From 86aaceba1a64255bf3ce46b6d2ea98615e6b21af Mon Sep 17 00:00:00 2001
From: Aaron LI <aly@aaronly.me>
Date: Tue, 30 Oct 2018 19:59:07 +0800
Subject: configs: Merge config specs into one single file
---
MANIFEST.in | 2 +-
fg21sim/configs/00-general.conf.spec | 151 ---------
fg21sim/configs/10-galactic.conf.spec | 89 ------
fg21sim/configs/20-extragalactic.conf.spec | 266 ----------------
fg21sim/configs/config.spec | 492 +++++++++++++++++++++++++++++
fg21sim/configs/manager.py | 19 +-
6 files changed, 495 insertions(+), 524 deletions(-)
delete mode 100644 fg21sim/configs/00-general.conf.spec
delete mode 100644 fg21sim/configs/10-galactic.conf.spec
delete mode 100644 fg21sim/configs/20-extragalactic.conf.spec
create mode 100644 fg21sim/configs/config.spec
diff --git a/MANIFEST.in b/MANIFEST.in
index 10eb325..580f3cc 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,5 @@
include LICENSE
include LICENSE-3RDPARTY
-include fg21sim/configs/*.conf.spec
+include fg21sim/configs/*.spec
include fg21sim/webui/templates/*.html
recursive-include fg21sim/webui/static *
diff --git a/fg21sim/configs/00-general.conf.spec b/fg21sim/configs/00-general.conf.spec
deleted file mode 100644
index 353e2cf..0000000
--- a/fg21sim/configs/00-general.conf.spec
+++ /dev/null
@@ -1,151 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-# This file contains the general configurations, which control the general
-# behaviors, or will be used in other configuration sections.
-
-
-# Foreground components to be simulated
-[foregrounds]
-# Diffuse Galactic synchrotron emission (unpolarized)
-galactic/synchrotron = boolean(default=False)
-
-# Diffuse Galactic free-free emission
-galactic/freefree = boolean(default=False)
-
-# Galactic supernova remnants emission
-galactic/snr = boolean(default=False)
-
-# Extragalactic clusters of galaxies emission
-extragalactic/clusters = boolean(default=False)
-
-# Emission from multiple types of extragalactic point sources
-# NOTE: This component is not well integrated and tested at the moment
-extragalactic/pointsources = boolean(default=False)
-
-
-# Simulation sky/region configurations
-[sky]
-# Type of the input/output simulation sky
-# + patch:
-# Input/output sky template is only a (square) patch of the sky.
-# The simulated output maps have the same coverage/field as the
-# input template, as well as the coordinate projection.
-# + healpix:
-# Input/output sky template covers (almost) all sky, and stored
-# in HEALPix format. The simulated output maps will also be
-# all-sky using the HEALPix projection.
-type = option("patch", "healpix", default="patch")
-
- # Configurations for input/output sky patch
- [[patch]]
- # The (R.A., Dec.) coordinate of the sky patch center
- # Unit: [deg]
- # (MWA EoR0 field center: (0, -27))
- xcenter = float(default=0.0, min=0.0, max=360.0)
- ycenter = float(default=-27.0, min=-90.0, max=90.0)
-
- # The image dimensions (i.e., number of pixels) of the sky patch,
- # along the X (R.A./longitude) and Y (Dec./latitude) axes.
- # Default: 1800x1800 => 10x10 [deg^2] (20 arcsec/pixel)
- xsize = integer(default=1800, min=1)
- ysize = integer(default=1800, min=1)
-
- # Pixel size [arcsec]
- pixelsize = float(default=20.0, min=0.0)
-
- # Configurations for input/output HEALPix sky
- [[healpix]]
- # HEALPix Nside value, i.e., pixel resolution
- nside = integer(default=1024, min=128)
-
-
-# Frequencies specification of the simulation products
-[frequency]
-# How to specify the frequencies
-# + custom:
-# directly specify the frequency values using the "frequencies" config
-# + calc:
-# calculate the frequency values by "start", "stop", and "step"
-type = option("custom", "calc", default="custom")
-
-# The frequency values to be simulated if above "type" is "custom".
-# Unit: [MHz]
-frequencies = float_list(default=list())
-
-# Parameters to calculate the frequencies
-# NOTE: "start" and "stop" frequencies are both inclusive.
-# Unit: [MHz]
-start = float(default=None, min=0.0)
-stop = float(default=None, min=0.0)
-step = float(default=None, min=0.0)
-
-
-# Configuration for output products
-[output]
-# Filename pattern for the output products, which will be finally
-# formatted using `str.format()`.
-filename_pattern = string(default="{prefix}_{frequency:06.2f}.fits")
-
-# Use single-precision float instead of double (to save spaces)
-float32 = boolean(default=True)
-
-# Whether to calculate the checksum for the output FITS file?
-# NOTE: May cost significantly more time on writing FITS file.
-checksum = boolean(default=False)
-
-# Whether to overwrite existing files (e.g., maps, catalogs, manifest, ...)
-clobber = boolean(default=False)
-
-# Filename of the simulation products manifest (JSON format), which
-# records all output products together with their sizes and MD5 hashes.
-# Do not create such a manifest if this option is not specified.
