + +If you do not intend to do any development you may choose instead to clone the most recent release tag. As of Oct., 2024 this is 1.7.0rc4 + +.. code-block:: sh + + git clone https://github.com/LSSTDESC/skyCatalogs.git --branch 1.7.0rc4 + + +Setup and Use *skyCatalogs* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +This setup step should be repeated for each new session. Here is a ``skycatalogs-setup.sh`` file you can use before each session + +.. code-block:: sh + + source /cvmfs/... # as above + setup lsst_distrib + + export SKYCATALOGS_HOME=*PUT YOUR INSTALL DIRECTORY HERE* + export RUBIN_SIM_DATA_DIR=$SKYCATALOGS_HOME/rubin_sim_data + export SIMS_SED_LIBRARY_DIR=$SKYCATALOGS_HOME/rubin_sim_data/sims_sed_library + + setup -k -r $SKYCATALOGS_HOME/skyCatalogs + +You should now be able to import the code you need from the skyCatalogs package, e.g. + +.. code-block:: python + + from skycatalogs.skyCatalogs import open_catalog + from skycatalogs.utils.shapes import Disk + + skycatalog_root = "path_to/skycatalog_files" # folder containing catalog + config_file = "some_folder/skyCatalog.yaml" + + cat = open_catalog(config_file, skycatalog_root=skycatalog_root) + + # define disk at ra, dec = 45.0, -9.0 of radius 100 arcseconds + disk = disk(45.0, -9.0, 100.0) + + # get galaxies and stars in the region + objects = cat.get_objects_by_region(disk, obj_type_set={'galaxy', 'star'}) diff --git a/_sources/ops-rehearsals-3-4/SSO.rst.txt b/_sources/ops-rehearsals-3-4/SSO.rst.txt new file mode 100644 index 0000000..fbc8246 --- /dev/null +++ b/_sources/ops-rehearsals-3-4/SSO.rst.txt @@ -0,0 +1,39 @@ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +Solar System Object (SSO) quantities for ops-rehearsals 3 and 4 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" and a flux file. The latter contains +for each object only fluxes for lsst bands, the object id and the time (mjd) +of the observation. The latter two fields may be used to join with the +main file. + +SSO main file +------------- + +======================== ============ ============== =========================== +Name Datatype Units Description +======================== ============ ============== =========================== +id string N/A Unique object identifier +mjd double days Time of observation +ra double degrees Object right ascension +dec double degrees Object declination +trailed_source_mag double N/A Mag. normalization for SED +ra_rate double deg/day RA rate of change * cos(dec) +dec_rate double deg/day Declination rate of change +======================== ============ ============== =========================== + +SSO flux file +---------------- + +============= ========= ================ ================================ +Name Datatype Units Description +============= ========= ================ ================================ +id string N/A Unique object identifier +mjd double days Time of observation (Julian date) +lsst_flux_u float photons/sec/cm^2 Flux integrated over lsst u-band +lsst_flux_g float photons/sec/cm^2 Flux integrated over lsst g-band +lsst_flux_r float photons/sec/cm^2 Flux integrated over lsst r-band +lsst_flux_i float photons/sec/cm^2 Flux integrated over lsst i-band +lsst_flux_z float photons/sec/cm^2 Flux integrated over lsst z-band +lsst_flux_y float photons/sec/cm^2 Flux integrated over lsst y-band +============= ========= ================ ================================ diff --git a/_sources/ops-rehearsals-3-4/UW_stars.rst.txt b/_sources/ops-rehearsals-3-4/UW_stars.rst.txt new file mode 100644 index 0000000..c1c64bf --- /dev/null +++ b/_sources/ops-rehearsals-3-4/UW_stars.rst.txt @@ -0,0 +1,59 @@ +++++++++++++++++++++++++++++++++++++++++++ +Star quantities for ops-rehearsals 3 and 4 +++++++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" (with information largely coming from the +UW star catalog) and a flux file. The latter contains for each object only +fluxes for lsst bands and the object id so it can be joined with the main +file. Both are parquet files. + +Star main file +---------------- +Note the same schema may be used for SNe. Some fields are unused for stars. + +======================== ============ ========== ========================= +Name Datatype Units Description +======================== ============ ========== ========================= +object_type string N/A In practice always 'star' +id string N/A Unique object identifier +ra double degrees Object right ascension +dec double degrees Object declination +host_galaxy_id int64 N/A Unused for stars +magnorm double N/A To be applied to SED +sed_filepath string N/A Path to object's SED file + relative to env variable + SIMS_SED_LIBRARY_DIR +MW_rv float N/A Extinction parameter +MW_av float N/A Extinction parameter + from F19 dust map +mura double milarcsec RA proper motion + per year +mudec double milarcsec Declin. proper motion + per year +radial_velocity double km/sec Radial velocity +parallax double milarcsec Parallax +variability_model string N/A Unused for stars +salt2_params int32 N/A Unused for stars +is_variable boolean N/A If true, the star has + sinusoidal variability + in magnitude +period double days period of variability +mag_amplitude double N/A amplitude of magnitude + variability +phase double radians phase of variability +======================== ============ ========== ========================= + +Star flux file +---------------- + +============= ========= ================ ================================ +Name Datatype Units Description +============= ========= ================ ================================ +id string N/A Unique object identifier +lsst_flux_u float photons/sec/cm^2 Flux integrated over lsst u-band +lsst_flux_g float photons/sec/cm^2 Flux integrated over lsst g-band +lsst_flux_r float photons/sec/cm^2 Flux integrated over lsst r-band +lsst_flux_i float photons/sec/cm^2 Flux integrated over lsst i-band +lsst_flux_z float photons/sec/cm^2 Flux integrated over lsst z-band +lsst_flux_y float photons/sec/cm^2 Flux integrated over lsst y-band +============= ========= ================ ================================ diff --git a/_sources/ops-rehearsals-3-4/galaxies.rst.txt b/_sources/ops-rehearsals-3-4/galaxies.rst.txt new file mode 100644 index 0000000..45a232f --- /dev/null +++ b/_sources/ops-rehearsals-3-4/galaxies.rst.txt @@ -0,0 +1,80 @@ +++++++++++++++++++++++++++++++++++++++++++++ +Galaxy quantities for ops-rehearsals 3 and 4 +++++++++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" (with information largely coming from the +cosmodc2 galaxy catalog) and a flux file. The latter contains +for each object only fluxes for lsst bands and the object id so it can be +joined with the main file. Both are parquet files. The main file can be +rather large (over 3 Gbytes) so, depending on your application, you may +want to iterate over row groups rather than reading it all in at once. + +Galaxy main file +---------------- + +======================== ============ ============== ======================== +Name Datatype Units Description +======================== ============ ============== ======================== +galaxy_id int64 N/A Unique object identifier +ra double degrees Object right ascension +dec double degrees Object declination +redshift double N/A Cosmological redshift + with line-of-sight motion +redshift_hubble double N/A Cosmological redshift +peculiar_velocity double km/sec Peculiar velocity +shear_1 double N/A Shear (gamma) component 1, + treecorr/Galsim convention +shear_2 double N/A Shear (gamma) component 2, + treecorr/Galsim convention +convergence double N/A Convergence (kappa) +size_bulge_true float arcsec Bulge half-light radius + (major axis) not lensed +size_minor_bulge_true float arcsec Bulge half-light radius + (minor axis) not lensed +sersic_bulge float N/A Sersic index of bulge + light profile +size_disk_true float arcsec Disk half-light radius + (major axis) not lensed +size_disk_bulge_true float arcsec Disk half-light radius + (minor axis) not lensed +sersic_disk float N/A Sersic index of disk + light profile +ellipticity_1_disk_true double N/A Ellipticity component 1 + for disk, not lensed +ellipticity_2_disk_true double N/A Ellipticity component 2 + for disk, not lensed +ellipticity_1_bulge_true double N/A Ellipticity component 1 + for bulge, not lensed +ellipticity_2_bulge_true double N/A Ellipticity component 2 + for bulge, not lensed +sed_val_bulge list(double) 4.4659e13 W/Hz Integrated rest-frame AB + luminosities for tophat + filters (bulge component) +sed_val_disk list(double) 4.4659e13 W/Hz Like sed_val_bulge +bulge_magnorm double N/A Normalization for SED +disk_magnorm double N/A Normalization for SED +MW_rv float N/A Extinction parameter +MW_av float N/A Extinction parameter + from F19 dust map +sed_val_knots list(double) 4.4659e13 W/Hz Like sed_val_bulge +n_knots float N/A Number of knots +knots_magnorm double N/A Normalization for SED +======================== ============ ============== ======================== + +NOTE: For tophat definitions (start and width in units of angstroms) see yaml +config file associated with the data. + +Galaxy flux file +---------------- + +============= ========= ================ ================================ +Name Datatype Units Description +============= ========= ================ ================================ +galaxy_id int64 N/A Unique object identifier +lsst_flux_u float photons/sec/cm^2 Flux integrated over lsst u-band +lsst_flux_g float photons/sec/cm^2 Flux integrated over lsst g-band +lsst_flux_r float photons/sec/cm^2 Flux integrated over lsst r-band +lsst_flux_i float photons/sec/cm^2 Flux integrated over lsst i-band +lsst_flux_z float photons/sec/cm^2 Flux integrated over lsst z-band +lsst_flux_y float photons/sec/cm^2 Flux integrated over lsst y-band +============= ========= ================ ================================ diff --git a/_sources/reference_python.rst.txt b/_sources/reference_python.rst.txt new file mode 100644 index 0000000..934a858 --- /dev/null +++ b/_sources/reference_python.rst.txt @@ -0,0 +1,57 @@ +=========================== +The ``skyCatalogs`` package +=========================== + +Reference documentation for core objects with the ``skyCatalogs`` package + +.. _skyCatalog_class: + +The skyCatalog class +===================== + +The ``skyCatalog`` class represents a catalog. Users gain access +to a catalog by calling its static method ``open_catalog``. + +.. autoclass:: skycatalogs.skyCatalogs.SkyCatalog + :members: + + .. automethod:: skycatalogs.skyCatalogs.open_catalog + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_objects_by_region + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_object_type_by_region + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_object_type_names + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_object_type_by_hp + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_hps_by_region + +.. + .. automethod:: skycatalogs.skyCatalogs.SkyCatalog.get_hps_by_type + +.. _baseobject_class: + +There are several classes (one per supported object type) representing +individual objects as observed at a particular time, all subclassing +``BaseObject``. + +.. autoclass:: skycatalogs.objects.base_object.BaseObject + :members: + + .. automethod:: skycatalogs.objects.base_object.BaseObject.id + .. automethod:: skycatalogs.objects.base_object.BaseObject.ra + .. automethod:: skycatalogs.objects.base_object.BaseObject.dec + .. automethod:: skycatalogs.objects.base_object.BaseObject.object_type + .. automethod:: skycatalogs.objects.base_object.BaseObject.get_native_attribute + .. automethod:: skycatalogs.objects.base_object.get_gsobject_components + .. automethod:: skycatalogs.objects.base_object.get_observer_sed_component + .. automethod:: skycatalogs.objects.base_object.get_observer_sed_components + .. automethod:: skycatalogs.objects.base_object.get_total_observer_sed + .. automethod:: skycatalogs.objects.base_object.get_flux + .. automethod:: skycatalogs.objects.base_object.get_LSST_flux + .. automethod:: skycatalogs.objects.base_object.get_LSST_fluxes + .. automethod:: skycatalogs.objects.base_object.get_roman_flux + .. automethod:: skycatalogs.objects.base_object.get_roman_fluxes + +.. _objectlist_class: + +The ``ObjectList`` class is a container for instances of ``BaseObject``. +It subclasses ``Sequence``. + +.. autoclass:: skycatalogs.objects.base_object.ObjectList diff --git a/_sources/roman-rubin-1.1.2/UW_stars.rst.txt b/_sources/roman-rubin-1.1.2/UW_stars.rst.txt new file mode 100644 index 0000000..a0ddc6f --- /dev/null +++ b/_sources/roman-rubin-1.1.2/UW_stars.rst.txt @@ -0,0 +1,52 @@ ++++++++++++++++++++++++++++++++++++++ +Star quantities for Roman-Rubin sims ++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" (with information largely coming from the +UW star catalog) and a flux file. The latter contains for each object only +fluxes for lsst bands and the object id so it can be joined with the main +file. Both are parquet files. + +Star main file +---------------- +Note the same schema may be used for SNe. Some fields are unused for stars. + +======================== ============ ========== ========================= +Name Datatype Units Description +======================== ============ ========== ========================= +object_type string N/A In practice always 'star' +id string N/A Unique object identifier +ra double degrees Object right ascension +dec double degrees Object declination +host_galaxy_id int64 N/A Unused for stars +magnorm double N/A To be applied to SED +sed_filepath string N/A Path to object's SED file + relative to env variable + SIMS_SED_LIBRARY_DIR +MW_rv float N/A Extinction parameter +MW_av float N/A Extinction parameter + from F19 dust map +mura double milarcsec RA proper motion + per year +mudec double milarcsec Declin. proper motion + per year +radial_velocity