From f27f9326554802ef21250587f0f2252c6a1d7139 Mon Sep 17 00:00:00 2001
From: Aaron LI <aaronly.me@outlook.com>
Date: Wed, 13 Jul 2016 17:11:06 +0800
Subject: calc_overdensity.py: Use class "SmoothSpline" from module "spline.py"

---
 calc_overdensity.py | 78 +++++++++++------------------------------------------
 1 file changed, 16 insertions(+), 62 deletions(-)

diff --git a/calc_overdensity.py b/calc_overdensity.py
index 562311e..501f5dd 100755
--- a/calc_overdensity.py
+++ b/calc_overdensity.py
@@ -2,9 +2,11 @@
 #
 # Aaron LI
 # Created: 2016-06-30
-# Updated: 2016-07-11
+# Updated: 2016-07-13
 #
 # Change logs:
+# 2016-07-13:
+#   * Use class 'SmoothSpline' from module 'spline.py'
 # 2016-07-11:
 #   * Use a default config to allow a minimal user config
 # 2016-07-04:
@@ -35,10 +37,8 @@ import astropy.units as au
 from astropy.cosmology import FlatLambdaCDM
 from configobj import ConfigObj
 
-import rpy2.robjects as ro
-from rpy2.robjects.packages import importr
-
 from astro_params import AstroParams
+from spline import SmoothSpline
 
 
 config_default = """
@@ -83,11 +83,7 @@ class MassProfile:
     redshift = None
     # fitted smoothing spline
     m_spline = None
-    m_spline_log10 = None
     od_spline = None
-    od_spline_log10 = None
-    # call R through `rpy2`
-    mgcv = importr("mgcv")
 
     def __init__(self, mass, mass_type="total"):
         self.load_data(data=mass, mass_type=mass_type)
@@ -130,7 +126,7 @@ class MassProfile:
         Calculate the radius at which the overdensity is delta.
         """
         if self.od_spline is None:
-            self.fit_spline(spline="overdensity", log10=True)
+            self.fit_spline(spline="overdensity", log10=["x", "y"])
         if min(self.overdensity) > delta:
             raise ValueError("min(overdensity) > %d" % delta)
         r = optimize.newton(
@@ -140,7 +136,7 @@ class MassProfile:
 
     def calc_mass_delta(self, r_delta):
         if self.m_spline is None:
-            self.fit_spline(spline="mass", log10=True)
+            self.fit_spline(spline="mass", log10=["x", "y"])
         return self.eval_spline(spline="mass", x=r_delta)
 
     def save(self, outfile):
@@ -153,49 +149,24 @@ class MassProfile:
         header = "radius[kpc]  radius_err[kpc]  overdensity"
         np.savetxt(outfile, data, header=header)
 
-    def fit_spline(self, spline, log10):
-        """
-        Fit a smoothing line to the specified spline data,
-        by utilizing the R `mgcv::gam()` function.
-
-        If 'log10' is True, the input data are first applied the log-scale
-        transform, and then fitted by the smoothing spline.
-
-        The fitted spline allows extrapolation.
-        """
+    def fit_spline(self, spline, log10=[]):
         if spline not in self.SPLINES:
             raise ValueError("invalid spline: %s" % spline)
         #
         if spline == "mass":
             # input gas/total mass profile
-            if log10:
-                x = ro.FloatVector(np.log10(self.r))
-                y = ro.FloatVector(np.log10(self.m))
-                self.m_spline_log10 = True
-            else:
-                x = ro.FloatVector(self.r)
-                y = ro.FloatVector(self.m)
-                self.m_spline_log10 = False
-            self.m_spline = self.mgcv.gam(
-                ro.Formula("y ~ s(x, bs='ps')"),
-                data=ro.DataFrame({"x": x, "y": y}),
-                method="REML")
+            x = self.r
+            y = self.m
+            spl = "m_spline"
         elif spline == "overdensity":
             # calculated overdensity profile
-            if log10:
-                x = ro.FloatVector(np.log10(self.r))
-                y = ro.FloatVector(np.log10(self.overdensity))
-                self.od_spline_log10 = True
-            else:
-                x = ro.FloatVector(self.radius)
-                y = ro.FloatVector(self.rho_total)
-                self.od_spline_log10 = False
-            self.od_spline = self.mgcv.gam(
-                ro.Formula("y ~ s(x, bs='ps')"),
-                data=ro.DataFrame({"x": x, "y": y}),
-                method="REML")
+            x = self.radius
+            y = self.rho_total
+            spl = "od_spline"
         else:
             raise ValueError("invalid spline: %s" % spline)
+        setattr(self, spl, SmoothSpline(x=x, y=y))
+        getattr(self, spl).fit(log10=log10)
 
     def eval_spline(self, spline, x):
         """
@@ -203,31 +174,14 @@ class MassProfile:
         Also check whether the spline was fitted in the log-scale space,
         and transform the evaluated values if necessary.
         """
-        x = np.array(x)
-        if x.shape == ():
-            x = x.reshape((1,))
         if spline == "mass":
             spl = self.m_spline
-            log10 = self.m_spline_log10
         elif spline == "overdensity":
             spl = self.od_spline
-            log10 = self.od_spline_log10
         else:
             raise ValueError("invalid spline: %s" % spline)
         #
-        if log10:
-            x_new = ro.ListVector({"x": ro.FloatVector(np.log10(x))})
-            y_pred = self.mgcv.predict_gam(spl, newdata=x_new)
-            y_pred = 10 ** np.array(y_pred)
-        else:
-            x_new = ro.ListVector({"x": ro.FloatVector(x)})
-            y_pred = self.mgcv.predict_gam(spl, newdata=x_new)
-            y_pred = np.array(y_pred)
-        #
-        if len(y_pred) == 1:
-            return y_pred[0]
-        else:
-            return y_pred
+        return spl.eval(x)
 
 
 def main():
-- 
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