Merge pull request #780 from sunpy/YOLO

Faster shortcut for working out coordinates values for non-correlated WCS

Author: DanRyanIrish

changelog/780.bugfix.rst

@@ -0,0 +1 @@
+Added an internal method to shortcut non-correlated axes avoiding the creation of a full coordinate grid, reducing memory use in specific circumstances.

ndcube/conftest.py

@@ -197,6 +197,30 @@ def wcs_3d_lt_ln_l():
     return WCS(header=header)
 
 
+@pytest.fixture
+def wcs_3d_wave_lt_ln():
+    header = {
+        'CTYPE1': 'WAVE    ',
+        'CUNIT1': 'Angstrom',
+        'CDELT1': 0.2,
+        'CRPIX1': 0,
+        'CRVAL1': 10,
+
+        'CTYPE2': 'HPLT-TAN',
+        'CUNIT2': 'deg',
+        'CDELT2': 0.5,
+        'CRPIX2': 2,
+        'CRVAL2': 0.5,
+
+        'CTYPE3': 'HPLN-TAN    ',
+        'CUNIT3': 'deg',
+        'CDELT3': 0.4,
+        'CRPIX3': 2,
+        'CRVAL3': 1,
+    }
+    return WCS(header=header)
+
+
 @pytest.fixture
 def wcs_2d_lt_ln():
     spatial = {
@@ -445,6 +469,24 @@ def ndcube_3d_ln_lt_l_ec_time(wcs_3d_l_lt_ln, time_and_simple_extra_coords_2d):
     return cube
 
 
+@pytest.fixture
+def ndcube_3d_wave_lt_ln_ec_time(wcs_3d_wave_lt_ln):
+    shape = (3, 4, 5)
+    wcs_3d_wave_lt_ln.array_shape = shape
+    data = data_nd(shape)
+    mask = data > 0
+    cube = NDCube(
+        data,
+        wcs_3d_wave_lt_ln,
+        mask=mask,
+        uncertainty=data,
+    )
+    base_time = Time('2000-01-01', format='fits', scale='utc')
+    timestamps = Time([base_time + TimeDelta(60 * i, format='sec') for i in range(data.shape[0])])
+    cube.extra_coords.add('time', 0, timestamps)
+    return cube
+
+
 @pytest.fixture
 def ndcube_3d_rotated(wcs_3d_ln_lt_t_rotated, simple_extra_coords_3d):
     data_rotated = np.array([[[1, 2, 3, 4, 6], [2, 4, 5, 3, 1], [0, -1, 2, 4, 2], [3, 5, 1, 2, 0]],

ndcube/ndcube.py

@@ -12,6 +12,9 @@
 import astropy.nddata
 import astropy.units as u
 from astropy.units import UnitsError
+from astropy.wcs.utils import _split_matrix
+
+from ndcube.utils.wcs import world_axis_to_pixel_axes
 
 try:
     # Import sunpy coordinates if available to register the frames and WCS functions with astropy
@@ -20,7 +23,6 @@
     pass
 
 from astropy.wcs import WCS
-from astropy.wcs.utils import _split_matrix
 from astropy.wcs.wcsapi import BaseHighLevelWCS, HighLevelWCSWrapper
 from astropy.wcs.wcsapi.high_level_api import values_to_high_level_objects
 
@@ -479,24 +481,76 @@ def quantity(self):
         """Unitful representation of the NDCube data."""
         return u.Quantity(self.data, self.unit, copy=_NUMPY_COPY_IF_NEEDED)
 