double km/sec Radial velocity +parallax double milarcsec Parallax +variability_model string N/A Unused for stars +salt2_params struct N/A Unused for stars +======================== ============ ========== ========================= + +Star flux file +---------------- + +============= ========= ================ ================================ +Name Datatype Units Description +============= ========= ================ ================================ +id string N/A Unique object identifier +lsst_flux_u float photons/sec/cm^2 Flux integrated over lsst u-band +lsst_flux_g float photons/sec/cm^2 Flux integrated over lsst g-band +lsst_flux_r float photons/sec/cm^2 Flux integrated over lsst r-band +lsst_flux_i float photons/sec/cm^2 Flux integrated over lsst i-band +lsst_flux_z float photons/sec/cm^2 Flux integrated over lsst z-band +lsst_flux_y float photons/sec/cm^2 Flux integrated over lsst y-band +============= ========= ================ ================================ diff --git a/_sources/roman-rubin-1.1.2/diffsky_galaxy.rst.txt b/_sources/roman-rubin-1.1.2/diffsky_galaxy.rst.txt new file mode 100644 index 0000000..b4ad853 --- /dev/null +++ b/_sources/roman-rubin-1.1.2/diffsky_galaxy.rst.txt @@ -0,0 +1,82 @@ +++++++++++++++++++++++++++++++++++++++++++++++++++ +Galaxy quantities for Roman-Rubin joint simulation +++++++++++++++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" (with information largely coming from the +diffsky galaxy catalog), a flux file and a SED file. The flux file contains for +each object only fluxes for lsst and Roman bands and the object id so it can be +joined with the main file. Both it and the main file are parquet files. The +SED file is in hdf5 format. The file names take the form galaxy_.parquet +(main file), galaxy_flux_.parquet (flux file) and galaxy_sed_.hdf5 for +SED files. In all cases is the id of the healpixel covered by the file. + +Galaxy main file +---------------- + +============================= ======== ========== ========================== +Name Datatype Units Description +============================= ======== ========== ========================== +galaxy_id int64 N/A Unique object identifier +ra double degrees Object right ascension +dec double degrees Object declination +redshift double N/A Cosmological redshift + with line-of-sight motion +redshiftHubble double N/A Cosmological redshift +peculiarVelocity double km/sec Peculiar velocity +shear1 double N/A Shear (gamma) component 1, + treecorr/Galsim convention +shear2 double N/A Shear (gamma) component 2, + treecorr/Galsim convention +convergence double N/A Convergence (kappa) +spheroidHalfLightRadiusArcsec float arcsec Bulge component half-light + radius +diskHalfLightRadiusArcsec float arcsec Disk component half-light + radius +diskEllipticity1 double N/A Ellipticity component 1 + for disk, not lensed +diskEllipticity2 double N/A Ellipticity component 2 + for disk, not lensed +spheroidEllipticity1 double N/A Ellipticity component 1 + for bulge, not lensed +spheroidEllipticity2 double N/A Ellipticity component 2 + for bulge, not lensed +um_source_galaxy_obs_sm float solar mass Stellar mass + (h=0.7) +MW_rv float N/A Extinction parameter +MW_av float N/A Extinction parameter + from F19 dust map +============================= ======== ========== ========================== + + + +Galaxy flux file +---------------- + +=============== ======== ================ ==================================== +Name Datatype Units Description +=============== ======== ================ ==================================== +galaxy_id int64 N/A Unique object identifier +lsst_flux_u float photons/sec/cm^2 Flux integrated over lsst u-band +lsst_flux_g float photons/sec/cm^2 Flux integrated over lsst g-band +lsst_flux_r float photons/sec/cm^2 Flux integrated over lsst r-band +lsst_flux_i float photons/sec/cm^2 Flux integrated over lsst i-band +lsst_flux_z float photons/sec/cm^2 Flux integrated over lsst z-band +lsst_flux_y float photons/sec/cm^2 Flux integrated over lsst y-band +roman_flux_W146 float photons/sec/cm^2 Flux integrated over roman W146-band +roman_flux_R062 float photons/sec/cm^2 Flux integrated over roman R062-band +roman_flux_Z087 float photons/sec/cm^2 Flux integrated over roman Z087-band +roman_flux_Y106 float photons/sec/cm^2 Flux integrated over roman Y106-band +roman_flux_J129 float photons/sec/cm^2 Flux integrated over roman J129-band +roman_flux_H158 float photons/sec/cm^2 Flux integrated over roman H158-band +roman_flux_F184 float photons/sec/cm^2 Flux integrated over roman F184-band +roman_flux_K213 float photons/sec/cm^2 Flux integrated over roman K213-band +=============== ======== ================ ==================================== + +Galaxy SED file +--------------- + +This file has two sections. One (**meta**) has an array **wave_list**, shape(312), +of wavelengths (angstroms), which is used for SEDs of all galaxies in the file's healpixel. +The other section, **galaxy**, contains groups of galaxies. Each group has entries +for individual galaxies, keyed by galaxy id. Such an entry is an array, shape(3, 312), +consisting of SEDs for the three galaxy components (disk, bulge, knot). Units are fnu. diff --git a/_sources/roman-rubin-1.1.2/snana.rst.txt b/_sources/roman-rubin-1.1.2/snana.rst.txt new file mode 100644 index 0000000..5b9ce18 --- /dev/null +++ b/_sources/roman-rubin-1.1.2/snana.rst.txt @@ -0,0 +1,77 @@ ++++++++++++++++++++++++++++++++++++++ +SNANA quantities for Roman-Rubin sims ++++++++++++++++++++++++++++++++++++++ +Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called "main file" in parquet format, containing static +quantities associated with each source, and an hdf5 file for quantities +which vary with time or wavelength or both. + + +SNANA main file +---------------- + +======================== ============ ========== ========================== +Name Datatype Units Description +======================== ============ ========== ========================== +id int64 N/A Unique object identifier +ra double degrees Object right ascension +dec double degrees Object declination +host_id int64 N/A Host galaxy +gentype int32 N/A Type of object simulated +model_name string N/A Type name +start_mjd float days Earliest visibility +end_mjd float days Latest visibility +z_CMB float N/A redshift +mw_EBV float N/A MW extinction parameter +mw_extinction_applied boolean N/A Here always False +AV float N/A For host galaxy, randomly + assigned +RV float N/A For host galaxy +v_pec float km/sec Peculiar velocity. Not + yet simulated so zero. +host_ra double degrees Host galaxy RA +host_dec double degrees Host galaxy decl. +host_mag_g float N/A Host mag. in Rubin g-band +host_mag_i float N/A Host mag. in Rubin i-band +host_mag_F float N/A Host mag. in Roman F-band +host_sn_sep float arcsec Separation from host +peak_mjd float days Time of peak flux + (model-dependent) +peak_mag_g float N/A g-band mag. at peak +peak_mag_i float N/A i-band mag. at peak +peak_mag_F float N/A F-band mag. at peak +lens_dmu_applied boolean N/A False (distance modulus + lensing shift not applied) +model_param_names list(string) N/A Model parameter names +model_param_values list(string) N/A Model parameter values +MW_av float N/A MW extinction parameter +MW_rv float N/A MW extinction parameter +======================== ============ ========== ========================== + +SNANA varying quantities +------------------------ + +The top-level keys for each file are the ids for sources in that pixel, the +same as the ids appearing in the parquet file but here stored as strings. +Under each id are the following keys + +============= =============== ================ =============================== +Name Datatype Units Description +============= =============== ================ =============================== +mjd float array days Time axis for flambda +lambda double array angstroms Wavelength axis for flambda +flambda float 2-d array erg/sec/A/cm^2 Flux indexed by (mjd,lambda) +mag_ float array N/A Magnitude for each mjd computed + using 5 angstrom bins. +magcor_ float array N/A Correction to magnitude + computed using flambda +synmag_ float array N/A Magnitude computed from flambda +============= =============== ================ =============================== + +where takes on values u, g, r, i, z, y (Rubin bandpasses) and F, H, J, +K, R, W, Y, Z (for Roman). + +mjd values have uniform spacing of 1 day. lambda values have uniform spacing +of 100 angstroms. + +synmag + magcor = mag diff --git a/_sources/usage_create.rst.txt b/_sources/usage_create.rst.txt new file mode 100644 index 0000000..8fb1973 --- /dev/null +++ b/_sources/usage_create.rst.txt @@ -0,0 +1,147 @@ +Creating New Catalogs +===================== +Catalogs - both the binary data files and yaml config - for some object types +can be created using the script `create_main.py` and +`create_flux.py`. Creation of the main catalog must precede +creation of the flux catalog for the same sky region. +For other object types the data are +created by other means, but it is still necessary to make a suitable +config fragment so that the skyCatalogs API can access the data. + + +The script ``create_main.py`` and its options +--------------------------------------------- +``create_main.py`` has a plethora of options, but few are of interest +for most invocations and even fewer are required. The options determine + +* object type for which files will be created (required) +* region of the sky for which files will be created. +* where the output goes +* inputs (usually defaulted, depending on object type) +* numerous options conditioning exactly how the output is to be created, + most of which are usually defaulted + +One particularly handy option, ``--options-file``, allows you to specify +everything else as key-value pairs in a yaml file. + +Options table ++++++++++++++ +Here is the complete list of options as they appear in an options file. +On the command line, prepend ``--`` and change all underscores to hyphens. + +===================== ========= ============ =============================== +Name Datatype Default Description +===================== ========= ============ =============================== +object_type string Required. One of {star, sso, + cosmodc2_galaxy, diffsky_galaxy} +catalog_dir string "." Location of catalog relative + to skycatalog_root + (see below) +catalog_name string "skyCatalog" Name of top-level yaml config + file +config_path string None where to write config. If + ``None``, same folder as data +dc2 boolean False Use dc2 conventions +galaxy_magnitude_cut float 29.0 Discard galaxies above cut. + Ignored for non-galaxy + object types +nside int 32 nside for healpixels +stride int 1_000_000 Max objects output per row + group +truth string None Default depends on object_type +knots_magnitude_cut float 27.0 Omit knots component from + galaxies with i-mag above cut +log_level string "INFO" Log level +no_knots boolean False Omit knot component +options_file string None Path to file where other + options are set +pixels int list [9556] healpix pixels for which + catalog will be created +skip_done boolean False do not overwrite existing files +skycatalog_root string None Abs. path. See catalog_dir +sso_sed string None Path to file to SED to be + used for all SSOs. Defaults + to `solar_sed_thin.txt`, + included in repo. +star_input_fmt string "sqlite" Format of star truth +===================== ========= ============ =============================== + +The script ``create_flux.py`` and its options +--------------------------------------------- +``create_flux.py`` has most of the same options as ``create_main.py`` +plus a couple new ones. Only ``object_type`` is required but several +others are specified for most invocations. + +Options table ++++++++++++++ +Here is the complete list of options as they appear in an options file. +On the command line, prepend ``--`` and change all underscores to hyphens. + +===================== ========= ============ =============================== +Name Datatype Default Description +===================== ========= ============ =============================== +object_type string Required. One of {star, sso, + cosmodc2_galaxy, diffsky_galaxy} +catalog_dir string "." Location of catalog relative + to skycatalog_root + (see below) +catalog_name string "skyCatalog" Name of top-level yaml config + file +config_path string None where to write config. If + ``None``, same folder as data +flux_parallel int 16 # processes to run in parallel + when computing fluxes +iclude_roman_flux boolean False If True calculate & store Roman + as well as Rubin fluxes. +log_level string "INFO" Log level +options_file string None Path to file where other + options are set +pixels int list [9556] healpix pixels for which + catalog will be created +skip_done boolean False do not overwrite existing files +skycatalog_root string None Abs. path. See catalog_dir +sso_sed string None Path to file to SED to be + used for all SSOs. Defaults + to `solar_sed_thin.txt`, + included in repo. +===================== ========= ============ =============================== + + +Example options files ++++++++++++++++++++++ +Create cosmodc2-style galaxies main file. This file was one I wrote +primarily for testing the creation code. In order to speed things up, I +set ``galaxy_magnitude_cut`` down to 20.0. The output file is about 1000 times +smaller than with the default cut. + +.. code-block:: yaml + + object_type: cosmodc2_galaxy + catalog_dir: just_testing + pixels: [9683] + galaxy_magnitude_cut: 20.0 # Default is 29.0 + log_level: DEBUG # Default is INFO + +Suppose the file is called `main_galaxy.yaml`. It can be invoked as follows: + +.. code-block:: sh + + python cosmodc2_galaxy --options-file main_galaxy.yaml + +.. note:: + Since ``object_type`` is required it must be specified both on the + command line and in the options file. + +Create star flux file for a couple healpixels. +The default value of ``flux_parallel`` is rather conservative for Perlmutter, +so use something higher to make the process go faster. + +.. code-block:: yaml + + catalog_dir: just_testing + pixels: [9683, 9684] + flux_parallel: 24 # Default is 16 + +.. note:: + The star main files for both healpixels must already exist in the output + directory since they are input to the flux generation. diff --git a/_sources/usage_read.rst.txt b/_sources/usage_read.rst.txt new file mode 100644 index 0000000..797d10a --- /dev/null +++ b/_sources/usage_read.rst.txt @@ -0,0 +1,196 @@ +Reading Catalogs with skyCatalogs +================================= +Typically making use of skyCatalogs involves three steps: + +1. "Open" the catalog. This is accomplished by reading a *config*: one or more + yaml files which describes features of the catalog. Config files will + be described in detail below. +2. Select objects of specified types (e.g. galaxies or stars or both) within + a region of the sky. +3. Obtain properties of the objects for use by your application. + +The last two steps are often executed multiple times. + +Opening a Catalog +----------------- +You open a catalog like this: + +.. code-block:: python + + from skycatalogs.skyCatalogs import open_catalog + + skycatalog_root = "some_path/data_folder" + config_file = "another_path/skyCatalog.yaml" + + cat = open_catalog(config_file, skycatalog_root=skycatalog_root) + +Often the config file is in the same folder as the data but it need not be. + +If ``skycatalog_root`` is not specified, the code will use the value of the +environment variable ``SKYCATALOG_ROOT`` if it exists, + +Structure of skyCatalogs Configs +================================ +Configs contain a variety of information. Some of it is required for the +skyCatalogs API to find and make sense of the binary data. Other quantities +are primarily for human consumption. An up-to-date config (version 1.3.0 +or later) is a mapping with only a few keys, currently ``skycatalog_root``, +``catalog_dir``, ``catalog_name``, ``schema_version`` and ``object_types``. The +first three are used to find the data. ``schema_version`` refers to the +version of the config structure. The value of ``object_types`` +is a mapping with a key for each object type having data in the catalog. +The bulk of the information may be found +under those keys. That information may be included literally in the +config file but it is preferable to isolate information pertaining to each +object type in its own yaml file and use the yaml **!include** +directive to incorporate it. + +Using !include +-------------- + +.. code-block:: yaml + + catalog_dir: . # See Note 1. + catalog_name: skyCatalog # default name for top-level yaml file + object_types: + galaxy: !include galaxy.yaml # See Note 2. + star: !include |- # The |- indicates continue to next line + star.yaml # & may appear in auto-generated top files + skycatalog_root: /some/path/often/absolute # see Note 3. + schema_version: 1.3.0 + +.. note:: + #. ``catalog_dir`` indicates where yaml and data files are to be found + relative to skycatalog_root. See also Note 3. + #. The **!include** directive is not supported by yaml natively, but one can + add an implementation. This has been done for the skyCatalogs API. + #. When the top-level yaml file is written, ``skycatalog_root`` is normally + an absolute path. That file is in the ``catalog_dir`` subdirectory of + ``skycatalog_root``. But, in case the catalog has been copied, + ``skycatalog_root`` may be overridden at run time when invoking + ``open_catalog``. ``catalog_dir`` is then interpreted to be relative to + the new value of ``skycatalog_root``. + +Description of an object type +----------------------------- +For the most part the configuration file fragment for an object type will +either be written by the code generating the binary data for that object +type or will be provided some other way by whoever provides the data. It +is not normally something users of the skyCatalogs API need be concerned with. +However, for those who are curious, such fragments usually include several +kinds of information: + +* information allowing the API to find the data files for the object type +* provenance, which in turn may consist of some or all of the following: + + * inputs used in the creation of the data files + + * run options supplied to the creating program + + * schema version + + * version of the program and information about the state of the git repo containing the program source + +* other information associated with the object type + + +Here is an example file for the ``star`` object type: + +.. code-block:: yaml + + area_partition: + nside: 32 + ordering: ring + type: healpix + data_file_type: parquet + file_template: pointsource_(?P\d+).parquet + flux_file_template: pointsource_flux_(?P\d+).parquet + provenance: + inputs: + star_truth: /global/cfs/cdirs/lsst/groups/SSim/DC2/dc2_stellar_healpixel.db + run_options: + catalog_dir: out_config + catalog_name: skyCatalog + config_path: null + dc2: false + flux_parallel: 16 + galaxy_magnitude_cut: 29.0 + galaxy_nside: 32 + galaxy_stride: 1000000 + galaxy_truth: null + galaxy_type: cosmodc2 + include_roman_flux: false + knots_magnitude_cut: 27.0 + log_level: DEBUG + no_flux: true + no_galaxies: true + no_knots: false + no_main: false + no_pointsources: false + options_file: local/out_config/star_main.yaml + pixels: + - 9556 + sed_subdir: galaxyTopHatSED + skip_done: true + skycatalog_root: null + sso: false + sso_sed: null + sso_truth: null + star_input_fmt: sqlite + skyCatalogs_repo: + git_branch: u/jrbogart/config_reorg + git_hash: 6da4f9636cc63010480c1a1c086cbde8f6ca4dd4 + git_status: + - UNCOMMITTED_FILES + - UNTRACKED_FILES + versioning: + code_version: 1.7.0-rc4 + schema_version: 1.3.0 + sed_file_root_env_var: SIMS_SED_LIBRARY_DIR + sed_model: file_nm + file_nm: + units: nm + internal_extinction: None + +Adding Supported Object Types to a Catalog +========================================== +We expect most users will use pre-assembled catalogs, already containing +all the kinds of objects they need, but it's possible someone will have to +add a new type to a collection. Assuming the data files and a suitable +config fragment for the new type exist somewhere else, one only needs to +copy them to the catalog directory, then edit the top-level config file +by adding a line to the ``object_types`` section: + +.. code-block:: yaml + + object_types: + galaxy: !include galaxy.yaml + star: !include star.yaml + sso: !include sso.yaml # the new one + +Of course the skyCatalogs API has to know how to handle the new type. + +Supported object types +---------------------- +As of August, 2024, the following object types are supported. + +.. glossary:: + + star + as in the DC2 simulation, generated from the UW database + + galaxy + as in the DC2 simulation, generated from the cosmodc2 catalog + + diffsky_galaxy + galaxies simulated from simple stellar populations + + snana + SNe generated by the SNANA simulation program, using either + galaxy or diffsky_galaxy objects as hosts + + sso + solar system objects generated by Sorcha + + gaia_star + Gaia catalog dr2 diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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+ document.dispatchEvent(event); + }); +}); \ No newline at end of file diff --git a/_static/language_data.js b/_static/language_data.js new file mode 100644 index 0000000..c7fe6c6 --- /dev/null +++ b/_static/language_data.js @@ -0,0 +1,192 @@ +/* + * This script contains the language-specific data used by searchtools.js, + * namely the list of stopwords, stemmer, scorer and splitter. + */ + +var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; + + +/* Non-minified version is copied as a separate JS file, if available */ + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; 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+ +/** + * Simple result scoring code. + */ +if (typeof Scorer === "undefined") { + var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [docname, title, anchor, descr, score, filename] + // and returns the new score. + /* + score: result => { + const [docname, title, anchor, descr, score, filename, kind] = result + return score + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: { + 0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5, // used to be unimportantResults + }, + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + partialTitle: 7, + // query found in terms + term: 5, + partialTerm: 2, + }; +} + +// Global search result kind enum, used by themes to style search results. +class SearchResultKind { + static get index() { return "index"; } + static get object() { return "object"; } + static get text() { return "text"; } + static get title() { return "title"; } +} + +const _removeChildren = (element) => { + while (element && element.lastChild) element.removeChild(element.lastChild); +}; + +/** + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping + */ +const _escapeRegExp = (string) => + string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string + +const _displayItem = (item, searchTerms, highlightTerms) => { + const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; + const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; + const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; + const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; + const contentRoot = document.documentElement.dataset.content_root; + + const [docName, title, anchor, descr, score, _filename, kind] = item; + + let listItem = document.createElement("li"); + // Add a class representing the item's type: + // can be used by a theme's CSS selector for styling + // See SearchResultKind for the class names. + listItem.classList.add(`kind-${kind}`); + let requestUrl; + let linkUrl; + if (docBuilder === "dirhtml") { + // dirhtml builder + let dirname = docName + "/"; + if (dirname.match(/\/index\/$/)) + dirname = dirname.substring(0, dirname.length - 6); + else if (dirname === "index/") dirname = ""; + requestUrl = contentRoot + dirname; + linkUrl = requestUrl; + } else { + // normal html builders + requestUrl = contentRoot + docName + docFileSuffix; + linkUrl = docName + docLinkSuffix; + } + let linkEl = listItem.appendChild(document.createElement("a")); + linkEl.href = linkUrl + anchor; + linkEl.dataset.score = score; + linkEl.innerHTML = title; + if (descr) { + listItem.appendChild(document.createElement("span")).innerHTML = + " (" + descr + ")"; + // highlight search terms in the description + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + } + else if (showSearchSummary) + fetch(requestUrl) + .then((responseData) => responseData.text()) + .then((data) => { + if (data) + listItem.appendChild( + Search.makeSearchSummary(data, searchTerms, anchor) + ); + // highlight search terms in the summary + if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js + highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); + }); + Search.output.appendChild(listItem); +}; +const _finishSearch = (resultCount) => { + Search.stopPulse(); + Search.title.innerText = _("Search Results"); + if (!resultCount) + Search.status.innerText = Documentation.gettext( + "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, + ).replace('${resultCount}', resultCount); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms, + highlightTerms, +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms, highlightTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; +// Helper function used by query() to order search results. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Order the results by score (in opposite order of appearance, since the +// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. +const _orderResultsByScoreThenName = (a, b) => { + const leftScore = a[4]; + const rightScore = b[4]; + if (leftScore === rightScore) { + // same score: sort alphabetically + const leftTitle = a[1].toLowerCase(); + const rightTitle = b[1].toLowerCase(); + if (leftTitle === rightTitle) return 0; + return leftTitle > rightTitle ? -1 : 1; // inverted is intentional + } + return leftScore > rightScore ? 1 : -1; +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings +} + +/** + * Search Module + */ +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString, anchor) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + for (const removalQuery of [".headerlink", "script", "style"]) { + htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); + } + if (anchor) { + const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); + if (anchorContent) return anchorContent.textContent; + + console.warn( + `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` + ); + } + + // if anchor not specified or not found, fall back to main content + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent) return docContent.textContent; + + console.warn( + "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." + ); + return ""; + }, + + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); + }, + + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), + + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); + } + }, + + hasIndex: () => Search._index !