Merge pull request #19 from wmfw23/master

Galaxy Dust Mass Functions
SWIFTSIM · Apr 1, 2020 · 45d3ff8 · 45d3ff8
2 parents 41d7975 + 21bc871
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diff --git a/data/GalaxyDustMassFunction/conversion/convertBeeston2018.py b/data/GalaxyDustMassFunction/conversion/convertBeeston2018.py
@@ -0,0 +1,143 @@
+from velociraptor.observations.objects import ObservationalData
+
+import unyt
+import numpy as np
+import os
+import re
+import sys
+import itertools as it
+
+ORIGINAL_H = 0.7
+
+
+def load_file_and_split_by_z(raw_file_name):
+    """
+    Read the data file and do all the mucking around needed to extract a list of the
+    redshift bins for which the GDMF is tabulated, along with the corresponding GDMF
+    values and their errors.
+    The number and spacing of the stellar mass bins vary with z; they are given in the
+    first column of the returned array.
+
+    raw_file_name: the file name of the raw data file to extract the GDMF from
+    """
+
+    data = np.genfromtxt(raw_file_name, comments="#")
+
+    # array of the lower redshift bin edges for each GDMF
+    z_bins_arr = np.unique(data[:, -2])
+
+    gdmf_arr = []
+    for zlow in z_bins_arr:
+        bdx = data[:, -2] == zlow
+        gdmf_arr.append(data[bdx, :-2])
+
+    return z_bins_arr, gdmf_arr
+
+
+def process_for_redshift(z, gdmf_and_Mstar_at_z):
+    """
+    Output an HDF5 file containing the GDMF at a given redshift.
+
+    z: the redshift to produce the GDMF for. The given value corresponds to the lower
+    edge of a range in redshift of width 0.5, except for the first bin 0.2 < z < 0.5,
+    and the last bin 3.0 < z < 4.0
+    gdmf_and_mstar_at_z: the array containing stellar mass bins and the GDMF at the
+    chosen redshift
+    """
+
+    processed = ObservationalData()
+
+    comment = (
+        "Beeston et al. (2018). Obtained using H-ATLAS+GAMA"
+        f"data, h-corrected for SWIFT using Cosmology: {cosmology.name}."
+    )
+    citation = "Beeston et al. (2018)"
+    bibcode = "2018MNRAS.479.1077B"
+    name = "GDMF from H-ATLAS+GAMA"
+    plot_as = "points"
+    redshift = z
+    h = cosmology.h
+
+    Mstar_bins = gdmf_and_Mstar_at_z[:, 0]
+    M = 10 ** Mstar_bins * (h / ORIGINAL_H) ** (-2) * unyt.Solar_Mass
+    Phi = 10 ** gdmf_and_Mstar_at_z[:, 1] * (h / ORIGINAL_H) ** 3 * unyt.Mpc ** (-3)
+    # y_scatter should be a 1xN or 2xN array describing offsets from
+    # the median point 'y'
+    # Errors are log error dz = 1/ln(10) dy/y
+    # We want dy = y ln(10) dz
+    M_err = (
+        (
+            10 ** gdmf_and_Mstar_at_z[:, 2][:, None]
+            * np.log(10)
+            * gdmf_and_Mstar_at_z[:, [2, 3]]
+        ).T
+        * (h / ORIGINAL_H) ** 3
+        * unyt.Solar_Mass
+    )
+
+    Phi_err = (
+        (
+            10 ** gdmf_and_Mstar_at_z[:, 2][:, None]
+            * np.log(10)
+            * gdmf_and_Mstar_at_z[:, [4, 5]]
+        ).T
+        * (h / ORIGINAL_H) ** 3
+        * unyt.Mpc ** (-3)
+    )
+
+    processed.associate_x(
+        M, scatter=M_err, comoving=True, description="Galaxy Dust Mass"
+    )
+    processed.associate_y(Phi, scatter=Phi_err, comoving=True, description="Phi (GDMF)")
+    processed.associate_citation(citation, bibcode)
+    processed.associate_name(name)
+    processed.associate_comment(comment)
+    processed.associate_redshift(redshift)
+    processed.associate_plot_as(plot_as)
+    processed.associate_cosmology(cosmology)
+
+    return processed
+
+
+def stringify_z(z):
+    """
+    Eagle-style text formatting of redshift label.
+    Example: z=1.5 will be printed as z001p500.