-manifest = string(default=None)
-
-
-# Cosmological parameters
-# References: Komatsu et al. 2011, ApJS, 192, 18; Tab.(1)
-[cosmology]
-# Hubble constant at z=0; [km/s/Mpc]
-H0 = float(default=71.0, min=0.0)
-# Density of non-relativistic matter in units of the critical density at z=0
-OmegaM0 = float(default=0.27, min=0.0, max=1.0)
-# Density of the baryon at present day
-Omegab0 = float(default=0.046, min=0.0, max=1.0)
-# Present-day CMB temperature; [K]
-Tcmb0 = float(default=2.725)
-# Present-day rms density fluctuations on a scale of 8 h^-1 [Mpc]
-sigma8 = float(default=0.81, min=0.0)
-# Scalar spectral index
-ns = float(default=0.96, min=0.0)
-
-
-# Configurations for initialization/reconfiguration of the `logging` module
-[logging]
-# debug: Detailed information, typically of interest only when diagnosing
-# problems.
-# info: Confirmation that things are working as expected.
-# warning: An indication that something unexpected happended, or indicative
-# of some problem in the near future (e.g., "disk space low").
-# The software is still working as expected.
-# error: Due to a more serious problem, the software has not been able to
-# perform some function.
-# critical: A serious error, indicating that the program itself may be unable
-# to continue running.
-level = option("debug", "info", "warning", "error", "critical", default="info")
-
-# Set the format of displayed messages
-format = string(default="%(asctime)s [%(levelname)s] <%(name)s:%(lineno)d> %(message)s")
-
-# Set the date/time format in messages
-datefmt = string(default="%H:%M:%S")
-
-# Set the logging filename (will create a `FileHandler`)
-# If set to "" (empty string), then the `FileHandler` will be disabled.
-filename = string(default="")
-
-# Set the stream used to initialize the `StreamHandler`
-# If set to "" (empty string), then the `StreamHandler` will be disabled.
-stream = option("stderr", "stdout", "", default="stderr")
diff --git a/fg21sim/configs/10-galactic.conf.spec b/fg21sim/configs/10-galactic.conf.spec
deleted file mode 100644
index 9185dc0..0000000
--- a/fg21sim/configs/10-galactic.conf.spec
+++ /dev/null
@@ -1,89 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-# This file contains the options corresponding the Galactic emission
-# components, which currently includes the following components:
-# - synchrotron
-# - freefree
-# - snr
-
-
-[galactic]
-
- # Synchrotron emission component (unpolarized)
- [[synchrotron]]
- # The template map for the simulation, e.g., Haslam 408 MHz survey.
- # Unit: [K] (Kelvin)
- template = string(default=None)
- # The frequency of the template map.
- # Unit: [MHz]
- template_freq = float(default=None, min=0.0)
-
- # Spectral index map
- indexmap = string(default=None)
-
- # Whether add fluctuations on the small scales according the angular
- # power spectrum prediction?
- add_smallscales = boolean(default=False)
- # Range of multipole moments (l) of the angular power spectrum.
- # The power spectrum will be cut off to a constant for multipole l < lmin.
- # NOTE: Update the ``lmax`` accordingly w.r.t. ``sky/healpix/nside``.
- # Generally, lmax = 3 * nside - 1
- lmin = integer(min=0, default=10)
- lmax = integer(min=1, default=3071)
-
- # Filename prefix for this component
- prefix = string(default="gsync")
- # Output directory to save the simulated results
- output_dir = string(default=None)
-
- # Free-free bremsstrahlung emission component
- [[freefree]]
- # The Hα map from which to derive the free-free emission
- # Unit: [Rayleigh]
- halphamap = string(default=None)
-
- # The 100-μm dust map used to correct Hα dust absorption
- # Unit: [MJy/sr]
- dustmap = string(default=None)
-
- # Effective dust fraction in the LoS actually absorbing Halpha
- dust_fraction = float(default=0.33, min=0.1, max=1.0)
-
- # Halpha absorption threshold:
- # When the dust absorption goes rather large, the true Halpha
- # absorption can not well determined. This configuration sets the
- # threshold below which the dust absorption can be well determined,
- # while the sky regions with higher absorption are masked out due
- # to unreliable absorption correction.
- # Unit: [mag]
- halpha_abs_th = float(default=1.0)
-
- # The electron temperature assumed for the ionized interstellar medium
- # that generating H{\alpha} emission.
- # Unit: [K]
- electron_temperature = float(default=7000.0, min=1000)
-
- # Filename prefix for this component
- prefix = string(default="gfree")
- # Output directory to save the simulated results
- output_dir = string(default=None)
-
- # Supernova remnants emission
- [[snr]]
- # The Galactic SNRs catalog data (CSV file)
- catalog = string(default=None)
- # Output the effective/inuse SNRs catalog data (CSV file)
- catalog_outfile = string(default=None)
-
- # Resolution for simulating each SNR template, which are finally
- # mapped to the all-sky HEALPix map if used.
- # Unit: [arcsec]
- resolution = float(default=30.0, min=5.0)
-
- # Filename prefix for this component
- prefix = string(default="gsnr")
- # Output directory to save the simulated results
- output_dir = string(default=None)
diff --git a/fg21sim/configs/20-extragalactic.conf.spec b/fg21sim/configs/20-extragalactic.conf.spec
deleted file mode 100644
index 943c7e0..0000000
--- a/fg21sim/configs/20-extragalactic.conf.spec
+++ /dev/null
@@ -1,266 +0,0 @@
-# Configurations for "fg21sim"
-# -*- mode: conf -*-
-#
-# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
-#
-# This file contains the options corresponding the extragalactic emission
-# components, which currently includes the following components:
-# - clusters: halos
-# - pointsources
-
-
-[extragalactic]
- #
- # Press-Schechter formalism to determine the cluster distributions
- # with respect to mass and redshift, from which to further determine
- # the total number of clusters within a sky patch and to sample the
- # masses and redshifts for each cluster.
