clusters: Use "hmf" to calculate halo mass functions/distributions

* New dependency "hmf" (halo mass functions) module
* Calculate halo mass distributions/functions (dndlnm) with respect to masses
  and redshifts, instead of use the previous data file ("ps_data")
* New section "[extragalactic][psformalism]" in configurations
* New functions to write and read the dndlnm data

TODO:
* update the method to sample (mass, redshift) for clusters from the dndlnm
  data

6 files changed, 230 insertions, 82 deletions

diff --git a/fg21sim/configs/20-extragalactic.conf.spec b/fg21sim/configs/20-extragalactic.conf.spec
index aa868ae..cda58b1 100644
--- a/fg21sim/configs/20-extragalactic.conf.spec
+++ b/fg21sim/configs/20-extragalactic.conf.spec
@@ -11,21 +11,51 @@
 
 [extragalactic]
 
+  # Press-Schechter formalism to determine the dark matter halos
+  # distribution with respect to masses and redshifts, from which
+  # to further determine the total number of halos within a sky
+  # patch and to sample the masses and redshifts for each halo.
+  # NOTE: only consider the *dark matter* mass within the halo!
+  [[psformalism]]
+  # The model of the fitting function for halo mass distribution
+  # For all models and more details:
+  # https://hmf.readthedocs.io/en/latest/_autosummary/hmf.fitting_functions.html
+  model = option("jenkins", "ps", "smt", default="smt")
+
+  # The minimum (inclusive) and maximum (exclusive) halo mass (dark
+  # matter only) within which to calculate the halo mass distribution.
+  # Unit: [Msun]
+  M_min = float(default=1e13, 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:
+  # * ``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)
+  # * ``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_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]]
-  # The Press-Schechter formalism predicted halo distribution densities.
-  # This data file is in plain text with 3 columns organized like:
-  # ---------------------
-  # z1  mass1  density1
-  # z1  mass2  density2
-  # z1  ..     density3
-  # z2  mass1  density4
-  # z2  mass2  density5
-  # z2  ..     density6
-  ps_data = string(default=None)
-
   # Output CSV file of the clusters catalog containing the simulated
   # mass, redshift, position, shape, and the recent major merger info.
   catalog_outfile = string(default=None)
diff --git a/fg21sim/configs/checkers.py b/fg21sim/configs/checkers.py
index 5316eac..76c99d3 100644
--- a/fg21sim/configs/checkers.py
+++ b/fg21sim/configs/checkers.py
@@ -150,13 +150,16 @@ def check_galactic_snr(configs):
 def check_extragalactic_clusters(configs):
     """
     Check the "[extragalactic][clusters]" section of the configurations.
+    The related sections ("[extragalactic][psformalism]",
+    "[extragalactic][halos]") are also checked.
     """
     comp = "extragalactic/clusters"
     comp_enabled = configs.foregrounds[0]
     results = {}
     if comp in comp_enabled:
-        # Only validate the configs if this component is enabled
-        results.update(_check_existence(configs, comp+"/ps_data"))
+        # output dndlnm data file required
+        key = "extragalactic/psformalism/dndlnm_outfile"
+        results.update(_check_missing(configs, key))
         # catalog required when enabled to use it
         if configs.get(comp+"/use_output_catalog"):
             results.update(_check_existence(configs, comp+"/catalog_outfile"))
diff --git a/fg21sim/extragalactic/clusters/psformalism.py b/fg21sim/extragalactic/clusters/psformalism.py
index 0ed19b0..899d94e 100644
--- a/fg21sim/extragalactic/clusters/psformalism.py
+++ b/fg21sim/extragalactic/clusters/psformalism.py
@@ -6,7 +6,7 @@ Press-Schechter (PS) formalism
 
 First determine the number of clusters within a sky patch (i.e., sky
 coverage) according to the cluster distribution predicted by the PS
-formalism; then sampling from the PS mass function to derive the mass
+formalism; then sampling from the halo mass function to derive the mass
 and redshift for each cluster.
 """
 