== null, + + deferQuery: (query) => (Search._queued_query = query), + + stopPulse: () => (Search._pulse_status = -1), + + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { + Search._pulse_status = (Search._pulse_status + 1) % 4; + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch: (query) => { + // create the required interface elements + const searchText = document.createElement("h2"); + searchText.textContent = _("Searching"); + const searchSummary = document.createElement("p"); + searchSummary.classList.add("search-summary"); + searchSummary.innerText = ""; + const searchList = document.createElement("ul"); + searchList.setAttribute("role", "list"); + searchList.classList.add("search"); + + const out = document.getElementById("search-results"); + Search.title = out.appendChild(searchText); + Search.dots = Search.title.appendChild(document.createElement("span")); + Search.status = out.appendChild(searchSummary); + Search.output = out.appendChild(searchList); + + const searchProgress = document.getElementById("search-progress"); + // Some themes don't use the search progress node + if (searchProgress) { + searchProgress.innerText = _("Preparing search..."); + } + Search.startPulse(); + + // index already loaded, the browser was quick! + if (Search.hasIndex()) Search.query(query); + else Search.deferQuery(query); + }, + + _parseQuery: (query) => { + // stem the search terms and add them to the correct list + const stemmer = new Stemmer(); + const searchTerms = new Set(); + const excludedTerms = new Set(); + const highlightTerms = new Set(); + const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); + splitQuery(query.trim()).forEach((queryTerm) => { + const queryTermLower = queryTerm.toLowerCase(); + + // maybe skip this "word" + // stopwords array is from language_data.js + if ( + stopwords.indexOf(queryTermLower) !== -1 || + queryTerm.match(/^\d+$/) + ) + return; + + // stem the word + let word = stemmer.stemWord(queryTermLower); + // select the correct list + if (word[0] === "-") excludedTerms.add(word.substr(1)); + else { + searchTerms.add(word); + highlightTerms.add(queryTermLower); + } + }); + + if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js + localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) + } + + // console.debug("SEARCH: searching for:"); + // console.info("required: ", [...searchTerms]); + // console.info("excluded: ", [...excludedTerms]); + + return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; + }, + + /** + * execute search (requires search index to be loaded) + */ + _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + const allTitles = Search._index.alltitles; + const indexEntries = Search._index.indexentries; + + // Collect multiple result groups to be sorted separately and then ordered. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + const normalResults = []; + const nonMainIndexResults = []; + + _removeChildren(document.getElementById("search-progress")); + + const queryLower = query.toLowerCase().trim(); + for (const [title, foundTitles] of Object.entries(allTitles)) { + if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { + for (const [file, id] of foundTitles) { + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles + normalResults.push([ + docNames[file], + titles[file] !== title ? `${titles[file]} > ${title}` : title, + id !== null ? "#" + id : "", + null, + score + boost, + filenames[file], + SearchResultKind.title, + ]); + } + } + } + + // search for explicit entries in index directives + for (const [entry, foundEntries] of Object.entries(indexEntries)) { + if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { + for (const [file, id, isMain] of foundEntries) { + const score = Math.round(100 * queryLower.length / entry.length); + const result = [ + docNames[file], + titles[file], + id ? "#" + id : "", + null, + score, + filenames[file], + SearchResultKind.index, + ]; + if (isMain) { + normalResults.push(result); + } else { + nonMainIndexResults.push(result); + } + } + } + } + + // lookup as object + objectTerms.forEach((term) => + normalResults.push(...Search.performObjectSearch(term, objectTerms)) + ); + + // lookup as search terms in fulltext + normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + normalResults.forEach((item) => (item[4] = Scorer.score(item))); + nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); + } + + // Sort each group of results by score and then alphabetically by name. + normalResults.sort(_orderResultsByScoreThenName); + nonMainIndexResults.sort(_orderResultsByScoreThenName); + + // Combine the result groups in (reverse) order. + // Non-main index entries are typically arbitrary cross-references, + // so display them after other results. + let results = [...nonMainIndexResults, ...normalResults]; + + // remove duplicate search results + // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept + let seen = new Set(); + results = results.reverse().reduce((acc, result) => { + let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); + if (!seen.has(resultStr)) { + acc.push(result); + seen.add(resultStr); + } + return acc; + }, []); + + return results.reverse(); + }, + + query: (query) => { + const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); + const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); + + // for debugging + //Search.lastresults = results.slice(); // a copy + // console.info("search results:", Search.lastresults); + + // print the results + _displayNextItem(results, results.length, searchTerms, highlightTerms); + }, + + /** + * search for object names + */ + performObjectSearch: (object, objectTerms) => { + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const objects = Search._index.objects; + const objNames = Search._index.objnames; + const titles = Search._index.titles; + + const results = []; + + const objectSearchCallback = (prefix, match) => { + const name = match[4] + const fullname = (prefix ? prefix + "." : "") + name; + const fullnameLower = fullname.toLowerCase(); + if (fullnameLower.indexOf(object) < 0) return; + + let score = 0; + const parts = fullnameLower.split("."); + + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullnameLower === object || parts.slice(-1)[0] === object) + score += Scorer.objNameMatch; + else if (parts.slice(-1)[0].indexOf(object) > -1) + score += Scorer.objPartialMatch; // matches in last name + + const objName = objNames[match[1]][2]; + const title = titles[match[0]]; + + // If more than one term searched for, we require other words to be + // found in the name/title/description + const otherTerms = new Set(objectTerms); + otherTerms.delete(object); + if (otherTerms.size > 0) { + const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); + if ( + [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) + ) + return; + } + + let anchor = match[3]; + if (anchor === "") anchor = fullname; + else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; + + const descr = objName + _(", in ") + title; + + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) + score += Scorer.objPrio[match[2]]; + else score += Scorer.objPrioDefault; + + results.push([ + docNames[match[0]], + fullname, + "#" + anchor, + descr, + score, + filenames[match[0]], + SearchResultKind.object, + ]); + }; + Object.keys(objects).forEach((prefix) => + objects[prefix].forEach((array) => + objectSearchCallback(prefix, array) + ) + ); + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch: (searchTerms, excludedTerms) => { + // prepare search + const terms = Search._index.terms; + const titleTerms = Search._index.titleterms; + const filenames = Search._index.filenames; + const docNames = Search._index.docnames; + const titles = Search._index.titles; + + const scoreMap = new Map(); + const fileMap = new Map(); + + // perform the search on the required terms + searchTerms.forEach((word) => { + const files = []; + const arr = [ + { files: terms[word], score: Scorer.term }, + { files: titleTerms[word], score: Scorer.title }, + ]; + // add support for partial matches + if (word.length > 2) { + const escapedWord = _escapeRegExp(word); + if (!terms.hasOwnProperty(word)) { + Object.keys(terms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: terms[term], score: Scorer.partialTerm }); + }); + } + if (!titleTerms.hasOwnProperty(word)) { + Object.keys(titleTerms).forEach((term) => { + if (term.match(escapedWord)) + arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); + }); + } + } + + // no match but word was a required one + if (arr.every((record) => record.files === undefined)) return; + + // found search word in contents + arr.forEach((record) => { + if (record.files === undefined) return; + + let recordFiles = record.files; + if (recordFiles.length === undefined) recordFiles = [recordFiles]; + files.push(...recordFiles); + + // set score for the word in each file + recordFiles.forEach((file) => { + if (!scoreMap.has(file)) scoreMap.set(file, {}); + scoreMap.get(file)[word] = record.score; + }); + }); + + // create the mapping + files.forEach((file) => { + if (!fileMap.has(file)) fileMap.set(file, [word]); + else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); + }); + }); + + // now check if the files don't contain excluded terms + const results = []; + for (const [file, wordList] of fileMap) { + // check if all requirements are matched + + // as search terms with length < 3 are discarded + const filteredTermCount = [...searchTerms].filter( + (term) => term.length > 2 + ).length; + if ( + wordList.length !== searchTerms.size && + wordList.length !== filteredTermCount + ) + continue; + + // ensure that none of the excluded terms is in the search result + if ( + [...excludedTerms].some( + (term) => + terms[term] === file || + titleTerms[term] === file || + (terms[term] || []).includes(file) || + (titleTerms[term] || []).includes(file) + ) + ) + break; + + // select one (max) score for the file. + const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); + // add result to the result list + results.push([ + docNames[file], + titles[file], + "", + null, + score, + filenames[file], + SearchResultKind.text, + ]); + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words. + */ + makeSearchSummary: (htmlText, keywords, anchor) => { + const text = Search.htmlToText(htmlText, anchor); + if (text === "") return null; + + const textLower = text.toLowerCase(); + const actualStartPosition = [...keywords] + .map((k) => textLower.indexOf(k.toLowerCase())) + .filter((i) => i > -1) + .slice(-1)[0]; + const startWithContext = Math.max(actualStartPosition - 120, 0); + + const top = startWithContext === 0 ? "" : "..."; + const tail = startWithContext + 240 < text.length ? "..." : ""; + + let summary = document.createElement("p"); + summary.classList.add("context"); + summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; + + return summary; + }, +}; + +_ready(Search.init); diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js new file mode 100644 index 0000000..8a96c69 --- /dev/null +++ b/_static/sphinx_highlight.js @@ -0,0 +1,154 @@ +/* Highlighting utilities for Sphinx HTML documentation. */ +"use strict"; + +const SPHINX_HIGHLIGHT_ENABLED = true + +/** + * highlight a given string on a node by wrapping it in + * span elements with the given class name. + */ +const _highlight = (node, addItems, text, className) => { + if (node.nodeType === Node.TEXT_NODE) { + const val = node.nodeValue; + const parent = node.parentNode; + const pos = val.toLowerCase().indexOf(text); + if ( + pos >= 0 && + !parent.classList.contains(className) && + !parent.classList.contains("nohighlight") + ) { + let span; + + const closestNode = parent.closest("body, svg, foreignObject"); + const isInSVG = closestNode && closestNode.matches("svg"); + if (isInSVG) { + span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); + } else { + span = document.createElement("span"); + span.classList.add(className); + } + + span.appendChild(document.createTextNode(val.substr(pos, text.length))); + const rest = document.createTextNode(val.substr(pos + text.length)); + parent.insertBefore( + span, + parent.insertBefore( + rest, + node.nextSibling + ) + ); + node.nodeValue = val.substr(0, pos); + /* There may be more occurrences of search term in this node. So call this + * function recursively on the remaining fragment. + */ + _highlight(rest, addItems, text, className); + + if (isInSVG) { + const rect = document.createElementNS( + "http://www.w3.org/2000/svg", + "rect" + ); + const bbox = parent.getBBox(); + rect.x.baseVal.value = bbox.x; + rect.y.baseVal.value = bbox.y; + rect.width.baseVal.value = bbox.width; + rect.height.baseVal.value = bbox.height; + rect.setAttribute("class", className); + addItems.push({ parent: parent, target: rect }); + } + } + } else if (node.matches && !node.matches("button, select, textarea")) { + node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); + } +}; +const _highlightText = (thisNode, text, className) => { + let addItems = []; + _highlight(thisNode, addItems, text, className); + addItems.forEach((obj) => + obj.parent.insertAdjacentElement("beforebegin", obj.target) + ); +}; + +/** + * Small JavaScript module for the documentation. + */ +const SphinxHighlight = { + + /** + * highlight the search words provided in localstorage in the text + */ + highlightSearchWords: () => { + if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight + + // get and clear terms from localstorage + const url = new URL(window.location); + const highlight = + localStorage.getItem("sphinx_highlight_terms") + || url.searchParams.get("highlight") + || ""; + localStorage.removeItem("sphinx_highlight_terms") + url.searchParams.delete("highlight"); + window.history.replaceState({}, "", url); + + // get individual terms from highlight string + const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); + if (terms.length === 0) return; // nothing to do + + // There should never be more than one element matching "div.body" + const divBody = document.querySelectorAll("div.body"); + const body = divBody.length ? divBody[0] : document.querySelector("body"); + window.setTimeout(() => { + terms.forEach((term) => _highlightText(body, term, "highlighted")); + }, 10); + + const searchBox = document.getElementById("searchbox"); + if (searchBox === null) return; + searchBox.appendChild( + document + .createRange() + .createContextualFragment( + '