- #
- [[psformalism]]
- # The model of the fitting function for halo/cluster mass distribution
- # For all models and more details:
- # https://hmf.readthedocs.io/en/latest/_autosummary/hmf.fitting_functions.html
- model = option("smt", "jenkins", "ps", default="ps")
-
- # The minimum (inclusive) and maximum (exclusive!) cluster mass
- # within which to calculate the halo mass distribution.
- # Unit: [Msun]
- M_min = float(default=1e12, min=1e10, max=1e14)
- M_max = float(default=1e16, min=1e14, max=1e18)
- # The logarithmic (base 10) step size for the halo masses; therefore
- # the number of intervals is: (log10(M_max) - log10(M_min)) / M_step
- M_step = float(default=0.01, min=0.001, max=0.1)
-
- # The minimum and maximum redshift within which to calculate the
- # halo mass distribution; as well as the step size.
- z_min = float(default=0.01, min=0.001, max=1.0)
- z_max = float(default=4.0, min=1.0, max=100)
- z_step = float(default=0.01, min=0.001, max=1.0)
-
- # Output file (NumPy ".npz" format) to save the calculated halo mass
- # distributions at every redshift.
- #
- # This file packs the following 3 NumPy arrays:
- # * ``z``:
- # Redshifts where the halo mass distribution is calculated.
- # * ``mass``:
- # (Logarithmic-distributed) masses points.
- # Unit: [Msun] (the little "h" is folded into the values)
- # * ``dndlnm``:
- # Shape: (len(z), len(mass))
- # Differential mass function in terms of natural log of M.
- # Unit: [Mpc^-3] (the little "h" is folded into the values)
- dndlnm_outfile = string(default=None)
-
-
- #
- # Extended emissions from the clusters of galaxies
- # The configurations in this ``[[clusters]]`` section may also be
- # used by the following ``[[halos]]`` section.
- #
- [[clusters]]
- # Output CSV file of the cluster catalog containing the simulated
- # mass, redshift, position, shape, recent merger info, etc.
- catalog_outfile = string(default=None)
-
- # Whether to dump the raw data of the simulated cluster catalog in
- # Python native pickle format (i.e., ".pkl") to a file with the same
- # basename as the above ``catalog_outfile``?
- # The dumped data can be easily loaded back for reuse.
- dump_catalog_data = boolean(default=True)
-
- # Whether to directly use the (previously simulated) catalog data as
- # specified by the above "catalog_outfile" and ``dump_catalog_data``
- # options?
- # NOTE:
- # By using an existing catalog, the steps to derive these data are
- # simply skipped.
- # Due to the small number density of the galaxy clusters, the simulated
- # results within a small patch of sky (e.g., 100 [deg^2]) show
- # significant fluctuations (several or even several tens of times
- # of differences between simulations). Therefore, one may run many
- # tests and only create images at some frequencies necessary for
- # testing, then select the satisfying one to continue the simulation
- # to generate images at all frequencies.
- use_dump_catalog_data = boolean(default=False)
-
- # Output CSV file of the halos catalog containing the calculated
- # properties of the simulated halos.
- halos_catalog_outfile = string(default=None)
-
- # Whether to dump the whole data of the simulated halos in Python
- # native pickle format (i.e., ".pkl") to a file with the same basename
- # as the above ``halos_catalog_outfile``?
- # The dumped data also includes the derived electron spectrum for
- # each halo, therefore this file can be reloaded back in order to
- # calculate the emissions at other frequencies.
- dump_halos_data = boolean(default=True)
-
- # Whether to directly use the (previously dumped) halos data (".pkl")
- # as specified by the above ``halos_catalog_outfile`` and
- # ``dump_halos_data`` options?
- # In this way, the radio emissions at additional frequencies can be
- # easily (and consistently) calculated.
- use_dump_halos_data = boolean(default=False)
-
- # The minimum mass for clusters when to determine the galaxy clusters
- # total counts and their distributions.
- # Unit: [Msun]
- mass_min = float(default=1e14, min=1e13)
-
- # Boost the number of expected cluster number within the sky coverage
- # by the specified times.
- # WARNING: for testing usage.
- boost = float(default=1.0, min=0.1, max=1e4)
-
- # Minimal elongated fraction for creating the images of radio halos
- # The ``felong`` is defined as ``felong = b/a``, similar to the Hubble
- # classification for the elliptical galaxies. ``felong_min = 1.0``
- # means no elongation, and ``felong_min = 0.6`` is a good choice as
- # the observed radio halos are generally regular.
- felong_min = float(default=1.0, min=0.1, max=1.0)
-
- # Number of most powerful halos to be dropped out.
- halo_dropout = integer(default=0, min=0)
-
- # Minimum mass change of the main cluster to be regarded as a merger
- # event instead of an accretion event.