@@ -15,10 +15,12 @@ import random
 
 import numpy as np
 import pandas as pd
+import hmf
 
 from ...share import CONFIGS, COSMO
 from ...utils.interpolate import bilinear
 from ...utils.units import UnitConversions as AUC
+from ...utils.io import write_dndlnm
 
 
 logger = logging.getLogger(__name__)
@@ -28,106 +30,171 @@ class PSFormalism:
     """
     Press-Schechter (PS) formalism
 
-    Simulate the clusters number and their distribution (mass and z)
-    within a sky patch of certain coverage.
+    Calculate the halo mass distribution with respect to mass and redshift,
+    determine the clusters number counts and generate their distribution
+    (mass and z) within a sky patch of certain coverage.
     """
     def __init__(self, configs=CONFIGS):
         self.configs = configs
         self._set_configs()
-        self._load_data()
 
     def _set_configs(self):
         """
         Load the required configurations and set them.
         """
+        comp = "extragalactic/psformalism"
+        self.model = self.configs.getn(comp+"/model")
+        self.M_min = self.configs.getn(comp+"/M_min")
+        self.M_max = self.configs.getn(comp+"/M_max")
+        self.M_step = self.configs.getn(comp+"/M_step")
+        self.z_min = self.configs.getn(comp+"/z_min")
+        self.z_max = self.configs.getn(comp+"/z_max")
+        self.z_step = self.configs.getn(comp+"/z_step")
+        self.dndlnm_outfile = self.configs.get_path(comp+"/dndlnm_outfile")
+
         comp = "extragalactic/clusters"
-        self.datafile = self.configs.get_path(comp+"/ps_data")
         self.Mmin_cluster = self.configs.getn(comp+"/mass_min")  # [Msun]
         self.boost = self.configs.getn(comp+"/boost")
 
+        self.clobber = self.configs.getn("output/clobber")
+
+    @property
+    def hmf_model(self):
+        return {"PS": "PS",
+                "SMT": "SMT",
+                "JENKINS": "Jenkins"}[self.model.upper()]
+
+    def hmf_massfunc(self, z=0.0):
+        """
+        Halo mass function as a `~hmf.MassFunction` instance.
+        """
+        if not hasattr(self, "_hmf_massfunc"):
+            h = COSMO.h
+            cosmo = COSMO._cosmo
+            self._hmf_massfunc = hmf.MassFunction(
+                Mmin=np.log10(self.M_min*h),
+                Mmax=np.log10(self.M_max*h),
+                dlog10m=self.M_step,
+                hmf_model=self.hmf_model,
+                cosmo_model=cosmo,
+                n=COSMO.ns,
+                sigma_8=COSMO.sigma8)
+            logger.info("Initialized '%s' halo mass function." %
+                        self.hmf_model)
+
+        massfunc = self._hmf_massfunc
+        massfunc.update(z=z)
+        return massfunc
+
+    @property
+    def z(self):
+        """
+        The redshift points where to calculate the dndlnm data.
+        """
+        return np.arange(self.z_min, self.z_max+self.z_step/2, self.z_step)
+
+    @property
+    def mass(self):
+        """
+        The mass points where to calculate the dndlnm data.
+
+        NOTE:
+        The maximum mass end is exclusive, to be  consistent with hmf's
+        mass function!
+        """
+        return 10 ** np.arange(np.log10(self.M_min),
+                               np.log10(self.M_max),
+                               self.M_step)
+
+    @property
+    def dndlnm(self):
+        """
+        The calculated halo mass distributions data.
+        """
+        if not hasattr(self, "_dndlnm"):
+            self._dndlnm = self.calc_dndlnm()
+        return self._dndlnm
+
+    def calc_dndlnm(self):
+        """
+        Calculate the halo mass distributions expressed in ``dndlnm``,
+        the differential mass distribution in terms of natural log of
+        masses.
+        Unit: [Mpc^-3] (the little "h" is folded into the values)
+
+        NOTE
+        ----
+        dndlnm = d n(M,z) / d ln(M); [Mpc^-3]
+        describes the number of halos per comoving volume (Mpc^3) at
+        redshift z per unit logarithmic mass interval at mass M.
+        """
+        logger.info("Calculating dndlnm data ...")
+        dndlnm = []
+        h = COSMO.h
+        for z_ in self.z:
+            massfunc = self.hmf_massfunc(z_)
+            dndlnm.append(massfunc.dndlnm * h**3)
+        self._dndlnm = np.array(dndlnm)
+        logger.info("Calculated dndlnm within redshift: %.1f - %.1f" %
+                    (self.z_min, self.z_max))
+        return self._dndlnm
+
+    def write(self, outfile=None):
+        """
+        Write the calculate dndlnm data into file as NumPy ".npz" format.
+        """
+        if outfile is None:
+            outfile = self.dndlnm_outfile
+        write_dndlnm(outfile, dndlnm=self.dndlnm, z=self.z, mass=self.mass,
+                     clobber=self.clobber)
+        logger.info("Wrote dndlnm data into file: %s" % outfile)
+
     @property
     def Mmin_halo(self):
         return self.Mmin_cluster * COSMO.darkmatter_fraction
 
