checking if streamline points are outside image

radtract/parcellation.py

@@ -19,7 +19,7 @@
 import multiprocessing
 import sys
 from radtract.tractdensity import tract_envelope
-from radtract.utils import load_trk_streamlines, save_as_vtk_fib, save_trk_streamlines
+from radtract.utils import load_trk_streamlines, save_as_vtk_fib, save_trk_streamlines, is_inside
 from fury.colormap import distinguishable_colormap
 import joblib
 
@@ -124,19 +124,6 @@ def split_parcellation(parcellation: nib.Nifti1Image):
     return parcels
 
 
-def is_inside(index, image):
-    """
-    Checks if a given index is inside the image.
-    :param index:
-    :param image:
-    :return:
-    """
-    for i in range(3):
-        if index[i] < 0 or index[i] > image.shape[i] - 1:
-            return False
-    return True
-
-
 def resample_streamlines(streamlines: nib.streamlines.array_sequence.ArraySequence,
                          nb_points: int):
     """
@@ -550,10 +537,14 @@ def parcellate_tract(streamlines: nib.streamlines.array_sequence.ArraySequence,
                 for j in range(num_points):
                     p_cont = s[j]
                     p = np.round(p_cont).astype('int64')
-                    label = envelope_data[p[0], p[1], p[2]]
-                    color = lut_cmap[label-1]*255.0
-                    color = np.append(color, 255.0)
-                    colors.append(color)
+
+                    if is_inside(p, envelope_data):
+                        label = envelope_data[p[0], p[1], p[2]]
+                        color = lut_cmap[label-1]*255.0
+                        color = np.append(color, 255.0)
+                        colors.append(color)
+                    else:
+                        colors.append(np.array([0, 0, 0, 0]))
 
     elif streamline_point_parcels is not None:
         parcellation = streamline_point_parcels

radtract/tractdensity.py

@@ -6,7 +6,7 @@
 import numpy as np
 import vtk
 from dipy.tracking.streamline import transform_streamlines
-from radtract.utils import load_trk_streamlines
+from radtract.utils import load_trk_streamlines, is_inside
 from skimage.morphology import binary_closing
 import argparse
 import sys
@@ -145,10 +145,11 @@ def tract_density(streamlines: nib.streamlines.array_sequence.ArraySequence, # i
 
             segments = intersect_image(spacing, start_index, end_index, start_index_cont, end_index_cont)
             for seg in segments:
-                if binary:
-                    image_data[seg[0][0], seg[0][1], seg[0][2]] = 1
-                else:
-                    image_data[seg[0][0], seg[0][1], seg[0][2]] += seg[1]
+                if is_inside(seg[0], image_data):
+                    if binary:
+                        image_data[seg[0][0], seg[0][1], seg[0][2]] = 1
+                    else:
+                        image_data[seg[0][0], seg[0][1], seg[0][2]] += seg[1]
 
     # Perform morphological closing if binary and do_closing is True
     if binary and do_closing:

radtract/utils.py

@@ -7,6 +7,10 @@
 from fury.utils import lines_to_vtk_polydata, numpy_to_vtk_colors
 from dipy.io.stateful_tractogram import Space, StatefulTractogram
 import nibabel as nib
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.colors import ListedColormap
+from fury.colormap import distinguishable_colormap
 
 
 def save_trk_streamlines(streamlines: nib.streamlines.array_sequence.ArraySequence, filename: str, reference_image: nib.Nifti1Image):
@@ -38,6 +42,36 @@ def save_as_vtk_fib(streamlines, out_filename, colors=None):
     save_polydata(polydata=polydata, file_name=out_filename, binary=True)
 
 
+def plot_parcellation(nifti_file, mip_axis):
+    """
+    
+    """
+
+    image = nib.load(nifti_file)
+    data = image.get_fdata()
+    mip = np.max(data, axis=mip_axis)
+    nb_labels = len(np.unique(mip)) - 1
+    fury_cmap = distinguishable_colormap(nb_colors=nb_labels)
+    fury_cmap = [np.array([0, 0, 0, 1])] + fury_cmap
+    mpl_cmap = ListedColormap(fury_cmap)
+    plt.imshow(mip.T, cmap=mpl_cmap, origin='lower')
+    plt.show()
+
+
+def is_inside(index, image):
+    """
+    Checks if a given index is inside the image.
+    :param index:
+    :param image:
+    :return:
+    """
+    for i in range(3):
+        if index[i] < 0 or index[i] > image.shape[i] - 1:
+            return False
+    return True
+
+
+
 def main():
     pass