' + + '' + + _("Hide Search Matches") + + "

" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/contact.html b/contact.html new file mode 100644 index 0000000..62d8eb3 --- /dev/null +++ b/contact.html @@ -0,0 +1,135 @@ + + + + + + + + + Contact — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Contact

+

If you need to contact someone directly for assistance we are happy to help!

+ +

For any bugs, or suggestions for additional features within the DESC data +management software, please raise an issue via the GitHub repository +(https://github.com/LSSTDESC/skyCatalogs/issues).

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..6c67c12 --- /dev/null +++ b/genindex.html @@ -0,0 +1,160 @@ + + + + + + + + Index — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ D + | G + | S + +
+

D

+ + +
+ +

G

+ + + +
+ +

S

+ + + +
+ + + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..b005ee8 --- /dev/null +++ b/index.html @@ -0,0 +1,205 @@ + + + + + + + + + skyCatalogs: provides API for simulated object catalogs — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • skyCatalogs: provides API for simulated object catalogs
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

skyCatalogs: provides API for simulated object catalogs

+

skyCatalogs both creates simulated object catalogs (from precursor catalogs) +and provides a uniform API to the catalogs it makes and to certain other +catalogs. These catalogs may be used as inputs to image simulation (originally +only for the Rubin Observatory; since also used in simulations for the +Roman Observatory) and as truth catalogs.

+

This documentation covers installation and usage instructions for the package.

+

The source code of skyCatalogs is hosted at +https://github.com/LSSTDESC/skyCatalogs.

+
+

Contents:

+ +
+
+
+
+
+
+

Indices and tables

+ +
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/installation.html b/installation.html new file mode 100644 index 0000000..dc6205f --- /dev/null +++ b/installation.html @@ -0,0 +1,220 @@ + + + + + + + + + Installation Instructions — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Installation Instructions

+
+

Note

+

Prerequisites:

+

To use skyCatalogs 1.7.x

+

all that is required is a reasonably current version of the LSST science pipelines . See installation instructions below.

+
+
+

Note

+

Use with imSim:

+

If you intend to use skyCatalogs with imSim, you should follow the imSim installation instructions . In that case, you need proceed no further with the instructions here; you’re all set. The remainder of these notes is largely extracted from the imSim instructions, omitting anything not required for skyCatalogs.

+
+
+

Installing LSST science pipelines

+

There are several methods of installation. Only the simplest (using a prebuilt cvmfs version) is described here. For other methods, see the imSim installation instructions.

+

If you are working at the USDF (Rubin Project computing) or at NERSC (DESC computing), perhaps the easiest way to setup and use skyCatalogs is to rely on the prebuilt versions of the pipelines contained in the cvmfs distribution which is installed there. This solution is also appropriate for personal laptops and university/lab based computing systems if you are able to install the cvmfs system.

+

The CernVM file system (cvmfs) is a distributed read-only file system developed at CERN for reliable low-maintenance world-wide software distribution. LSST-France distributes weekly builds of the Rubin science pipelines for both Linux and MacOS. Details and installation instructions can be found at sw.lsst.eu . The distribution includes conda and skyCatalogs dependencies from conda-forge along with the science pipelines.

+
+

Load and setup the science pipelines

+

First you need to setup the science pipelines. This involves sourcing a setup file and then using the Rubin eups commands to set them up.

+
+

Note

+

Version w_2024_20 or later of the science pipelines is recommended. This will guarantee other dependencies of skyCatalogs, such as GalSim, are new enough.

+

Also note: the cvmfs distribution is a read-only distribution. This means you cannot add packages to the included conda environment and packages you install via pip will be installed in the user area. If you need a conda environment you will need to use a different installation method.

+
+

Source the appropriate setup script (note the -ext in the name) and then setup the distribution (if you are on MacOS use darwin-x86_64 instead of linux-x86_64).

+
source /cvmfs/sw.lsst.eu/linux-x86_64/lsst_distrib/w_2024_20/loadLSST-ext.bash
+setup lsst_distrib
+
+
+
+
+

Install needed data files

+

Now go to where you would like to install skyCatalogs and download some needed data files (you will only need to do this once).

+
mkdir -p rubin_sim_data/sims_sed_library
+curl https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/rubin_sim_data/throughputs_2023_09_07.tgz | tar -C rubin_sim_data -xz
+curl https://s3df.slac.stanford.edu/groups/rubin/static/sim-data/sed_library/seds_170124.tar.gz  | tar -C rubin_sim_data/sims_sed_library -xz
+
+
+
+
+

Set up skyCatalogs itself

+

Clone the skyCatalogs package from GitHub:

+
git clone https://github.com/LSSTDESC/skyCatalogs
+
+
+

at this point if you would only like to use skyCatalogs you can pip install skyCatalog/ however we instead suggest using the eups tool to simply setup the package for use without installing it. This will allow you to edit the package in place, use multiple versions, change branches etc. You should definitely do this if you plan to do any skyCatalogs development.

+

If you do not intend to do any development you may choose instead to clone the most recent release tag. As of Oct., 2024 this is 1.7.0rc4

+
git clone https://github.com/LSSTDESC/skyCatalogs.git --branch 1.7.0rc4
+
+
+
+
+

Setup and Use skyCatalogs

+

This setup step should be repeated for each new session. Here is a skycatalogs-setup.sh file you can use before each session

+
source /cvmfs/...            # as above
+setup lsst_distrib
+
+export SKYCATALOGS_HOME=*PUT YOUR INSTALL DIRECTORY HERE*
+export RUBIN_SIM_DATA_DIR=$SKYCATALOGS_HOME/rubin_sim_data
+export SIMS_SED_LIBRARY_DIR=$SKYCATALOGS_HOME/rubin_sim_data/sims_sed_library
+
+setup -k -r $SKYCATALOGS_HOME/skyCatalogs
+
+
+

You should now be able to import the code you need from the skyCatalogs package, e.g.

+
from skycatalogs.skyCatalogs import open_catalog
+from skycatalogs.utils.shapes import Disk
+
+skycatalog_root = "path_to/skycatalog_files"  # folder containing catalog
+config_file = "some_folder/skyCatalog.yaml"
+
+cat = open_catalog(config_file, skycatalog_root=skycatalog_root)
+
+# define disk at ra, dec = 45.0, -9.0 of radius 100 arcseconds
+disk = disk(45.0, -9.0, 100.0)
+
+# get galaxies and stars in the region
+objects = cat.get_objects_by_region(disk, obj_type_set={'galaxy', 'star'})
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..f1d72bf Binary files /dev/null and b/objects.inv differ diff --git a/ops-rehearsals-3-4/SSO.html b/ops-rehearsals-3-4/SSO.html new file mode 100644 index 0000000..18b9cf0 --- /dev/null +++ b/ops-rehearsals-3-4/SSO.html @@ -0,0 +1,241 @@ + + + + + + + + + Solar System Object (SSO) quantities for ops-rehearsals 3 and 4 — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Solar System Object (SSO) quantities for ops-rehearsals 3 and 4
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

Solar System Object (SSO) quantities for ops-rehearsals 3 and 4

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” and a flux file. The latter contains +for each object only fluxes for lsst bands, the object id and the time (mjd) +of the observation. The latter two fields may be used to join with the +main file.

+
+

SSO main file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

id

string

N/A

Unique object identifier

mjd

double

days

Time of observation

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

trailed_source_mag

double

N/A

Mag. normalization for SED

ra_rate

double

deg/day

RA rate of change * cos(dec)

dec_rate

double

deg/day

Declination rate of change

+
+
+

SSO flux file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

id

string

N/A

Unique object identifier

mjd

double

days

Time of observation (Julian date)

lsst_flux_u

float

photons/sec/cm^2

Flux integrated over lsst u-band

lsst_flux_g

float

photons/sec/cm^2

Flux integrated over lsst g-band

lsst_flux_r

float

photons/sec/cm^2

Flux integrated over lsst r-band

lsst_flux_i

float

photons/sec/cm^2

Flux integrated over lsst i-band

lsst_flux_z

float

photons/sec/cm^2

Flux integrated over lsst z-band

lsst_flux_y

float

photons/sec/cm^2

Flux integrated over lsst y-band

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ops-rehearsals-3-4/UW_stars.html b/ops-rehearsals-3-4/UW_stars.html new file mode 100644 index 0000000..cc81d2c --- /dev/null +++ b/ops-rehearsals-3-4/UW_stars.html @@ -0,0 +1,305 @@ + + + + + + + + + Star quantities for ops-rehearsals 3 and 4 — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Star quantities for ops-rehearsals 3 and 4

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” (with information largely coming from the +UW star catalog) and a flux file. The latter contains for each object only +fluxes for lsst bands and the object id so it can be joined with the main +file. Both are parquet files.

+
+

Star main file

+

Note the same schema may be used for SNe. Some fields are unused for stars.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

object_type

string

N/A

In practice always ‘star’

id

string

N/A

Unique object identifier

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

host_galaxy_id

int64

N/A

Unused for stars

magnorm

double

N/A

To be applied to SED

sed_filepath

string

N/A

Path to object’s SED file +relative to env variable +SIMS_SED_LIBRARY_DIR

MW_rv

float

N/A

Extinction parameter

MW_av

float

N/A

Extinction parameter +from F19 dust map

mura

double

milarcsec +per year

RA proper motion

mudec

double

milarcsec +per year

Declin. proper motion

radial_velocity

double

km/sec

Radial velocity

parallax

double

milarcsec

Parallax

variability_model

string

N/A

Unused for stars

salt2_params

int32

N/A

Unused for stars

is_variable

boolean

N/A

If true, the star has +sinusoidal variability +in magnitude

period

double

days

period of variability

mag_amplitude

double

N/A

amplitude of magnitude +variability

phase

double

radians

phase of variability

+
+
+

Star flux file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

id

string

N/A

Unique object identifier

lsst_flux_u

float

photons/sec/cm^2

Flux integrated over lsst u-band

lsst_flux_g

float

photons/sec/cm^2

Flux integrated over lsst g-band

lsst_flux_r

float

photons/sec/cm^2

Flux integrated over lsst r-band

lsst_flux_i

float

photons/sec/cm^2

Flux integrated over lsst i-band

lsst_flux_z

float

photons/sec/cm^2

Flux integrated over lsst z-band

lsst_flux_y

float

photons/sec/cm^2

Flux integrated over lsst y-band

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ops-rehearsals-3-4/galaxies.html b/ops-rehearsals-3-4/galaxies.html new file mode 100644 index 0000000..cd266ae --- /dev/null +++ b/ops-rehearsals-3-4/galaxies.html @@ -0,0 +1,361 @@ + + + + + + + + + Galaxy quantities for ops-rehearsals 3 and 4 — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Galaxy quantities for ops-rehearsals 3 and 4

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” (with information largely coming from the +cosmodc2 galaxy catalog) and a flux file. The latter contains +for each object only fluxes for lsst bands and the object id so it can be +joined with the main file. Both are parquet files. The main file can be +rather large (over 3 Gbytes) so, depending on your application, you may +want to iterate over row groups rather than reading it all in at once.

