def test_contour_from_label(interactive=False): # Render volumne scene = window.Scene() data = np.zeros((50, 50, 50)) data[5:15, 1:10, 25] = 1. data[25:35, 1:10, 25] = 2. data[40:49, 1:10, 25] = 3. color = np.array([[255, 0, 0, 0.6], [0, 255, 0, 0.5], [0, 0, 255, 1.0]]) surface = actor.contour_from_label(data, color=color) scene.add(surface) scene.reset_camera() scene.reset_clipping_range() if interactive: window.show(scene) # Test Errors with npt.assert_raises(ValueError): actor.contour_from_label(data, color=np.array([1, 2, 3])) actor.contour_from_label(np.ones(50)) # Test binarization scene2 = window.Scene() data2 = np.zeros((50, 50, 50)) data2[20:30, 25, 25] = 1. data2[25, 20:30, 25] = 2. color2 = np.array([[255, 0, 255], [255, 255, 0]]) surface2 = actor.contour_from_label(data2, color=color2) scene2.add(surface2) scene2.reset_camera() scene2.reset_clipping_range() if interactive: window.show(scene2) arr = window.snapshot(scene, 'test_surface.png', offscreen=True, order_transparent=False) arr2 = window.snapshot(scene2, 'test_surface2.png', offscreen=True, order_transparent=True) report = window.analyze_snapshot(arr, colors=[(255, 0, 0), (0, 255, 0), (0, 0, 255)], find_objects=True) report2 = window.analyze_snapshot(arr2, find_objects=True) npt.assert_equal(report.objects, 3) npt.assert_equal(report2.objects, 1) actor.contour_from_label(data)
def main(): parser = _build_arg_parser() args = parser.parse_args() assert_inputs_exist(parser, args.in_seed_map, [args.tractogram]) # Seed map informations seed_map_img = nib.load(args.in_seed_map) seed_map_data = seed_map_img.get_fdata().astype(np.uint8) seed_map_affine = seed_map_img.affine # Load seed density as labels values = np.delete(np.unique(seed_map_data), 0) # Create colormap based on labels cmap = actor.create_colormap(values, name=args.colormap, auto=False) # Append opacity to colormap cmap = np.concatenate((cmap, np.full( (cmap.shape[0], 1), args.seed_opacity)), axis=-1) scene = window.Scene() scene.background(tuple(map(int, args.background))) seedroi_actor = actor.contour_from_label(seed_map_data, seed_map_affine, color=cmap) scene.add(seedroi_actor) # Load tractogram as tubes or lines, with color if specified if args.tractogram: tractogram = nib.streamlines.load(args.tractogram).tractogram color = None if args.tractogram_color: color = tuple(map(int, args.tractogram_color)) line_actor = streamline_actor[args.tractogram_shape]( tractogram.streamlines, opacity=args.tractogram_opacity, colors=color, linewidth=args.tractogram_width) scene.add(line_actor) # Showtime ! showm = window.ShowManager(scene, reset_camera=True) showm.initialize() showm.start()
from fury import actor, window import numpy as np scene = window.Scene() data = np.zeros((50, 50, 50)) data[15:20, 25, 25] = 1. data[25, 20:30, 25] = 2. data[25, 40:50, 30:50] = 3. surface = actor.contour_from_label(data, color=np.random.rand(3, 3), opacity=0.6) scene.add(surface) scene.reset_camera() scene.reset_clipping_range() window.show(scene)
def test_manifest_standard(interactive=False): scene = window.Scene() # Setup scene # Setup surface surface_actor = _generate_surface() material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(surface_actor) arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 1) scene.clear() # Reset scene # Contour from roi setup data = np.zeros((50, 50, 50)) data[20:30, 25, 25] = 1. data[25, 20:30, 25] = 1. affine = np.eye(4) surface = actor.contour_from_roi(data, affine, color=np.array([1, 0, 1])) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(surface) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 1) scene.clear() # Reset scene # Contour from label setup data = np.zeros((50, 50, 50)) data[5:15, 1:10, 25] = 1. data[25:35, 1:10, 25] = 2. data[40:49, 1:10, 25] = 3. color = np.array([[255, 0, 0], [0, 255, 0], [0, 0, 255]]) surface = actor.contour_from_label(data, color=color) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(surface) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 3) scene.clear() # Reset scene # Streamtube setup data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]]) data2 = data1 + np.array([0.5, 0., 0.]) data = [data1, data2] colors = np.array([[1, 0, 0], [0, 0, 1.]]) tubes = actor.streamtube(data, colors, linewidth=.1) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(tubes) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 2) scene.clear() # Reset scene # ODF slicer setup if have_dipy: from dipy.data import get_sphere from tempfile import mkstemp sphere = get_sphere('symmetric362') shape = (11, 11, 