WIP "Fake" ambiant occlusion for MI-Brain

scilpy/viz/color.py

@@ -1,9 +1,11 @@
 # -*- coding: utf-8 -*-
 
-from fury.colormap import distinguishable_colormap
+from dipy.io.stateful_tractogram import StatefulTractogram
+from fury import colormap
 import matplotlib.pyplot as plt
-from matplotlib import colors
+from matplotlib import colors as mcolors
 import numpy as np
+from scipy.spatial import KDTree
 
 from scilpy.viz.backends.vtk import get_color_by_name, lut_from_colors
 
@@ -38,7 +40,7 @@ def convert_color_names_to_rgb(names):
                                              "Brown"])
 
 
-def generate_n_colors(n, generator=distinguishable_colormap,
+def generate_n_colors(n, generator=colormap.distinguishable_colormap,
                       pick_from_base10=True, shuffle=False):
     """
     Generate a set of N colors. When using the default parameters, colors will
@@ -98,8 +100,8 @@ def get_lookup_table(name):
 
     if '-' in name:
         name_list = name.split('-')
-        colors_list = [colors.to_rgba(color)[0:3] for color in name_list]
-        cmap = colors.LinearSegmentedColormap.from_list('CustomCmap',
+        colors_list = [mcolors.to_rgba(color)[0:3] for color in name_list]
+        cmap = mcolors.LinearSegmentedColormap.from_list('CustomCmap',
                                                         colors_list)
         return cmap
 
@@ -279,3 +281,76 @@ def prepare_colorbar_figure(cmap, lbound, ubound, nb_values=255, nb_ticks=10,
         ax.set_xticklabels(ticks_labels)
         ax.set_yticks([])
     return fig
+
+
+def ambiant_occlusion(sft, colors, factor=4):
+    """
+    Apply ambiant occlusion to a set of colors based on point density
+    around each points. 
+
+    Parameters
+    ----------
+    sft : StatefulTractogram
+        The streamlines.
+    colors : np.ndarray
+        The original colors to modify.
+    factor : float
+        The factor of occlusion (how density will affect the saturation).
+
+    Returns
+    -------
+    np.ndarray
+        The modified colors.
+    """
+
+    pts = sft.streamlines._data
+    hsv = mcolors.rgb_to_hsv(colors)
+
+    tree = KDTree(pts)
+    nb_neighbor = np.array(tree.query_ball_point(pts, 1,
+                                                 return_length=True),
+                           dtype=float)
+    nb_neighbor /= np.max(nb_neighbor)
+    occlusion_w = np.exp(-factor * nb_neighbor)
+
+    hsv[:, 1] = np.clip(hsv[:, 1], max(1 / factor, np.min(hsv[:, 1])),
+                        min(1 - 1 / factor, np.max(hsv[:, 1])))
+    hsv[:, 1] -= (occlusion_w / factor)
+
+    occlusion_w = np.clip(occlusion_w, 0.5 + (1 / factor), 1)
+    hsv[:, 2] *= occlusion_w
+    hsv[:, 0:2] = np.clip(hsv[:, 0:2], 0, 1)
+    hsv[:, 2] = np.clip(hsv[:, 2], 0, 255)
+
+    return mcolors.hsv_to_rgb(hsv)
+
+def generate_local_coloring(sft):
+    """
+    Generate a coloring based on the local orientation of the streamlines.
+
+    Parameters
+    ----------
+    sft : StatefulTractogram / ArraySequence / List
+        The tractogram / streamlines to generate the coloring from.
+
+    Returns
+    -------
+    np.ndarray
+        The generated colors.
+    """
+    if isinstance(sft, StatefulTractogram):
+        streamlines = sft.streamlines
+    else:
+        streamlines = sft
+
+    # Compute segment orientation
+    diff = [np.diff(list(s), axis=0) for s in streamlines]
+    # Repeat first segment so that the number of segments matches
+    # the number of points
+    diff = [[d[0]] + list(d) for d in diff]
+    # Flatten the list of segments
+    orientations = np.asarray([o for d in diff for o in d])
+    # Turn the segments into colors
+    color = colormap.orient2rgb(orientations)
+
+    return color

scripts/scil_tractogram_assign_custom_color.py

@@ -50,6 +50,7 @@
 import logging
 
 from dipy.io.streamline import save_tractogram
+from fury import colormap
 import nibabel as nib
 import numpy as np
 import matplotlib.pyplot as plt
@@ -65,8 +66,9 @@
 from scilpy.tractograms.dps_and_dpp_management import add_data_as_color_dpp
 from scilpy.tractograms.streamline_operations import (
     get_streamlines_as_linspaces, get_angles)
-from scilpy.viz.color import get_lookup_table
-from scilpy.viz.color import prepare_colorbar_figure
+from scilpy.viz.color import (
+    get_lookup_table, prepare_colorbar_figure, ambiant_occlusion,
+    generate_local_coloring)
 
 
 def _build_arg_parser():
@@ -105,12 +107,19 @@ def _build_arg_parser():
     p1.add_argument('--along_profile', action='store_true',
                     help='Color streamlines according to each point position'
                          'along its length.')
+    p1.add_argument('--local_orientation', action='store_true',
+                    help="Color streamlines according to the angle between "
+                         "each segment (in degree). \nAngles at first and "
+                         "last points are set to 0.")
     p1.add_argument('--local_angle', action='store_true',
                     help="Color streamlines according to the angle between "
                          "each segment (in degree). \nAngles at first and "
                          "last points are set to 0.")
 
