diff --git a/specreduce/background.py b/specreduce/background.py
index a2829622..d8b7def3 100644
--- a/specreduce/background.py
+++ b/specreduce/background.py
@@ -26,7 +26,7 @@ class Background:
Parameters
----------
- image : `~astropy.nddata.NDData` or array-like
+ image : `~astropy.nddata.NDData`-like or array-like
image with 2-D spectral image data
traces : List
list of trace objects (or integers to define FlatTraces) to
@@ -59,7 +59,7 @@ def __post_init__(self):
Parameters
----------
- image : `~astropy.nddata.NDData` or array-like
+ image : `~astropy.nddata.NDData`-like or array-like
image with 2-D spectral image data
traces : List
list of trace objects (or integers to define FlatTraces) to
@@ -85,6 +85,11 @@ def _to_trace(trace):
raise ValueError('trace_object.trace_pos must be >= 1')
return trace
+ if isinstance(self.image, NDData):
+ # NOTE: should the NDData structure instead be preserved?
+ # (NDData includes Spectrum1D under its umbrella)
+ self.image = self.image.data
+
bkg_wimage = np.zeros_like(self.image, dtype=np.float64)
for trace in self.traces:
trace = _to_trace(trace)
@@ -132,7 +137,7 @@ def two_sided(cls, image, trace_object, separation, **kwargs):
Parameters
----------
- image : nddata-compatible image
+ image : `~astropy.nddata.NDData`-like or array-like
image with 2-D spectral image data
trace_object: Trace
estimated trace of the spectrum to center the background traces
@@ -165,7 +170,7 @@ def one_sided(cls, image, trace_object, separation, **kwargs):
Parameters
----------
- image : nddata-compatible image
+ image : `~astropy.nddata.NDData`-like or array-like
image with 2-D spectral image data
trace_object: Trace
estimated trace of the spectrum to center the background traces
@@ -192,7 +197,7 @@ def bkg_image(self, image=None):
Parameters
----------
- image : nddata-compatible image or None
+ image : `~astropy.nddata.NDData`-like, array-like, or None
image with 2-D spectral image data. If None, will use ``image`` passed
to extract the background.
@@ -211,7 +216,7 @@ def sub_image(self, image=None):
Parameters
----------
- image : nddata-compatible image or None
+ image : `~astropy.nddata.NDData`-like, array-like, or None
image with 2-D spectral image data. If None, will use ``image`` passed
to extract the background.
diff --git a/specreduce/extract.py b/specreduce/extract.py
index 2537d7ba..768c6160 100644
--- a/specreduce/extract.py
+++ b/specreduce/extract.py
@@ -116,15 +116,15 @@ class BoxcarExtract(SpecreduceOperation):
Parameters
----------
- image : nddata-compatible image
+ image : `~astropy.nddata.NDData`-like or array-like, required
image with 2-D spectral image data
- trace_object : Trace
+ trace_object : Trace, required
trace object
- width : float
+ width : float, optional
width of extraction aperture in pixels
- disp_axis : int
+ disp_axis : int, optional
dispersion axis
- crossdisp_axis : int
+ crossdisp_axis : int, optional
cross-dispersion axis
Returns
@@ -150,15 +150,15 @@ def __call__(self, image=None, trace_object=None, width=None,
Parameters
----------
- image : nddata-compatible image
+ image : `~astropy.nddata.NDData`-like or array-like, required
image with 2-D spectral image data
- trace_object : Trace
+ trace_object : Trace, required
trace object
- width : float
+ width : float, optional
width of extraction aperture in pixels [default: 5]
- disp_axis : int
+ disp_axis : int, optional
dispersion axis [default: 1]
- crossdisp_axis : int
+ crossdisp_axis : int, optional
cross-dispersion axis [default: 0]
@@ -174,25 +174,33 @@ def __call__(self, image=None, trace_object=None, width=None,
disp_axis = disp_axis if disp_axis is not None else self.disp_axis
crossdisp_axis = crossdisp_axis if crossdisp_axis is not None else self.crossdisp_axis
+ # handle image processing based on its type
+ if isinstance(image, Spectrum1D):
+ img = image.data
+ unit = image.unit
+ else:
+ img = image
+ unit = getattr(image, 'unit', u.DN)
+
# TODO: this check can be removed if/when implemented as a check in FlatTrace
if isinstance(trace_object, FlatTrace):
if trace_object.trace_pos < 1:
raise ValueError('trace_object.trace_pos must be >= 1')
# weight image to use for extraction
- wimage = _ap_weight_image(
+ wimg = _ap_weight_image(
trace_object,
width,
disp_axis,
crossdisp_axis,
- image.shape)
+ img.shape)
# extract
- ext1d = np.sum(image * wimage, axis=crossdisp_axis)
+ ext1d = np.sum(img * wimg, axis=crossdisp_axis) * unit
- # 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))
+ # TODO: add wavelength units, uncertainty and mask to Spectrum1D object
+ pixels = np.arange(ext1d.shape[crossdisp_axis]) * u.pixel
+ spec = Spectrum1D(spectral_axis=pixels, flux=ext1d)
return spec
@@ -206,7 +214,7 @@ class HorneExtract(SpecreduceOperation):
Parameters
----------
- image : `~astropy.nddata.NDData` or array-like, required
+ image : `~astropy.nddata.NDData`-like or array-like, required
The input 2D spectrum from which to extract a source. An
NDData object must specify uncertainty and a mask. An array
requires use of the ``variance``, ``mask``, & ``unit`` arguments.