-    def _generate_world_coords(self, pixel_corners, wcs, needed_axes=None, *, units):
-        # Create meshgrid of all pixel coordinates.
-        # If user wants pixel_corners, set pixel values to pixel corners.
-        # Else make pixel centers.
+    def _generate_independent_world_coords(self, pixel_corners, wcs, needed_axes, units):
+        """
+        Generate world coordinates for independent axes.
+
+        The idea is to workout only the specific grid that is needed for independent axes.
+        This speeds up the calculation of world coordinates and reduces memory usage.
+
+        Parameters
+        ----------
+        pixel_corners : bool
+            If one needs pixel corners, otherwise pixel centers.
+        wcs : astropy.wcs.WCS
+            The WCS.
+        needed_axes : array-like
+            The required pixel axes.
+        units : bool
+            If units are needed.
+
+        Returns
+        -------
+        array-like
+            The world coordinates.
+        """
+        needed_axes = np.array(needed_axes).squeeze()
+        if self.data.ndim in needed_axes:
+            required_axes = needed_axes - 1
+        else:
+            required_axes = needed_axes
+        lims = (-0.5, self.data.shape[::-1][required_axes] + 1) if pixel_corners else (0, self.data.shape[::-1][required_axes])
+        indices = [np.arange(lims[0], lims[1]) if wanted else [0] for wanted in wcs.axis_correlation_matrix[required_axes]]
+        world_coords = wcs.pixel_to_world_values(*indices)
+        if units:
+            world_coords = world_coords << u.Unit(wcs.world_axis_units[needed_axes])
+        return world_coords
+
+    def _generate_dependent_world_coords(self, pixel_corners, wcs, needed_axes, units):
+        """
+        Generate world coordinates for dependent axes.
+
+        This will work out the exact grid that is needed for dependent axes
+        and can be time and memory consuming.
+
+        Parameters
+        ----------
+        pixel_corners : bool
+            If one needs pixel corners, otherwise pixel centers.
+        wcs : astropy.wcs.WCS
+            The WCS.
+        needed_axes : array-like
+            The required pixel axes.
+        units : bool
+            If units are needed.
+
+        Returns
+        -------
+        array-like
+            The world coordinates.
+        """
         pixel_shape = self.data.shape[::-1]
         if pixel_corners:
             pixel_shape = tuple(np.array(pixel_shape) + 1)
             ranges = [np.arange(i) - 0.5 for i in pixel_shape]
         else:
             ranges = [np.arange(i) for i in pixel_shape]
-
         # Limit the pixel dimensions to the ones present in the ExtraCoords
         if isinstance(wcs, ExtraCoords):
             ranges = [ranges[i] for i in wcs.mapping]
             wcs = wcs.wcs
             if wcs is None:
-                return []
-
+                return ()
         # This value of zero will be returned as a throwaway for unneeded axes, and a numerical value is
         # required so values_to_high_level_objects in the calling function doesn't crash or warn
         world_coords = [0] * wcs.world_n_dim
@@ -528,71 +582,92 @@ def _generate_world_coords(self, pixel_corners, wcs, needed_axes=None, *, units)
                 array_slice[wcs.axis_correlation_matrix[idx]] = slice(None)
                 tmp_world = world[idx][tuple(array_slice)].T
                 world_coords[idx] = tmp_world
-
         if units:
             for i, (coord, unit) in enumerate(zip(world_coords, wcs.world_axis_units)):
                 world_coords[i] = coord << u.Unit(unit)
+        return world_coords
+
+    def _generate_world_coords(self, pixel_corners, wcs, *, needed_axes, units=None):
+        """
+        Private method to generate world coordinates.
+
+        Handles both dependent and independent axes.
+
+        Parameters
+        ----------
+        pixel_corners : bool
+            If one needs pixel corners, otherwise pixel centers.
+        wcs : astropy.wcs.WCS
+            The WCS.
+        needed_axes : array-like
+            The axes that are needed.
+        units : bool
+            If units are needed.
 
