Merge pull request #88 from Carifio24/utils-tests

Add tests of utility functions

glue_ar/tests/test_utils.py

@@ -0,0 +1,360 @@
+from itertools import product
+from numpy import arange, array, array_equal, nan, ones
+import pytest
+
+from glue.core import Data
+from glue.viewers.common.viewer import LayerArtist
+from glue_vispy_viewers.volume.volume_viewer import Vispy3DVolumeViewerState
+
+from glue_ar.utils import alpha_composite, binned_opacity, clamp, clamped_opacity, \
+                          clip_linear_transformations, clip_sides, data_count, data_for_layer, \
+                          export_label_for_layer, get_resolution, hex_to_components, is_volume_viewer, \
+                          iterable_has_nan, iterator_count, layer_color, mask_for_bounds, ndarray_has_nan, \
+                          offset_triangles, slope_intercept_between, unique_id, xyz_bounds
+
+
+def package_installed(package):
+    from importlib.util import find_spec
+    return find_spec(package) is not None
+
+
+GLUE_QT_INSTALLED = package_installed("glue_qt")
+GLUE_JUPYTER_INSTALLED = package_installed("glue_jupyter")
+
+
+try:
+    from glue_qt.app import GlueApplication
+    from glue_vispy_viewers.scatter.qt.scatter_viewer import VispyScatterViewer
+    from glue_vispy_viewers.volume.qt.volume_viewer import VispyVolumeViewer
+except ImportError:
+    pass
+
+try:
+    from glue_jupyter.app import JupyterApplication
+    from glue_jupyter.ipyvolume import IpyvolumeScatterView, IpyvolumeVolumeView
+    from glue_vispy_viewers.scatter.jupyter.scatter_viewer import JupyterVispyScatterViewer
+    from glue_vispy_viewers.volume.jupyter.volume_viewer import JupyterVispyVolumeViewer
+except ImportError:
+    pass
+
+
+def test_data_count():
+    data1 = Data(label="Data 1")
+    data2 = Data(label="Data 2")
+    viewer_state = Vispy3DVolumeViewerState()
+
+    layer1 = LayerArtist(viewer_state, layer=data1)
+    layer1_2 = LayerArtist(viewer_state, layer=data1)
+    layer2 = LayerArtist(viewer_state, layer=data2)
+
+    assert data_count((layer1,)) == 1
+    assert data_count((layer1, layer1_2)) == 1
+    assert data_count((layer1, layer2)) == 2
+
+    subset = data1.new_subset()
+    subset_layer = LayerArtist(viewer_state, layer=subset)
+
+    assert data_count((subset_layer,)) == 1
+    assert data_count((layer1, subset_layer)) == 1
+    assert data_count((layer2, subset_layer)) == 2
+
+
+def test_export_label_for_layer():
+    data = Data(label="Data")
+    subset = data.new_subset(label="Subset")
+    viewer_state = Vispy3DVolumeViewerState()
+    data_layer = LayerArtist(viewer_state, layer=data)
+    subset_layer = LayerArtist(viewer_state, layer=subset)
+
+    assert export_label_for_layer(data_layer, add_data_label=True) == "Data"
+    assert export_label_for_layer(data_layer, add_data_label=False) == "Data"
+
+    assert export_label_for_layer(subset_layer, add_data_label=True) == "Subset (Data)"
+    assert export_label_for_layer(subset_layer, add_data_label=False) == "Subset"
+
+
+def test_slope_intercept_between():
+    assert slope_intercept_between((3, 3), (1, 1)) == (1, 0)
+    assert slope_intercept_between((3, 4), (1, 2)) == (1, 1)
+    assert slope_intercept_between((-1, 5), (1, 5)) == (0, 5)
+    assert slope_intercept_between((-1, 5), (1, 15)) == (5, 10)
+
+
+def test_clip_linear_transformations():
+    bounds = [(0, 2), (0, 8), (2, 6)]
+
+    assert clip_linear_transformations(bounds) == [
+        (0.25, -0.25),
+        (0.25, -1),
