Merge pull request dipy#1502 from skoudoro/fix-doc-issue

[DOC] Fix doc generation

doc/examples/bundle_registration.py

@@ -67,6 +67,7 @@ def show_both_bundles(bundles, colors=None, show=True, fname=None):
 
 show_both_bundles([cb_subj1, cb_subj2],
                   colors=[window.colors.orange, window.colors.red],
+                  show=False,
                   fname='before_registration.png')
 
 """
@@ -78,6 +79,7 @@ def show_both_bundles(bundles, colors=None, show=True, fname=None):
 
 show_both_bundles([cb_subj1, cb_subj2_aligned],
                   colors=[window.colors.orange, window.colors.red],
+                  show=False,
                   fname='after_registration.png')
 
 """

doc/examples/linear_fascicle_evaluation.py

@@ -23,6 +23,7 @@
 import numpy as np
 import os.path as op
 import nibabel as nib
+from dipy.io.streamline import load_trk
 import dipy.core.optimize as opt
 if not op.exists('lr-superiorfrontal.trk'):
     from streamline_tools import *
@@ -39,8 +40,10 @@
     t1_data = t1.get_data()
     data = hardi_img.get_data()
 # Read the candidates from file in voxel space:
-candidate_sl = [s[0] for s in nib.trackvis.read('lr-superiorfrontal.trk',
-                                                  points_space='voxel')[0]]
+
+candidate_sl, hdr = load_trk('lr-superiorfrontal.trk')
+# candidate_sl = [s[0] for s in nib.trackvis.read('lr-superiorfrontal.trk',
+#                                                  points_space='voxel')[0]]
 
 """
 

doc/examples/sfm_tracking.py

@@ -118,7 +118,7 @@
 color = line_colors(streamlines)
 
 # Enables/disables interactive visualization
-interactive = True
+interactive = False
 
 """
 To speed up visualization, we will select a random sub-set of streamlines to

doc/examples/streamline_length.py

@@ -61,7 +61,7 @@ def simulated_bundles(no_streamlines=50, n_pts=100):
 ax.hist(lengths, color='burlywood')
 ax.set_xlabel('Length')
 ax.set_ylabel('Count')
-plt.show()
+# plt.show()
 plt.legend()
 plt.savefig('length_histogram.png')
 
@@ -132,7 +132,7 @@ def simulated_bundles(no_streamlines=50, n_pts=100):
 ren.add(bundle_actor3)
 
 ren.set_camera(position=(0, 0, 0), focal_point=(30, 0, 0))
-window.record(out_path='simulated_cosine_bundle.png', size=(900, 900))
+window.record(ren, out_path='simulated_cosine_bundle.png', size=(900, 900))
 if interactive:
     window.show(ren)
 
@@ -157,7 +157,7 @@ def simulated_bundles(no_streamlines=50, n_pts=100):
 ax.hist(n_pts_ds2, color='b', histtype='step', label='approx_polygon_track (0.25)')
 ax.set_xlabel('Number of points')
 ax.set_ylabel('Count')
-plt.show()
+# plt.show()
 plt.legend()
 plt.savefig('n_pts_histogram.png')
 
@@ -180,7 +180,7 @@ def simulated_bundles(no_streamlines=50, n_pts=100):
 ax.plot(lengths_downsampled2, color='b', label='approx_polygon_track (0.25)')
 ax.set_xlabel('Streamline ID')
 ax.set_ylabel('Length')
-plt.show()
+# plt.show()
 plt.legend()
 plt.savefig('lengths_plots.png')
 

doc/examples/streamline_tools.py

@@ -231,10 +231,10 @@
 # Move streamlines to "trackvis space"
 voxel_size = labels_img.header.get_zooms()
 trackvis_point_space = utils.affine_for_trackvis(voxel_size)
-lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track,
-                                   trackvis_point_space, input_space=affine)
+# lr_sf_trk = utils.move_streamlines(lr_superiorfrontal_track,
+#                                   trackvis_point_space, input_space=affine)
 
-lr_sf_trk = Streamlines(lr_sf_trk)
+lr_sf_trk = Streamlines(lr_superiorfrontal_track)
 
 # Save streamlines
 save_trk("lr-superiorfrontal.trk", lr_sf_trk, shape=shape, vox_size=voxel_size, affine=affine)
@@ -262,7 +262,7 @@
 as long as we specify the right coordinate system.
 """
 
-dm_trackvis = utils.density_map(lr_sf_trk, shape, affine=trackvis_point_space)
+dm_trackvis = utils.density_map(lr_sf_trk, shape, affine=np.eye(4))
 assert np.all(dm == dm_trackvis)
 
 """

doc/examples/valid_examples.txt

@@ -50,7 +50,7 @@
  tissue_classification.py
  bundle_registration.py
  tracking_tissue_classifier.py
- tracking_comparison_direction_getters.py
+ tracking_bootstrap_peaks.py
 # piesno.py
  viz_advanced.py
  viz_slice.py

doc/examples/viz_roi_contour.py

@@ -63,6 +63,7 @@
 a decimal between zero and one. Here, we set the color as blue/green with
 50% opacity.
 """
+
 surface_opacity = 0.5
 surface_color = [0, 1, 1]
 
@@ -82,6 +83,7 @@
 If you uncomment the following line, the rendering will pop up in an
 interactive window.
 """
+
 interactive = False
 if interactive:
     window.show(ren)

doc/examples/viz_ui.py

@@ -9,6 +9,7 @@
 First, a bunch of imports.
 
 """
+
 import os
 
 from dipy.data import read_viz_icons, fetch_viz_icons