11, sphere.vertices.shape[0]) fid, fname = mkstemp(suffix='_odf_slicer.mmap') odfs = np.memmap(fname, dtype=np.float64, mode='w+', shape=shape) odfs[:] = 1 affine = np.eye(4) mask = np.ones(odfs.shape[:3]) mask[:4, :4, :4] = 0 odfs[..., 0] = 1 odf_actor = actor.odf_slicer(odfs, affine, mask=mask, sphere=sphere, scale=.25, colormap='blues') material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) k = 5 I, J, _ = odfs.shape[:3] odf_actor.display_extent(0, I, 0, J, k, k) odf_actor.GetProperty().SetOpacity(1.0) scene.add(odf_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 11 * 11) scene.clear() # Reset scene # Tensor slicer setup if have_dipy: from dipy.data import get_sphere sphere = get_sphere('symmetric724') evals = np.array([1.4, .35, .35]) * 10 ** (-3) evecs = np.eye(3) mevals = np.zeros((3, 2, 4, 3)) mevecs = np.zeros((3, 2, 4, 3, 3)) mevals[..., :] = evals mevecs[..., :, :] = evecs affine = np.eye(4) scene = window.Scene() tensor_actor = actor.tensor_slicer(mevals, mevecs, affine=affine, sphere=sphere, scale=.3) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) _, J, K = mevals.shape[:3] tensor_actor.display_extent(0, 1, 0, J, 0, K) scene.add(tensor_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 4) scene.clear() # Reset scene # Point setup points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]]) colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) opacity = 0.5 points_actor = actor.point(points, colors, opacity=opacity) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(points_actor) arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 3) scene.clear() # Reset scene # Sphere setup xyzr = np.array([[0, 0, 0, 10], [100, 0, 0, 25], [200, 0, 0, 50]]) colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]]) opacity = 0.5 sphere_actor = actor.sphere(centers=xyzr[:, :3], colors=colors[:], radii=xyzr[:, 3], opacity=opacity) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(sphere_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 3) scene.clear() # Reset scene # Advanced geometry actors setup (Arrow, cone, cylinder) xyz = np.array([[0, 0, 0], [50, 0, 0], [100, 0, 0]]) dirs = np.array([[0, 1, 0], [1, 0, 0], [0, 0.5, 0.5]]) colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [1, 1, 0, 1]]) heights = np.array([5, 7, 10]) actor_list = [[actor.cone, {'directions': dirs, 'resolution': 8}], [actor.arrow, {'directions': dirs, 'resolution': 9}], [actor.cylinder, {'directions': dirs}]] for act_func, extra_args in actor_list: aga_actor = act_func(centers=xyz, colors=colors[:], heights=heights, **extra_args) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(aga_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 3) scene.clear() # Basic geometry actors (Box, cube, frustum, octagonalprism, rectangle, # square) centers = np.array([[4, 0, 0], [0, 4, 0], [0, 0, 0]]) colors = np.array([[1, 0, 0, 0.4], [0, 1, 0, 0.8], [0, 0, 1, 0.5]]) directions = np.array([[1, 1, 0]]) scale_list = [1, 2, (1, 1, 1), [3, 2, 1], np.array([1, 2, 3]), np.array([[1, 2, 3], [1, 3, 2], [3, 1, 2]])] actor_list = [[actor.box, {}], [actor.cube, {}], [actor.frustum, {}], [actor.octagonalprism, {}], [actor.rectangle, {}], [actor.square, {}]] for act_func, extra_args in actor_list: for scale in scale_list: scene = window.Scene() bga_actor = act_func(centers=centers, directions=directions, colors=colors, scales=scale, **extra_args) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(bga_actor) arr = window.snapshot(scene) report = window.analyze_snapshot(arr) msg = 'Failed with {}, scale={}'.format(act_func.__name__, scale) npt.assert_equal(report.objects, 3, err_msg=msg) scene.clear() # Cone setup using vertices centers = np.array([[0, 0, 0], [20, 0, 0], [40, 0, 0]]) directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]]) colors = np.array([[1, 0, 0, 0.3], [0, 1, 0, 0.4], [0, 0, 1., 0.99]]) vertices = np.array([[0.0, 0.0, 0.0], [0.0, 10.0, 0.0], [10.0, 0.0, 0.0], [0.0, 0.0, 10.0]]) faces = np.array([[0, 1, 3], [0, 1, 2]]) cone_actor = actor.cone(centers=centers, directions=directions, colors=colors[:], vertices=vertices, faces=faces) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(cone_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 3) scene.clear() # Reset scene # Superquadric setup centers = np.array([[8, 0, 0], [0, 8, 0], [0, 0, 0]]) colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) directions = np.random.rand(3, 3) scales = [1, 2, 3] roundness = np.array([[1, 1], [1, 2], [2, 1]]) sq_actor = actor.superquadric(centers, roundness=roundness, directions=directions, colors=colors.astype(np.uint8), scales=scales) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(sq_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) ft.assert_greater_equal(report.objects, 3) scene.clear() # Reset scene # Label setup text_actor = actor.label("Hello") material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(text_actor) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 5) scene.clear() # Reset scene # Texture setup arr = (255 * np.ones((512, 212, 4))).astype('uint8') arr[20:40, 20:40, :] = np.array([255, 0, 0, 255], dtype='uint8') tp2 = actor.texture(arr) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(tp2) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 1) scene.clear() # Reset scene # Texture on sphere setup arr = 255 * np.ones((810, 1620, 3), dtype='uint8') rows, cols, _ = arr.shape rs = rows // 2 cs = cols // 2 w = 150 // 2 arr[rs - w: rs + w, cs - 10 * w: cs + 10 * w] = np.array([255, 127, 0]) tsa = actor.texture_on_sphere(arr) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(tsa) scene.reset_camera() scene.reset_clipping_range() arr = window.snapshot(scene) report = window.analyze_snapshot(arr) npt.assert_equal(report.objects, 1) # NOTE: From this point on, these actors don't have full support for PBR # interpolation. This is, the test passes but there is no evidence of the # desired effect. """ # Setup slicer data = (255 * np.random.rand(50, 50, 50)) affine = np.eye(4) slicer = actor.slicer(data, affine, value_range=[data.min(), data.max()]) slicer.display(None, None, 25) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(slicer) """ """ # Line setup data1 = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 2.]]) data2 = data1 + np.array([0.5, 0., 0.]) data = [data1, data2] colors = np.array([[1, 0, 0], [0, 0, 1.]]) lines = actor.line(data, colors, linewidth=5) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(lines) """ """ # Scalar bar setup lut = actor.colormap_lookup_table( scale_range=(0., 100.), hue_range=(0., 0.1), saturation_range=(1, 1), value_range=(1., 1)) sb_actor = actor.scalar_bar(lut, ' ') material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(sb_actor) """ """ # Axes setup axes = actor.axes() material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(axes) """ """ # Peak slicer setup _peak_dirs = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], dtype='f4') # peak_dirs.shape = (1, 1, 1) + peak_dirs.shape peak_dirs = np.zeros((11, 11, 11, 3, 3)) peak_dirs[:, :, :] = _peak_dirs peak_actor = actor.peak_slicer(peak_dirs) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(peak_actor) """ """ # Dots setup points = np.array([[0, 0, 0], [0, 1, 0], [1, 0, 0]]) dots_actor = actor.dots(points, color=(0, 255, 0)) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(dots_actor) """ """ # Text3D setup msg = 'I \nlove\n FURY' txt_actor = actor.text_3d(msg) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(txt_actor) """ """ # Figure setup arr = (255 * np.ones((512, 212, 4))).astype('uint8') arr[20:40, 20:40, 3] = 0 tp = actor.figure(arr) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(tp) """ """ # SDF setup centers = np.array([[2, 0, 0], [0, 2, 0], [0, 0, 0]]) * 11 colors = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]) directions = np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]]) scales = [1, 2, 3] primitive = ['sphere', 'ellipsoid', 'torus'] sdf_actor = actor.sdf(centers, directions=directions, colors=colors, primitives=primitive, scales=scales) material.manifest_standard(surface_actor, ambient_level=.3, diffuse_level=.25) scene.add(sdf_actor) """ # NOTE: For these last set of actors, there is not support for PBR # interpolation at all. """ # Billboard setup centers = np.array([[0, 0, 0], [5, -5, 5], [-7, 7, -7], [10, 10, 10], [10.5, 11.5, 11.5], [12, -12, -12], [-17, 17, 17], [-22, -22, 22]]) colors = np.array([[1, 1, 0], [0, 0, 0], [1, 0, 1], [0, 0, 1], [1, 1, 1], [1, 0, 0], [0, 1, 0], [0, 1, 1]]) scales = [6, .4, 1.2, 1, .2, .7, 3, 2] """ fake_sphere = \ """ float len = length(point); float radius = 1.; if (len > radius) discard; vec3 normalizedPoint = normalize(vec3(point.xy, sqrt(1. - len))); vec3 direction = normalize(vec3(1., 1., 1.)); float df_1 = max(0, dot(direction, normalizedPoint)); float sf_1 = pow(df_1, 24); fragOutput0 = vec4(max(df_1 * color, sf_1 * vec3(1)), 1); """ """ billboard_actor = actor.billboard(centers, colors=colors, scales=scales, fs_impl=fake_sphere) material.manifest_pbr(billboard_actor) scene.add(billboard_actor) """ if interactive: window.show(scene)