+        Returns
+        -------
+        array-like
+            The world coordinates.
+        """
+        axes_are_independent = []
+        pixel_axes = set()
+        for world_axis in needed_axes:
+            pix_ax = world_axis_to_pixel_axes(world_axis, wcs.axis_correlation_matrix)
+            axes_are_independent.append(len(pix_ax) == 1)
+            pixel_axes = pixel_axes.union(set(pix_ax))
+        pixel_axes = list(pixel_axes)
+        if all(axes_are_independent) and len(pixel_axes) == len(needed_axes) and len(needed_axes) != 0:
+            world_coords = self._generate_independent_world_coords(pixel_corners, wcs, needed_axes, units)
+        else:
+            world_coords = self._generate_dependent_world_coords(pixel_corners, wcs, needed_axes, units)
         return world_coords
 
     @utils.cube.sanitize_wcs
     def axis_world_coords(self, *axes, pixel_corners=False, wcs=None):
         # Docstring in NDCubeABC.
         if isinstance(wcs, BaseHighLevelWCS):
             wcs = wcs.low_level_wcs
-
         orig_wcs = wcs
         if isinstance(wcs, ExtraCoords):
             wcs = wcs.wcs
             if not wcs:
                 return ()
-
         object_names = np.array([wao_comp[0] for wao_comp in wcs.world_axis_object_components])
         unique_obj_names = utils.misc.unique_sorted(object_names)
         world_axes_for_obj = [np.where(object_names == name)[0] for name in unique_obj_names]
-
         # Create a mapping from world index in the WCS to object index in axes_coords
         world_index_to_object_index = {}
         for object_index, world_axes in enumerate(world_axes_for_obj):
             for world_index in world_axes:
                 world_index_to_object_index[world_index] = object_index
-
         world_indices = utils.wcs.calculate_world_indices_from_axes(wcs, axes)
         object_indices = utils.misc.unique_sorted(
             [world_index_to_object_index[world_index] for world_index in world_indices]
         )
-
-        axes_coords = self._generate_world_coords(pixel_corners, orig_wcs, world_indices, units=False)
-
+        axes_coords = self._generate_world_coords(pixel_corners, orig_wcs, needed_axes=world_indices, units=False)
         axes_coords = values_to_high_level_objects(*axes_coords, low_level_wcs=wcs)
-
         if not axes:
             return tuple(axes_coords)
-
         return tuple(axes_coords[i] for i in object_indices)
 
     @utils.cube.sanitize_wcs
     def axis_world_coords_values(self, *axes, pixel_corners=False, wcs=None):
         # Docstring in NDCubeABC.
         if isinstance(wcs, BaseHighLevelWCS):
             wcs = wcs.low_level_wcs
-
         orig_wcs = wcs
         if isinstance(wcs, ExtraCoords):
             wcs = wcs.wcs
-
+            if not wcs:
+                return ()
         world_indices = utils.wcs.calculate_world_indices_from_axes(wcs, axes)
-
-        axes_coords = self._generate_world_coords(pixel_corners, orig_wcs, world_indices, units=True)
-
+        axes_coords = self._generate_world_coords(pixel_corners, orig_wcs, needed_axes=world_indices, units=True)
         world_axis_physical_types = wcs.world_axis_physical_types
-
         # If user has supplied axes, extract only the
         # world coords that correspond to those axes.
         if axes:
             axes_coords = [axes_coords[i] for i in world_indices]
             world_axis_physical_types = tuple(np.array(world_axis_physical_types)[world_indices])
-
         # Return in array order.
         # First replace characters in physical types forbidden for namedtuple identifiers.
         identifiers = []

ndcube/tests/test_ndcube.py

@@ -12,6 +12,7 @@
 from astropy.coordinates import SkyCoord, SpectralCoord
 from astropy.io import fits
 from astropy.nddata import UnknownUncertainty
+from astropy.tests.helper import assert_quantity_allclose
 from astropy.time import Time
 from astropy.units import UnitsError
 from astropy.wcs import WCS
@@ -177,9 +178,19 @@ def test_axis_world_coords_wave_ec(ndcube_3d_l_ln_lt_ectime):
 
     coords = cube.axis_world_coords()
     assert len(coords) == 2
+    assert isinstance(coords[0], SkyCoord)
+    assert coords[0].shape == (5, 8)
+    assert isinstance(coords[1], SpectralCoord)
+    assert coords[1].shape == (10,)
 
