Merge d4c3674 into bb63852

spacetelescope · Dec 20, 2019 · 712dbe5 · 712dbe5
2 parents bb63852 + d4c3674
commit 712dbe5
Show file tree

Hide file tree

Showing 4 changed files with 26 additions and 11 deletions.
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -4,6 +4,7 @@
 - Doc update (explain time column) [#19]
 - Adding img_cut and normalize_img [#21]
 - Improve cutout filenames, change minmax_cut to minmax_value [#24]
+- Add error handling when reading data raises an exception [#28]
 
 0.4 (2019-06-21)
 ----------------

diff --git a/astrocut/cube_cut.py b/astrocut/cube_cut.py
@@ -158,8 +158,6 @@ def _get_cutout_limits(self, cutout_size):
 
         Parameters
         ----------
-        center_coord : `~astropy.coordinates.SkyCoord`
-            The central coordinate for the cutout
         cutout_size : array
             [ny,nx] in with ints (pixels) or astropy quantities
 
@@ -759,12 +757,12 @@ def cube_cut(self, cube_file, coordinates, cutout_size,
 
         if not target_pixel_file:
             _, flename = os.path.split(cube_file)
-            tpf_name = "{}_{:7f}_{:7f}_{}x{}_astrocut.fits".format(flename.rstrip('.fits').rstrip("-cube"),
+            target_pixel_file = "{}_{:7f}_{:7f}_{}x{}_astrocut.fits".format(flename.rstrip('.fits').rstrip("-cube"),
                                                                    self.center_coord.ra.value,
                                                                    self.center_coord.dec.value,
                                                                    self.cutout_lims[0, 1]-self.cutout_lims[0, 0],
                                                                    self.cutout_lims[1, 1]-self.cutout_lims[1, 0])
-            target_pixel_file = os.path.join(output_path, tpf_name)
+        target_pixel_file = os.path.join(output_path, target_pixel_file)
 
 
         if verbose:

diff --git a/astrocut/cutouts.py b/astrocut/cutouts.py
@@ -21,7 +21,7 @@
 import warnings
 
 from . import __version__
-from .exceptions import InputWarning, InvalidQueryError, InvalidInputError
+from .exceptions import InputWarning, DataWarning, InvalidQueryError, InvalidInputError
 
 
 #### FUNCTIONS FOR UTILS ####
@@ -168,7 +168,8 @@ def _hducut(img_hdu, center_coord, cutout_size, correct_wcs=False, drop_after=No
         try:
             max_ind = img_hdu.header.index(drop_after)
         except ValueError:
-            warnings.warn("Last desired keyword not found in image header, using the entire header.")
+            warnings.warn("Last desired keyword not found in image header, using the entire header.",
+                          DataWarning)
 
     hdu_header = fits.Header(img_hdu.header[:max_ind], copy=True)
     img_wcs = wcs.WCS(hdu_header)
@@ -402,8 +403,14 @@ def fits_cut(input_files, coordinates, cutout_size, correct_wcs=False, drop_afte
         if verbose:
             print("\n{}".format(in_fle))
         hdulist = fits.open(in_fle)
-        cutout = _hducut(hdulist[0], coordinates, cutout_size,
-                         correct_wcs=correct_wcs, drop_after=drop_after, verbose=verbose)
+
+        try:
+            cutout = _hducut(hdulist[0], coordinates, cutout_size,
+                             correct_wcs=correct_wcs, drop_after=drop_after, verbose=verbose)
+        except OSError as err:
+            warnings.warn("Error {} encountered when performing cutout on {}.\nFile will be skipped".format(err, in_fle),
+                          DataWarning)
+
         hdulist.close()
 
         # Check that there is data in the cutout image
@@ -415,7 +422,7 @@ def fits_cut(input_files, coordinates, cutout_size, correct_wcs=False, drop_afte
 
     # If no cutouts contain data, raise exception
     if num_empty == len(input_files):
-        raise InvalidQueryError("Cutout contains to data! (Check image footprint.)")
+        raise InvalidQueryError("Cutout contains no data! (Check image footprint.)")
 
     # Make sure the output directory exists
     if not os.path.exists(output_dir):
@@ -441,7 +448,8 @@ def fits_cut(input_files, coordinates, cutout_size, correct_wcs=False, drop_afte
         for fle in input_files:
             cutout = cutout_hdu_dict[fle]
             if cutout.header.get("EMPTY"):
-                warnings.warn("Cutout of {} contains to data and will not be written.".format(fle))
+                warnings.warn("Cutout of {} contains to data and will not be written.".format(fle),
+                              DataWarning)
                 continue
 
             cutout_hdus.append(cutout)
@@ -684,7 +692,8 @@ def img_cut(input_files, coordinates, cutout_size, stretch='asinh', minmax_perce
         for fle in input_files:
             cutout = cutout_hdu_dict.get(fle)
             if cutout is None:
-                warnings.warn("Cutout of {} contains to data and will not be written.".format(fle))
+                warnings.warn("Cutout of {} contains to data and will not be written.".format(fle),
+                              DataWarning)
                 continue
 
             file_path = "{}_{:7f}_{:7f}_{}-x-{}_astrocut.{}".format(os.path.basename(fle).rstrip('.fits'),

diff --git a/astrocut/exceptions.py b/astrocut/exceptions.py
@@ -35,3 +35,10 @@ class TypeWarning(AstropyWarning):
     Warnings to do with data types.
     """
     pass
+
+
+class DataWarning(AstropyWarning):
+    """
+    Warnings to do with data content.
+    """
+    pass