Fix tests and improve pad_input handling

Author: nabobalis

sunkit_image/coalignment/match_template.py

@@ -106,15 +106,27 @@ def match_template_coalign(target_array, reference_array, **kwargs):
             The rotation angle in radians, which is fixed at 0.0 in this function.
         - translation : `tuple`
             A tuple containing the x and y translation values.
+
+    Notes
+    -----
+    This uses `skimage.feature.match_template` to perform the cross correlation.
+    Please check the documentation of that function for details on the available keyword arguments
+    and the details of the algorithm.
     """
     from sunkit_image.coalignment.interface import AffineParams  # NOQA: PLC0415
 
     corr = match_template(np.float64(reference_array), np.float64(target_array), **kwargs)
-    # TODO: Work out what is going on
-    if corr.ndim != target_array.ndim:
-        raise ValueError("The correlation output failed to work out a match.")
+    if len(corr) < 2:
+        raise ValueError(
+            "match_template returned an array with fewer than two values, and cannot be used for coalignment. "
+            "This implies the cross-correlation failed to find a match."
+            )
     # Find the best match location
     y_shift, x_shift = _find_best_match_location(corr)
+    if kwargs.get("pad_input"):
+        # For pad_input=True matches correspond to the center
+        y_shift -= target_array.shape[0] // 2
+        x_shift -= target_array.shape[1] // 2
     log.debug(f"Match template shift: x: {x_shift}, y: {y_shift}")
     # Particularly for this method, there is no change in the rotation or scaling,
     # hence the hardcoded values of scale to 1.0 & rotation to identity matrix

sunkit_image/coalignment/phase_cross_correlation.py

@@ -35,6 +35,12 @@ def phase_cross_correlation_coalign(target_array, reference_array, **kwargs):
             The rotation angle in radians, which is fixed at 0.0 in this function.
         - translation : `tuple`
             A tuple containing the x and y translation values.
+
+    Notes
+    -----
+    This uses `skimage.registration.phase_cross_correlation` to perform the cross correlation.
+    Please check the documentation of that function for details on the available keyword arguments
+    and the details of the algorithm.
     """
     from sunkit_image.coalignment.interface import AffineParams  # NOQA: PLC0415
 

sunkit_image/coalignment/tests/test_coalignment.py

@@ -5,8 +5,10 @@
 import astropy.units as u
 from astropy.coordinates import SkyCoord
 from astropy.io import fits
+from astropy.tests.helper import assert_quantity_allclose
 
 import sunpy.map
+from sunpy.map.maputils import all_coordinates_from_map, coordinate_is_on_solar_disk
 from sunpy.util.exceptions import SunpyUserWarning
 
 from sunkit_image.coalignment import coalign
@@ -70,50 +72,63 @@ def test_coalignment_eis_aia(eis_test_map, aia193_test_map):
     aia193_test_downsampled_map = aia193_test_map.resample(u.Quantity([nx, ny]))
     coaligned_eis_map = coalign(eis_test_map, aia193_test_downsampled_map, method='match_template')
     # Check that correction is as expected based on known pointing offset
-    assert u.allclose(
+    assert_quantity_allclose(
         eis_test_map.reference_coordinate.separation(coaligned_eis_map.reference_coordinate),
         5.95935177*u.arcsec,
     )
 
 
 def test_coalignment_match_template_full_map(incorrect_pointing_map_and_shift, aia171_test_map):
     incorrect_pointing_map, pointing_shift = incorrect_pointing_map_and_shift
-    fixed_map = coalign(incorrect_pointing_map, aia171_test_map)
+    # Crop out the array that is outside the solar disk to have something to align to
+    hpc_coords = all_coordinates_from_map(incorrect_pointing_map)
+    mask = coordinate_is_on_solar_disk(hpc_coords)
+    masked_map = sunpy.map.Map(np.abs(incorrect_pointing_map.data*mask), incorrect_pointing_map.meta)
+    # We have to pad the input map because otherwise match_template cannot find a good match
+    fixed_map = coalign(masked_map, aia171_test_map, pad_input=True)
     # The actual shifts applied by coalignment should be equal to the expected shifts
-    u.allclose(
-        np.fabs(incorrect_pointing_map.reference_coordinate.Tx-fixed_map.reference_coordinate.Tx),
+    assert_quantity_allclose(
+        (incorrect_pointing_map.reference_coordinate.Tx-fixed_map.reference_coordinate.Tx),
         pointing_shift[0],
+        # Not as precise for full map
+        atol=0.6*u.arcsec,
     )
-    u.allclose(
-        np.fabs(incorrect_pointing_map.reference_coordinate.Ty-fixed_map.reference_coordinate.Ty),
+    assert_quantity_allclose(
+        (incorrect_pointing_map.reference_coordinate.Ty-fixed_map.reference_coordinate.Ty),
         pointing_shift[1],
+        # Not as precise for full map
+        atol=0.6*u.arcsec,
     )
 
