Merge pull request #409 from esheldon/slice-fix

check TBIT for slices/rows read

CHANGES.md

@@ -1,3 +1,10 @@
+version 1.2.5 (not yet released)
+-------------
+
+Bug Fixes
+
+    - Fig bug slicing tables that have TBIT columns
+
 version 1.2.4
 -------------
 

fitsio/__init__.py

@@ -5,7 +5,7 @@
 usage.
 """
 
-__version__ = '1.2.4'
+__version__ = '1.2.5'
 
 from . import fitslib
 

fitsio/hdu/table.py

@@ -896,6 +896,8 @@ def read_rows(self, rows, vstorage=None,
         dtype, offsets, isvar = self.get_rec_dtype(vstorage=vstorage)
 
         w, = np.where(isvar == True)  # noqa
+        has_tbit = self._check_tbit()
+
         if w.size > 0:
             if vstorage is None:
                 _vstorage = self._vstorage
@@ -905,6 +907,14 @@ def read_rows(self, rows, vstorage=None,
             return self._read_rec_with_var(
                 colnums, rows, sortind, dtype, offsets, isvar, _vstorage,
             )
+        elif has_tbit:
+            # drop down to read_columns since we can't stuff into a
+            # contiguous array
+            colnums = self._extract_colnums()
+            array = self.read_columns(
+                colnums, rows=rows, vstorage=vstorage, upper=upper,
+                lower=lower, trim_strings=trim_strings,
+            )
         else:
             array = np.zeros(rows.size, dtype=dtype)
             self._FITS.read_rows_as_rec(self._ext+1, array, rows, sortind)
@@ -1094,6 +1104,8 @@ def read_slice(self, firstrow, lastrow, step=1,
         dtype, offsets, isvar = self.get_rec_dtype(vstorage=vstorage)
 
         w, = np.where(isvar == True)  # noqa
+        has_tbit = self._check_tbit()
+
         if w.size > 0:
             if vstorage is None:
                 _vstorage = self._vstorage
@@ -1104,6 +1116,15 @@ def read_slice(self, firstrow, lastrow, step=1,
             colnums = self._extract_colnums()
             array = self._read_rec_with_var(
                 colnums, rows, sortind, dtype, offsets, isvar, _vstorage)
+        elif has_tbit:
+            # drop down to read_columns since we can't stuff into a
+            # contiguous array
+            colnums = self._extract_colnums()
+            rows = np.arange(firstrow, lastrow, step, dtype='i8')
+            array = self.read_columns(
+                colnums, rows=rows, vstorage=vstorage, upper=upper,
+                lower=lower, trim_strings=trim_strings,
+            )
         else:
             if step != 1:
                 rows = np.arange(firstrow, lastrow, step, dtype='i8')

fitsio/tests/test_table.py

@@ -1257,6 +1257,13 @@ def test_table_bitcol_read_write():
             d = fits[1].read()
             compare_rec(bdata, d, "table read/write")
 
+            rows = [0, 2]
+            d = fits[1].read(rows=rows)
+            compare_rec(bdata[rows], d, "table read/write rows")
+
+            d = fits[1][:2]
+            compare_rec(bdata[:2], d, "table read/write slice")
+
         # now test read_column
         with FITS(fname) as fits:
 

setup.py

@@ -318,7 +318,7 @@ def check_system_cfitsio_objects(self, obj_name):
 
 setup(
     name="fitsio",
-    version="1.2.4",
+    version="1.2.5",
     description=description,
     long_description=long_description,
     long_description_content_type='text/markdown; charset=UTF-8; variant=GFM',