Merge pull request #116 from p-slash/v1.1.2-dev

v1.1.2 - remove outlier masking

py/qsonic/__init__.py

@@ -1,6 +1,6 @@
 __author__ = 'Naim Goksel Karacayli'
 __email__ = '[email protected]'
-__version__ = '1.1.1'
+__version__ = '1.1.2'
 
 
 class QsonicException(Exception):

py/qsonic/spectrum.py

@@ -2,8 +2,7 @@
 
 import numpy as np
 
-from qsonic.mathtools import (
-    _zero_function, _one_function, get_smooth_ivar, get_median_outlier_mask)
+from qsonic.mathtools import _zero_function, _one_function, get_smooth_ivar
 
 
 def add_wave_region_parser(parser=None):
@@ -303,11 +302,11 @@ def slice(self, arm, i1, i2):
                 self.cont_params['cont'][arm][i1:i2]
 
     def set_forest_region(self, w1, w2, lya1, lya2):
-        """ Sets slices for the forest region. Masks outliers in each arm
-        separately based on moving median statistics
-        (see :func:`qsonic.mathtools.get_median_outlier_mask`). Also calculates
+        """ Sets slices for the forest region. Also calculates
         the mean SNR in the forest and an initial guess for the continuum
-        amplitude.
+        amplitude. This is currently turned off, but it can mask outliers in
+        each arm separately based on moving median statistics
+        (see :func:`qsonic.mathtools.get_median_outlier_mask`).
 
         Arguments
         ---------
@@ -337,11 +336,6 @@ def set_forest_region(self, w1, w2, lya1, lya2):
             if self.reso:
                 self._forestreso[arm] = self.reso[arm][:, ii1:ii2].copy()
 
-            w = get_median_outlier_mask(
-                self._forestflux[arm], self._forestivar[arm])
-            self._forestflux[arm][w] = 0
-            self._forestivar[arm][w] = 0
-
         self._forestivar_sm = self._forestivar
         self._forestweight = self._forestivar
         self._set_forest_related_parameters()
@@ -611,8 +605,10 @@ def coadd_arms_forest(
         min_wave = np.min([wave[0] for wave in self.forestwave.values()])
         max_wave = np.max([wave[-1] for wave in self.forestwave.values()])
 
-        nwaves = int((max_wave - min_wave) / self.dwave + 0.1) + 1
-        coadd_wave = np.linspace(min_wave, max_wave, nwaves)
+        nwaves = round((max_wave - min_wave) / self.dwave + 0.1)
+        coadd_wave = np.linspace(
+            min_wave, min_wave + nwaves * self.dwave, nwaves + 1)
+        nwaves += 1
         coadd_flux = np.zeros(nwaves)
         coadd_ivar = np.zeros(nwaves)
         coadd_norm = np.zeros(nwaves)

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.1
+current_version = 1.1.2
 commit = True
 tag = False
 message = [skip ci] Bump version: {current_version} → {new_version}

tests/test_spectrum.py

@@ -57,9 +57,10 @@ def test_set_forest_region(self, setup_data):
         assert ('R' not in spec.forestflux.keys())
         assert (not spec.forestreso)
 
-        spec.flux['B'][10:15] = 1e2
-        spec.set_forest_region(3600., 6000., 1050., 1180.)
-        npt.assert_equal(spec.forestflux['B'][10:15], 0)
+        # Test outlier masking (turned off)
+        # spec.flux['B'][10:15] = 1e2
+        # spec.set_forest_region(3600., 6000., 1050., 1180.)
+        # npt.assert_equal(spec.forestflux['B'][10:15], 0)
 
     def test_drop_short_arms(self, setup_data):
         cat_by_survey, _, data = setup_data(1)