 
 def test_coalignment_match_template_cutout(incorrect_pointing_cutout_map_and_shift, aia171_test_map):
     incorrect_pointing_cutout_map, pointing_shift = incorrect_pointing_cutout_map_and_shift
     fixed_cutout_map = coalign(incorrect_pointing_cutout_map, aia171_test_map)
     # The actual shifts applied by coalignment should be equal to the expected shifts
-    u.allclose(
-        np.fabs(incorrect_pointing_cutout_map.reference_coordinate.Tx-fixed_cutout_map.reference_coordinate.Tx),
+    assert_quantity_allclose(
+        (incorrect_pointing_cutout_map.reference_coordinate.Tx-fixed_cutout_map.reference_coordinate.Tx),
         pointing_shift[0],
+        # For example, a shift is 25 arcsec but the returned shift is 24.9 arcsec
+        atol=0.1*u.arcsec,
     )
-    u.allclose(
-        np.fabs(incorrect_pointing_cutout_map.reference_coordinate.Ty-fixed_cutout_map.reference_coordinate.Ty),
+    assert_quantity_allclose(
+        (incorrect_pointing_cutout_map.reference_coordinate.Ty-fixed_cutout_map.reference_coordinate.Ty),
         pointing_shift[1],
+        # For example, a shift is 25 arcsec but the returned shift is 24.9 arcsec
+        atol=0.1*u.arcsec,
     )
 
 
 def test_coalign_phase_cross_correlation(incorrect_pointing_map_and_shift, aia171_test_map):
     incorrect_pointing_map, pointing_shift = incorrect_pointing_map_and_shift
     fixed_map = coalign(incorrect_pointing_map, aia171_test_map, method='phase_cross_correlation')
     # The actual shifts applied by coalignment should be equal to the expected shifts
-    u.allclose(
-        np.fabs(incorrect_pointing_map.reference_coordinate.Tx-fixed_map.reference_coordinate.Tx),
+    assert_quantity_allclose(
+        (incorrect_pointing_map.reference_coordinate.Tx-fixed_map.reference_coordinate.Tx),
         pointing_shift[0],
     )
-    u.allclose(
-        np.fabs(incorrect_pointing_map.reference_coordinate.Ty-fixed_map.reference_coordinate.Ty),
+    assert_quantity_allclose(
+        (incorrect_pointing_map.reference_coordinate.Ty-fixed_map.reference_coordinate.Ty),
         pointing_shift[1],
     )
 
@@ -158,10 +173,10 @@ def test_warnings_coalign(incorrect_shifted_once_map, aia171_test_map):
     time_shift_meta = incorrect_shifted_once_map.meta.copy()
     time_shift_meta['DATE-OBS'] = '2014-01-08T09:57:30.84'
     time_shift = sunpy.map.Map(incorrect_shifted_once_map.data, time_shift_meta)
-    with pytest.warns(SunpyUserWarning, match=r"The time difference between the reference and target maps in time is large."):
-        with pytest.raises(ValueError, match=r"attempt to get argmax of an empty sequence"):
+    with pytest.warns(SunpyUserWarning, match=r"The difference in observation times of the reference and target maps is large."):
+        with pytest.raises(ValueError, match=r"match_template returned an array with fewer than two values,"):
             coalign(time_shift, aia171_test_map)
 
     resampled_map = incorrect_shifted_once_map.resample([100,100]*u.pix)
-    with pytest.warns(SunpyUserWarning, match=r"There is a plate scale difference between the reference and target maps."):
+    with pytest.warns(SunpyUserWarning, match=r"The reference and target maps have different plate scales."):
         coalign(resampled_map, aia171_test_map)