+
+

Galaxy main file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

galaxy_id

int64

N/A

Unique object identifier

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

redshift

double

N/A

Cosmological redshift +with line-of-sight motion

redshift_hubble

double

N/A

Cosmological redshift

peculiar_velocity

double

km/sec

Peculiar velocity

shear_1

double

N/A

Shear (gamma) component 1, +treecorr/Galsim convention

shear_2

double

N/A

Shear (gamma) component 2, +treecorr/Galsim convention

convergence

double

N/A

Convergence (kappa)

size_bulge_true

float

arcsec

Bulge half-light radius +(major axis) not lensed

size_minor_bulge_true

float

arcsec

Bulge half-light radius +(minor axis) not lensed

sersic_bulge

float

N/A

Sersic index of bulge +light profile

size_disk_true

float

arcsec

Disk half-light radius +(major axis) not lensed

size_disk_bulge_true

float

arcsec

Disk half-light radius +(minor axis) not lensed

sersic_disk

float

N/A

Sersic index of disk +light profile

ellipticity_1_disk_true

double

N/A

Ellipticity component 1 +for disk, not lensed

ellipticity_2_disk_true

double

N/A

Ellipticity component 2 +for disk, not lensed

ellipticity_1_bulge_true

double

N/A

Ellipticity component 1 +for bulge, not lensed

ellipticity_2_bulge_true

double

N/A

Ellipticity component 2 +for bulge, not lensed

sed_val_bulge

list(double)

4.4659e13 W/Hz

Integrated rest-frame AB +luminosities for tophat +filters (bulge component)

sed_val_disk

list(double)

4.4659e13 W/Hz

Like sed_val_bulge

bulge_magnorm

double

N/A

Normalization for SED

disk_magnorm

double

N/A

Normalization for SED

MW_rv

float

N/A

Extinction parameter

MW_av

float

N/A

Extinction parameter +from F19 dust map

sed_val_knots

list(double)

4.4659e13 W/Hz

Like sed_val_bulge

n_knots

float

N/A

Number of knots

knots_magnorm

double

N/A

Normalization for SED

+

NOTE: For tophat definitions (start and width in units of angstroms) see yaml +config file associated with the data.

+
+
+

Galaxy flux file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

galaxy_id

int64

N/A

Unique object identifier

lsst_flux_u

float

photons/sec/cm^2

Flux integrated over lsst u-band

lsst_flux_g

float

photons/sec/cm^2

Flux integrated over lsst g-band

lsst_flux_r

float

photons/sec/cm^2

Flux integrated over lsst r-band

lsst_flux_i

float

photons/sec/cm^2

Flux integrated over lsst i-band

lsst_flux_z

float

photons/sec/cm^2

Flux integrated over lsst z-band

lsst_flux_y

float

photons/sec/cm^2

Flux integrated over lsst y-band

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/reference_python.html b/reference_python.html new file mode 100644 index 0000000..88c6c70 --- /dev/null +++ b/reference_python.html @@ -0,0 +1,143 @@ + + + + + + + + + The skyCatalogs package — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

The skyCatalogs package

+

Reference documentation for core objects with the skyCatalogs package

+
+

The skyCatalog class

+

The skyCatalog class represents a catalog. Users gain access +to a catalog by calling its static method open_catalog.

+

There are several classes (one per supported object type) representing +individual objects as observed at a particular time, all subclassing +BaseObject.

+

The ObjectList class is a container for instances of BaseObject. +It subclasses Sequence.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/roman-rubin-1.1.2/UW_stars.html b/roman-rubin-1.1.2/UW_stars.html new file mode 100644 index 0000000..6f6abaa --- /dev/null +++ b/roman-rubin-1.1.2/UW_stars.html @@ -0,0 +1,282 @@ + + + + + + + + + Star quantities for Roman-Rubin sims — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Star quantities for Roman-Rubin sims

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” (with information largely coming from the +UW star catalog) and a flux file. The latter contains for each object only +fluxes for lsst bands and the object id so it can be joined with the main +file. Both are parquet files.

+
+

Star main file

+

Note the same schema may be used for SNe. Some fields are unused for stars.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

object_type

string

N/A

In practice always ‘star’

id

string

N/A

Unique object identifier

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

host_galaxy_id

int64

N/A

Unused for stars

magnorm

double

N/A

To be applied to SED

sed_filepath

string

N/A

Path to object’s SED file +relative to env variable +SIMS_SED_LIBRARY_DIR

MW_rv

float

N/A

Extinction parameter

MW_av

float

N/A

Extinction parameter +from F19 dust map

mura

double

milarcsec +per year

RA proper motion

mudec

double

milarcsec +per year

Declin. proper motion

radial_velocity

double

km/sec

Radial velocity

parallax

double

milarcsec

Parallax

variability_model

string

N/A

Unused for stars

salt2_params

struct

N/A

Unused for stars

+
+
+

Star flux file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

id

string

N/A

Unique object identifier

lsst_flux_u

float

photons/sec/cm^2

Flux integrated over lsst u-band

lsst_flux_g

float

photons/sec/cm^2

Flux integrated over lsst g-band

lsst_flux_r

float

photons/sec/cm^2

Flux integrated over lsst r-band

lsst_flux_i

float

photons/sec/cm^2

Flux integrated over lsst i-band

lsst_flux_z

float

photons/sec/cm^2

Flux integrated over lsst z-band

lsst_flux_y

float

photons/sec/cm^2

Flux integrated over lsst y-band

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/roman-rubin-1.1.2/diffsky_galaxy.html b/roman-rubin-1.1.2/diffsky_galaxy.html new file mode 100644 index 0000000..78024c2 --- /dev/null +++ b/roman-rubin-1.1.2/diffsky_galaxy.html @@ -0,0 +1,354 @@ + + + + + + + + + Galaxy quantities for Roman-Rubin joint simulation — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Galaxy quantities for Roman-Rubin joint simulation

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” (with information largely coming from the +diffsky galaxy catalog), a flux file and a SED file. The flux file contains for +each object only fluxes for lsst and Roman bands and the object id so it can be +joined with the main file. Both it and the main file are parquet files. The +SED file is in hdf5 format. The file names take the form galaxy_<hp>.parquet +(main file), galaxy_flux_<hp>.parquet (flux file) and galaxy_sed_<hp>.hdf5 for +SED files. In all cases <hp> is the id of the healpixel covered by the file.

+
+

Galaxy main file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

galaxy_id

int64

N/A

Unique object identifier

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

redshift

double

N/A

Cosmological redshift +with line-of-sight motion

redshiftHubble

double

N/A

Cosmological redshift

peculiarVelocity

double

km/sec

Peculiar velocity

shear1

double

N/A

Shear (gamma) component 1, +treecorr/Galsim convention

shear2

double

N/A

Shear (gamma) component 2, +treecorr/Galsim convention

convergence

double

N/A

Convergence (kappa)

spheroidHalfLightRadiusArcsec

float

arcsec

Bulge component half-light +radius

diskHalfLightRadiusArcsec

float

arcsec

Disk component half-light +radius

diskEllipticity1

double

N/A

Ellipticity component 1 +for disk, not lensed

diskEllipticity2

double

N/A

Ellipticity component 2 +for disk, not lensed

spheroidEllipticity1

double

N/A

Ellipticity component 1 +for bulge, not lensed

spheroidEllipticity2

double

N/A

Ellipticity component 2 +for bulge, not lensed

um_source_galaxy_obs_sm

float

solar mass +(h=0.7)

Stellar mass

MW_rv

float

N/A

Extinction parameter

MW_av

float

N/A

Extinction parameter +from F19 dust map

+
+
+

Galaxy flux file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

galaxy_id

int64

N/A

Unique object identifier

lsst_flux_u

float

photons/sec/cm^2

Flux integrated over lsst u-band

lsst_flux_g

float

photons/sec/cm^2

Flux integrated over lsst g-band

lsst_flux_r

float

photons/sec/cm^2

Flux integrated over lsst r-band

lsst_flux_i

float

photons/sec/cm^2

Flux integrated over lsst i-band

lsst_flux_z

float

photons/sec/cm^2

Flux integrated over lsst z-band

lsst_flux_y

float

photons/sec/cm^2

Flux integrated over lsst y-band

roman_flux_W146

float

photons/sec/cm^2

Flux integrated over roman W146-band

roman_flux_R062

float

photons/sec/cm^2

Flux integrated over roman R062-band

roman_flux_Z087

float

photons/sec/cm^2

Flux integrated over roman Z087-band

roman_flux_Y106

float

photons/sec/cm^2

Flux integrated over roman Y106-band

roman_flux_J129

float

photons/sec/cm^2

Flux integrated over roman J129-band

roman_flux_H158

float

photons/sec/cm^2

Flux integrated over roman H158-band

roman_flux_F184

float

photons/sec/cm^2

Flux integrated over roman F184-band

roman_flux_K213

float

photons/sec/cm^2

Flux integrated over roman K213-band

+
+
+

Galaxy SED file

+

This file has two sections. One (meta) has an array wave_list, shape(312), +of wavelengths (angstroms), which is used for SEDs of all galaxies in the file’s healpixel. +The other section, galaxy, contains groups of galaxies. Each group has entries +for individual galaxies, keyed by galaxy id. Such an entry is an array, shape(3, 312), +consisting of SEDs for the three galaxy components (disk, bulge, knot). Units are fnu.

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+ + + + \ No newline at end of file diff --git a/roman-rubin-1.1.2/snana.html b/roman-rubin-1.1.2/snana.html new file mode 100644 index 0000000..f47d873 --- /dev/null +++ b/roman-rubin-1.1.2/snana.html @@ -0,0 +1,354 @@ + + + + + + + + + SNANA quantities for Roman-Rubin sims — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
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SNANA quantities for Roman-Rubin sims

+

Data are partitioned by (nside=32, ring ordering) healpixel. For each pixel +there is a so-called “main file” in parquet format, containing static +quantities associated with each source, and an hdf5 file for quantities +which vary with time or wavelength or both.

+
+

SNANA main file

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

id

int64

N/A

Unique object identifier

ra

double

degrees

Object right ascension

dec

double

degrees

Object declination

host_id

int64

N/A

Host galaxy

gentype

int32

N/A

Type of object simulated

model_name

string

N/A

Type name

start_mjd

float

days

Earliest visibility

end_mjd

float

days

Latest visibility

z_CMB

float

N/A

redshift

mw_EBV

float

N/A

MW extinction parameter

mw_extinction_applied

boolean

N/A

Here always False

AV

float

N/A

For host galaxy, randomly +assigned

RV

float

N/A

For host galaxy

v_pec

float

km/sec

Peculiar velocity. Not +yet simulated so zero.

host_ra

double

degrees

Host galaxy RA

host_dec

double

degrees

Host galaxy decl.

host_mag_g

float

N/A

Host mag. in Rubin g-band

host_mag_i

float

N/A

Host mag. in Rubin i-band

host_mag_F

float

N/A

Host mag. in Roman F-band

host_sn_sep

float

arcsec

Separation from host

peak_mjd

float

days

Time of peak flux +(model-dependent)

peak_mag_g

float

N/A

g-band mag. at peak

peak_mag_i

float

N/A

i-band mag. at peak

peak_mag_F

float

N/A

F-band mag. at peak

lens_dmu_applied

boolean

N/A

False (distance modulus +lensing shift not applied)

model_param_names

list(string)

N/A

Model parameter names

model_param_values

list(string)

N/A

Model parameter values

MW_av

float

N/A

MW extinction parameter

MW_rv

float

N/A

MW extinction parameter

+
+
+

SNANA varying quantities

+

The top-level keys for each file are the ids for sources in that pixel, the +same as the ids appearing in the parquet file but here stored as strings. +Under each id are the following keys

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Units

Description

mjd

float array

days

Time axis for flambda

lambda

double array

angstroms

Wavelength axis for flambda

flambda

float 2-d array

erg/sec/A/cm^2

Flux indexed by (mjd,lambda)

mag_<band>

float array

N/A

Magnitude for each mjd computed +using 5 angstrom bins.

magcor_<band>

float array

N/A

Correction to magnitude +computed using flambda

synmag_<band>

float array

N/A

Magnitude computed from flambda

+

where <band> takes on values u, g, r, i, z, y (Rubin bandpasses) and F, H, J, +K, R, W, Y, Z (for Roman).

+

mjd values have uniform spacing of 1 day. lambda values have uniform spacing +of 100 angstroms.

