Merge pull request #374 from CHrlS98/odf_slicer

ENH: Refactor actor.odf_slicer for increased performances

docs/examples/viz_fiber_odf.py

@@ -0,0 +1,224 @@
+"""
+====================================
+Brain Fiber ODF Visualisation
+====================================
+
+This example demonstrate how to create a simple viewer for fiber
+orientation distribution functions (ODF) using fury's odf_slicer.
+"""
+
+# First, we import some useful modules and methods.
+import numpy as np
+import nibabel as nib
+from fury import actor, window, ui
+from fury.data import read_viz_dmri, fetch_viz_dmri, fetch_viz_icons
+from fury.utils import fix_winding_order
+from dipy.reconst.shm import sh_to_sf_matrix
+from dipy.data import get_sphere
+
+###############################################################################
+# Here, we fetch and load the fiber ODF volume to display. The ODF are
+# expressed as spherical harmonics (SH) coefficients in a 3D grid.
+fetch_viz_dmri()
+fetch_viz_icons()
+
+fodf_img = nib.load(read_viz_dmri('fodf.nii.gz'))
+sh = fodf_img.get_fdata()
+affine = fodf_img.affine
+grid_shape = sh.shape[:-1]
+
+###############################################################################
+# We then define a low resolution sphere used to visualize SH coefficients
+# as spherical functions (SF) as well as a matrix `B_low` to project SH
+# onto the sphere.
+sphere_low = get_sphere('repulsion100')
+B_low = sh_to_sf_matrix(sphere_low, 8, return_inv=False)
+
+###############################################################################
+# Now, we create a slicer for each orientation to display a slice in
+# the middle of the volume and we add them to a `scene`.
+
+# Change these values to test various parameters combinations.
+scale = 0.5
+norm = False
+colormap = None
+radial_scale = True
+opacity = 1.0
+global_cm = False
+
+# ODF slicer for axial slice
+odf_actor_z = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
+                               scale=scale, norm=norm,
+                               radial_scale=radial_scale, opacity=opacity,
+                               colormap=colormap, global_cm=global_cm,
+                               B_matrix=B_low)
+
+# ODF slicer for coronal slice
+odf_actor_y = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
+                               scale=scale, norm=norm,
+                               radial_scale=radial_scale, opacity=opacity,
+                               colormap=colormap, global_cm=global_cm,
+                               B_matrix=B_low)
+odf_actor_y.display_extent(0, grid_shape[0] - 1, grid_shape[1]//2,
+                           grid_shape[1]//2, 0, grid_shape[2] - 1)
+
+# ODF slicer for sagittal slice
+odf_actor_x = actor.odf_slicer(sh, affine=affine, sphere=sphere_low,
+                               scale=scale, norm=norm,
+                               radial_scale=radial_scale, opacity=opacity,
+                               colormap=colormap, global_cm=global_cm,
+                               B_matrix=B_low)
+odf_actor_x.display_extent(grid_shape[0]//2, grid_shape[0]//2, 0,
+                           grid_shape[1] - 1, 0, grid_shape[2] - 1)
+
+scene = window.Scene()
+scene.add(odf_actor_z)
+scene.add(odf_actor_y)
+scene.add(odf_actor_x)
+
+show_m = window.ShowManager(scene, reset_camera=True, size=(1200, 900))
+show_m.initialize()
+
+###############################################################################
+# Now that we have a `ShowManager` containing our slicer, we can go on and
+# configure our UI for changing the slices to visualize.
+line_slider_z = ui.LineSlider2D(min_value=0,
+                                max_value=grid_shape[2] - 1,
+                                initial_value=grid_shape[2] / 2,
+                                text_template="{value:.0f}",
+                                length=140)
+
+line_slider_y = ui.LineSlider2D(min_value=0,
+                                max_value=grid_shape[1] - 1,
+                                initial_value=grid_shape[1] / 2,
+                                text_template="{value:.0f}",
+                                length=140)
+
+line_slider_x = ui.LineSlider2D(min_value=0,
+                                max_value=grid_shape[0] - 1,
+                                initial_value=grid_shape[0] / 2,
