fix HI masses

SAGA/objects/build.py

@@ -894,24 +894,33 @@ def add_stellar_mass(base):
     if "z_cosmo" not in base.colnames:
         base = add_z_cosmo(base)
 
+    # HOST_ZCOSMO is calculated using host's distance, not measured redshift
     z = np.where(np.isfinite(base["z_cosmo"]), base["z_cosmo"], base["HOST_ZCOSMO"])
     z = np.clip(z, np.finfo(np.float32).eps, None)
     gr = base["g_mag"] - base["r_mag"]
 
     with np.errstate(invalid="ignore"):
-        base["Mr_phony"] = (base["r_mag"] - z2m(z) - calc_kcor("r", z, "g - r", gr)).astype(np.float32)
-        base["log_sm_phony"] = (1.254 + 1.0976 * gr - 0.4 * base["Mr_phony"]).astype(np.float32)
+        base["Mr_phony"] = (base["r_mag"] - z2m(z) - calc_kcor("r", z, "g - r", gr))
+        base["log_sm_phony"] = (1.254 + 1.0976 * gr - 0.4 * base["Mr_phony"])
+        base["log_MHI_phony"] = np.log10(2.356e5 / (z + 1.0) * (z2d(z) ** 2) * base["HI_FLUX"])
 
     ok_to_calculate = Query(
         QueryMaker.isfinite("Mr_phony"),
-        QueryMaker.isfinite("z_cosmo"),
         "z_cosmo >= 0.001",
         "z_cosmo < 0.5",
         "abs(g_mag - r_mag) < 10",
     ).mask(base)
 
-    base["Mr"] = np.where(ok_to_calculate, base["Mr_phony"], np.float32(np.nan))
-    base["log_sm"] = np.where(ok_to_calculate, base["log_sm_phony"], np.float32(np.nan))
+    base["Mr"] = np.where(ok_to_calculate, base["Mr_phony"], np.nan).astype(np.float32)
+    base["log_sm"] = np.where(ok_to_calculate, base["log_sm_phony"], np.nan).astype(np.float32)
+
+    ok_to_calculate = Query(
+        "HI_FLUX > 0",
+        "z_cosmo >= 0.001",
+        "z_cosmo < 0.5",
+    ).mask(base)
+
+    base["log_MHI"] = np.where(ok_to_calculate, base["log_MHI_phony"], np.nan).astype(np.float32)
 
     return base
 

SAGA/objects/build2.py

@@ -740,9 +740,11 @@ def get_tel_rank(
             set(specs_to_merge["TELNAME"][mask_within_dz & mask_same_zq_class])
         )
         specs["SPEC_REPEAT_ALL"][best_spec_index] = "+".join(set(specs_to_merge["TELNAME"]))
-        log_MHI = specs_to_merge["LOG_MHI"][mask_within_dz & np.isfinite(specs_to_merge["LOG_MHI"])]
-        if len(log_MHI):
-            specs["LOG_MHI"][best_spec_index] = log_MHI[0]
+        has_HI = mask_within_dz & (specs_to_merge["HI_FLUX"] > 0)
+        if has_HI.any():
+            has_HI = np.argmax(has_HI)
+            for c in ["HI_FLUX", "HI_FLUX_ERR"]:
+                specs[c][best_spec_index] = specs_to_merge[c][has_HI]
 
         nsa_specs = specs_to_merge[specs_to_merge["TELNAME"] == "NSA"]
         specs["OBJ_NSAID"][best_spec_index] = int(nsa_specs["SPECOBJID"][0]) if len(nsa_specs) else -1

SAGA/spectra/common.py

@@ -15,7 +15,8 @@
     ("MASKNAME", "<U48"),
     ("TELNAME", "<U6"),
     ("HELIO_CORR", "|b1"),
-    ("LOG_MHI", "<f4"),
+    ("HI_FLUX", "<f4"),
+    ("HI_FLUX_ERR", "<f4"),
 )
 
 SPECS_COLUMNS = dict(_SPECS_COLUMNS)

SAGA/spectra/read_external.py

@@ -302,19 +302,21 @@ def read_alfalfa(file_path):
         "RAdeg_OC",
         "DECdeg_OC",
         "Vhelio",
-        "W50",
-        "logMH",
+        "sigW",
+        "HIflux",
+        "sigflux",
     ]
 
     specs.rename_column("AGCNr", "SPECOBJID")
-    specs.rename_column("logMH", "LOG_MHI")
+    specs.rename_column("HIflux", "HI_FLUX")
+    specs.rename_column("sigflux", "HI_FLUX_ERR")
 
     valid_oc_coord = Query("abs(RAdeg_OC) + abs(DECdeg_OC) > 0").mask(specs)
     specs["RA"] = np.where(valid_oc_coord, specs["RAdeg_OC"], specs["RAdeg_HI"])
     specs["DEC"] = np.where(valid_oc_coord, specs["DECdeg_OC"], specs["DECdeg_HI"])
 
     specs["SPEC_Z"] = specs["Vhelio"].astype(np.float64) / SPEED_OF_LIGHT
-    specs["SPEC_Z_ERR"] = specs["W50"].astype(np.float64) / SPEED_OF_LIGHT / np.sqrt(2 * np.log(2))
+    specs["SPEC_Z_ERR"] = specs["sigW"].astype(np.float64) * 0.5 / SPEED_OF_LIGHT
     specs["ZQUALITY"] = np.where(valid_oc_coord, 3, 2)
 
     specs["TELNAME"] = "ALFALF"
@@ -335,12 +337,15 @@ def read_fashi(file_path):
     specs.rename_column("ID_FASHI", "SPECOBJID")
     specs.rename_column("z", "SPEC_Z")
     specs.rename_column("z_err", "SPEC_Z_ERR")
-    specs.rename_column("log10Mass", "LOG_MHI")
+    specs.rename_column("S_bf", "HI_FLUX")
+    specs.rename_column("S_bf_err", "HI_FLUX_ERR")
 
     valid_oc_coord = Query("oc_flag > 0.9995", "abs(RA_oc) + abs(DEC_oc) > 0").mask(specs)
     specs["RA"] = np.where(valid_oc_coord, specs["RA_oc"], specs["RA"])
     specs["DEC"] = np.where(valid_oc_coord, specs["DEC_oc"], specs["DEC"])
     specs["ZQUALITY"] = np.where(valid_oc_coord, 3, 2)
+    specs["HI_FLUX"] *= 1.0e-3  # convret from mJy to Jy
+    specs["HI_FLUX_ERR"] *= 1.0e-3  # convret from mJy to Jy
 
     specs["TELNAME"] = "FASHI"
     specs["MASKNAME"] = "FASHI"

SAGA/version.py

@@ -1,4 +1,4 @@
 """
 SAGA package version
 """
-__version__ = "0.68.0"
+__version__ = "0.68.1"