@@ -269,7 +277,7 @@ def __call__(self, image=None, trace_object=None,
Parameters
----------
- image : `~astropy.nddata.NDData` or array-like, required
+ image : `~astropy.nddata.NDData`-like or array-like, required
The input 2D spectrum from which to extract a source. An
NDData object must specify uncertainty and a mask. An array
requires use of the ``variance``, ``mask``, & ``unit`` arguments.
@@ -322,6 +330,7 @@ def __call__(self, image=None, trace_object=None,
# handle image and associated data based on image's type
if isinstance(image, NDData):
+ # (NDData includes Spectrum1D under its umbrella)
img = np.ma.array(image.data, mask=image.mask)
unit = image.unit if image.unit is not None else u.Unit()
diff --git a/specreduce/tracing.py b/specreduce/tracing.py
index 6b2557ca..23ec9d08 100644
--- a/specreduce/tracing.py
+++ b/specreduce/tracing.py
@@ -8,6 +8,7 @@
from astropy.nddata import CCDData, NDData
from astropy.stats import gaussian_sigma_to_fwhm
from scipy.interpolate import UnivariateSpline
+from specutils import Spectrum1D
import numpy as np
__all__ = ['Trace', 'FlatTrace', 'ArrayTrace', 'KosmosTrace']
@@ -20,7 +21,7 @@ class Trace:
Parameters
----------
- image : `~astropy.nddata.CCDData`
+ image : `~astropy.nddata.NDData`-like or array-like, required
Image to be traced
Properties
@@ -28,7 +29,7 @@ class Trace:
shape : tuple
Shape of the array describing the trace
"""
- image: CCDData
+ image: NDData
def __post_init__(self):
self.trace_pos = self.image.shape[0] / 2
@@ -37,6 +38,11 @@ def __post_init__(self):
def __getitem__(self, i):
return self.trace[i]
+ def _parse_image(self):
+ if isinstance(self.image, Spectrum1D):
+ # NOTE: should the Spectrum1D structure instead be preserved?
+ self.image = self.image.data
+
@property
def shape(self):
return self.trace.shape
@@ -95,6 +101,8 @@ class FlatTrace(Trace):
trace_pos: float
def __post_init__(self):
+ super()._parse_image()
+
self.set_position(self.trace_pos)
def set_position(self, trace_pos):
@@ -124,6 +132,8 @@ class ArrayTrace(Trace):
trace: np.ndarray
def __post_init__(self):
+ super()._parse_image()
+
nx = self.image.shape[1]
nt = len(self.trace)
if nt != nx:
@@ -158,7 +168,7 @@ class KosmosTrace(Trace):
Parameters
----------
- image : `~astropy.nddata.NDData` or array-like, required
+ image : `~astropy.nddata.NDData`-like or array-like, required
The image over which to run the trace. Assumes cross-dispersion
(spatial) direction is axis 0 and dispersion (wavelength)
direction is axis 1.
@@ -200,6 +210,8 @@ class KosmosTrace(Trace):
_disp_axis = 1
def __post_init__(self):
+ super()._parse_image()
+
# handle multiple image types and mask uncaught invalid values
if isinstance(self.image, NDData):
img = np.ma.masked_invalid(np.ma.masked_array(self.image.data,