+        (0.25, -1)
+    ]
+
+    assert clip_linear_transformations(bounds, clip_size=2) == [
+        (0.5, -0.5),
+        (0.5, -2),
+        (0.5, -2)
+    ]
+
+    assert clip_linear_transformations(bounds, stretches=(4, 0.5, 0.25)) == [
+        (1, -1),
+        (0.125, -0.5),
+        (0.0625, -0.25)
+    ]
+
+    assert clip_linear_transformations(bounds, clip_size=4,
+                                       stretches=(4, 0.5, 0.25)) == [
+        (4, -4),
+        (0.5, -2),
+        (0.25, -1)
+    ]
+
+
+def test_layer_color():
+    data = Data(label="Data")
+    viewer_state = Vispy3DVolumeViewerState()
+    layer = LayerArtist(viewer_state, layer=data)
+    layer.state.color = "#abcdef"
+
+    assert layer_color(layer.state) == "#abcdef"
+
+    layer.state.color = "0.35"
+    assert layer_color(layer.state) == "#808080"
+
+    layer.state.color = "0.75"
+    assert layer_color(layer.state) == "#808080"
+
+
+def test_clip_sides_non_native():
+    viewer_state = Vispy3DVolumeViewerState()
+    viewer_state.native_aspect = False
+
+    viewer_state.x_min = 0
+    viewer_state.x_max = 8
+    viewer_state.y_min = -2
+    viewer_state.y_max = 2
+    viewer_state.z_min = -1
+    viewer_state.z_max = 1
+
+    resolutions = (32, 64, 128, 256, 512)
+    clip_sizes = (1, 2, 3, 5, 10)
+    for resolution, clip_size in product(resolutions, clip_sizes):
+        viewer_state.resolution = resolution
+        size = 2 * clip_size / resolution
+        assert clip_sides(viewer_state, clip_size=clip_size) == (size, size, size)
+
+
+def test_clip_sides_native():
+    viewer_state = Vispy3DVolumeViewerState()
+    viewer_state.native_aspect = True
+
+    viewer_state.x_min = 0
+    viewer_state.x_max = 8
+    viewer_state.y_min = -2
+    viewer_state.y_max = 2
+    viewer_state.z_min = -1
+    viewer_state.z_max = 1
+
+    resolutions = (32, 64, 128, 256, 512)
+    clip_sizes = (1, 2, 3, 5, 10)
+    for resolution, clip_size in product(resolutions, clip_sizes):
+        viewer_state.resolution = resolution
+        max_size = 2 * clip_size / resolution
+        assert clip_sides(viewer_state, clip_size=clip_size) == (max_size, max_size / 2, max_size / 4)
+
+
+def test_mask_for_bounds():
+    x_values = range(10, 25)
+    y_values = range(130, 145)
+    z_values = range(-50, -35)
+    data = Data(x=x_values, y=y_values, z=z_values)
+    try:
+        app = GlueApplication()
+        app.add_data(data)
+        viewer = app.new_data_viewer(VispyScatterViewer, data=data)
+    except NameError:
+        app = JupyterApplication()
+        app.add_data(data)
+        viewer = app.new_data_viewer(JupyterVispyScatterViewer, data=data)
+    viewer.state.x_att = data.id['x']
+    viewer.state.y_att = data.id['y']
+    viewer.state.z_att = data.id['z']
+    viewer.add_data(data)
+    layer_state = viewer.layers[0].state
+
+    viewer.state.x_min = 12  # Cuts off the first two points
+    viewer.state.x_max = 25
+    viewer.state.y_min = 130
+    viewer.state.y_max = 141  # Cuts off the last three points
+    viewer.state.z_min = -70
+    viewer.state.z_max = -30
+
+    bounds = xyz_bounds(viewer.state, with_resolution=False)
+    mask = array([i not in (0, 1, 12, 13, 14) for i in range(15)])
+    assert array_equal(mask_for_bounds(viewer.state, layer_state, bounds), mask)
+
+
+def test_hex_to_components():
+    assert hex_to_components("#7f11e0") == [127, 17, 224]
+    assert hex_to_components("#abcdef47") == [171, 205, 239, 71]
+    assert hex_to_components("#000000") == [0, 0, 0]
