Fix another VTK issue, and minor test_pipeline tweak (#71)

tests/test_pipeline.sh

@@ -1,31 +1,34 @@
+#set -x # show commands as-run
+#set -e # fail on error
+
 test_out_dir=$1 # need to specify an output folder
 
 mkdir ${test_out_dir}
 
-# Step 1. tractography quality control:
+echo "#### Step 1. tractography quality control:"
 
 wm_quality_control_tractography.py test_data_small ${test_out_dir}/S1_QC
 
-# Step 2. groupwise tract registration:
+echo "#### Step 2. groupwise tract registration:"
 
 wm_register_multisubject_faster.py -l 20 -f 200 -j 2 -midsag_symmetric -mode affine test_data_small/ ${test_out_dir}/S2_GroupRegistration/
 
-# Step 3. atlas generation:
+echo "#### Step 3. atlas generation:"
 
 wm_cluster_atlas.py -l 20 -f 200 -nystrom_sample 250 -k 10 -j 2 ${test_out_dir}/S2_GroupRegistration/output_tractography/ ${test_out_dir}/S3_Atlas
 
-# Step 4. subject registration: 
+echo "#### Step 4. subject registration:"
 
 wm_register_to_atlas_new.py -l 40 -mode affine test_data_small/brain_0001.vtk ${test_out_dir}/S2_GroupRegistration/registration_atlas.vtk ${test_out_dir}/S4_RegisteredSubject
 
-# Step 5. subject clustering:
+echo "#### Step 5. subject clustering:"
 
 wm_cluster_from_atlas.py -j 4 -l 40  ${test_out_dir}/S4_RegisteredSubject/brain_0001/output_tractography/brain_0001_reg.vtk ${test_out_dir}/S3_Atlas/iteration_00002/initial_clusters/ ${test_out_dir}/S5_ClusteredSubject
 
-# Step 6. subject outlier removal:
+echo "#### Step 6. subject outlier removal:"
 
 wm_cluster_remove_outliers.py ${test_out_dir}/S5_ClusteredSubject/brain_0001_reg ${test_out_dir}/S3_Atlas/iteration_00002/initial_clusters/ ${test_out_dir}/S6_OutlierRemovedSubject
 
-# Step 7. subject hemisphere separation:
+echo "#### Step 7. subject hemisphere separation:"
 
-wm_separate_clusters_by_hemisphere.py -pthresh 0.6 -atlasMRML ${test_out_dir}/S3_Atlas/iteration_00002/initial_clusters/clustered_tracts_display_100_percent.mrml ${test_out_dir}/S6_OutlierRemovedSubject/brain_0001_reg_outlier_removed ${test_out_dir}/S7_HemisphereSeparatedSubject
+wm_separate_clusters_by_hemisphere.py -pthresh 0.6 -atlasMRML ${test_out_dir}/S3_Atlas/iteration_00002/initial_clusters/clustered_tracts_display_100_percent.mrml ${test_out_dir}/S6_OutlierRemovedSubject/brain_0001_reg_outlier_removed ${test_out_dir}/S7_HemisphereSeparatedSubject

whitematteranalysis/cluster.py

@@ -825,7 +825,10 @@ def _format_output_polydata(output_polydata, cluster_idx, color, embed, estimate
         embed_colors.InsertNextTuple3(
             color[lidx, 0], color[lidx, 1], color[lidx, 2])
         cluster_colors.InsertNextTuple1(int(cluster_idx[lidx]))
-        embed_data.InsertNextTupleValue(embed[lidx, :])
+        if (vtk.vtkVersion().GetVTKMajorVersion() >= 7.1):
+          embed_data.InsertNextTypedTuple(embed[lidx, :])
+        else:
+          embed_data.InsertNextTupleValue(embed[lidx, :])
         row_sum_data.InsertNextTuple1(float(estimated_row_sum[lidx]))
         col_sum_data.InsertNextTuple1(float(computed_column_sum[lidx]))
 
@@ -1229,4 +1232,4 @@ def mask_all_clusters(inpd, cluster_numbers_s, number_of_clusters, color=None, p
         if verbose:
             print "<cluster.py> Cluster", c_idx," have fibers ", outpd_list[c_idx].GetNumberOfLines(), "/", inpd.GetNumberOfLines(), ", points ", outpd_list[c_idx].GetNumberOfPoints()
 
-    return outpd_list
+    return outpd_list