+

synmag + magcor = mag

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+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..5f8fba1 --- /dev/null +++ b/search.html @@ -0,0 +1,138 @@ + + + + + + + + Search — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + + +
+ + +
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+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..72fc1b1 --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"alltitles": {"Adding Supported Object Types to a Catalog": [[11, "adding-supported-object-types-to-a-catalog"]], "Contact": [[0, null]], "Contents:": [[1, null]], "Creating New Catalogs": [[10, null]], "Description of an object type": [[11, "description-of-an-object-type"]], "Example options files": [[10, "example-options-files"]], "Galaxy SED file": [[8, "galaxy-sed-file"]], "Galaxy flux file": [[5, "galaxy-flux-file"], [8, "galaxy-flux-file"]], "Galaxy main file": [[5, "galaxy-main-file"], [8, "galaxy-main-file"]], "Galaxy quantities for Roman-Rubin joint simulation": [[8, null]], "Galaxy quantities for ops-rehearsals 3 and 4": [[5, null]], "Indices and tables": [[1, "indices-and-tables"]], "Install needed data files": [[2, "install-needed-data-files"]], "Installation Instructions": [[2, null]], "Installing LSST science pipelines": [[2, "installing-lsst-science-pipelines"]], "Load and setup the science pipelines": [[2, "load-and-setup-the-science-pipelines"]], "Opening a Catalog": [[11, "opening-a-catalog"]], "Options table": [[10, "options-table"], [10, "id1"]], "Reading Catalogs with skyCatalogs": [[11, null]], "SNANA main file": [[9, "snana-main-file"]], "SNANA quantities for Roman-Rubin sims": [[9, null]], "SNANA varying quantities": [[9, "snana-varying-quantities"]], "SSO flux file": [[3, "sso-flux-file"]], "SSO main file": [[3, "sso-main-file"]], "Set up skyCatalogs itself": [[2, "set-up-skycatalogs-itself"]], "Setup and Use skyCatalogs": [[2, "setup-and-use-skycatalogs"]], "Solar System Object (SSO) quantities for ops-rehearsals 3 and 4": [[3, null]], "Star flux file": [[4, "star-flux-file"], [7, "star-flux-file"]], "Star main file": [[4, "star-main-file"], [7, "star-main-file"]], "Star quantities for Roman-Rubin sims": [[7, null]], "Star quantities for ops-rehearsals 3 and 4": [[4, null]], "Structure of skyCatalogs Configs": [[11, "structure-of-skycatalogs-configs"]], "Supported object types": [[11, "supported-object-types"]], "The script create_flux.py and its options": [[10, "the-script-create-flux-py-and-its-options"]], "The script create_main.py and its options": [[10, "the-script-create-main-py-and-its-options"]], "The skyCatalog class": [[6, "the-skycatalog-class"]], "The skyCatalogs package": [[6, null]], "Using !include": [[11, "using-include"]], "skyCatalogs: provides API for simulated object catalogs": [[1, null]]}, "docnames": ["contact", "index", "installation", "ops-rehearsals-3-4/SSO", "ops-rehearsals-3-4/UW_stars", "ops-rehearsals-3-4/galaxies", "reference_python", "roman-rubin-1.1.2/UW_stars", "roman-rubin-1.1.2/diffsky_galaxy", "roman-rubin-1.1.2/snana", "usage_create", "usage_read"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 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"pipelin": 1, "pixel": [3, 4, 5, 7, 8, 9, 10, 11], "place": 2, "plan": 2, "pleas": 0, "plethora": 10, "plu": 10, "point": 2, "pointsource_": 11, "pointsource_flux_": 11, "popul": 11, "possibl": 11, "practic": [4, 7], "pre": 11, "prebuilt": 2, "preced": 10, "precursor": 1, "prefer": 11, "prepend": 10, "prerequisit": 2, "primarili": [10, 11], "proce": 2, "process": 10, "profil": 5, "program": 11, "project": 2, "proper": [4, 7], "properti": 11, "proven": 11, "provid": 11, "put": 2, "py": 1, "python": 10, "quantiti": [1, 11], "r": [2, 3, 4, 5, 7, 8, 9], "r062": 8, "ra": [2, 3, 4, 5, 7, 8, 9], "ra_rat": 3, "radial": [4, 7], "radial_veloc": [4, 7], "radian": 4, "radiu": [2, 5, 8], "rais": 0, "randomli": 9, "rate": 3, "rather": [5, 10], "rc4": 11, "re": 2, "read": [1, 2, 5], "reason": 2, "recent": 2, "recommend": 2, "redshift": [5, 8, 9], "redshift_hubbl": 5, "redshifthubbl": 8, "refer": [6, 11], "region": [2, 10, 11], "rehears": 1, "rel": [4, 7, 10, 11], "releas": 2, "reli": 2, "reliabl": 2, "remaind": 2, "repeat": 2, "repo": [10, 11], "repositori": 0, "repres": 6, "requir": [2, 10, 11], "rest": 5, "right": [3, 4, 5, 7, 8, 9], "ring": [3, 4, 5, 7, 8, 9, 11], "roman": [1, 10], "roman_flux_f184": 8, "roman_flux_h158": 8, "roman_flux_j129": 8, "roman_flux_k213": 8, "roman_flux_r062": 8, "roman_flux_w146": 8, "roman_flux_y106": 8, "roman_flux_z087": 8, "row": [5, 10], "rubin": [1, 2, 10], "rubin_sim_data": 2, "rubin_sim_data_dir": 2, "run": [10, 11], "run_opt": 11, "rv": 9, "s3df": 2, "salt2_param": [4, 7], "same": [4, 7, 9, 10, 11], "schema": [4, 7, 11], "schema_vers": 11, "scienc": 1, "script": [1, 2], "search": 1, "sec": [3, 4, 5, 7, 8, 9], "section": [8, 11], "sed": [1, 3, 4, 5, 7, 10], "sed_file_root_env_var": 11, "sed_filepath": [4, 7], "sed_librari": 2, "sed_model": 11, "sed_subdir": 11, "sed_val_bulg": 5, "sed_val_disk": 5, "sed_val_knot": 5, "seds_170124": 2, "see": [2, 5, 10, 11], "select": 11, "sens": 11, "separ": 9, "sequenc": 6, "sersic": 5, "sersic_bulg": 5, "sersic_disk": 5, "session": 2, "set": 10, "sever": [2, 6, 10, 11], "sh": 2, "shape": [2, 8], "shear": [5, 8], "shear1": 8, "shear2": 8, "shear_1": 5, "shear_2": 5, "shift": 9, "should": 2, "sight": [5, 8], "sim": [1, 2], "simpl": 11, "simplest": 2, "simpli": 2, "sims_sed_librari": 2, "sims_sed_library_dir": [2, 4, 7, 11], "simul": [9, 11], "sinc": [1, 10], "sinusoid": 4, "size_bulge_tru": 5, "size_disk_bulge_tru": 5, "size_disk_tru": 5, "size_minor_bulge_tru": 5, "skip_don": [10, 11], "sky": [10, 11], "skycatalog": [0, 10], "skycatalog_fil": 2, "skycatalog_root": [2, 10, 11], "skycatalogs_hom": 2, "skycatalogs_repo": 11, "slac": 2, "smaller": 10, "snana": [1, 11], "sne": [4, 7, 11], "so": [3, 4, 5, 7, 8, 9, 10], "softwar": [0, 2], "solar": [1, 8, 11], "solar_sed_thin": 10, "solut": 2, "some": [2, 4, 7, 10, 11], "some_fold": 2, "some_path": 11, "someon": [0, 11], "someth": [10, 11], "somewher": 11, "sorcha": 11, "sourc": [1, 2, 9, 11], "space": 9, "specifi": [10, 11], "speed": 10, "spheroidellipticity1": 8, "spheroidellipticity2": 8, "spheroidhalflightradiusarcsec": 8, "sqlite": [10, 11], "ssim": 11, "sso": [1, 10, 11], "sso_s": [10, 11], "sso_truth": 11, "stanford": 2, "star": [1, 2, 10, 11], "star_input_fmt": [10, 11], "star_main": 11, "star_truth": 11, "start": 5, "start_mjd": 9, "state": 11, "static": [2, 6, 9], "stellar": [8, 11], "step": [2, 11], "still": 10, "store": [9, 10], "stride": 10, "string": [3, 4, 7, 9, 10], "struct": 7, "structur": 1, "style": 10, "subclass": 6, "subdirectori": 11, "suggest": [0, 2], "suitabl": [10, 11], "suppli": 11, "support": [1, 6], "suppos": 10, "sw": 2, "synmag": 9, "synmag_": 9, "system": [1, 2, 11], "tag": 2, "take": [8, 9], "tar": 2, "test": 10, "tgz": 2, "than": [5, 10], "thei": [10, 11], "them": [2, 11], "thi": [1, 2, 8, 10, 11], "thing": 10, "those": 11, "three": [8, 11], "throughputs_2023_09_07": 2, "time": [3, 6, 9, 10, 11], "tool": 2, "top": [9, 10, 11], "tophat": 5, "trailed_source_mag": 3, "treecorr": [5, 8], "true": [4, 10, 11], "truth": [1, 10], "turn": 11, "two": [3, 8, 11], "txt": 10, "type": [1, 6, 9, 10], "typic": 11, "u": [3, 4, 5, 7, 8, 9, 11], "um_source_galaxy_obs_sm": 8, "uncommitted_fil": 11, "under": [9, 11], "underscor": 10, "uniform": [1, 9], "uniqu": [3, 4, 5, 7, 8, 9], "unit": [3, 4, 5, 7, 8, 9, 11], "univers": 2, "untracked_fil": 11, "unus": [4, 7], "up": [10, 11], "us": [1, 3, 4, 7, 8, 9, 10], "usag": 1, "usdf": 2, "user": [2, 6, 11], "usual": [10, 11], "util": 2, "uw": [4, 7, 11], "v_pec": 9, "valu": [9, 10, 11], "vari": 1, "variability_model": [4, 7], "variabl": [4, 7, 11], "varieti": 11, "veloc": [4, 5, 7, 8, 9], "version": [2, 11], "via": [0, 2], "visibl": 9, "w": [5, 9], "w146": 8, "w_2024_20": 2, "wa": 10, "wai": [2, 11], "want": 5, "wave_list": 8, "wavelength": [8, 9], "we": [0, 2, 11], "weekli": 2, "well": 10, "when": [10, 11], "where": [2, 9, 10, 11], "which": [2, 8, 9, 10, 11], "who": 11, "whoever": 11, "wide": 2, "width": 5, "within": [0, 11], "without": 2, "work": 2, "world": 2, "would": 2, "write": 10, "written": 11, "wrote": 10, "x": 2, "x86_64": 2, "xz": 2, "y": [3, 4, 5, 7, 8, 9], "y106": 8, "yaml": [2, 5, 10, 11], "year": [4, 7], "yet": 9, "you": [0, 2, 5, 10, 11], "your": [2, 5, 11], "z": [3, 4, 5, 7, 8, 9], "z087": 8, "z_cmb": 9, "zero": 9}, "titles": ["Contact", "skyCatalogs: provides API for simulated object catalogs", "Installation Instructions", "Solar System Object (SSO) quantities for ops-rehearsals 3 and 4", "Star quantities for ops-rehearsals 3 and 4", "Galaxy quantities for ops-rehearsals 3 and 4", "The skyCatalogs package", "Star quantities for Roman-Rubin sims", "Galaxy quantities for Roman-Rubin joint simulation", "SNANA quantities for Roman-Rubin sims", "Creating New Catalogs", "Reading Catalogs with skyCatalogs"], "titleterms": {"3": [3, 4, 5], "4": [3, 4, 5], "The": [6, 10], "ad": 11, "an": 11, "api": 1, "catalog": [1, 10, 11], "class": 6, "config": 11, "contact": 0, "content": 1, "creat": 10, "create_flux": 10, "create_main": 10, "data": 2, "descript": 11, "exampl": 10, "file": [2, 3, 4, 5, 7, 8, 9, 10], "flux": [3, 4, 5, 7, 8], "galaxi": [5, 8], "includ": 11, "indic": 1, "instal": 2, "instruct": 2, "its": 10, "itself": 2, "joint": 8, "load": 2, "lsst": 2, "main": [3, 4, 5, 7, 8, 9], "need": 2, "new": 10, "object": [1, 3, 11], "op": [3, 4, 5], "open": 11, "option": 10, "packag": 6, "pipelin": 2, "provid": 1, "py": 10, "quantiti": [3, 4, 5, 7, 8, 9], "read": 11, "rehears": [3, 4, 5], "roman": [7, 8, 9], "rubin": [7, 8, 9], "scienc": 2, "script": 10, "sed": 8, "set": 2, "setup": 2, "sim": [7, 9], "simul": [1, 8], "skycatalog": [1, 2, 6, 11], "snana": 9, "solar": 3, "sso": 3, "star": [4, 7], "structur": 11, "support": 11, "system": 3, "tabl": [1, 10], "type": 11, "up": 2, "us": [2, 11], "vari": 9}}) \ No newline at end of file diff --git a/usage_create.html b/usage_create.html new file mode 100644 index 0000000..8c1ec0d --- /dev/null +++ b/usage_create.html @@ -0,0 +1,412 @@ + + + + + + + + + Creating New Catalogs — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Creating New Catalogs

+

Catalogs - both the binary data files and yaml config - for some object types +can be created using the script create_main.py and +create_flux.py. Creation of the main catalog must precede +creation of the flux catalog for the same sky region. +For other object types the data are +created by other means, but it is still necessary to make a suitable +config fragment so that the skyCatalogs API can access the data.

