From 6a5b036e4c9f40c8c30ef9aaee9faa690f8b74e5 Mon Sep 17 00:00:00 2001
From: Thomas Robitaille <thomas.robitaille@gmail.com>
Date: Thu, 9 Apr 2020 22:36:37 +0100
Subject: [PATCH] Fix bug that caused errors when slicing a cube with a mask
 set to None

---
 CHANGES.rst                                   |   1 +
 spectral_cube/spectral_cube.py                |   4 +--
 .../data/nomask.image/logtable/table.dat      | Bin 0 -> 1392 bytes
 .../tests/data/nomask.image/logtable/table.f0 | Bin 0 -> 98816 bytes
 .../data/nomask.image/logtable/table.info     |   4 +++
 .../data/nomask.image/logtable/table.lock     | Bin 0 -> 325 bytes
 .../tests/data/nomask.image/table.dat         | Bin 0 -> 8753 bytes
 .../tests/data/nomask.image/table.f0          | Bin 0 -> 293 bytes
 .../tests/data/nomask.image/table.f0_TSM0     | Bin 0 -> 480 bytes
 .../tests/data/nomask.image/table.info        |   3 +++
 .../tests/data/nomask.image/table.lock        | Bin 0 -> 325 bytes
 spectral_cube/tests/test_casafuncs.py         |  25 ++++++++++++++++++
 spectral_cube/tests/test_spectral_cube.py     |  17 ++++++++++++
 13 files changed, 52 insertions(+), 2 deletions(-)
 create mode 100644 spectral_cube/tests/data/nomask.image/logtable/table.dat
 create mode 100644 spectral_cube/tests/data/nomask.image/logtable/table.f0
 create mode 100644 spectral_cube/tests/data/nomask.image/logtable/table.info
 create mode 100644 spectral_cube/tests/data/nomask.image/logtable/table.lock
 create mode 100644 spectral_cube/tests/data/nomask.image/table.dat
 create mode 100644 spectral_cube/tests/data/nomask.image/table.f0
 create mode 100644 spectral_cube/tests/data/nomask.image/table.f0_TSM0
 create mode 100644 spectral_cube/tests/data/nomask.image/table.info
 create mode 100644 spectral_cube/tests/data/nomask.image/table.lock

diff --git a/CHANGES.rst b/CHANGES.rst
index ef8a66ca7..32431c38a 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -5,6 +5,7 @@
   run a script to generate test files. #598
 - Refactor package infrastructure to no longer use astropy-helpers. #599
 - Switch to using unified I/O infrastructure from Astropy. #600
+- Bugfix: fix slicing of cubes with mask set to None. #621
 - Refactor CASA I/O to use dask to access the array/mask data directly
   and to use only Python and Numpy to access image metadata. CASA images
   can now be read without CASA installed. #607, #609, #613
diff --git a/spectral_cube/spectral_cube.py b/spectral_cube/spectral_cube.py
index 4df521f0f..d5ff86a86 100644
--- a/spectral_cube/spectral_cube.py
+++ b/spectral_cube/spectral_cube.py
@@ -1223,7 +1223,7 @@ def __getitem__(self, view):
                                            copy=False,
                                            unit=self.unit,
                                            spectral_unit=self._spectral_unit,
-                                           mask=self.mask[view],
+                                           mask=self.mask[view] if self.mask is not None else None,
                                            meta=meta,
                                            **bmarg
                                           )
@@ -1239,7 +1239,7 @@ def __getitem__(self, view):
                 header['CUNIT3'] = self._spectral_unit.to_string(format='FITS')
 
