Merge pull request #361 from simontorres/fix_mask_issue

Extracted spectrum (1 dimension) had mask it wasn't updated so saving the file would fail.
- Test updated to include a mask
- Set mask to `None` for extracted spectrum files.

docs/change_history.rst

@@ -3,12 +3,15 @@ Change History
 
 .. _v1.3.5:
 
-V1.3.5 Not Released
-^^^^^^^^^^^^^^^^^^^
+V1.3.5 24-11-2021
+^^^^^^^^^^^^^^^^^
 
 - Created `--target-min-width` and `--target-max-width` flags to allow extraction of extended sources.
 - Replaced coveralls with codecov for code coverage.
 - Documentation improvements and updates.
+- Fixed issue with extracted spectrum that where masked in 2D.
+- Code style improvements.
+
 
 .. _v1.3.4:
 

goodman_pipeline/core/__init__.py

@@ -42,7 +42,7 @@
                    identify_technique,
                    image_overscan,
                    image_trim,
-                   interpolate,
+                   interpolate_spectrum,
                    is_file_saturated,
                    linearize_spectrum,
                    name_master_flats,

goodman_pipeline/core/core.py

@@ -13,7 +13,6 @@
 import pandas
 import random
 import re
-import scipy
 import subprocess
 import sys
 import time
@@ -30,7 +29,7 @@
 from astropy.time import Time
 from astroscrappy import detect_cosmics
 from matplotlib import pyplot as plt
-from scipy import signal
+from scipy import signal, interpolate
 from threading import Timer
 
 from . import check_version
@@ -1296,6 +1295,8 @@ def extract_fractional_pixel(ccd, target_trace, target_fwhm, extraction_width,
 
     new_ccd = ccd.copy()
     new_ccd.data = np.asarray(extracted_spectrum)
+    log.warning("Setting mask to None, otherwise saving will fail.")
+    new_ccd.mask = None
     if new_ccd.header['NAXIS'] != 1:
         for i in range(int(new_ccd.header['NAXIS']), 1, -1):
             new_ccd.header.remove(keyword="NAXIS{:d}".format(i))
@@ -2062,7 +2063,7 @@ def image_trim(ccd, trim_section, trim_type='trimsec', add_keyword=False):
     return ccd
 
 
-def interpolate(spectrum, interpolation_size):
+def interpolate_spectrum(spectrum, interpolation_size):
     """Creates an interpolated version of the input spectrum
 
     This method creates an interpolated version of the input array, it is
@@ -2089,8 +2090,8 @@ def interpolate(spectrum, interpolation_size):
                              last_x,
                              spectrum.size * interpolation_size)
 
-    tck = scipy.interpolate.splrep(x_axis, spectrum, s=0)
-    new_spectrum = scipy.interpolate.splev(new_x_axis, tck, der=0)
+    tck = interpolate.splrep(x_axis, spectrum, s=0)
+    new_spectrum = interpolate.splev(new_x_axis, tck, der=0)
     return [new_x_axis, new_spectrum]
 
 
@@ -2169,10 +2170,8 @@ def linearize_spectrum(data, wavelength_solution, plots=False):
         except TypeError:
             pass
         new_x_axis = np.linspace(x_axis[0], x_axis[-1], len(data))
-        tck = scipy.interpolate.splrep(x_axis, data, s=0)
-        linearized_data = scipy.interpolate.splev(new_x_axis,
-                                                  tck,
-                                                  der=0)
+        tck = interpolate.splrep(x_axis, data, s=0)
+        linearized_data = interpolate.splev(new_x_axis, tck, der=0)
 
         smoothed_linearized_data = signal.medfilt(linearized_data)
         if plots:  # pragma: no cover

goodman_pipeline/core/tests/test_core.py

@@ -62,7 +62,7 @@
                     identify_targets,
                     image_overscan,
                     image_trim,
-                    interpolate,
+                    interpolate_spectrum,
                     is_file_saturated,
                     linearize_spectrum,
                     name_master_flats,
@@ -821,6 +821,7 @@ def setUp(self):
         self.fake_image = CCDData(data=np.ones((100, 100)),
                                   meta=fits.Header(),
                                   unit='adu')
+        self.fake_image.mask = np.zeros((100, 100), dtype=bool)
         self.fake_image.header.set('NAXIS', value=2)
         self.fake_image.header.set('NAXIS1', value=100)
         self.fake_image.header.set('NAXIS2', value=100)
@@ -1259,12 +1260,12 @@ def test__get_spectral_characteristics(self):
 
 class InterpolationTest(TestCase):
 
-    def test_interpolate(self):
+    def test_interpolate_spectrum(self):
         initial_array = np.sin(np.arange(0, 3 * np.pi))
         initial_length = len(initial_array)
 
-        new_x_axis, new_array = interpolate(spectrum=initial_array,
-                                            interpolation_size=100)
+        new_x_axis, new_array = interpolate_spectrum(spectrum=initial_array,
+                                                     interpolation_size=100)
 
         self.assertEqual(len(new_x_axis), len(new_array))
         self.assertEqual(len(new_array), initial_length * 100)

goodman_pipeline/spectroscopy/wavelength.py

@@ -337,7 +337,7 @@ def _automatic_wavelength_solution(self,
         except NoMatchFound as error:
             raise NoMatchFound(error)
         except NotImplementedError as error:
-            raise NotImplemented(error)
+            raise NotImplementedError(error)
 
         # TODO (simon): Evaluate possibility to read iraf wcs. [#304]
 

goodman_pipeline/version.py

@@ -1,2 +1,2 @@
 # This is an automatic generated file please do not edit
-__version__ = '1.3.5.dev2'
+__version__ = '1.3.5'

setup.cfg

@@ -32,4 +32,4 @@ install_requires =
     ccdproc
     astroplan
 # version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 1.3.5.dev2
+version = 1.3.5