Increasing Test coverage

changelog/59.bugfix.rst

@@ -0,0 +1 @@
+Changed minimum version of `skimage` to 0.18.0, preventing faulty code in :meth:`sunkit-image.utils.points_in_poly`.

changelog/59.trivial.rst

@@ -0,0 +1 @@
+Added multiple unit tests to increase code coverage.

setup.cfg

@@ -31,7 +31,7 @@ include_package_data = True
 setup_requires =
   setuptools_scm
 install_requires =
-  scikit-image>=0.16.2
+  scikit-image>=0.18.0
   sunpy>=2.0.0
 
 [options.extras_require]

sunkit_image/tests/test_radial.py

@@ -230,3 +230,70 @@ def test_set_attenuation_coefficients():
         _ = rad.set_attenuation_coefficients(order, cutoff=5)
 
     assert str(record.value) == "Cutoff cannot be greater than order + 1."
+
+
+def test_fit_polynomial_to_log_radial_intensity():
+
+    radii = (0.001, 0.002) * u.R_sun
+    intensity = np.asarray([1, 2])
+    degree = 1
+    expected = np.polyfit(radii.to(u.R_sun).value, np.log(intensity), degree)
+
+    assert np.allclose(rad.fit_polynomial_to_log_radial_intensity(radii, intensity, degree), expected)
+
+
+def test_calculate_fit_radial_intensity():
+
+    polynomial = np.asarray([1, 2, 3])
+    radii = (0.001, 0.002) * u.R_sun
+    expected = np.exp(np.poly1d(polynomial)(radii.to(u.R_sun).value))
+
+    assert np.allclose(rad.calculate_fit_radial_intensity(radii, polynomial), expected)
+
+
+def test_normalize_fit_radial_intensity():
+    polynomial = np.asarray([1, 2, 3])
+    radii = (0.001, 0.002) * u.R_sun
+    normalization_radii = (0.003, 0.004) * u.R_sun
+    expected = rad.calculate_fit_radial_intensity(radii, polynomial) / rad.calculate_fit_radial_intensity(
+        normalization_radii, polynomial
+    )
+
+    assert np.allclose(rad.normalize_fit_radial_intensity(radii, polynomial, normalization_radii), expected)
+
+
+def test_intensity_enhance(map_test1):
+    degree = 1
+    fit_range = [1, 1.5] * u.R_sun
+    normalization_radius = 1 * u.R_sun
+    summarize_bin_edges = "center"
+    scale = 1 * map_test1.rsun_obs
+    radial_bin_edges = u.Quantity(utils.equally_spaced_bins()) * u.R_sun
+
+    radial_intensity = utils.get_radial_intensity_summary(map_test1, radial_bin_edges, scale=scale)
+
+    map_r = utils.find_pixel_radii(map_test1).to(u.R_sun)
+
+    radial_bin_summary = utils.bin_edge_summary(radial_bin_edges, summarize_bin_edges).to(u.R_sun)
+
+    fit_here = np.logical_and(
+        fit_range[0].to(u.R_sun).value <= radial_bin_summary.to(u.R_sun).value,
+        radial_bin_summary.to(u.R_sun).value <= fit_range[1].to(u.R_sun).value,
+    )
+
+    polynomial = rad.fit_polynomial_to_log_radial_intensity(
+        radial_bin_summary[fit_here], radial_intensity[fit_here], degree
+    )
+
+    enhancement = 1 / rad.normalize_fit_radial_intensity(map_r, polynomial, normalization_radius)
+    enhancement[map_r < normalization_radius] = 1
+
+    with pytest.raises(ValueError, match="The fit range must be strictly increasing."):
+        rad.intensity_enhance(
+            smap=map_test1, radial_bin_edges=radial_bin_edges, scale=scale, fit_range=fit_range[::-1]
+        )
+
+    assert np.allclose(
+        enhancement * map_test1.data,
+        rad.intensity_enhance(smap=map_test1, radial_bin_edges=radial_bin_edges, scale=scale).data,
+    )

sunkit_image/utils/tests/test_utils.py

@@ -1,10 +1,14 @@
+import warnings
+
 import numpy as np
 import pytest
 
 import astropy.units as u
 from astropy.tests.helper import assert_quantity_allclose
 
-from sunkit_image.utils import bin_edge_summary, equally_spaced_bins, find_pixel_radii
+import sunkit_image.utils as utils
+from sunkit_image import asda
+from sunkit_image.data.test import get_test_filepath
 
 
 @pytest.fixture
@@ -18,31 +22,31 @@ def smap():
 
 def test_equally_spaced_bins():
     # test the default
-    esb = equally_spaced_bins()
+    esb = utils.equally_spaced_bins()
     assert esb.shape == (2, 100)
     assert esb[0, 0] == 1.0
     assert esb[1, 0] == 1.01
     assert esb[0, 99] == 1.99
     assert esb[1, 99] == 2.00
 
     # Bins are 0.015 wide
-    esb2 = equally_spaced_bins(inner_value=0.5)
+    esb2 = utils.equally_spaced_bins(inner_value=0.5)
     assert esb2.shape == (2, 100)
     assert esb2[0, 0] == 0.5
     assert esb2[1, 0] == 0.515
     assert esb2[0, 99] == 1.985
     assert esb2[1, 99] == 2.00
 
     # Bins are 0.2 wide
-    esb2 = equally_spaced_bins(outer_value=3.0)
+    esb2 = utils.equally_spaced_bins(outer_value=3.0)
     assert esb2.shape == (2, 100)
     assert esb2[0, 0] == 1.0
     assert esb2[1, 0] == 1.02
     assert esb2[0, 99] == 2.98
     assert esb2[1, 99] == 3.00
 
     # Bins are 0.01 wide
-    esb2 = equally_spaced_bins(nbins=1000)
+    esb2 = utils.equally_spaced_bins(nbins=1000)
     assert esb2.shape == (2, 1000)
     assert esb2[0, 0] == 1.0
     assert esb2[1, 0] == 1.001
@@ -51,42 +55,42 @@ def test_equally_spaced_bins():
 
     # The radii have the correct relative sizes
     with pytest.raises(ValueError):
-        equally_spaced_bins(inner_value=1.0, outer_value=1.0)
+        utils.equally_spaced_bins(inner_value=1.0, outer_value=1.0)
     with pytest.raises(ValueError):
-        equally_spaced_bins(inner_value=1.5, outer_value=1.0)
+        utils.equally_spaced_bins(inner_value=1.5, outer_value=1.0)
 
     # The number of bins is strictly greater than 0
     with pytest.raises(ValueError):
-        equally_spaced_bins(nbins=0)
+        utils.equally_spaced_bins(nbins=0)
 
 
 def test_bin_edge_summary():
-    esb = equally_spaced_bins()
+    esb = utils.equally_spaced_bins()
 
-    center = bin_edge_summary(esb, "center")
+    center = utils.bin_edge_summary(esb, "center")
     assert center.shape == (100,)
     assert center[0] == 1.005
     assert center[99] == 1.995
 
-    left = bin_edge_summary(esb, "left")
+    left = utils.bin_edge_summary(esb, "left")
     assert left.shape == (100,)
     assert left[0] == 1.0
     assert left[99] == 1.99
 
-    right = bin_edge_summary(esb, "right")
+    right = utils.bin_edge_summary(esb, "right")
     assert right.shape == (100,)
     assert right[0] == 1.01
     assert right[99] == 2.0
 
     # Correct selection of summary type
     with pytest.raises(ValueError):
-        bin_edge_summary(esb, "should raise the error")
+        utils.bin_edge_summary(esb, "should raise the error")
 
     # The correct shape of bin edges are passed in
     with pytest.raises(ValueError):
-        bin_edge_summary(np.arange(0, 10), "center")
+        utils.bin_edge_summary(np.arange(0, 10), "center")
     with pytest.raises(ValueError):
-        bin_edge_summary(np.zeros((3, 4)), "center")
+        utils.bin_edge_summary(np.zeros((3, 4)), "center")
 
 
 @pytest.mark.remote_data
@@ -95,7 +99,7 @@ def test_find_pixel_radii(smap):
     known_maximum_pixel_radius = 1.84183121
 
     # Calculate the pixel radii
-    pixel_radii = find_pixel_radii(smap)
+    pixel_radii = utils.find_pixel_radii(smap)
 
     # The shape of the pixel radii is the same as the input map
     assert pixel_radii.shape[0] == int(smap.dimensions[0].value)
@@ -108,10 +112,103 @@ def test_find_pixel_radii(smap):
     assert_quantity_allclose((np.max(pixel_radii)).value, known_maximum_pixel_radius)
 
     # Test that the new scale is used
-    pixel_radii = find_pixel_radii(smap, scale=2 * smap.rsun_obs)
+    pixel_radii = utils.find_pixel_radii(smap, scale=2 * smap.rsun_obs)
     assert_quantity_allclose(np.max(pixel_radii).value, known_maximum_pixel_radius / 2)
 