     coords = cube.axis_world_coords(wcs=cube.combined_wcs)
     assert len(coords) == 3
+    assert isinstance(coords[0], SkyCoord)
+    assert coords[0].shape == (5, 8)
+    assert isinstance(coords[1], SpectralCoord)
+    assert coords[1].shape == (10,)
+    assert isinstance(coords[2], Time)
+    assert coords[2].shape == (5,)
 
     coords = cube.axis_world_coords(wcs=cube.extra_coords)
     assert len(coords) == 1
@@ -199,8 +210,6 @@ def test_axis_world_coords_empty_ec(ndcube_3d_l_ln_lt_ectime):
     # slice the cube so extra_coords is empty, and then try and run axis_world_coords
     awc = sub_cube.axis_world_coords(wcs=sub_cube.extra_coords)
     assert awc == ()
-    sub_cube._generate_world_coords(pixel_corners=False, wcs=sub_cube.extra_coords, units=True)
-    assert awc == ()
 
 
 @pytest.mark.xfail(reason=">1D Tables not supported")
@@ -235,13 +244,31 @@ def test_axis_world_coords_single(axes, ndcube_3d_ln_lt_l):
     assert u.allclose(coords[0], [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
 
 
+def test_axis_world_coords_combined_wcs(ndcube_3d_wave_lt_ln_ec_time):
+    # This replicates a specific NDCube object in visualization.rst
+    coords = ndcube_3d_wave_lt_ln_ec_time.axis_world_coords('time', wcs=ndcube_3d_wave_lt_ln_ec_time.combined_wcs)
+    assert len(coords) == 1
+    assert isinstance(coords[0], Time)
+    assert np.all(coords[0] == Time(['2000-01-01T00:00:00.000', '2000-01-01T00:01:00.000', '2000-01-01T00:02:00.000']))
+
+    coords = ndcube_3d_wave_lt_ln_ec_time.axis_world_coords_values('time', wcs=ndcube_3d_wave_lt_ln_ec_time.combined_wcs)
+    assert len(coords) == 1
+    assert isinstance(coords.time, u.Quantity)
+    assert_quantity_allclose(coords.time, [0, 60, 120] * u.second)
+
+
 @pytest.mark.parametrize("axes", [[-1], [2], ["em"]])
 def test_axis_world_coords_single_pixel_corners(axes, ndcube_3d_ln_lt_l):
+
+    # We go from 4 pixels to 6 pixels when we add pixel corners
+    coords = ndcube_3d_ln_lt_l.axis_world_coords_values(*axes, pixel_corners=False)
+    assert u.allclose(coords[0], [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
+
     coords = ndcube_3d_ln_lt_l.axis_world_coords_values(*axes, pixel_corners=True)
-    assert u.allclose(coords, [1.01e-09, 1.03e-09, 1.05e-09, 1.07e-09, 1.09e-09] * u.m)
+    assert u.allclose(coords[0], [1.01e-09, 1.03e-09, 1.05e-09, 1.07e-09, 1.09e-09, 1.11e-09] * u.m)
 
     coords = ndcube_3d_ln_lt_l.axis_world_coords(*axes, pixel_corners=True)
-    assert u.allclose(coords, [1.01e-09, 1.03e-09, 1.05e-09, 1.07e-09, 1.09e-09] * u.m)
+    assert u.allclose(coords[0], [1.01e-09, 1.03e-09, 1.05e-09, 1.07e-09, 1.09e-09, 1.11e-09] * u.m)
 
 
 @pytest.mark.parametrize(("ndc", "item"),
@@ -252,10 +279,10 @@ def test_axis_world_coords_single_pixel_corners(axes, ndcube_3d_ln_lt_l):
                          indirect=("ndc",))
 def test_axis_world_coords_sliced_all_3d(ndc, item):
     coords = ndc[item].axis_world_coords_values()
-    assert u.allclose(coords, [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
+    assert u.allclose(coords[0], [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
 
     coords = ndc[item].axis_world_coords()
-    assert u.allclose(coords, [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
+    assert u.allclose(coords[0], [1.02e-09, 1.04e-09, 1.06e-09, 1.08e-09] * u.m)
 
 
 @pytest.mark.parametrize(("ndc", "item"),