     g2 = p.add_argument_group(title='Coloring options')
+    g2.add_argument('--ambiant_occlusion', nargs='?', const=4, type=int,
+                    help='Impact factor of the ambiant occlusion '
+                    'approximation. [%(default)s]')
     g2.add_argument('--colormap', default='jet',
                     help='Select the colormap for colored trk (dps/dpp) '
                     '[%(default)s].\nUse two Matplotlib named color separeted '
@@ -128,8 +137,7 @@ def _build_arg_parser():
     g2.add_argument('--max_cmap', type=float,
                     help='Set the maximum value of the colormap.')
     g2.add_argument('--log', action='store_true',
-                    help='Apply a base 10 logarithm for colored trk (dps/dpp).'
-                    )
+                    help='Apply a base 10 logarithm for colored trk (dps/dpp).')
     g2.add_argument('--LUT', metavar='FILE',
                     help='If the dps/dpp or anatomy contain integer labels, '
                          'the value will be substituted.\nIf the LUT has 20 '
@@ -148,6 +156,9 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
+    if args.local_orientation and args.out_colorbar:
+        parser.error("Cannot save a colorbar with local orientation coloring.")
+
     # Verifications
     assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
@@ -206,16 +217,26 @@ def main():
     elif args.along_profile:
         data = get_streamlines_as_linspaces(sft)
         data = np.hstack(data)
+    elif args.local_orientation:
+        data = generate_local_coloring(sft)
     else:  # args.local_angle:
         data = get_angles(sft, add_zeros=True)
         data = np.hstack(data)
 
     # Processing
-    sft, lbound, ubound = add_data_as_color_dpp(
-        sft, cmap, data, args.clip_outliers, args.min_range, args.max_range,
-        args.min_cmap, args.max_cmap, args.log, LUT)
+    if not args.local_orientation:
+        sft, lbound, ubound = add_data_as_color_dpp(
+            sft, cmap, data, args.clip_outliers, args.min_range, args.max_range,
+            args.min_cmap, args.max_cmap, args.log, LUT)
+    else:
+        sft.data_per_point['color'] = sft.streamlines.copy()
+        data *= 255
+        sft.data_per_point['color']._data = data.astype(np.uint8)
 
     # Saving
+    if args.ambiant_occlusion:
+        sft.data_per_point['color']._data = ambiant_occlusion(
+            sft, sft.data_per_point['color']._data, args.ambiant_occlusion)
     save_tractogram(sft, args.out_tractogram)
 
     if args.out_colorbar:

scripts/scil_tractogram_assign_uniform_color.py

@@ -30,7 +30,7 @@
                              add_overwrite_arg,
                              add_verbose_arg,
                              add_reference_arg, assert_headers_compatible)
-from scilpy.viz.color import format_hexadecimal_color_to_rgb
+from scilpy.viz.color import format_hexadecimal_color_to_rgb, ambiant_occlusion
 
 
 def _build_arg_parser():
@@ -41,6 +41,11 @@ def _build_arg_parser():
     p.add_argument('in_tractograms', nargs='+',
                    help='Input tractograms (.trk or .tck).')
 
+    p.add_argument('--ambiant_occlusion', nargs='?', const=4, type=int,
+                   help='Impact factor of the ambiant occlusion '
+                   'approximation.\n Use factor or 2. Decrease for '
+                   'lighter and increase for darker [%(default)s].')
+
     g1 = p.add_argument_group(title='Coloring Methods')
     p1 = g1.add_mutually_exclusive_group(required=True)
     p1.add_argument('--fill_color', metavar='str',
@@ -116,6 +121,10 @@ def main():
 
         sft = load_tractogram_with_reference(parser, args, filename)
 
+        sft.data_per_point['color'] = sft.streamlines.copy()
+        sft.data_per_point['color']._data = np.zeros(
+            (len(sft.streamlines._data), 3), dtype=np.uint8)
+
         if args.dict_colors:
             base, ext = os.path.splitext(filename)
             pos = base.index('__') if '__' in base else -2
@@ -132,11 +141,11 @@ def main():
 
         red, green, blue = format_hexadecimal_color_to_rgb(color)
 
-        tmp = [np.tile([red, green, blue], (len(i), 1))
-               for i in sft.streamlines]
-        sft.data_per_point['color'] = tmp
-
-        # Saving
+        colors = np.tile([red, green, blue], (len(sft.streamlines._data), 1))
+        if args.ambiant_occlusion:
+            colors = ambiant_occlusion(sft, colors,
+                                       factor=args.ambiant_occlusion)
+        sft.data_per_point['color']._data = colors
         save_tractogram(sft, out_filenames[i])
 
 

scripts/scil_viz_bundle.py

@@ -30,11 +30,12 @@
 import random
 
 from dipy.tracking.streamline import set_number_of_points
-from fury import window, actor, colormap
+from fury import window, actor
 
 from scilpy.io.utils import (assert_inputs_exist,
                              add_verbose_arg,
                              parser_color_type)
+from scilpy.viz.color import generate_local_coloring
 
 
 streamline_actor = {'tube': actor.streamtube,
@@ -185,15 +186,7 @@ def subsample(list_obj):
         elif args.uniform_coloring:  # Assign uniform coloring to streamlines
             color = tuple(np.asarray(args.uniform_coloring) / 255)
         elif args.local_coloring:  # Compute coloring from local orientations
-            # Compute segment orientation
-            diff = [np.diff(list(s), axis=0) for s in streamlines]
-            # Repeat first segment so that the number of segments matches
-            # the number of points
-            diff = [[d[0]] + list(d) for d in diff]
-            # Flatten the list of segments
-            orientations = np.asarray([o for d in diff for o in d])
-            # Turn the segments into colors
-            color = colormap.orient2rgb(orientations)
+            color = generate_local_coloring(streamlines)
         else:  # Streamline color will depend on the streamlines' endpoints.
             color = None
         # TODO: Coloring from a volume of local orientations