- # Unit: [Msun]
- merger_mass_min = float(default=1e13, min=1e11, max=1e14)
-
- # The trace back time when to stop tracing the merging history of
- # clusters. ~2-3 Gyr should be enough since the turbulence acceleration
- # effective time ~<1 Gyr and the halo lifetime is also short compared
- # to mergers.
- # Unit: [Gyr]
- time_traceback = float(default=3.0, min=1.0, max=5.0)
-
- # The fraction of the magnetic field energy density w.r.t. the ICM
- # thermal energy density, which is used to determine the mean magnetic
- # field strength within the ICM and is also assumed to be uniform.
- # * ~< 0.4% (Ref: Pfrommer & Ensslin 2004, MNRAS)
- # * ~0.3%-1% (Ref: Bohringer et al. 2016, A&A)
- eta_b = float(default=0.001, min=1e-5, max=0.1)
-
- # The temperature of the outer gas surrounding the cluster. Accretion
- # shocks form near the cluster virial radius during the cluster formation,
- # which can heat the cluster ICM to have a higher temperature than the
- # virial temperature:
- # kT_icm ~ kT_vir + 1.5 * kT_out,
- # with: kT_out ~ 0.5 [keV]
- # Reference: Fujita et al. 2003, ApJ, 584, 190; Eq.(49)
- # Unit: [keV]
- kT_out = float(default=0.0, min=0.0)
-
- # Filename prefix for this component
- prefix = string(default="cluster")
- # Output directory to save the simulated results
- output_dir = string(default=None)
-
-
- #
- # Giant radio halos
- #
- [[halos]]
- # A custom parameter to tune the turbulent acceleration efficiency.
- # NOTE: The smaller this parameter, the shorter the acceleration
- # timescale, therefore more efficient acceleration.
- f_acc = float(default=1.0, min=0.1, max=10)
-
- # The turbulence is generally injected at the cluster center during
- # a merger. This option parameterize the turbulence injection scale
- # to be a fraction of the virial radius of the cluster, which is also
- # used to determine the radio halo size.
- f_lturb = float(default=0.33, min=0.1, max=1.0)
-
- # An efficiency factor describing the effectiveness of plasma
- # instabilities (e.g., due to spatial or temporal intermittency).
- zeta_ins = float(default=0.1, min=0.1, max=1.0)
-
- # The fraction of merger energy transferred into the turbulence.
- eta_turb = float(default=0.1, min=0.1, max=0.5)
-
- # The fraction of the thermal energy injected into the cosmic-ray
- # electrons during the cluster life time.
- eta_e = float(default=0.003, min=0.001, max=0.1)
-
- # The ratio of cosmic ray (including protons and electrons) energy
- # density (i.e., pressure) to the thermal energy density.
- # NOTE: Fermi-LAT has placed an upper limit of ~1.25%-1.4%
- # (Ackermann et al. 2014, ApJ, 787, 18)
- # NOTE: The energy ratio of cosmic-ray electrons to protons K_ep ~0.01
- # for our Galaxy (Pinzke et al. 2017, MNRAS, 465, 4800)
- x_cr = float(default=0.015, min=0.001, max=0.1)
-
- # Electron injection, which is assumed to have a constant injection
- # rate and a power-law spectrum.
- injection_index = float(default=2.3, min=2.1, max=3.0)
-
- # Minimum and maximum Lorentz factor (i.e., energy) of the relativistic
- # electron spectrum.
- gamma_min = float(default=1)
- gamma_max = float(default=1e5)
- # Number of cells on the logarithmic momentum grid used to solve the
- # Fokker-Planck equation.
- gamma_np = integer(default=200)
-
- # Number of cells used as the buffer regions near both the lower
- # and upper boundaries, within which the values will be replaced by
- # extrapolating from the inner-region data, in order to avoid the
- # unphysical particle pile-ups.
- # It is suggested to be about 5%-10% of the above ``gamma_np``.
- # NOTE: * set to 0 to disable boundary fixes;
- # * otherwise, set to a number >= 2.
- buffer_np = integer(default=10, min=0)
-
- # Time step for solving the Fokker-Planck equation
- # Unit: [Gyr]
- time_step = float(default=0.02, min=1e-4, max=0.1)
-
- # How long the period before the merger begins, which is used to derive
- # an approximately steady initial electron spectrum. During this period,
- # the acceleration is turned off and only leaves energy loss mechanisms.
