Merge pull request #407 from hamogu/patchwcs

Extend list of hacks for reading non-standard complied 1d WCS fits files

specutils/tests/test_loaders.py

@@ -1,3 +1,4 @@
+import logging
 import os
 import shutil
 import tempfile
@@ -36,7 +37,7 @@ def test_spectrum1d_GMOSfits(remote_data_path):
 
 
 @remote_access([{'id': '1481190', 'filename': 'L5g_0355+11_Cruz09.fits'}])
-def test_spectrumlist_GMOSfits(remote_data_path):
+def test_spectrumlist_GMOSfits(remote_data_path, caplog):
     with warnings.catch_warnings():
         warnings.simplefilter('ignore', (VerifyWarning, UnitsWarning))
         spectrum_list = SpectrumList.read(remote_data_path, format='wcs1d-fits')
@@ -46,6 +47,11 @@ def test_spectrumlist_GMOSfits(remote_data_path):
     spec = spectrum_list[0]
     assert len(spec.data) == 3020
 
+    logmsg = caplog.record_tuples[0]
+    assert logmsg[1] == logging.WARN
+    assert "Assuming the axis 0 labeled 'linear' is spectral" in logmsg[2]
+
+
 
 @remote_access([{'id': '1481190', 'filename': 'L5g_0355+11_Cruz09.fits'}])
 def test_specific_spec_axis_unit(remote_data_path):
@@ -57,6 +63,15 @@ def test_specific_spec_axis_unit(remote_data_path):
 
     assert optical_spec.spectral_axis.unit == "Angstrom"
 
+@remote_access([{'id': '2656720', 'filename': '_v1410ori_20181204_261_Forrest%20Sims.fit'}])
+def test_ctypye_not_compliant(remote_data_path, caplog):
+    optical_spec = Spectrum1D.read(remote_data_path,
+                                   spectral_axis_unit="Angstrom",
+                                   format='wcs1d-fits')
+    logmsg = caplog.record_tuples[0]
+    assert logmsg[1] == logging.WARN
+    assert "Assuming the axis 0 labeled 'wavelength' is spectral" in logmsg[2]
+
 
 def test_generic_ecsv_reader(tmpdir):
     # Create a small data set

specutils/wcs/adapters/fitswcs_adapter.py

@@ -1,3 +1,4 @@
+import logging
 import astropy.units as u
 from astropy.wcs import (WCS, WCSSUB_CELESTIAL, WCSSUB_CUBEFACE,
                          WCSSUB_LATITUDE, WCSSUB_LONGITUDE, WCSSUB_SPECTRAL,
@@ -14,10 +15,18 @@
 class FITSWCSAdapter(WCSAdapter):
     """
     Adapter class that adds support for FITSWCS objects.
+
+    In the wild, fits WCS headers are often non-standard compliant, but
+    can be interpreted with little ambiguity (e.g. the CTYPE of the
+    wavelength axis is called "Wavelength" instead of the standard fits
+    "WAVE"). In some common cases, this class will thus read files that
+    are not fully compliant. In these cases, it prints a warning message.
     """
     wrapped_class = WCS
     axes = None
 
+    substitute_spec_axis_names = ['linear', 'wavelength']
+
     def __init__(self, wcs):
         super(FITSWCSAdapter, self).__init__(wcs)
         self._spec_axis = None
@@ -71,17 +80,18 @@ def spec_axis(self):
         """
         self._spec_axis = self.wcs.wcs.spec
 
-        if self._spec_axis < 0:
-            try:
-                idx = list(self.wcs.wcs.ctype).index('LINEAR')
-            except ValueError:
+        if (self._spec_axis < 0) and (self._wcs.wcs.spec) < 0:
+            ctypelist = [c.lower() for c in self.wcs.wcs.ctype]
+            for n in self.substitute_spec_axis_names:
+                if n in ctypelist:
+                    self._spec_axis = ctypelist.index(n)
+                    logging.warning("WCS has a non-standard spectral axis, 'ctype's might be incorrect. Assuming the axis {} labeled '{}' is spectral and proceeding.".format(self._spec_axis, n))
+                    break
+            else:
                 raise InvalidSubimageSpecificationError(
                     "Cannot find a spectral axis in the provided WCS."
                     "Are your 'ctype's correct?")
 
-            if self._wcs.wcs.spec < 0:
-                self._spec_axis = idx
-
         return self._spec_axis
 
     @property