Add a smooth SFH quenching module

Rename (and correct a bug into) the SFH quenching module to sfh_quenching_trunk
and add a sfh_quenching_smooth version where the SFR is linearly decreasing
after the quenching.

pcigale/sed_modules/sfh_quenching_smooth.py

+# -*- coding: utf-8 -*-
+
+# Copyright (C) 2015-2016 Laboratoire d'Astrophysique de Marseille
+# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
+# Author: Yannick Roehlly
+
+"""
+Star Formation History quenching (smooth) module
+================================================
+
+This module performs a smooth quenching on the Star Formation History. Below a
+given age, the Star Formation Rate becomes linear to be multiplied by
+1- quenching_factor at the end of the history.
+
+"""
+
+from collections import OrderedDict
+
+import numpy as np
+
+from . import SedModule
+
+
+class SfhQuenchSmooth(SedModule):
+    """Star Formation History Quenching
+
+    This module implements a quenching of the Star Formation History.
+
+    """
+
+    parameter_list = OrderedDict([
+        ("quenching_time", (
+            "cigale_list(dtype=int, minvalue=0.)",
+            "Look-back time when the quenching starts in Myr.",
+            0
+        )),
+        ("quenching_factor", (
+            "cigale_list(minvalue=0., maxvalue=1.)",
+            "Quenching factor applied to the SFH. After the quenching time, "
+            "the SFR is multiplied by 1 - quenching factor and made constant. "
+            "The factor must be between 0 (no quenching) and 1 (no more star "
+            "formation).",
+            0.
+        )),
+        ("normalise", (
+            "boolean()",
+            "Normalise the SFH to produce one solar mass.",
+            True
+        ))
+    ])
+
+    def _init_code(self):
+        self.quenching_age = int(self.parameters["quenching_time"])
+        self.quenching_factor = float(self.parameters["quenching_factor"])
+        self.normalise = bool(self.parameters["normalise"])
+
+    def process(self, sed):
+        """
+        Parameters
+        ----------
+        sed : pcigale.sed.SED object
+
+        """
+
+        # Read the star formation history of the SED
+        sfr = sed.sfh
+
+        if self.quenching_age > sfr.size:
+            raise Exception("[sfh_quenching] The quenching age is greater "
+                            "than the galaxy age. Please fix your parameters.")
+
+        # We assume the time in the star formation history is evenly spaced to
+        # compute the reverse index (i.e. from the end of the array) of the SFH
+        # step corresponding to the quenching age.
+        # We make the computation only if the quenching age and the quenching
+        # factor are not 0.
+        if self.quenching_age > 0 and self.quenching_factor > 0.:
+            sfr0 = sfr[-self.quenching_age]
+            sfr1 = sfr[-self.quenching_age] * (1. - self.quenching_factor)
+            sfr[-self.quenching_age:] = sfr0 + (sfr1 - sfr0) * np.linspace(
+                0, 1, self.quenching_age)
+
+            # Compute the galaxy mass and normalise the SFH to 1 solar mass
+            # produced if asked to.
+            sfr_integrated = np.sum(sfr) * 1e6
+            if self.normalise:
+                sfr /= sfr_integrated
+                sfr_integrated = 1.
+
+            sed.sfh = sfr
+            sed.add_info("sfh.integrated", sfr_integrated, True, force=True)
+
+        sed.add_module(self.name, self.parameters)
+
+        sed.add_info("sfh.quenching_time", self.quenching_age)
+        sed.add_info("sfh.quenching_factor", self.quenching_factor)
+
+# SedModule to be returned by get_module
+Module = SfhQuenchSmooth

pcigale/sed_modules/sfh_quenching.py → pcigale/sed_modules/sfh_quenching_trunk.py

 # -*- coding: utf-8 -*-
 
-# Copyright (C) 2015 Laboratoire d'Astrophysique de Marseille
+# Copyright (C) 2015-2016 Laboratoire d'Astrophysique de Marseille
 # Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt
 # Author: Yannick Roehlly
 
 """
-Star Formation History quenching module
-=======================================
+Star Formation History quenching (trunk) module
+===============================================
 
 This module performs a quenching on the Star Formation History. Below a given
 age, the Star Formation Rate in multiplied by 1 - quenching_factor and is set
@@ -21,7 +21,7 @@ import numpy as np
 from . import SedModule
 
 
-class SfhQuench(SedModule):
+class SfhQuenchTrunk(SedModule):
     """Star Formation History Quenching
 
     This module implements a quenching of the Star Formation History.
@@ -74,7 +74,7 @@ class SfhQuench(SedModule):
         # We make the computation only if the quenching age and the quenching
         # factor are not 0.
         if self.quenching_age > 0 and self.quenching_factor > 0.:
-            sfr[-self.quenching_age:] = sfr[-quenching_idx] * (
+            sfr[-self.quenching_age:] = sfr[-self.quenching_age] * (
                 1. - self.quenching_factor)
 
             # Compute the galaxy mass and normalise the SFH to 1 solar mass
@@ -93,4 +93,4 @@ class SfhQuench(SedModule):
         sed.add_info("sfh.quenching_factor", self.quenching_factor)
 
 # SedModule to be returned by get_module
-Module = SfhQuench
+Module = SfhQuenchTrunk