- # Unit: [Gyr]
- time_init = float(default=1.0, min=0)
-
-
- #
- # Extragalactic point sources
- #
- [[pointsources]]
- # Output directory to save the simulated catalog
- output_dir = string(default="PS_tables")
- # PS components to be simulated
- pscomponents = string_list(default=list())
- # Resolution [arcmin]
- resolution = float(default=0.6, min=0.0)
-
- [[[starforming]]]
- # Number of samples
- numps = integer(default=1000)
- # Prefix
- prefix = string(default="SF")
-
- [[[starbursting]]]
- # Number of samples
- numps = integer(default=1000)
- # Prefix
- prefix = string(default="SB")
-
- [[[radioquiet]]]
- # Number of samples
- numps = integer(default=1000)
- # Prefix
- prefix = string(default="RQ")
-
- [[[FRI]]]
- # Number of samples
- numps = integer(default=1000)
- # Prefix
- prefix = string(default="FRI")
-
- [[[FRII]]]
- # Number of samples
- numps = integer(default=1000)
- # Prefix
- prefix = string(default="FRII")
diff --git a/fg21sim/configs/config.spec b/fg21sim/configs/config.spec
new file mode 100644
index 0000000..6b871e4
--- /dev/null
+++ b/fg21sim/configs/config.spec
@@ -0,0 +1,492 @@
+#
+# Configurations for "fg21sim"
+# Syntax: `ConfigObj`, https://github.com/DiffSK/configobj
+#
+
+
+# Foreground components to be simulated
+[foregrounds]
+# Diffuse Galactic synchrotron emission (unpolarized)
+galactic/synchrotron = boolean(default=False)
+
+# Diffuse Galactic free-free emission
+galactic/freefree = boolean(default=False)
+
+# Galactic supernova remnants emission
+galactic/snr = boolean(default=False)
+
+# Extragalactic clusters of galaxies emission
+extragalactic/clusters = boolean(default=False)
+
+# Emission from multiple types of extragalactic point sources
+# NOTE: This component is not well integrated and tested at the moment
+extragalactic/pointsources = boolean(default=False)
+
+
+# Simulation sky/region configurations
+[sky]
+# Type of the input/output simulation sky
+# + patch:
+# Input/output sky template is only a (square) patch of the sky.
+# The simulated output maps have the same coverage/field as the
+# input template, as well as the coordinate projection.
+# + healpix:
+# Input/output sky template covers (almost) all sky, and stored
+# in HEALPix format. The simulated output maps will also be
+# all-sky using the HEALPix projection.
+type = option("patch", "healpix", default="patch")
+
+ # Configurations for input/output sky patch
+ [[patch]]
+ # The (R.A., Dec.) coordinate of the sky patch center
+ # Unit: [deg]
+ # (MWA EoR0 field center: (0, -27))
+ xcenter = float(default=0.0, min=0.0, max=360.0)
+ ycenter = float(default=-27.0, min=-90.0, max=90.0)
+
+ # The image dimensions (i.e., number of pixels) of the sky patch,
+ # along the X (R.A./longitude) and Y (Dec./latitude) axes.
+ # Default: 1800x1800 => 10x10 [deg^2] (20 arcsec/pixel)
+ xsize = integer(default=1800, min=1)
+ ysize = integer(default=1800, min=1)
+
+ # Pixel size [arcsec]
+ pixelsize = float(default=20.0, min=0.0)
+
+ # Configurations for input/output HEALPix sky
+ [[healpix]]
+ # HEALPix Nside value, i.e., pixel resolution
+ nside = integer(default=1024, min=128)
+
+
+# Frequencies specification of the simulation products
+[frequency]
+# How to specify the frequencies
+# + custom:
+# directly specify the frequency values using the "frequencies" config
+# + calc:
+# calculate the frequency values by "start", "stop", and "step"
+type = option("custom", "calc", default="custom")
+
+# The frequency values to be simulated if above "type" is "custom".
+# Unit: [MHz]
+frequencies = float_list(default=list())
+
+# Parameters to calculate the frequencies
+# NOTE: "start" and "stop" frequencies are both inclusive.
+# Unit: [MHz]
+start = float(default=None, min=0.0)
+stop = float(default=None, min=0.0)
+step = float(default=None, min=0.0)
+
+
+# Configuration for output products
+[output]
+# Filename pattern for the output products, which will be finally
+# formatted using `str.format()`.
+filename_pattern = string(default="{prefix}_{frequency:06.2f}.fits")
+
+# Use single-precision float instead of double (to save spaces)
+float32 = boolean(default=True)
+
+# Whether to calculate the checksum for the output FITS file?
+# NOTE: May cost significantly more time on writing FITS file.
+checksum = boolean(default=False)
+
+# Whether to overwrite existing files (e.g., maps, catalogs, manifest, ...)
+clobber = boolean(default=False)
+
+# Filename of the simulation products manifest (JSON format), which
+# records all output products together with their sizes and MD5 hashes.
+# Do not create such a manifest if this option is not specified.
+manifest = string(default=None)
+
+
+# Cosmological parameters
+# References: Komatsu et al. 2011, ApJS, 192, 18; Tab.(1)
+[cosmology]
+# Hubble constant at z=0; [km/s/Mpc]
+H0 = float(default=71.0, min=0.0)
+# Density of non-relativistic matter in units of the critical density at z=0
+OmegaM0 = float(default=0.27, min=0.0, max=1.0)
+# Density of the baryon at present day
+Omegab0 = float(default=0.046, min=0.0, max=1.0)
+# Present-day CMB temperature; [K]
+Tcmb0 = float(default=2.725)
+# Present-day rms density fluctuations on a scale of 8 h^-1 [Mpc]
+sigma8 = float(default=0.81, min=0.0)
+# Scalar spectral index
+ns = float(default=0.96, min=0.0)
+
+
+# Configurations for initialization/reconfiguration of the `logging` module
+[logging]
+# debug: Detailed information, typically of interest only when diagnosing
+# problems.
+# info: Confirmation that things are working as expected.
+# warning: An indication that something unexpected happended, or indicative
+# of some problem in the near future (e.g., "disk space low").
+# The software is still working as expected.
+# error: Due to a more serious problem, the software has not been able to
+# perform some function.
+# critical: A serious error, indicating that the program itself may be unable
+# to continue running.
