Merge d004813 into 51f02cd

ccdproc/ccddata.py

@@ -11,7 +11,7 @@
 from astropy.io import fits, registry
 from astropy.utils.compat.odict import OrderedDict
 from astropy import units as u
-import astropy
+from astropy import log
 
 from .utils.collections import CaseInsensitiveOrderedDict
 
@@ -39,7 +39,7 @@ class CCDData(NDData):
         make copy the `data` before passing it in if that's the  desired
         behavior.
 
-    uncertainty : `~astropy.nddata.StdDevUncertainty`, optional
+    uncertainty : `~astropy.nddata.StdDevUncertainty` or `~numpy.ndarray`, optional
         Uncertainties on the data.
 
     mask : `~numpy.ndarray`, optional
@@ -143,10 +143,17 @@ def uncertainty(self, value):
         if value is not None:
             if isinstance(value, NDUncertainty):
                 self._uncertainty = value
-                self._uncertainty._parent_nddata = self
+            elif isinstance(value, np.ndarray):
+                if value.shape != self.shape:
+                    raise ValueError("Uncertainty must have same shape as "
+                                     "data")
+                self._uncertainty = StdDevUncertainty(value)
+                log.info("Array provided for uncertainty; assuming it is a "
+                         "StdDevUncertainty.")
             else:
                 raise TypeError("Uncertainty must be an instance of a "
-                                "NDUncertainty object")
+                                "NDUncertainty object or a numpy array.")
+            self._uncertainty._parent_nddata = self
         else:
             self._uncertainty = value
 
@@ -262,8 +269,10 @@ def fits_ccddata_reader(filename, hdu=0, unit=None, **kwd):
     hdu : int, optional
         FITS extension from which CCDData should be initialized.
 
-    unit : astropy.units.Unit
-        Units of the image data
+    unit : astropy.units.Unit, optional
+        Units of the image data. If this argument is provided and there is a
+        unit for the image in the FITS header (the keyword ``BUNIT`` is used
+        as the unit, if present), this argument is used for the unit.
 
     kwd :
         Any additional keyword parameters are passed through to the FITS reader
@@ -286,7 +295,19 @@ def fits_ccddata_reader(filename, hdu=0, unit=None, **kwd):
             prefix = 'Unsupported keyword: {0}.'.format(key)
             raise TypeError(' '.join([prefix, msg]))
     hdus = fits.open(filename, **kwd)
-    ccd_data = CCDData(hdus[hdu].data, meta=hdus[hdu].header, unit=unit)
+    hdr = hdus[hdu].header
+
+    try:
+        fits_unit_string = hdr['bunit']
+    except KeyError:
+        fits_unit_string = None
+
+    if unit is not None and fits_unit_string:
+        log.info("Using the unit {0} passed to the FITS reader instead of "
+                 "the unit {1} in the FITS file.", unit, fits_unit_string)
+
+    use_unit = unit or fits_unit_string
+    ccd_data = CCDData(hdus[hdu].data, meta=hdus[hdu].header, unit=use_unit)
     hdus.close()
     return ccd_data
 

ccdproc/tests/test_ccddata.py

@@ -48,6 +48,21 @@ def test_initialize_from_FITS(ccd_data, tmpdir):
         assert cd.meta[k] == v
 
 
+def test_initialize_from_fits_with_unit_in_header(tmpdir):
+    fake_img = np.random.random(size=(100, 100))
+    hdu = fits.PrimaryHDU(fake_img)
+    hdu.header['bunit'] = u.adu.to_string()
+    filename = tmpdir.join('afile.fits').strpath
+    hdu.writeto(filename)
+    ccd = CCDData.read(filename)
+    # ccd should pick up the unit adu from the fits header...did it?
+    assert ccd.unit is u.adu
+
+    # An explicit unit in the read overrides any unit in the FITS file
+    ccd2 = CCDData.read(filename, unit="photon")
+    assert ccd2.unit is u.photon
+
+
 def test_initialize_from_FITS_bad_keyword_raises_error(ccd_data, tmpdir):
     # There are two fits.open keywords that are not permitted in ccdpro:
     #     do_not_scale_image_data and scale_back
@@ -135,6 +150,18 @@ def test_setting_bad_uncertainty_raises_error(ccd_data):
         ccd_data.uncertainty = 10
 
 
+def test_setting_uncertainty_with_array(ccd_data):
+    ccd_data.uncertainty = None
+    fake_uncertainty = np.sqrt(np.abs(ccd_data.data))
+    ccd_data.uncertainty = fake_uncertainty.copy()
+    np.testing.assert_array_equal(ccd_data.uncertainty.array, fake_uncertainty)
+
+
+def test_setting_uncertainty_wrong_shape_raises_error(ccd_data):
+    with pytest.raises(ValueError):
+        ccd_data.uncertainty = np.random.random(size=2 * ccd_data.shape)
+
+
 def test_to_hdu(ccd_data):
     ccd_data.meta = {'observer': 'Edwin Hubble'}
     fits_hdulist = ccd_data.to_hdu()

docs/ccdproc/ccddata.rst

@@ -45,8 +45,9 @@ A `~ccdproc.ccddata.CCDData` object can also be initialized from a FITS file:
 
     >>> ccd = ccdproc.CCDData.read('my_file.fits', unit="adu")  # doctest: +SKIP
 
-but for the moment you need to set the unit explicitly, even if it is in the
-FITS header.
+If there is a unit in the FITS file (in the ``BUNIT`` keyword), that will be
+used, but a unit explicitly provided in ``read`` will override any unit in the
+FITS file.
 
 There is no restriction at all on what the unit can be -- any unit in
 `astropy.units` or that you create yourself will work.
@@ -131,16 +132,22 @@ Pixel-by-pixel uncertainty can be calculated for you:
 
 See :ref:`create_variance` for more details.
 
-You can also set the uncertainty directly but need to create a
+You can also set the uncertainty directly, either by creating a
 `~astropy.nddata.StdDevUncertainty` object first:
 
     >>> from astropy.nddata.nduncertainty import StdDevUncertainty
     >>> uncertainty = 0.1 * ccd.data  # can be any array whose shape matches the data
     >>> my_uncertainty = StdDevUncertainty(uncertainty)
     >>> ccd.uncertainty = my_uncertainty
 
-Using `~astropy.nddata.StdDevUncertainty` is required to enable error
-propagation in `~ccdproc.ccddata.CCDData`
+or by providing a `~numpy.ndarray` with the same shape as the data:
+
+    >>> ccd.uncertainty = 0.1 * ccd.data
+    INFO: Array provided for uncertainty; assuming it is a StdDevUncertainty. [ccdproc.ccddata]
+
+In this case the uncertainty is assumed to be
+`~astropy.nddata.StdDevUncertainty`. Using `~astropy.nddata.StdDevUncertainty`
+is required to enable error propagation in `~ccdproc.ccddata.CCDData`
 
 If you want access to the underlying uncertainty use its ``.array`` attribute: