Merge pull request #143 from kecnry/bg-spectrum

Background.bkg_spectrum and sub_spectrum

CHANGES.rst

@@ -15,6 +15,8 @@ New Features
 ^^^^^^^^^^^^
 
 - ``peak_method`` as an optional argument to ``KosmosTrace`` [#115]
+- ``Background`` has new methods for exposing the 1D spectrum of the background or
+  background-subtracted regions [#143]
 
 API Changes
 ^^^^^^^^^^^

specreduce/background.py

@@ -5,8 +5,9 @@
 
 import numpy as np
 from astropy.nddata import NDData
+from astropy import units as u
 
-from specreduce.extract import _ap_weight_image
+from specreduce.extract import _ap_weight_image, _to_spectrum1d_pixels
 from specreduce.tracing import Trace, FlatTrace
 
 __all__ = ['Background']
@@ -193,8 +194,8 @@ def bkg_image(self, image=None):
         Parameters
         ----------
         image : nddata-compatible image or None
-            image with 2-D spectral image data.  If None, will use ``image`` passed
-            to extract the background.
+            image with 2-D spectral image data.  If None, will extract
+            the background from ``image`` used to initialize the class.
 
         Returns
         -------
@@ -205,15 +206,37 @@ def bkg_image(self, image=None):
 
         return np.tile(self.bkg_array, (image.shape[0], 1))
 
+    def bkg_spectrum(self, image=None):
+        """
+        Expose the 1D spectrum of the background.
+
+        Parameters
+        ----------
+        image : nddata-compatible image or None
+            image with 2-D spectral image data.  If None, will extract
+            the background from ``image`` used to initialize the class.
+
+        Returns
+        -------
+        spec : `~specutils.Spectrum1D`
+            The background 1-D spectrum, with flux expressed in the same
+            units as the input image (or u.DN if none were provided) and
+            the spectral axis expressed in pixel units.
+        """
+        bkg_image = self.bkg_image(image=image)
+
+        ext1d = np.sum(bkg_image, axis=self.crossdisp_axis)
+        return _to_spectrum1d_pixels(ext1d * getattr(image, 'unit', u.DN))
+
     def sub_image(self, image=None):
         """
         Subtract the computed background from ``image``.
 
         Parameters
         ----------
         image : nddata-compatible image or None
-            image with 2-D spectral image data.  If None, will use ``image`` passed
-            to extract the background.
+            image with 2-D spectral image data.  If None, will extract
+            the background from ``image`` used to initialize the class.
 
         Returns
         -------
@@ -228,6 +251,28 @@ def sub_image(self, image=None):
         else:
             return image - self.bkg_image(image)
 
+    def sub_spectrum(self, image=None):
+        """
+        Expose the 1D spectrum of the background-subtracted image.
+
+        Parameters
+        ----------
+        image : nddata-compatible image or None
+            image with 2-D spectral image data.  If None, will extract
+            the background from ``image`` used to initialize the class.
+
+        Returns
+        -------
+        spec : `~specutils.Spectrum1D`
+            The background 1-D spectrum, with flux expressed in the same
+            units as the input image (or u.DN if none were provided) and
+            the spectral axis expressed in pixel units.
+        """
+        sub_image = self.sub_image(image=image)
+
+        ext1d = np.sum(sub_image, axis=self.crossdisp_axis)
+        return _to_spectrum1d_pixels(ext1d * getattr(image, 'unit', u.DN))
+
     def __rsub__(self, image):
         """
         Subtract the background from an image.

specreduce/extract.py

@@ -102,6 +102,12 @@ def _ap_weight_image(trace, width, disp_axis, crossdisp_axis, image_shape):
     return wimage
 
 
+def _to_spectrum1d_pixels(fluxes):
+    # TODO: add wavelength units, uncertainty and mask to spectrum1D object
+    return Spectrum1D(spectral_axis=np.arange(len(fluxes)) * u.pixel,
+                      flux=fluxes)
+
+
 @dataclass
 class BoxcarExtract(SpecreduceOperation):
     """
@@ -189,12 +195,7 @@ def __call__(self, image=None, trace_object=None, width=None,
 
         # extract
         ext1d = np.sum(image * wimage, axis=crossdisp_axis)
-
-        # TODO: add wavelenght units, uncertainty and mask to spectrum1D object
-        spec = Spectrum1D(spectral_axis=np.arange(len(ext1d)) * u.pixel,
-                          flux=ext1d * getattr(image, 'unit', u.DN))
-
-        return spec
+        return _to_spectrum1d_pixels(ext1d * getattr(image, 'unit', u.DN))
 
 
 @dataclass
@@ -432,10 +433,7 @@ def __call__(self, image=None, trace_object=None,
         extraction = result * norms
 
         # convert the extraction to a Spectrum1D object
-        pixels = np.arange(img.shape[disp_axis]) * u.pix
-        spec_1d = Spectrum1D(spectral_axis=pixels, flux=extraction * unit)
-
-        return spec_1d
+        return _to_spectrum1d_pixels(extraction * unit)
 
 
 @dataclass

specreduce/tests/test_background.py

@@ -3,6 +3,7 @@
 
 import astropy.units as u
 from astropy.nddata import CCDData
+from specutils import Spectrum1D
 
 from specreduce.background import Background
 from specreduce.tracing import FlatTrace
@@ -44,6 +45,11 @@ def test_background():
     assert np.allclose(sub1, sub2)
     assert np.allclose(sub1, sub3)
 
+    bkg_spec = bg1.bkg_spectrum()
+    assert isinstance(bkg_spec, Spectrum1D)
+    sub_spec = bg1.sub_spectrum()
+    assert isinstance(sub_spec, Spectrum1D)
+
 
 def test_oob():
     # image.shape (30, 10)