+level = option("debug", "info", "warning", "error", "critical", default="info")
+
+# Set the format of displayed messages
+format = string(default="%(asctime)s [%(levelname)s] <%(name)s:%(lineno)d> %(message)s")
+
+# Set the date/time format in messages
+datefmt = string(default="%H:%M:%S")
+
+# Set the logging filename (will create a `FileHandler`)
+# If set to "" (empty string), then the `FileHandler` will be disabled.
+filename = string(default="")
+
+# Set the stream used to initialize the `StreamHandler`
+# If set to "" (empty string), then the `StreamHandler` will be disabled.
+stream = option("stderr", "stdout", "", default="stderr")
+
+
+#
+# Galactic emission components
+#
+
+[galactic]
+
+ # Synchrotron emission component (unpolarized)
+ [[synchrotron]]
+ # The template map for the simulation, e.g., Haslam 408 MHz survey.
+ # Unit: [K] (Kelvin)
+ template = string(default=None)
+ # The frequency of the template map.
+ # Unit: [MHz]
+ template_freq = float(default=None, min=0.0)
+
+ # Spectral index map
+ indexmap = string(default=None)
+
+ # Whether add fluctuations on the small scales according the angular
+ # power spectrum prediction?
+ add_smallscales = boolean(default=False)
+ # Range of multipole moments (l) of the angular power spectrum.
+ # The power spectrum will be cut off to a constant for multipole l < lmin.
+ # NOTE: Update the ``lmax`` accordingly w.r.t. ``sky/healpix/nside``.
+ # Generally, lmax = 3 * nside - 1
+ lmin = integer(min=0, default=10)
+ lmax = integer(min=1, default=3071)
+
+ # Filename prefix for this component
+ prefix = string(default="gsync")
+ # Output directory to save the simulated results
+ output_dir = string(default=None)
+
+ # Free-free bremsstrahlung emission component
+ [[freefree]]
+ # The Hα map from which to derive the free-free emission
+ # Unit: [Rayleigh]
+ halphamap = string(default=None)
+
+ # The 100-μm dust map used to correct Hα dust absorption
+ # Unit: [MJy/sr]
+ dustmap = string(default=None)
+
+ # Effective dust fraction in the LoS actually absorbing Halpha
+ dust_fraction = float(default=0.33, min=0.1, max=1.0)
+
+ # Halpha absorption threshold:
+ # When the dust absorption goes rather large, the true Halpha
+ # absorption can not well determined. This configuration sets the
+ # threshold below which the dust absorption can be well determined,
+ # while the sky regions with higher absorption are masked out due
+ # to unreliable absorption correction.
+ # Unit: [mag]
+ halpha_abs_th = float(default=1.0)
+
+ # The electron temperature assumed for the ionized interstellar medium
+ # that generating H{\alpha} emission.
+ # Unit: [K]
+ electron_temperature = float(default=7000.0, min=1000)
+
+ # Filename prefix for this component
+ prefix = string(default="gfree")
+ # Output directory to save the simulated results
+ output_dir = string(default=None)
+
+ # Supernova remnants emission
+ [[snr]]
+ # The Galactic SNRs catalog data (CSV file)
+ catalog = string(default=None)
+ # Output the effective/inuse SNRs catalog data (CSV file)
+ catalog_outfile = string(default=None)
+
+ # Resolution for simulating each SNR template, which are finally
+ # mapped to the all-sky HEALPix map if used.
+ # Unit: [arcsec]
+ resolution = float(default=30.0, min=5.0)
+
+ # Filename prefix for this component
+ prefix = string(default="gsnr")
+ # Output directory to save the simulated results
+ output_dir = string(default=None)
+
+
+#
+# Extragalactic emission components
+#
+
+[extragalactic]
+ #
+ # Press-Schechter formalism to determine the cluster distributions
+ # with respect to mass and redshift, from which to further determine
+ # the total number of clusters within a sky patch and to sample the
+ # masses and redshifts for each cluster.
+ #
+ [[psformalism]]
+ # The model of the fitting function for halo/cluster mass distribution
+ # For all models and more details:
+ # https://hmf.readthedocs.io/en/latest/_autosummary/hmf.fitting_functions.html
+ model = option("smt", "jenkins", "ps", default="ps")
+
+ # The minimum (inclusive) and maximum (exclusive!) cluster mass
+ # within which to calculate the halo mass distribution.
+ # Unit: [Msun]
+ M_min = float(default=1e12, min=1e10, max=1e14)
+ M_max = float(default=1e16, min=1e14, max=1e18)
+ # The logarithmic (base 10) step size for the halo masses; therefore
+ # the number of intervals is: (log10(M_max) - log10(M_min)) / M_step
+ M_step = float(default=0.01, min=0.001, max=0.1)
+
+ # The minimum and maximum redshift within which to calculate the
+ # halo mass distribution; as well as the step size.
+ z_min = float(default=0.01, min=0.001, max=1.0)
+ z_max = float(default=4.0, min=1.0, max=100)
+ z_step = float(default=0.01, min=0.001, max=1.0)
+
+ # Output file (NumPy ".npz" format) to save the calculated halo mass
+ # distributions at every redshift.
+ #
+ # This file packs the following 3 NumPy arrays:
+ # * ``z``:
+ # Redshifts where the halo mass distribution is calculated.
+ # * ``mass``:
+ # (Logarithmic-distributed) masses points.
+ # Unit: [Msun] (the little "h" is folded into the values)
+ # * ``dndlnm``:
+ # Shape: (len(z), len(mass))
+ # Differential mass function in terms of natural log of M.