-    def _load_data(self, filepath=None):
-        """
-        Load dndM data and reformat into a 2D density grid together with
-        redshifts and masses vectors.
-
-        Data File Description
-        ---------------------
-        z1  mass1  density1
-        z1  mass2  density2
-        z1  ..     density3
-        z2  mass1  density4
-        z2  mass2  density5
-        z2  ..     density6
-        ...
-
-        where,
-        * Redshifts: 0.0 -> 3.02, even-spacing, step 0.02
-        * Mass: unit 1e12 -> 9.12e15 [Msun], log-even (dark matter)
-        * Density: [number]/dVc/dM
-          with,
-          - dVc: differential comvoing volume, [Mpc^3]/[sr]/[unit redshift]
-        """
-        if filepath is None:
-            filepath = self.datafile
-        data = np.loadtxt(filepath)
-        redshifts = data[:, 0]
-        masses = data[:, 1]
-        densities = data[:, 2]
-
-        redshifts = np.array(list(set(redshifts)))
-        redshifts.sort()
-        masses = np.array(list(set(masses)))
-        masses.sort()
-        densities = densities.reshape((len(redshifts), len(masses)))
-
-        logger.info("Loaded PS data from file: %s" % filepath)
-        logger.info("Number of redshift bins: %d" % len(redshifts))
-        logger.info("Number of mass bins: %d" % len(masses))
-        self.redshifts = redshifts
-        self.masses = masses
-        self.densities = densities
-
     @staticmethod
     def delta(x, logeven=False):
         """
         Calculate the delta values for each element of a vector,
         assuming they are evenly or log-evenly distributed,
-        with extrapolating.
+        by extrapolating.
         """
         x = np.asarray(x)
         if logeven:
-            x = np.log(x)
-        step = x[1] - x[0]
-        x1 = np.concatenate([[x[0]-step], x[:-1]])
-        x2 = np.concatenate([x[1:], [x[-1]+step]])
-        dx = (x2 - x1) * 0.5
-        if logeven:
-            dx = np.exp(dx)
+            ratio = x[1] / x[0]
+            x_left = x[0] / ratio
+            x_right = x[-1] * ratio
+        else:
+            step = x[1] - x[0]
+            x_left = x[0] - step
+            x_right = x[-1] + step
+        x2 = np.concatenate([[x_left], x, [x_right]])
+        dx = (x2[2:] - x2[:-2]) / 2
         return dx
 
     @property
     def number_grid(self):
         """
-        Calculate the number distribution w.r.t. redshift, mass, and
-        unit coverage [sr] from the density distribution.
+        The halo number per unit solid angle [sr] distribution w.r.t.
+        mass and redshift.
+        Unit: [/sr]
         """
-        dz = self.delta(self.redshifts)
-        dM = self.delta(self.masses)
-        dMgrip, dzgrip = np.meshgrid(dM, dz)
-        Mgrip, zgrip = np.meshgrid(self.masses, self.redshifts)
-        dVcgrip = COSMO.dVc(zgrip)  # [Mpc^3/sr]
-        numgrid = self.densities * dVcgrip * dzgrip * dMgrip
-        return numgrid
+        if not hasattr(self, "_number_grid"):
+            dz = self.delta(self.z)
+            dM = self.delta(self.mass, logeven=True)
+            dlnM = dM / self.mass
+            dlnMgrid, dzgrid = np.meshgrid(dlnM, dz)
+            __, zgrid = np.meshgrid(self.mass, self.z)
+            dVcgrid = COSMO.dVc(zgrid)  # [Mpc^3/sr]
+            self._number_grid = self.dndlnm * dlnMgrid * (dVcgrid*dzgrid)
+
+        return self._number_grid
 