+
+    z: The redshift to produce a label for
+    """
+    whole = int(z)
+    frac = int(1000 * (z - whole))
+    return f"z{whole:03d}p{frac:03d}"
+
+
+# Exec the master cosmology file passed as first argument
+# These lines are _required_ and you are required to use
+# the cosmology specified (this is an astropy.cosmology
+# instance)
+with open(sys.argv[1], "r") as handle:
+    exec(handle.read())
+
+input_filename = "../raw/Beeston2018.txt"
+
+output_filename = "Beeston2018_{}.hdf5"
+output_directory = "../"
+
+if not os.path.exists(output_directory):
+    os.mkdir(output_directory)
+
+# z_bins is a 1-D ndarray containing the lower edges of the redshift bins
+# gdmf_and_Mstar is a list of 2D ndarrays, one per redshift
+# Each contains five columns as follows:
+# log(Mstar) bins, Mstar errors, log(GDMF), GDMF +- errors
+z_bins, gdmf_and_Mstar = load_file_and_split_by_z(input_filename)
+
+for z, gdmf_and_Mstar_at_z in zip(z_bins, gdmf_and_Mstar):
+    processed = process_for_redshift(z, gdmf_and_Mstar_at_z)
+
+    output_path = f"{output_directory}/{output_filename.format(stringify_z(z))}"
+
+    if os.path.exists(output_path):
+        os.remove(output_path)
+
+    processed.write(filename=output_path)
diff --git a/data/GalaxyDustMassFunction/conversion/convertPozzi2020.py b/data/GalaxyDustMassFunction/conversion/convertPozzi2020.py
@@ -0,0 +1,143 @@
+from velociraptor.observations.objects import ObservationalData
+
+import unyt
+import numpy as np
+import os
+import re
+import sys
+import itertools as it
+
+ORIGINAL_H = 0.7
+
+
+def load_file_and_split_by_z(raw_file_name):
+    """
+    Read the data file and do all the mucking around needed to extract a list of the
+    redshift bins for which the GDMF is tabulated, along with the corresponding GDMF
+    values and their errors.
+    The number and spacing of the stellar mass bins vary with z; they are given in the
+    first column of the returned array.
+
+    raw_file_name: the file name of the raw data file to extract the GDMF from
+    """
+
+    data = np.genfromtxt(raw_file_name, comments="#")
+
+    # array of the lower redshift bin edges for each GDMF
+    z_bins_arr = np.unique(data[:, -2])
+
+    gdmf_arr = []
+    for zlow in z_bins_arr:
+        bdx = data[:, -2] == zlow
+        gdmf_arr.append(data[bdx, :-2])
+    return z_bins_arr, gdmf_arr
+
+
+def process_for_redshift(z, gdmf_and_Mstar_at_z):
+    """
+    Output an HDF5 file containing the GDMF at a given redshift.
+
+    z: the redshift to produce the GDMF for. The given value corresponds to the lower
+    edge of a range in redshift of width 0.5, except for the first bin 0.2 < z < 0.5,
+    and the last bin 3.0 < z < 4.0
+    gdmf_and_mstar_at_z: the array containing stellar mass bins and the GDMF at the
+    chosen redshift
+    """
+
+    processed = ObservationalData()
+
+    comment = (
+        "Pozzi et al. (2020), Figure 5. Obtained using Herschel+GAMA"
+        "data, and derived using the MAGPHYS SED fitting package."
+        f"h-corrected for SWIFT using Cosmology: {cosmology.name}."
+    )
+    citation = "Pozzi et al. (2020)"
+    bibcode = "2020MNRAS.491.5073P"
+    name = "GDMF from Herschel+GAMA"
+    plot_as = "points"
+    redshift = z
+    h = cosmology.h
+
+    Mstar_bins = gdmf_and_Mstar_at_z[:, 0]
+    M = 10 ** Mstar_bins * (h / ORIGINAL_H) ** (-2) * unyt.Solar_Mass
+    Phi = 10 ** gdmf_and_Mstar_at_z[:, 1] * (h / ORIGINAL_H) ** 3 * unyt.Mpc ** (-3)
+    # y_scatter should be a 1xN or 2xN array describing offsets from
+    # the median point 'y'
+    # Errors are log error dz = 1/ln(10) dy/y
+    # We want dy = y ln(10) dz
+    M_err = (
+        (
+            10 ** gdmf_and_Mstar_at_z[:, 2][:, None]
+            * np.log(10)
+            * gdmf_and_Mstar_at_z[:, [2, 3]]
+        ).T
+        * (h / ORIGINAL_H) ** 3
+        * unyt.Solar_Mass
+    )
+
+    Phi_err = (
+        (
+            10 ** gdmf_and_Mstar_at_z[:, 2][:, None]
+            * np.log(10)
+            * gdmf_and_Mstar_at_z[:, [4, 5]]
+        ).T
+        * (h / ORIGINAL_H) ** 3
+        * unyt.Mpc ** (-3)
+    )
+
+    processed.associate_x(
+        M, scatter=M_err, comoving=True, description="Galaxy Dust Mass"
+    )
+    processed.associate_y(Phi, scatter=Phi_err, comoving=True, description="Phi (GDMF)")
+    processed.associate_citation(citation, bibcode)
+    processed.associate_name(name)
+    processed.associate_comment(comment)
+    processed.associate_redshift(redshift)
+    processed.associate_plot_as(plot_as)
+    processed.associate_cosmology(cosmology)
+
+    return processed
+
+
+def stringify_z(z):
+    """
+    Eagle-style text formatting of redshift label.