+                                text_template="{value:.0f}",
+                                length=140)
+
+###############################################################################
+# We also define a high resolution sphere to demonstrate the capability to
+# dynamically change the sphere used for SH to SF projection.
+sphere_high = get_sphere('symmetric362')
+
+# We fix the order of the faces' three vertices to a clockwise winding. This
+# ensures all faces have a normal going away from the center of the sphere.
+sphere_high.faces = fix_winding_order(sphere_high.vertices,
+                                      sphere_high.faces, True)
+B_high = sh_to_sf_matrix(sphere_high, 8, return_inv=False)
+
+###############################################################################
+# We add a combobox for choosing the sphere resolution during execution.
+sphere_dict = {'Low resolution': (sphere_low, B_low),
+               'High resolution': (sphere_high, B_high)}
+combobox = ui.ComboBox2D(items=list(sphere_dict))
+scene.add(combobox)
+
+###############################################################################
+# Here we will write callbacks for the sliders and combo box and register them.
+
+
+def change_slice_z(slider):
+    i = int(np.round(slider.value))
+    odf_actor_z.slice_along_axis(i)
+
+
+def change_slice_y(slider):
+    i = int(np.round(slider.value))
+    odf_actor_y.slice_along_axis(i, 'yaxis')
+
+
+def change_slice_x(slider):
+    i = int(np.round(slider.value))
+    odf_actor_x.slice_along_axis(i, 'xaxis')
+
+
+def change_sphere(combobox):
+    sphere, B = sphere_dict[combobox.selected_text]
+    odf_actor_x.update_sphere(sphere.vertices, sphere.faces, B)
+    odf_actor_y.update_sphere(sphere.vertices, sphere.faces, B)
+    odf_actor_z.update_sphere(sphere.vertices, sphere.faces, B)
+
+
+line_slider_z.on_change = change_slice_z
+line_slider_y.on_change = change_slice_y
+line_slider_x.on_change = change_slice_x
+combobox.on_change = change_sphere
+
+###############################################################################
+# We then add labels for the sliders and position them inside a panel.
+
+
+def build_label(text):
+    label = ui.TextBlock2D()
+    label.message = text
+    label.font_size = 18
+    label.font_family = 'Arial'
+    label.justification = 'left'
+    label.bold = False
+    label.italic = False
+    label.shadow = False
+    label.background_color = (0, 0, 0)
+    label.color = (1, 1, 1)
+
+    return label
+
+
+line_slider_label_z = build_label(text="Z Slice")
+line_slider_label_y = build_label(text="Y Slice")
+line_slider_label_x = build_label(text="X Slice")
+
+panel = ui.Panel2D(size=(300, 200),
+                   color=(1, 1, 1),
+                   opacity=0.1,
+                   align="right")
+panel.center = (1030, 120)
+
+panel.add_element(line_slider_label_x, (0.1, 0.75))
+panel.add_element(line_slider_x, (0.38, 0.75))
+panel.add_element(line_slider_label_y, (0.1, 0.55))
+panel.add_element(line_slider_y, (0.38, 0.55))
+panel.add_element(line_slider_label_z, (0.1, 0.35))
+panel.add_element(line_slider_z, (0.38, 0.35))
+
+show_m.scene.add(panel)
+
+###############################################################################
+# Then, we can render all the widgets and everything else in the screen and
+# start the interaction using ``show_m.start()``.
+#
+# However, if you change the window size, the panel will not update its
+# position properly. The solution to this issue is to update the position of
+# the panel using its ``re_align`` method every time the window size changes.
+size = scene.GetSize()
+
+
+def win_callback(obj, _event):
+    global size
+    if size != obj.GetSize():
+        size_old = size
+        size = obj.GetSize()
+        size_change = [size[0] - size_old[0], 0]
+        panel.re_align(size_change)
+
+
+show_m.initialize()
+
+###############################################################################
+# Finally, please set the following variable to ``True`` to interact with the
+# datasets in 3D.
+interactive = False
+
+if interactive:
+    show_m.add_window_callback(win_callback)
+    show_m.render()
+    show_m.start()
+else:
+    window.record(scene, out_path='odf_slicer_3D.png', size=(1200, 900),
+                  reset_camera=False)
+
+del show_m