+ # Unit: [Mpc^-3] (the little "h" is folded into the values)
+ dndlnm_outfile = string(default=None)
+
+
+ #
+ # Extended emissions from the clusters of galaxies
+ # The configurations in this ``[[clusters]]`` section may also be
+ # used by the following ``[[halos]]`` section.
+ #
+ [[clusters]]
+ # Output CSV file of the cluster catalog containing the simulated
+ # mass, redshift, position, shape, recent merger info, etc.
+ catalog_outfile = string(default=None)
+
+ # Whether to dump the raw data of the simulated cluster catalog in
+ # Python native pickle format (i.e., ".pkl") to a file with the same
+ # basename as the above ``catalog_outfile``?
+ # The dumped data can be easily loaded back for reuse.
+ dump_catalog_data = boolean(default=True)
+
+ # Whether to directly use the (previously simulated) catalog data as
+ # specified by the above "catalog_outfile" and ``dump_catalog_data``
+ # options?
+ # NOTE:
+ # By using an existing catalog, the steps to derive these data are
+ # simply skipped.
+ # Due to the small number density of the galaxy clusters, the simulated
+ # results within a small patch of sky (e.g., 100 [deg^2]) show
+ # significant fluctuations (several or even several tens of times
+ # of differences between simulations). Therefore, one may run many
+ # tests and only create images at some frequencies necessary for
+ # testing, then select the satisfying one to continue the simulation
+ # to generate images at all frequencies.
+ use_dump_catalog_data = boolean(default=False)
+
+ # Output CSV file of the halos catalog containing the calculated
+ # properties of the simulated halos.
+ halos_catalog_outfile = string(default=None)
+
+ # Whether to dump the whole data of the simulated halos in Python
+ # native pickle format (i.e., ".pkl") to a file with the same basename
+ # as the above ``halos_catalog_outfile``?
+ # The dumped data also includes the derived electron spectrum for
+ # each halo, therefore this file can be reloaded back in order to
+ # calculate the emissions at other frequencies.
+ dump_halos_data = boolean(default=True)
+
+ # Whether to directly use the (previously dumped) halos data (".pkl")
+ # as specified by the above ``halos_catalog_outfile`` and
+ # ``dump_halos_data`` options?
+ # In this way, the radio emissions at additional frequencies can be
+ # easily (and consistently) calculated.
+ use_dump_halos_data = boolean(default=False)
+
+ # The minimum mass for clusters when to determine the galaxy clusters
+ # total counts and their distributions.
+ # Unit: [Msun]
+ mass_min = float(default=1e14, min=1e13)
+
+ # Boost the number of expected cluster number within the sky coverage
+ # by the specified times.
+ # WARNING: for testing usage.
+ boost = float(default=1.0, min=0.1, max=1e4)
+
+ # Minimal elongated fraction for creating the images of radio halos
+ # The ``felong`` is defined as ``felong = b/a``, similar to the Hubble
+ # classification for the elliptical galaxies. ``felong_min = 1.0``
+ # means no elongation, and ``felong_min = 0.6`` is a good choice as
+ # the observed radio halos are generally regular.
+ felong_min = float(default=1.0, min=0.1, max=1.0)
+
+ # Number of most powerful halos to be dropped out.
+ halo_dropout = integer(default=0, min=0)
+
+ # Minimum mass change of the main cluster to be regarded as a merger
+ # event instead of an accretion event.
+ # Unit: [Msun]
+ merger_mass_min = float(default=1e13, min=1e11, max=1e14)
+
+ # The trace back time when to stop tracing the merging history of
+ # clusters. ~2-3 Gyr should be enough since the turbulence acceleration
+ # effective time ~<1 Gyr and the halo lifetime is also short compared
+ # to mergers.
+ # Unit: [Gyr]
+ time_traceback = float(default=3.0, min=1.0, max=5.0)
+
+ # The fraction of the magnetic field energy density w.r.t. the ICM
+ # thermal energy density, which is used to determine the mean magnetic
+ # field strength within the ICM and is also assumed to be uniform.
+ # * ~< 0.4% (Ref: Pfrommer & Ensslin 2004, MNRAS)
+ # * ~0.3%-1% (Ref: Bohringer et al. 2016, A&A)
+ eta_b = float(default=0.001, min=1e-5, max=0.1)
+
+ # The temperature of the outer gas surrounding the cluster. Accretion
+ # shocks form near the cluster virial radius during the cluster formation,
+ # which can heat the cluster ICM to have a higher temperature than the
+ # virial temperature:
+ # kT_icm ~ kT_vir + 1.5 * kT_out,
+ # with: kT_out ~ 0.5 [keV]
+ # Reference: Fujita et al. 2003, ApJ, 584, 190; Eq.(49)
+ # Unit: [keV]
+ kT_out = float(default=0.0, min=0.0)
+
+ # Filename prefix for this component
+ prefix = string(default="cluster")
+ # Output directory to save the simulated results
+ output_dir = string(default=None)
+
+
+ #
+ # Giant radio halos
+ #
+ [[halos]]
+ # A custom parameter to tune the turbulent acceleration efficiency.
+ # NOTE: The smaller this parameter, the shorter the acceleration
+ # timescale, therefore more efficient acceleration.