+    Example: z=1.5 will be printed as z001p500.
+
+    z: The redshift to produce a label for
+    """
+    whole = int(z)
+    frac = int(1000 * (z - whole))
+    return f"z{whole:03d}p{frac:03d}"
+
+
+# Exec the master cosmology file passed as first argument
+# These lines are _required_ and you are required to use
+# the cosmology specified (this is an astropy.cosmology
+# instance)
+with open(sys.argv[1], "r") as handle:
+    exec(handle.read())
+
+input_filename = "../raw/Pozzi2020.txt"
+
+output_filename = "Pozzi2020_{}.hdf5"
+output_directory = "../"
+
+if not os.path.exists(output_directory):
+    os.mkdir(output_directory)
+
+# z_bins is a 1-D ndarray containing the lower edges of the redshift bins
+# gdmf_and_Mstar is a list of 2D ndarrays, one per redshift
+# Each contains five columns as follows:
+# log(Mstar) bins, Mstar errors, log(GDMF), GDMF +- errors
+z_bins, gdmf_and_Mstar = load_file_and_split_by_z(input_filename)
+
+for z, gdmf_and_Mstar_at_z in zip(z_bins, gdmf_and_Mstar):
+    processed = process_for_redshift(z, gdmf_and_Mstar_at_z)
+
+    output_path = f"{output_directory}/{output_filename.format(stringify_z(z))}"
+
+    if os.path.exists(output_path):
+        os.remove(output_path)
+
+    processed.write(filename=output_path)
diff --git a/data/GalaxyDustMassFunction/raw/Beeston2018.txt b/data/GalaxyDustMassFunction/raw/Beeston2018.txt
@@ -0,0 +1,22 @@
+#
+# Galaxy Dust Mass Function from Beeston+18, columns:
+# | log10 (Mdust/Msun) | phi [cMpc^-3] | Mdust err + | Mdust err - | phi err + | phi err - | redshift edge lower | redshift edge upper |
+#
+4.12808  -1.30441	0	0	0	0	0.	0.06
+4.37931  -1.30441	0	0	0	0	0.	0.06
+4.63054  -1.59813	0	0	0	0	0.	0.06
+4.88177  -1.48598	0	0	0	0	0.	0.06
+5.12808  -1.45394	0	0	0	0	0.	0.06
+5.37931  -1.71562	0	0	0	0	0.	0.06
+5.63054  -1.70494	0	0	0	0	0.	0.06
+5.87685  -1.73698	0	0	0	0	0.	0.06
+6.12808  -1.80641	0	0	0	0	0.	0.06
+6.37931  -1.95594	0	0	0	0	0.	0.06
+6.62562  -2.04139	0	0	0	0	0.	0.06
+6.88177  -2.13218	0	0	0	0	0.	0.06
+7.12808  -2.22296	0	0	0	0	0.	0.06
+7.37931  -2.29773	0	0	0	0	0.	0.06
+7.63054  -2.54339	0	0	0	0	0.	0.06
+7.88177  -2.97063	0	0	0	0	0.	0.06
+8.12808  -3.73965	0	0	0	0	0.	0.06
+8.37931  -4.60481	0	0	0	0	0.	0.06
diff --git a/data/GalaxyDustMassFunction/raw/Pozzi2020.txt b/data/GalaxyDustMassFunction/raw/Pozzi2020.txt
@@ -0,0 +1,19 @@
+#
+# Galaxy Dust Mass Function from Pozzi+2020, columns:
+# | log10 (Mdust/Msun) | phi [cMpc^-3] | Mdust err + | Mdust err - | phi err + | phi err - | redshift edge lower | redshift edge upper |
+#
+6.69767	-1.75705	0	0	0	0	0.1	0.25
+6.90439	-2.07041	0	0	0	0	0.1 	0.25
+7.09819	-2.21705	0	0 	0	0	0.1 	0.25
+7.29199	-2.46786	0	0 	0	0	0.1	0.25
+7.49871	-2.61456	0	0	0	0	0.1	0.25
+7.70543	-2.90708	0	0	0	0	0.1	0.25
+7.89922	-3.32456	0	0	0	0	0.1	0.25
+8.09302	-4.24203	0	0	0	0	0.1	0.25
+8.70026	-4.41123	0	0	0	0	0.1	0.25
+8.70898  -3.71850	0	0	0	0	1.8	2.5
+8.89474  -4.16943	0	0	0	0	1.8	2.5
+9.09598  -4.57043	0	0	0	0	1.8	2.5
+9.29721  -4.94644	0	0	0	0	1.8	2.5
+9.49845  -5.82245	0	0	0	0	1.8	2.5
+10.10217  -6.45046	0	0	0	0	1.8	2.5