Merge pull request #11 from kadrlica/marigo2017

Remove spurious point in Marigo 2017 isochrone
DarkEnergySurvey · May 12, 2018 · ccb503d · ccb503d
2 parents 85faa65 + f8603d9
commit ccb503d
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Showing 5 changed files with 32 additions and 14 deletions.
diff --git a/.gitignore b/.gitignore
@@ -10,4 +10,6 @@ dist/
 
 ### ugali data files
 ugali/data/*/
+healpix
+mask
 *.tar.gz
diff --git a/tests/test_loglike.py b/tests/test_loglike.py
@@ -19,27 +19,34 @@ def test_loglike():
     loglike = ugali.analysis.loglike.createLoglike(CONFIG,lon=LON,lat=LAT)
 
     source = loglike.source
+    np.testing.assert_equal(source.isochrone.name,'Bressan2012')
+    np.testing.assert_equal(source.kernel.name,'RadialPlummer')
     np.testing.assert_equal(source.richness,1000.)
 
     # Probability calculations
-    np.testing.assert_allclose(loglike.f,0.1945461,rtol=1e-6)
+    np.testing.assert_allclose(loglike.f,0.08614111,rtol=1e-6)
+
     np.testing.assert_allclose(loglike.u[IDX],
-                               [1.11721569e-11, 3.67872840e-03, 3.25216604e-02])
+                               [5.29605173e-03, 1.80040569e-03, 5.52283081e-09],
+                               rtol=1e-6)
     np.testing.assert_allclose(loglike.b[IDX],
-                               [4215.31143651, 9149.29106545, 1698.22182173])
+                               [4215.31143651, 9149.29106545, 1698.22182173],
+                               rtol=1e-6)
     np.testing.assert_allclose(loglike.p[IDX],
-                               [2.65037519e-12, 4.01916371e-04, 1.87905722e-02])
-    np.testing.assert_allclose(loglike(),390.153891)
-    np.testing.assert_allclose(loglike.ts(),780.30778)
-    np.testing.assert_allclose(loglike.nobs,194.546134)
+                               [1.25480793e-03, 1.96742181e-04, 3.25212568e-09],
+                               rtol=1e-6)
+    np.testing.assert_allclose(loglike(),3947.9703876)
+    np.testing.assert_allclose(loglike.ts(),7895.94077)
+    np.testing.assert_allclose(loglike.nobs,86.1411187)
 
     # Fit the richness
     interval = loglike.richness_interval()
-    np.testing.assert_allclose(interval,(1713.4082, 1969.1216))
+    np.testing.assert_allclose(interval,(31516.82584, 32836.37888))
+
     lnl,rich,para = loglike.fit_richness()
-    np.testing.assert_allclose(lnl,418.666213)
-    np.testing.assert_allclose(rich,1839.005237)
-    np.testing.assert_allclose(loglike.source.richness,1839.005237)
+    np.testing.assert_allclose(lnl,8443.79621)
+    np.testing.assert_allclose(rich,32171.788052)
+    np.testing.assert_allclose(loglike.source.richness,32171.78805)
 
     # Write membership
     filename = 'test-membership.fits'

diff --git a/ugali/analysis/imf.py b/ugali/analysis/imf.py
@@ -61,10 +61,11 @@ def integrate(self, mass_min, mass_max, log_mode=True, weight=False, steps=10000
             else:
                 return np.sum(d_mass * self.pdf(mass, log_mode=False))
 
-    def sample(self, n, mass_min=0.1, mass_max=10., steps=10000):
+    def sample(self, n, mass_min=0.1, mass_max=10., steps=10000, seed=None):
         """
         Sample n initial mass values between mass_min and mass_max, following the IMF distribution.
         """
+        if seed is not None: np.random.seed(seed)
         d_mass = (mass_max - mass_min) / float(steps)
         mass = numpy.linspace(mass_min, mass_max, steps)
         cdf = numpy.insert(numpy.cumsum(d_mass * self.pdf(mass[1:], log_mode=False)), 0, 0.)

diff --git a/ugali/config/config_test.yaml b/ugali/config/config_test.yaml
@@ -92,18 +92,23 @@ kernel: &kernel
 isochrone: &isochrone
    name: Bressan2012
    age: 12.0
-   z: 0.0001
+   z: 0.00010
    distance_modulus : 17.0
    band_1 : *band1
    band_2 : *band2
    band_1_detection : *detection
+
+# Default source specification
+source: &source
+  kernel   : *kernel
+  isochrone: *isochrone
 
 likelihood:
   #delta_mag: 0.01 # 1.e-3 
   delta_mag: 0.01 # 1.e-3 
 
 ### ### ### ### ### ### ### ### ### ### 
-### Options for analysis components ###
+### Options for pipeline components ###
 ### ### ### ### ### ### ### ### ### ### 
 
 output:

diff --git a/ugali/isochrone/parsec.py b/ugali/isochrone/parsec.py
@@ -375,6 +375,9 @@ def _parse(self,filename):
 
         kwargs = dict(usecols=list(columns.keys()),dtype=list(columns.values()))
         self.data = np.genfromtxt(filename,**kwargs)
+        # cut out anomalous point:
+        # https://github.com/DarkEnergySurvey/ugali/issues/29
+        self.data = self.data[self.data['stage'] != 9]
 
         self.mass_init = self.data['mass_init']
         self.mass_act  = self.data['mass_act']