+ f_acc = float(default=1.0, min=0.1, max=10)
+
+ # The turbulence is generally injected at the cluster center during
+ # a merger. This option parameterize the turbulence injection scale
+ # to be a fraction of the virial radius of the cluster, which is also
+ # used to determine the radio halo size.
+ f_lturb = float(default=0.33, min=0.1, max=1.0)
+
+ # An efficiency factor describing the effectiveness of plasma
+ # instabilities (e.g., due to spatial or temporal intermittency).
+ zeta_ins = float(default=0.1, min=0.1, max=1.0)
+
+ # The fraction of merger energy transferred into the turbulence.
+ eta_turb = float(default=0.1, min=0.1, max=0.5)
+
+ # The fraction of the thermal energy injected into the cosmic-ray
+ # electrons during the cluster life time.
+ eta_e = float(default=0.003, min=0.001, max=0.1)
+
+ # The ratio of cosmic ray (including protons and electrons) energy
+ # density (i.e., pressure) to the thermal energy density.
+ # NOTE: Fermi-LAT has placed an upper limit of ~1.25%-1.4%
+ # (Ackermann et al. 2014, ApJ, 787, 18)
+ # NOTE: The energy ratio of cosmic-ray electrons to protons K_ep ~0.01
+ # for our Galaxy (Pinzke et al. 2017, MNRAS, 465, 4800)
+ x_cr = float(default=0.015, min=0.001, max=0.1)
+
+ # Electron injection, which is assumed to have a constant injection
+ # rate and a power-law spectrum.
+ injection_index = float(default=2.3, min=2.1, max=3.0)
+
+ # Minimum and maximum Lorentz factor (i.e., energy) of the relativistic
+ # electron spectrum.
+ gamma_min = float(default=1)
+ gamma_max = float(default=1e5)
+ # Number of cells on the logarithmic momentum grid used to solve the
+ # Fokker-Planck equation.
+ gamma_np = integer(default=200)
+
+ # Number of cells used as the buffer regions near both the lower
+ # and upper boundaries, within which the values will be replaced by
+ # extrapolating from the inner-region data, in order to avoid the
+ # unphysical particle pile-ups.
+ # It is suggested to be about 5%-10% of the above ``gamma_np``.
+ # NOTE: * set to 0 to disable boundary fixes;
+ # * otherwise, set to a number >= 2.
+ buffer_np = integer(default=10, min=0)
+
+ # Time step for solving the Fokker-Planck equation
+ # Unit: [Gyr]
+ time_step = float(default=0.02, min=1e-4, max=0.1)
+
+ # How long the period before the merger begins, which is used to derive
+ # an approximately steady initial electron spectrum. During this period,
+ # the acceleration is turned off and only leaves energy loss mechanisms.
+ # Unit: [Gyr]
+ time_init = float(default=1.0, min=0)
+
+
+ #
+ # Extragalactic point sources
+ #
+ [[pointsources]]
+ # Output directory to save the simulated catalog
+ output_dir = string(default="PS_tables")
+ # PS components to be simulated
+ pscomponents = string_list(default=list())
+ # Resolution [arcmin]
+ resolution = float(default=0.6, min=0.0)
+
+ [[[starforming]]]
+ # Number of samples
+ numps = integer(default=1000)
+ # Prefix
+ prefix = string(default="SF")
+
+ [[[starbursting]]]
+ # Number of samples
+ numps = integer(default=1000)
+ # Prefix
+ prefix = string(default="SB")
+
+ [[[radioquiet]]]
+ # Number of samples
+ numps = integer(default=1000)
+ # Prefix
+ prefix = string(default="RQ")
+
+ [[[FRI]]]
+ # Number of samples
+ numps = integer(default=1000)
+ # Prefix
+ prefix = string(default="FRI")
+
+ [[[FRII]]]
+ # Number of samples
+ numps = integer(default=1000)
+ # Prefix
+ prefix = string(default="FRII")
diff --git a/fg21sim/configs/manager.py b/fg21sim/configs/manager.py
index e2103da..07f6f77 100644
--- a/fg21sim/configs/manager.py
+++ b/fg21sim/configs/manager.py
@@ -31,22 +31,6 @@ from ..errors import ConfigError
logger = logging.getLogger(__name__)
-def _get_configspec():
- """Found and read all the configuration specifications"""
- files = sorted(pkg_resources.resource_listdir(__name__, ""))
- specfiles = [fn for fn in files if fn.endswith(".conf.spec")]
- if os.environ.get("DEBUG_FG21SIM"):
- print("DEBUG: Found config specifications: %s" % ", ".join(specfiles),
- file=sys.stderr)
- # NOTE:
- # `resource_string()` returns the resource in *binary/bytes* string
- configspec = "\n".join([
- pkg_resources.resource_string(__name__, fn).decode("utf-8")
- for fn in specfiles
- ]).split("\n")
- return configspec
-
-
def _flatten_dict(d, sep="/", parent_key=""):
"""
Recursively flatten a nested dictionary with keys compressed.
@@ -147,7 +131,8 @@ class ConfigManager:
If the ``userconfig`` provided, the user configurations is also
loaded, validated, and merged.
"""
- configspec = _get_configspec()
+ configspec = pkg_resources.resource_string(
+ __name__, "config.spec").decode("utf-8")
self._configspec = ConfigObj(configspec, interpolation=False,
list_values=False, _inspec=True,
encoding="utf-8")
--
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