     def calc_cluster_counts(self, coverage):
         """
         Calculate the total number of clusters (>= minimum mass) within
-        the FoV coverage according to the number density distribution
-        (e.g., predicted by the Press-Schechter mass function)
+        the FoV coverage according to the halo number density distribution.
 
         Parameters
         ----------
@@ -145,10 +212,10 @@ class PSFormalism:
         ----------
         counts
         """
-        logger.info("Determine the total number of clusters within "
+        logger.info("Calculating the total number of clusters within "
                     "sky patch of coverage %.1f [deg^2]" % coverage)
         coverage *= AUC.deg2rad**2  # [deg^2] -> [rad^2] = [sr]
-        midx = (self.masses >= self.Mmin_halo)
+        midx = (self.mass >= self.Mmin_halo)
         numgrid = self.number_grid
         counts = np.sum(numgrid[:, midx]) * coverage
         counts *= self.boost  # number boost factor
@@ -159,7 +226,7 @@ class PSFormalism:
     def sample_z_m(self, counts=None):
         """
         Randomly generate the requested number of pairs of (z, M) following
-        the specified number distribution.
+        the halo number distribution.
 
         Parameters
         ----------
diff --git a/fg21sim/utils/io.py b/fg21sim/utils/io.py
index 2449ca5..b3666b6 100644
--- a/fg21sim/utils/io.py
+++ b/fg21sim/utils/io.py
@@ -380,3 +380,49 @@ def write_fits_healpix(outfile, hpmap, header=None, float32=False,
     ], header=hdr)
     hdu.writeto(outfile, checksum=checksum)
     logger.info("Wrote HEALPix map to FITS file: %s" % outfile)
+
+
+def write_dndlnm(outfile, dndlnm, z, mass, clobber=False):
+    """
+    Write the halo mass distribution data into file in NumPy's ".npz"
+    format, which packs the ``dndlnm``, ``z``, and ``mass`` arrays.
+
+    Parameters
+    ----------
+    outfile : str
+        The output file to store the dndlnm data, in ".npz" format.
+    dndlnm : 2D float `~numpy.ndarray`
+        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)
+    z : 1D float `~numpy.ndarray`
+        Redshifts where the halo mass distribution is calculated.
+    mass : 1D float `~numpy.ndarray`
+        (Logarithmic-distributed) masses points.
+        Unit: [Msun] (the little "h" is folded into the values)
+    clobber : bool, optional
+        Whether to overwrite the existing output file?
+    """
+    _create_dir(outfile)
+    _check_existence(outfile, clobber=clobber, remove=True)
+    np.savez(outfile, dndlnm=dndlnm, z=z, mass=mass)
+
+
+def read_dndlnm(infile):
+    """
+    Read the halo mass distribution data from the above saved file.
+
+    Parameters
+    ----------
+    infile : str
+        The ".npz" file from which to read the dndlnm data.
+
+    Returns
+    -------
+    (dndlnm, z, mass)
+    """
+    with np.load(infile) as npzfile:
+        dndlnm = npzfile["dndlnm"]
+        z = npzfile["z"]
+        mass = npzfile["mass"]
+    return (dndlnm, z, mass)
diff --git a/requirements.txt b/requirements.txt
index 0833028..d898ab2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,4 +9,5 @@ beautifulsoup4
 requests
 tornado
 reproject
+hmf
 git+https://github.com/astropy/regions.git
diff --git a/setup.py b/setup.py
index 63ef7b0..00bd96e 100755
--- a/setup.py
+++ b/setup.py
@@ -89,6 +89,7 @@ setup(
         "requests",
         "tornado",
         "reproject",
+        "hmf",
     ],
     dependency_links=[
         "git+https://github.com/astropy/regions.git",