Merge pull request #220 from naplab/brain_sulc_alpha

Create sulcus alpha and light source for brain plots

Author: vinaysraghavan

naplib/localization/freesurfer.py

@@ -124,6 +124,7 @@ def __init__(
         except Exception as e:
             logger.warning(f'No {hemi}.sulc file found. No sulcus information will be used.')
             self.sulc = None
+        self.sulc_alpha = 1.0
 
 
         self.load_labels()

naplib/utils/surfdist.py

@@ -5,6 +5,7 @@
 
 import gdist
 import matplotlib.pyplot as plt
+from matplotlib.colors import LightSource
 import numpy as np
 from nibabel.freesurfer.io import read_annot
 
@@ -124,17 +125,19 @@ def surfdist_viz(
     alpha="auto",
     bg_map=None,
     bg_on_stat=False,
+    bg_alpha=1.0,
     figsize=None,
     ax=None,
     vmin=None,
     vmax=None,
+    light_source=None,
 ):
     """Visualize results on cortical surface using matplotlib.
 
     Parameters
     ----------
     coords : numpy array of shape (n_nodes,3), each row specifying the x,y,z
-            coordinates of one node of surface mesh
+             coordinates of one node of surface mesh
     faces : numpy array of shape (n_faces, 3), each row specifying the indices
             of the three nodes building one node of the surface mesh
     stat_map : numpy array of shape (n_nodes,) containing the values to be
@@ -158,9 +161,16 @@ def surfdist_viz(
                  multiplied with the background map for shadowing. Otherwise,
                  only areas that are not covered by the statsitical map after
                  thresholding will show shadows.
+    bg_alpha : float, determines the opacity of the background map.
+               bg_alpha defaults to 1.0 and is only relevant if bg_on_stat
     figsize : tuple of intergers, dimensions of the figure that is produced.
     ax : Axis
         Axis to plot on, with 3d projection.
+    light_source: None, bool, or tuple of int, optional
+        Whether to apply a light source for shading. If True, the light
+        source position is inferred from `elev` and `azim`. If a tuple of
+        (alt, az), these values will be used to specify the light source
+        position. If None or False, no shading is applied. Default is None.
 
     Returns
     -------
@@ -226,7 +236,7 @@ def surfdist_viz(
             bg_faces = np.mean(bg_data[faces], axis=1)
             bg_faces = bg_faces - bg_faces.min()
             bg_faces = bg_faces / bg_faces.max()
-            face_colors = plt.cm.gray_r(bg_faces)
+            face_colors = plt.cm.gray_r(bg_faces * bg_alpha)
 
         # modify alpha values of background
         face_colors[:, 3] = alpha * face_colors[:, 3]
@@ -260,6 +270,41 @@ def surfdist_viz(
                 else:
                     face_colors = cmap(stat_map_faces)
 
+        if light_source:
+            if hasattr(light_source, '__len__'):
+                if len(light_source) == 2:
+                    ls = LightSource(azdeg=light_source[1], altdeg=light_source[0])
+            else:
+                # Apply lighting to the face colors for shading
+                ls = LightSource(azdeg=azim, altdeg=elev)
+
+            # Manually calculate the light vector since the 'light_vector'
+            # attribute is not accessible in some matplotlib versions.
+            az = np.radians(ls.azdeg)
+            alt = np.radians(ls.altdeg)
+            light_vec = np.array([
+                np.cos(az) * np.cos(alt),
+                np.sin(az) * np.cos(alt),
+                np.sin(alt)
+            ])
+
+            # Calculate face normals
+            v0 = coords[faces[:, 0]]
+            v1 = coords[faces[:, 1]]
+            v2 = coords[faces[:, 2]]
+            face_normals = np.cross(v1 - v0, v2 - v0)
+            face_normals /= np.linalg.norm(face_normals, axis=1)[:, np.newaxis]
+
+            # The shade is the dot product of the light vector and face normals
+            shade = np.dot(face_normals, light_vec)
+
+            # Modulate the RGB colors by the shade, keeping the alpha channel
+            # Use np.clip to keep shade values between 0 and 1
+            illuminated_rgb = face_colors[:, :3] * np.clip(shade, 0, 1)[:, np.newaxis]
+
+            # Combine illuminated RGB with the original alpha channel
+            face_colors = np.hstack((illuminated_rgb, face_colors[:, 3:]))
+
         p3dcollec.set_facecolors(face_colors)
 
     if not premade_ax:

naplib/visualization/brain_plots.py

@@ -90,7 +90,7 @@ def _view(hemi, mode: str = "lateral", backend: str = "mpl"):
     raise ValueError(f"Unknown `mode`: {mode}.")
 
 
-def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", threshold=None, vmin=None, vmax=None):
+def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", threshold=None, vmin=None, vmax=None, light_source=False):
     if isinstance(view, tuple):
         elev, azim = view
     else:
@@ -105,16 +105,18 @@ def _plot_hemi(hemi, cmap="coolwarm", ax=None, view="best", threshold=None, vmin
         alpha=hemi.alpha,
         bg_map=hemi.sulc,
         bg_on_stat=True,
+        bg_alpha=hemi.sulc_alpha,
         ax=ax,
         vmin=vmin,
-        vmax=vmax
+        vmax=vmax,
+        light_source=light_source
     )
     ax.axes.set_axis_off()
     ax.grid(False)
 
 
 def plot_brain_overlay(
-    brain, cmap="coolwarm", ax=None, hemi='both', view="best", vmin=None, vmax=None, cmap_quantile=1.0, threshold=None, **kwargs
+    brain, cmap="coolwarm", ax=None, hemi='both', view="best", vmin=None, vmax=None, cmap_quantile=1.0, threshold=None, light_source=False, **kwargs
 ):
     """
     Plot brain overlay on the 3D cortical surface using matplotlib.
@@ -149,6 +151,11 @@ def plot_brain_overlay(
     threshold : positive float, optional
         If given, then only values on the overlay which are less -threshold or greater than threshold will
         be shown.
+    light_source: None, bool, or tuple of int, optional
+        Whether to apply a light source for shading. If True, the light
+        source position is inferred from `elev` and `azim`. If a tuple of
+        (alt, az), these values will be used to specify the light source
+        position. If None or False, no shading is applied. Default is True.
     **kwargs : kwargs
         Any other kwargs to pass to matplotlib.pyplot.figure (such as figsize)
 
@@ -216,9 +223,9 @@ def plot_brain_overlay(
 
 
     if ax[0] is not None:
-        _plot_hemi(brain.lh, cmap, ax[0], view=view, vmin=vmin, vmax=vmax, threshold=threshold)
+        _plot_hemi(brain.lh, cmap, ax[0], view=view, vmin=vmin, vmax=vmax, threshold=threshold, light_source=light_source)
     if ax[1] is not None:
-        _plot_hemi(brain.rh, cmap, ax[1], view=view, vmin=vmin, vmax=vmax, threshold=threshold)
+        _plot_hemi(brain.rh, cmap, ax[1], view=view, vmin=vmin, vmax=vmax, threshold=threshold, light_source=light_source)
 
     return fig, ax