Merge pull request #513 from 36000/plotly_viz_fixes

FIX: Plotly viz bug fixes, and update to custom bundles

AFQ/viz/fury_backend.py

@@ -47,6 +47,9 @@ def visualize_bundles(sft, affine=None, n_points=None, bundle_dict=None,
     sft : Stateful Tractogram, str
         A Stateful Tractogram containing streamline information
         or a path to a trk file
+        In order to visualize individual bundles, the Stateful Tractogram
+        must contain a bundle key in it's data_per_streamline which is a list
+        of bundle `'uid'`.
 
     affine : ndarray, optional
        An affine transformation to apply to the streamlines before
@@ -69,7 +72,8 @@ def visualize_bundles(sft, affine=None, n_points=None, bundle_dict=None,
     colors : dict or list
         If this is a dict, keys are bundle names and values are RGB tuples.
         If this is a list, each item is an RGB tuple. Defaults to a list
-        with Tableau 20 RGB values
+        with Tableau 20 RGB values if bundle_dict is None, or dict from
+        bundles to Tableau 20 RGB values if bundle_dict is not None.
 
     background : tuple, optional
         RGB values for the background. Default: (1, 1, 1), which is white

AFQ/viz/plotly_backend.py

@@ -152,7 +152,10 @@ def visualize_bundles(sft, affine=None, n_points=None, bundle_dict=None,
     ----------
     sft : Stateful Tractogram, str
         A Stateful Tractogram containing streamline information
-        or a path to a trk file
+        or a path to a trk file.
+        In order to visualize individual bundles, the Stateful Tractogram
+        must contain a bundle key in it's data_per_streamline which is a list
+        of bundle `'uid'`.
 
     affine : ndarray, optional
        An affine transformation to apply to the streamlines before
@@ -175,7 +178,8 @@ def visualize_bundles(sft, affine=None, n_points=None, bundle_dict=None,
     colors : dict or list
         If this is a dict, keys are bundle names and values are RGB tuples.
         If this is a list, each item is an RGB tuple. Defaults to a list
-        with Tableau 20 RGB values
+        with Tableau 20 RGB values if bundle_dict is None, or dict from
+        bundles to Tableau 20 RGB values if bundle_dict is not None.
 
     background : tuple, optional
         RGB values for the background. Default: (1, 1, 1), which is white

AFQ/viz/utils.py

@@ -75,6 +75,41 @@
     {'dti_md': 0.001}
 
 
+def gen_color_dict(bundles):
+    """
+    Helper function.
+    Generate a color dict given a list of bundles.
+    """
+    def incr_color_idx(color_idx):
+        return (color_idx + 1) % 20
+    custom_color_dict = {}
+    color_idx = 0
+    for bundle in bundles:
+        if bundle not in custom_color_dict.keys():
+            if bundle in COLOR_DICT.keys():
+                custom_color_dict[bundle] = COLOR_DICT[bundle]
+            else:
+                other_bundle = list(bundle)
+                if bundle[-2:] == '_L':
+                    other_bundle[-2:] = '_R'
+                elif bundle[-2:] == '_R':
+                    other_bundle[-2:] = '_L'
+                other_bundle = str(other_bundle)
+
+                if other_bundle == bundle:  # lone bundle
+                    custom_color_dict[bundle] = tableau_20_sns[color_idx]
+                    color_idx = incr_color_idx(color_idx)
+                else:  # right left pair
+                    if color_idx % 2 != 0:
+                        color_idx = incr_color_idx(color_idx)
+                    custom_color_dict[bundle] =\
+                        tableau_20_sns[color_idx]
+                    custom_color_dict[other_bundle] =\
+                        tableau_20_sns[color_idx + 1]
+                    color_idx = incr_color_idx(incr_color_idx(color_idx))
+    return custom_color_dict
+
+
 def viz_import_msg_error(module):
     """Alerts user to install the appropriate viz module """
     msg = f"To use {module.upper()} visualizations in pyAFQ, you will need "
@@ -182,8 +217,11 @@ def tract_generator(sft, affine, bundle, bundle_dict, colors, n_points,
     -------
     Statefule Tractogram streamlines, RGB numpy array, str
     """
-    bundle_dict = bundle_dict.copy()
-    bundle_dict.pop('whole_brain', None)
+    if colors is None:
+        if bundle_dict is None:
+            colors = tableau_20_sns
+        else:
+            colors = gen_color_dict(bundle_dict.keys())
 
     if isinstance(sft, str):
         viz_logger.info("Loading Stateful Tractogram...")
@@ -199,18 +237,18 @@ def tract_generator(sft, affine, bundle, bundle_dict, colors, n_points,
     streamlines = sft.streamlines
     viz_logger.info("Generating colorful lines from tractography...")
 
-    if colors is None:
-        # Use the color dict provided
-        colors = COLOR_DICT
-
     if list(sft.data_per_streamline.keys()) == []:
         # There are no bundles in here:
         if n_points is not None:
             streamlines = dps.set_number_of_points(streamlines, n_points)
-        yield streamlines, [0.5, 0.5, 0.5], "all_bundles"
+        yield streamlines, colors[0], "all_bundles"
 
     else:
         # There are bundles:
+        if bundle_dict is not None:
+            bundle_dict = bundle_dict.copy()
+            bundle_dict.pop('whole_brain', None)
+
         if bundle is None:
             # No selection: visualize all of them:
 
@@ -674,6 +712,7 @@ def __init__(self, out_folder, csv_fnames, names, is_mats=False,
             self.bundles.sort()
         else:
             self.bundles = bundles
+        self.color_dict = gen_color_dict(self.bundles)
 
     def _threshold_scalar(self, bound, threshold, val):
         """
@@ -842,7 +881,7 @@ def tract_profiles(self, names=None, scalar="dti_fa",
                     {
                         "dashes": [(2**i, 2**i)],
                         "hue": "tractID",
-                        "palette": [COLOR_DICT[bundle]]},
+                        "palette": [self.color_dict[bundle]]},
                     plot_subject_lines=plot_subject_lines)
                 if j == 0:
                     line = Line2D(
@@ -938,7 +977,7 @@ def contrast_index(self, names=None, scalar="dti_fa",
                 [bundle], names, scalar)
             ba.plot_line(
                 bundle, "nodeID", "diff", ci_df, "C.I. * 2", (-1, 1),
-                n_boot, 1.0, {"color": COLOR_DICT[bundle]},
+                n_boot, 1.0, {"color": self.color_dict[bundle]},
                 plot_subject_lines=plot_subject_lines)
             ci_all_df[j] = ci_df["diff"]
         ba.fig.legend([scalar], loc='center', fontsize=medium_font)
@@ -1004,7 +1043,7 @@ def lateral_contrast_index(self, name, scalar="dti_fa",
                 [bundle, other_bundle], [name], scalar)
             ba.plot_line(
                 bundle, "nodeID", "diff", ci_df, "C.I. * 2", (-1, 1),
-                n_boot, 1.0, {"color": COLOR_DICT[bundle]},
+                n_boot, 1.0, {"color": self.color_dict[bundle]},
                 plot_subject_lines=plot_subject_lines)
 
         ba.fig.legend([scalar], loc='center', fontsize=medium_font)