 
-def test_get_radial_intensity_summary():
-    # TODO: Write some tests.
-    pass
+@pytest.mark.remote_data
+def test_get_radial_intensity_summary(smap):
+
+    radial_bin_edges = u.Quantity(utils.equally_spaced_bins()) * u.R_sun
+    summary = np.mean
+
+    map_r = utils.find_pixel_radii(smap, scale=smap.rsun_obs).to(u.R_sun)
+
+    nbins = radial_bin_edges.shape[1]
+
+    lower_edge = [map_r > radial_bin_edges[0, i].to(u.R_sun) for i in range(0, nbins)]
+    upper_edge = [map_r < radial_bin_edges[1, i].to(u.R_sun) for i in range(0, nbins)]
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", category=RuntimeWarning)
+        expected = np.asarray([summary(smap.data[lower_edge[i] * upper_edge[i]]) for i in range(0, nbins)])
+
+    assert np.allclose(utils.get_radial_intensity_summary(smap, radial_bin_edges=radial_bin_edges), expected)
+
+
+def test_calculate_gamma():
+    vel_file = get_test_filepath("asda_vxvy.npz")
+    get_test_filepath("asda_correct.npz")
+    vxvy = np.load(vel_file, allow_pickle=True)
+    vx = vxvy["vx"]
+    vy = vxvy["vy"]
+    vxvy["data"]
+
+    factor = 1
+    lo = asda.Asda(vx, vy, factor=factor)
+
+    shape = vx.shape
+    r = 3
+
+    index = np.array([[i, j] for i in np.arange(r, shape[0] - r) for j in np.arange(r, shape[1] - r)])
+
+    vel = lo.gen_vel(index[1], index[0])
+
+    pm = np.array(
+        [[i, j] for i in np.arange(-lo.r, lo.r + 1) for j in np.arange(-lo.r, lo.r + 1)],
+        dtype=float,
+    )
+
+    N = (2 * lo.r + 1) ** 2
+
+    pnorm = np.linalg.norm(pm, axis=1)
+
+    cross = np.cross(pm, vel[..., 0])
+    vel_norm = np.linalg.norm(vel[..., 0], axis=2)
+    sint = cross / (pnorm * vel_norm + 1e-10)
+
+    expected = np.nansum(sint, axis=1) / N
+
+    assert np.allclose(expected, utils.calc_gamma(pm, vel[..., 0], pnorm, N))
+
+
+def test_remove_duplicate():
+
+    test_data = np.random.rand(5, 2)
+    data_ = np.append(test_data, [test_data[0]], axis=0)
+    expected = np.delete(data_, -1, 0)
+    assert (utils.remove_duplicate(data_) == expected).all()
+
+
+def test_points_in_poly():
+
+    test_data = np.asarray([[0, 0], [0, 1], [0, 2], [1, 2], [2, 2], [2, 0]])
+
+    with pytest.raises(ValueError, match="Polygon must be defined as a n x 2 array!"):
+        utils.points_in_poly(test_data.T)
+
+    expected = [[0, 0], [0, 1], [0, 2], [1, 0], [1, 1], [1, 2], [2, 0], [2, 1], [2, 2]]
+    assert expected == utils.points_in_poly(test_data)
+
+
+def test_reform_2d():
+
+    test_data = np.asarray([[0, 0], [1, 2], [3, 4]])
+
+    with pytest.raises(ValueError, match="Parameter 'factor' must be an integer!"):
+        utils.reform2d(test_data, 2.2)
+    with pytest.raises(ValueError, match="Input array must be 2d!"):
+        utils.reform2d(test_data[0], 2)
+
+    expected = np.asarray(
+        [
+            [0.0, 0.0, 0.0, 0.0],
+            [0.5, 0.75, 1.0, 1.0],
+            [1.0, 1.5, 2.0, 2.0],
+            [2.0, 2.5, 3.0, 3.0],
+            [3.0, 3.5, 4.0, 4.0],
+            [3.0, 3.5, 4.0, 4.0],
+        ]
+    )
+
+    assert np.allclose(utils.reform2d(test_data, 2), expected)

tox.ini

@@ -54,7 +54,7 @@ deps =
 
     # Oldest deps we pin against.
     oldestdeps: sunpy<2.1
-    oldestdeps: scikit-image<0.17.0
+    oldestdeps: scikit-image<=0.18.0
 
     # These are specific online extras we use to run the online tests.
     online: pytest-rerunfailures