             return Slice(value=self.filled_data[view],
-                         mask=self.mask[view],
+                         mask=self.mask[view] if self.mask is not None else None,
                          wcs=newwcs,
                          copy=False,
                          unit=self.unit,
diff --git a/spectral_cube/tests/data/nomask.image/logtable/table.dat b/spectral_cube/tests/data/nomask.image/logtable/table.dat
new file mode 100644
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diff --git a/spectral_cube/tests/data/nomask.image/logtable/table.info b/spectral_cube/tests/data/nomask.image/logtable/table.info
new file mode 100644
index 000000000..dfeff77ec
--- /dev/null
+++ b/spectral_cube/tests/data/nomask.image/logtable/table.info
@@ -0,0 +1,4 @@
+Type = Log message
+SubType = 
+
+Repository for software-generated logging messages
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diff --git a/spectral_cube/tests/data/nomask.image/table.f0 b/spectral_cube/tests/data/nomask.image/table.f0
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diff --git a/spectral_cube/tests/data/nomask.image/table.f0_TSM0 b/spectral_cube/tests/data/nomask.image/table.f0_TSM0
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diff --git a/spectral_cube/tests/data/nomask.image/table.info b/spectral_cube/tests/data/nomask.image/table.info
new file mode 100644
index 000000000..cbab78e3a
--- /dev/null
+++ b/spectral_cube/tests/data/nomask.image/table.info
@@ -0,0 +1,3 @@
+Type = Image
+SubType = 
+
diff --git a/spectral_cube/tests/data/nomask.image/table.lock b/spectral_cube/tests/data/nomask.image/table.lock
new file mode 100644
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diff --git a/spectral_cube/tests/test_casafuncs.py b/spectral_cube/tests/test_casafuncs.py
index afe684d3e..f0111465d 100644
--- a/spectral_cube/tests/test_casafuncs.py
+++ b/spectral_cube/tests/test_casafuncs.py
@@ -95,6 +95,31 @@ def test_casa_read_basic():
     assert_quantity_allclose(cube.unmasked_data[0, 1, 2], 1 * u.Jy / u.beam)
 
 
+def test_casa_read_basic_nomask():
+
+    # Make sure things work well if there is no mask in the data
+
+    cube = SpectralCube.read(os.path.join(DATA, 'nomask.image'))
+    assert cube.shape == (3, 4, 5)
+    assert_allclose(cube.wcs.pixel_to_world_values(1, 2, 3),
+                    [2.406271e+01, 2.993521e+01, 1.421911e+09])
+
+    # Carry out an operation to make sure the underlying data array works
+
+    cube.moment0()
+
+    # Slice the dataset
+
+    assert_quantity_allclose(cube.unmasked_data[0, 0, :],
+                             [1, 1, 1, 1, 1] * u.Jy / u.beam)
+    assert_quantity_allclose(cube.unmasked_data[0, 1, 2], 1 * u.Jy / u.beam)
+
+    # Slice the cube
+
+    assert_quantity_allclose(cube[:, 0, 0],
+                             [1, 1, 1] * u.Jy / u.beam)
+
+
 @pytest.mark.skipif(not CASA_INSTALLED, reason='CASA tests must be run in a CASA environment.')
 @pytest.mark.parametrize('filename', ('data_adv', 'data_advs', 'data_sdav',
                                       'data_vad', 'data_vsad'),
diff --git a/spectral_cube/tests/test_spectral_cube.py b/spectral_cube/tests/test_spectral_cube.py
index 851e876b4..a76e263c0 100644
--- a/spectral_cube/tests/test_spectral_cube.py
+++ b/spectral_cube/tests/test_spectral_cube.py
@@ -2207,3 +2207,20 @@ def test_varyres_mask(data_vda_beams):
         assert mcube[:5].unmasked_beams == cube[:5].beams
     except ValueError:
         assert np.all(mcube[:5].unmasked_beams == cube[:5].beams)
+
+
+def test_mask_none():
+
+    # Regression test for issues that occur when mask is None
+
+    data = np.arange(24).reshape((2, 3, 4))
+
+    wcs = WCS(naxis=3)
+    wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN', 'VELO-HEL']
+
+    cube = SpectralCube(data * u.Jy / u.beam, wcs=wcs)
+
+    assert_quantity_allclose(cube[0, :, :],
+                             [[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11]] * u.Jy / u.beam)
+    assert_quantity_allclose(cube[:, 0, 0],
+                             [0, 12] * u.Jy / u.beam)