Image data handling refactor

.github/dependabot.yml

@@ -0,0 +1,15 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: ".github/workflows" # Location of package manifests
+    schedule:
+      interval: "monthly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/cron-tests.yml

@@ -22,7 +22,7 @@ concurrency:
 jobs:
   tests:
     if: (github.repository == 'astropy/specreduce' && (github.event_name == 'schedule' || github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'Extra CI')))
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@924441154cf3053034c6513d5e06c69d262fb9a6  # v1.13.0
     with:
       submodules: false
       coverage: ''

.github/workflows/publish-to-pypi.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   publish:
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@924441154cf3053034c6513d5e06c69d262fb9a6  # v1.13.0
     # NOTE: Uncomment "if" if you do not want this to run for every PR.
     # if: ((github.event_name == 'push' && startsWith(github.ref, 'refs/tags')) || contains(github.event.pull_request.labels.*.name, 'Build wheels'))
     with:

.github/workflows/tox-tests.yml

@@ -21,7 +21,7 @@ concurrency:
 
 jobs:
   tests:
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@924441154cf3053034c6513d5e06c69d262fb9a6  # v1.13.0
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV }}
     with:

CHANGES.rst

@@ -70,7 +70,12 @@ Bug Fixes
   peaks. Previously for Gaussian, the entire fit failed. [#205, #206]
 
 - Fixed input of `traces` in `Background`. Added a condition to 'FlatTrace' that
-  trace position must be a positive number. [#211]
+
+- Fix in FitTrace to set fully-masked column bin peaks to NaN. Previously, for
+  peak_method='max' these were set to 0.0, and for peak_method='centroid' they
+  were set to the number of rows in the image, biasing the final fit to all bin
+  peaks. [#206]
+
 
 Other changes
 ^^^^^^^^^^^^^

specreduce/core.py

@@ -1,5 +1,6 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 
+from copy import deepcopy
 import inspect
 from dataclasses import dataclass
 
@@ -11,88 +12,8 @@
 __all__ = ['SpecreduceOperation']
 
 
-class _ImageParser:
-    """
-    Coerces images from accepted formats to Spectrum1D objects for
-    internal use in specreduce's operation classes.
-
-    Fills any and all of uncertainty, mask, units, and spectral axis
-    that are missing in the provided image with generic values.
-    Accepted image types are:
-
-        - `~specutils.spectra.spectrum1d.Spectrum1D` (preferred)
-        - `~astropy.nddata.ccddata.CCDData`
-        - `~astropy.nddata.ndddata.NDDData`
-        - `~astropy.units.quantity.Quantity`
-        - `~numpy.ndarray`
-    """
-
-    def _parse_image(self, image, disp_axis=1):
-        """
-        Convert all accepted image types to a consistently formatted
-        Spectrum1D object.
-
-        Parameters
-        ----------
-        image : `~astropy.nddata.NDData`-like or array-like, required
-            The image to be parsed. If None, defaults to class' own
-            image attribute.
-        disp_axis : int, optional
-            The index of the image's dispersion axis. Should not be
-            changed until operations can handle variable image
-            orientations. [default: 1]
-        """
-
-        # would be nice to handle (cross)disp_axis consistently across
-        # operations (public attribute? private attribute? argument only?) so
-        # it can be called from self instead of via kwargs...
-
-        if image is None:
-            # useful for Background's instance methods
-            return self.image
-
-        img = self._get_data_from_image(image, disp_axis=disp_axis)
-
-        return img
-
-    @staticmethod
-    def _get_data_from_image(image, disp_axis=1):
-        """Extract data array from various input types for `image`.
-           Retruns `np.ndarray` of image data."""
-
-        if isinstance(image, u.quantity.Quantity):
-            img = image.value
-        elif isinstance(image, np.ndarray):
-            img = image
-        else:  # NDData, including CCDData and Spectrum1D
-            img = image.data
-
-        # mask and uncertainty are set as None when they aren't specified upon
-        # creating a Spectrum1D object, so we must check whether these
-        # attributes are absent *and* whether they are present but set as None
-        if getattr(image, 'mask', None) is not None:
-            mask = image.mask
-        else:
-            mask = ~np.isfinite(img)
-
-        if getattr(image, 'uncertainty', None) is not None:
-            uncertainty = image.uncertainty
-        else:
-            uncertainty = VarianceUncertainty(np.ones(img.shape))
-
-        unit = getattr(image, 'unit', u.Unit('DN'))
-
-        spectral_axis = getattr(image, 'spectral_axis',
-                                np.arange(img.shape[disp_axis]) * u.pix)
-
-        return Spectrum1D(img * unit, spectral_axis=spectral_axis,
-                          uncertainty=uncertainty, mask=mask)
-
-        return img
-
-
 @dataclass
-class SpecreduceOperation(_ImageParser):
+class SpecreduceOperation:
     """
     An operation to perform as part of a spectroscopic reduction pipeline.