+    assert hex_to_components("#00000000") == [0, 0, 0, 0]
+    assert hex_to_components("#26e04a") == [38, 224, 74]
+    assert hex_to_components("#ff021706") == [255, 2, 23, 6]
+
+
+def test_unique_id():
+    ids = [unique_id() for _ in range(25)]
+    assert all(len(id) == 32 for id in ids)
+    assert len(set(ids)) == 25
+
+
+def test_alpha_composite():
+    over = [110, 206, 15, 0.3]
+    under = [89, 97, 202, 0.4]
+    alpha_combined = 0.3 + 0.4 * 0.7
+    rgb_new = [(o * 0.3 + u * 0.4 * 0.7) / alpha_combined for o, u in zip(over[:3], under[:3])]
+    assert alpha_composite(over, under) == rgb_new + [alpha_combined]
+
+    over = [110, 206, 15, 0.6]
+    under = [89, 97, 202, 0.7]
+    alpha_combined = 0.6 + 0.7 * 0.4
+    rgb_new = [(o * 0.6 + u * 0.7 * 0.4) / alpha_combined for o, u in zip(over[:3], under[:3])]
+    assert alpha_composite(over, under) == rgb_new + [alpha_combined]
+
+    # Here over has full opacity, so the composition should just be the over color
+    over = [255, 10.5, 176]
+    under = [12, 116, 175, 0.5]
+    assert alpha_composite(over, under) == over + [1]
+
+
+def test_data_for_layer():
+    data = Data(label="Data")
+    subset = data.new_subset(label="Subset")
+    viewer_state = Vispy3DVolumeViewerState()
+    data_layer = LayerArtist(viewer_state, layer=data)
+    subset_layer = LayerArtist(viewer_state, layer=subset)
+
+    assert data_for_layer(data_layer) == data
+    assert data_for_layer(subset_layer) == data
+
+
+def test_ndarray_has_nan():
+    assert ndarray_has_nan(array([3.0, nan, -4.7, 2, nan]))
+    assert not ndarray_has_nan(array([3.0, 2.6, -4.7, 2, -10.5]))
+
+
+def test_iterable_has_nan():
+    assert iterable_has_nan((nan, 2.7, 3.5))
+    assert iterable_has_nan([2.1, nan, 11.0, 2.6])
+    assert not iterable_has_nan([2.1, -3.5, 4.6])
+    assert not iterable_has_nan((2.2, 4.6, -0.7))
+
+
+def test_iterator_count():
+    assert iterator_count(iter([1, 2, 3, 4, 5])) == 5
+    assert iterator_count(iter(range(11))) == 11
+
+
+@pytest.mark.skipif(not GLUE_QT_INSTALLED,
+                    reason="Requires glue-qt to test Qt VisPy volume viewer")
+def test_is_volume_viewer_qt():
+    qt_app = GlueApplication()
+    vispy_scatter = qt_app.new_data_viewer(VispyScatterViewer)
+    vispy_volume = qt_app.new_data_viewer(VispyVolumeViewer)
+    assert not is_volume_viewer(vispy_scatter)
+    assert is_volume_viewer(vispy_volume)
+
+
+@pytest.mark.skipif(not GLUE_JUPYTER_INSTALLED,
+                    reason="Requires glue-jupyter to test Jupyter VisPy and ipyvolume viewers")
+def test_is_volume_viewer_jupyter():
+    jupyter_app = JupyterApplication()
+
+    vispy_scatter = jupyter_app.new_data_viewer(JupyterVispyScatterViewer)
+    vispy_volume = jupyter_app.new_data_viewer(JupyterVispyVolumeViewer)
+    assert not is_volume_viewer(vispy_scatter)
+    assert is_volume_viewer(vispy_volume)
+
+    ipv_scatter = jupyter_app.new_data_viewer(IpyvolumeScatterView)
+    ipv_volume = jupyter_app.new_data_viewer(IpyvolumeVolumeView)
+    assert not is_volume_viewer(ipv_scatter)
+    assert is_volume_viewer(ipv_volume)
+
+
+@pytest.mark.skipif(not GLUE_QT_INSTALLED,
+                    reason="Requires glue-qt to test Qt VisPy volume viewer")
+def test_get_resolution_qt():
+    qt_app = GlueApplication()
+
+    vispy_volume = qt_app.new_data_viewer(VispyVolumeViewer)
+    vispy_volume.state.resolution = 64
+    assert get_resolution(vispy_volume.state) == 64
+
+    # Check default behavior