+
+

The script create_main.py and its options

+

create_main.py has a plethora of options, but few are of interest +for most invocations and even fewer are required. The options determine

+
    +

  • object type for which files will be created (required)

    • +

  • region of the sky for which files will be created.

    • +

  • where the output goes

    • +

  • inputs (usually defaulted, depending on object type)

    • +

  • numerous options conditioning exactly how the output is to be created, +most of which are usually defaulted

    • +
+

One particularly handy option, --options-file, allows you to specify +everything else as key-value pairs in a yaml file.

+
+

Options table

+

Here is the complete list of options as they appear in an options file. +On the command line, prepend -- and change all underscores to hyphens.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Default

Description

object_type

string

Required. One of {star, sso, +cosmodc2_galaxy, diffsky_galaxy}

catalog_dir

string

“.”

Location of catalog relative +to skycatalog_root +(see below)

catalog_name

string

“skyCatalog”

Name of top-level yaml config +file

config_path

string

None

where to write config. If +None, same folder as data

dc2

boolean

False

Use dc2 conventions

galaxy_magnitude_cut

float

29.0

Discard galaxies above cut. +Ignored for non-galaxy +object types

nside

int

32

nside for healpixels

stride

int

1_000_000

Max objects output per row +group

truth

string

None

Default depends on object_type

knots_magnitude_cut

float

27.0

Omit knots component from +galaxies with i-mag above cut

log_level

string

“INFO”

Log level

no_knots

boolean

False

Omit knot component

options_file

string

None

Path to file where other +options are set

pixels

int list

[9556]

healpix pixels for which +catalog will be created

skip_done

boolean

False

do not overwrite existing files

skycatalog_root

string

None

Abs. path. See catalog_dir

sso_sed

string

None

Path to file to SED to be +used for all SSOs. Defaults +to solar_sed_thin.txt, +included in repo.

star_input_fmt

string

“sqlite”

Format of star truth

+
+
+
+

The script create_flux.py and its options

+

create_flux.py has most of the same options as create_main.py +plus a couple new ones. Only object_type is required but several +others are specified for most invocations.

+
+

Options table

+

Here is the complete list of options as they appear in an options file. +On the command line, prepend -- and change all underscores to hyphens.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Name

Datatype

Default

Description

object_type

string

Required. One of {star, sso, +cosmodc2_galaxy, diffsky_galaxy}

catalog_dir

string

“.”

Location of catalog relative +to skycatalog_root +(see below)

catalog_name

string

“skyCatalog”

Name of top-level yaml config +file

config_path

string

None

where to write config. If +None, same folder as data

flux_parallel

int

16

# processes to run in parallel +when computing fluxes

iclude_roman_flux

boolean

False

If True calculate & store Roman +as well as Rubin fluxes.

log_level

string

“INFO”

Log level

options_file

string

None

Path to file where other +options are set

pixels

int list

[9556]

healpix pixels for which +catalog will be created

skip_done

boolean

False

do not overwrite existing files

skycatalog_root

string

None

Abs. path. See catalog_dir

sso_sed

string

None

Path to file to SED to be +used for all SSOs. Defaults +to solar_sed_thin.txt, +included in repo.

+
+
+

Example options files

+

Create cosmodc2-style galaxies main file. This file was one I wrote +primarily for testing the creation code. In order to speed things up, I +set galaxy_magnitude_cut down to 20.0. The output file is about 1000 times +smaller than with the default cut.

+
object_type:          cosmodc2_galaxy
+catalog_dir:          just_testing
+pixels:               [9683]
+galaxy_magnitude_cut: 20.0    # Default is 29.0
+log_level:            DEBUG   # Default is INFO
+
+
+

Suppose the file is called main_galaxy.yaml. It can be invoked as follows:

+
python cosmodc2_galaxy --options-file main_galaxy.yaml
+
+
+
+

Note

+

Since object_type is required it must be specified both on the +command line and in the options file.

+
+

Create star flux file for a couple healpixels. +The default value of flux_parallel is rather conservative for Perlmutter, +so use something higher to make the process go faster.

+
catalog_dir:          just_testing
+pixels:               [9683, 9684]
+flux_parallel:        24      # Default is 16
+
+
+
+

Note

+

The star main files for both healpixels must already exist in the output +directory since they are input to the flux generation.

+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/usage_read.html b/usage_read.html new file mode 100644 index 0000000..6f5a875 --- /dev/null +++ b/usage_read.html @@ -0,0 +1,320 @@ + + + + + + + + + Reading Catalogs with skyCatalogs — skyCatalogs 1.7.0-rc4 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Reading Catalogs with skyCatalogs

+

Typically making use of skyCatalogs involves three steps:

+
    +

  1. “Open” the catalog. This is accomplished by reading a config: one or more +yaml files which describes features of the catalog. Config files will +be described in detail below.

    2. +

  2. Select objects of specified types (e.g. galaxies or stars or both) within +a region of the sky.

    3. +

  3. Obtain properties of the objects for use by your application.

    4. +
+

The last two steps are often executed multiple times.

+
+

Opening a Catalog

+

You open a catalog like this:

+
from skycatalogs.skyCatalogs import open_catalog
+
+skycatalog_root = "some_path/data_folder"
+config_file = "another_path/skyCatalog.yaml"
+
+cat = open_catalog(config_file, skycatalog_root=skycatalog_root)
+
+
+

Often the config file is in the same folder as the data but it need not be.

+

If skycatalog_root is not specified, the code will use the value of the +environment variable SKYCATALOG_ROOT if it exists,

+
+
+
+

Structure of skyCatalogs Configs

+

Configs contain a variety of information. Some of it is required for the +skyCatalogs API to find and make sense of the binary data. Other quantities +are primarily for human consumption. An up-to-date config (version 1.3.0 +or later) is a mapping with only a few keys, currently skycatalog_root, +catalog_dir, catalog_name, schema_version and object_types. The +first three are used to find the data. schema_version refers to the +version of the config structure. The value of object_types +is a mapping with a key for each object type having data in the catalog. +The bulk of the information may be found +under those keys. That information may be included literally in the +config file but it is preferable to isolate information pertaining to each +object type in its own yaml file and use the yaml !include +directive to incorporate it.

+
+

Using !include

+
catalog_dir:        .             # See Note 1.
+catalog_name:       skyCatalog    # default name for top-level yaml file
+object_types:
+  galaxy: !include galaxy.yaml    # See Note 2.
+  star: !include |-               # The  |- indicates continue to next line
+    star.yaml                     # & may appear in auto-generated top files
+skycatalog_root:    /some/path/often/absolute   # see Note 3.
+schema_version:     1.3.0
+
+
+
+

Note

+
    +

  1. catalog_dir indicates where yaml and data files are to be found +relative to skycatalog_root. See also Note 3.

    2. +

  2. The !include directive is not supported by yaml natively, but one can +add an implementation. This has been done for the skyCatalogs API.

    3. +

  3. When the top-level yaml file is written, skycatalog_root is normally +an absolute path. That file is in the catalog_dir subdirectory of +skycatalog_root. But, in case the catalog has been copied, +skycatalog_root may be overridden at run time when invoking +open_catalog. catalog_dir is then interpreted to be relative to +the new value of skycatalog_root.

    4. +
+
+
+
+

Description of an object type

+

For the most part the configuration file fragment for an object type will +either be written by the code generating the binary data for that object +type or will be provided some other way by whoever provides the data. It +is not normally something users of the skyCatalogs API need be concerned with. +However, for those who are curious, such fragments usually include several +kinds of information:

+
    +

  • information allowing the API to find the data files for the object type

    • +

  • provenance, which in turn may consist of some or all of the following:

    +
      +

    • inputs used in the creation of the data files

      • +

    • run options supplied to the creating program

      • +

    • schema version

      • +

    • version of the program and information about the state of the git repo containing the program source

      • +
    +
    • +

  • other information associated with the object type

    • +
+

Here is an example file for the star object type:

+
area_partition:
+  nside: 32
+  ordering: ring
+  type: healpix
+data_file_type: parquet
+file_template: pointsource_(?P<healpix>\d+).parquet
+flux_file_template: pointsource_flux_(?P<healpix>\d+).parquet
+provenance:
+  inputs:
+    star_truth: /global/cfs/cdirs/lsst/groups/SSim/DC2/dc2_stellar_healpixel.db
+  run_options:
+    catalog_dir: out_config
+    catalog_name: skyCatalog
+    config_path: null
+    dc2: false
+    flux_parallel: 16
+    galaxy_magnitude_cut: 29.0
+    galaxy_nside: 32
+    galaxy_stride: 1000000
+    galaxy_truth: null
+    galaxy_type: cosmodc2
+    include_roman_flux: false
+    knots_magnitude_cut: 27.0
+    log_level: DEBUG
+    no_flux: true
+    no_galaxies: true
+    no_knots: false
+    no_main: false
+    no_pointsources: false
+    options_file: local/out_config/star_main.yaml
+    pixels:
+    - 9556
+    sed_subdir: galaxyTopHatSED
+    skip_done: true
+    skycatalog_root: null
+    sso: false
+    sso_sed: null
+    sso_truth: null
+    star_input_fmt: sqlite
+  skyCatalogs_repo:
+    git_branch: u/jrbogart/config_reorg
+    git_hash: 6da4f9636cc63010480c1a1c086cbde8f6ca4dd4
+    git_status:
+    - UNCOMMITTED_FILES
+    - UNTRACKED_FILES
+  versioning:
+    code_version: 1.7.0-rc4
+    schema_version: 1.3.0
+sed_file_root_env_var: SIMS_SED_LIBRARY_DIR
+sed_model: file_nm
+file_nm:
+  units: nm
+internal_extinction: None
+
+
+
+
+
+

Adding Supported Object Types to a Catalog

+

We expect most users will use pre-assembled catalogs, already containing +all the kinds of objects they need, but it’s possible someone will have to +add a new type to a collection. Assuming the data files and a suitable +config fragment for the new type exist somewhere else, one only needs to +copy them to the catalog directory, then edit the top-level config file +by adding a line to the object_types section:

+
object_types:
+  galaxy: !include galaxy.yaml
+  star: !include star.yaml
+  sso: !include sso.yaml      # the new one
+
+
+

Of course the skyCatalogs API has to know how to handle the new type.

+
+

Supported object types

+

As of August, 2024, the following object types are supported.

+
+
star

as in the DC2 simulation, generated from the UW database

+
+
galaxy

as in the DC2 simulation, generated from the cosmodc2 catalog

+
+
diffsky_galaxy

galaxies simulated from simple stellar populations

+
+
snana

SNe generated by the SNANA simulation program, using either +galaxy or diffsky_galaxy objects as hosts

+
+
sso

solar system objects generated by Sorcha

+
+
gaia_star

Gaia catalog dr2

+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file