+    vispy_scatter = qt_app.new_data_viewer(VispyScatterViewer)
+    assert get_resolution(vispy_scatter) == 256
+
+
+@pytest.mark.skipif(not GLUE_JUPYTER_INSTALLED,
+                    reason="Requires glue-jupyter to test Jupyter VisPy and ipyvolume viewers")
+def test_get_resolution_jupyter():
+    jupyter_app = JupyterApplication()
+    volume_data1 = Data(label='Volume Data',
+                        x=arange(24).reshape((2, 3, 4)),
+                        y=ones((2, 3, 4)),
+                        z=arange(100, 124).reshape((2, 3, 4)))
+    jupyter_app.add_data(volume_data1)
+
+    vispy_volume = jupyter_app.new_data_viewer(JupyterVispyVolumeViewer)
+    vispy_volume.add_data(volume_data1)
+    vispy_volume.state.resolution = 32
+    assert get_resolution(vispy_volume.state) == 32
+
+    ipv_volume = jupyter_app.new_data_viewer(IpyvolumeVolumeView)
+    ipv_volume.add_data(volume_data1)
+    ipv_volume.layers[-1].state.max_resolution = 128
+    assert get_resolution(ipv_volume.state) == 128
+
+    volume_data2 = Data(label='Volume Data',
+                        x=arange(24).reshape((2, 3, 4)),
+                        y=ones((2, 3, 4)),
+                        z=arange(100, 124).reshape((2, 3, 4)))
+    jupyter_app.add_data(volume_data2)
+    vispy_volume.add_data(volume_data2)
+    ipv_volume.add_data(volume_data2)
+    ipv_volume.layers[-1].state.max_resolution = 64
+    assert get_resolution(vispy_volume.state) == 32
+    assert get_resolution(ipv_volume.state) == 128
+
+    ipv_volume.layers[-1].state.max_resolution = 512
+    assert get_resolution(ipv_volume.state) == 512
+
+
+def test_clamp():
+    assert clamp(2, 0, 1) == 1
+    assert clamp(-1, 0, 1) == 0
+    assert clamp(0.5, 0, 1) == 0.5
+    assert clamp(9, 5, 7) == 7
+    assert clamp(16.2, 20.5, 31.6) == 20.5
+    assert clamp(5.6, 4.8, 7.2) == 5.6
+
+
+def test_clamped_opacity():
+    assert clamped_opacity(0.1) == 0.1
+    assert clamped_opacity(0.77) == 0.77
+    assert clamped_opacity(-2) == 0
+    assert clamped_opacity(1.6) == 1
+
+
+def test_binned_opacity():
+    assert binned_opacity(0.13, 0.2) == 0.2
+    assert binned_opacity(0.3, 0.25) == 0.25
+    assert binned_opacity(-1.3, 0.1) == 0
+    assert binned_opacity(2.46, 0.01) == 1
+    assert binned_opacity(0.775, 0.02) == 0.78
+
+
+def test_offset_triangles():
+    assert offset_triangles([[0, 1, 2], [1, 2, 3], [0, 2, 3]], 6) == [(6, 7, 8), (7, 8, 9), (6, 8, 9)]
+    assert offset_triangles([[2, 1, 6], [5, 7, 4]], 5) == [(7, 6, 11), (10, 12, 9)]
+    assert offset_triangles([[0, 1, 2], [2, 3, 0], [3, 1, 2]], 0) == [(0, 1, 2), (2, 3, 0), (3, 1, 2)]

glue_ar/utils.py

@@ -188,7 +188,7 @@ def clip_sides(viewer_state: Viewer3DState,
         return tuple(s * transform[0] for s, transform in zip(sides, clip_transforms))
     else:
         max_stretch = max(stretches)
-        return tuple(2 * stretch / (max_stretch * resolution) for stretch in stretches)
+        return tuple(2 * clip_size * stretch / (max_stretch * resolution) for stretch in stretches)
 
 
 def bring_into_clip(data,
@@ -256,8 +256,8 @@ def unique_id() -> str:
 
 
 def alpha_composite(over: List[float], under: List[float]) -> List[float]:
-    alpha_o = over[3] if len(over) == 4 else over[2]
-    alpha_u = under[3] if len(under) == 4 else under[2]
+    alpha_o = over[3] if len(over) == 4 else 1
+    alpha_u = under[3] if len(under) == 4 else 1
     rgb_o = over[:3]
     rgb_u = under[:3]
     alpha_new = alpha_o + alpha_u * (1 - alpha_o)