Merge pull request #131 from jhlegarreta/FixHemisphereLocationArrayNa…

…meTpo

STYLE: Fix typo in hemisphere location array name

bin/wm_assess_cluster_location_by_hemisphere.py

@@ -17,11 +17,11 @@
 import shutil
 import vtk
 import glob
+import warnings
 
 import whitematteranalysis as wma
 
 
-
 def _build_arg_parser():
 
     parser = argparse.ArgumentParser(
@@ -77,11 +77,17 @@ def write_mask_location_to_vtk(inpd, mask_location):
             for idx in point_data_array_indices:
                 array = inpointdata.GetArray(idx)
                 if array.GetName() == 'HemisphereLocataion':
+                    warnings.warn(
+                        wma.utils.hemisphere_loc_name_typo_warn_msg,
+                        PendingDeprecationWarning)
                     print('  -- HemisphereLocataion is in the input data: skip updating the vtk file.')
                     return inpd
+                elif array.GetName() == 'HemisphereLocation':
+                    print('  -- HemisphereLocation is in the input data: skip updating the vtk file.')
+                    return inpd
 
         vtk_array = vtk.vtkDoubleArray()
-        vtk_array.SetName('HemisphereLocataion')
+        vtk_array.SetName('HemisphereLocation')
 
         inpd.GetLines().InitTraversal()
         for lidx in range(0, inpd.GetNumberOfLines()):
@@ -96,7 +102,19 @@ def write_mask_location_to_vtk(inpd, mask_location):
         return inpd
 
     def read_mask_location_from_vtk(inpd):
-
+
+        def _read_location(_inpd):
+            _flag_location = True
+
+            _inpd.GetLines().InitTraversal()
+            for lidx in range(0, _inpd.GetNumberOfLines()):
+                ptids = vtk.vtkIdList()
+                _inpd.GetLines().GetNextCell(ptids)
+                for pidx in range(0, ptids.GetNumberOfIds()):
+                    mask_location[lidx] = array.GetTuple(ptids.GetId(pidx))[0]
+
+            return _flag_location
+
         mask_location = numpy.zeros(pd.GetNumberOfLines())
 
         inpointdata = inpd.GetPointData()
@@ -106,17 +124,15 @@ def read_mask_location_from_vtk(inpd):
             for idx in point_data_array_indices:
                 array = inpointdata.GetArray(idx)
                 if array.GetName() == 'HemisphereLocataion':
-                    flag_location = True
-
-                    inpd.GetLines().InitTraversal()
-                    for lidx in range(0, inpd.GetNumberOfLines()):
-                        ptids = vtk.vtkIdList()
-                        inpd.GetLines().GetNextCell(ptids)
-                        for pidx in range(0, ptids.GetNumberOfIds()):
-                            mask_location[lidx] = array.GetTuple(ptids.GetId(pidx))[0]
-
+                    warnings.warn(
+                        wma.utils.hemisphere_loc_name_typo_warn_msg,
+                        PendingDeprecationWarning)
+                    flag_location = _read_location(inpd)
                     break
-
+                elif array.GetName() == 'HemisphereLocation':
+                    flag_location = _read_location(inpd)
+                    break
+
         return flag_location, mask_location
 
     parser = _build_arg_parser()
@@ -214,7 +230,7 @@ def read_mask_location_from_vtk(inpd):
 
         flag_location, mask_location = read_mask_location_from_vtk(pd)
 
-         # If HemisphereLocataion is not defined in the input vtk file, the location of each fiber in the cluster is decided.
+         # If HemisphereLocation is not defined in the input vtk file, the location of each fiber in the cluster is decided.
         if not flag_location:
             if clusterLocationFile is None:
                 # internal representation for fast similarity computation

bin/wm_separate_clusters_by_hemisphere.py

@@ -17,6 +17,7 @@
 import shutil
 import vtk
 import glob
+import warnings
 
 import whitematteranalysis as wma
 
@@ -88,11 +89,17 @@ def write_mask_location_to_vtk(inpd, mask_location):
             for idx in point_data_array_indices:
                 array = inpointdata.GetArray(idx)
                 if array.GetName() == 'HemisphereLocataion':
+                    warnings.warn(
+                        wma.utils.hemisphere_loc_name_typo_warn_msg,
+                        PendingDeprecationWarning)
                     print('  -- HemisphereLocataion is in the input data: skip updating the vtk file.')
                     return inpd
+                elif array.GetName() == 'HemisphereLocation':
+                    print('  -- HemisphereLocation is in the input data: skip updating the vtk file.')
+                    return inpd
 
         vtk_array = vtk.vtkDoubleArray()
-        vtk_array.SetName('HemisphereLocataion')
+        vtk_array.SetName('HemisphereLocation')
 
         inpd.GetLines().InitTraversal()
         for lidx in range(0, inpd.GetNumberOfLines()):
@@ -107,7 +114,19 @@ def write_mask_location_to_vtk(inpd, mask_location):
         return inpd
 
     def read_mask_location_from_vtk(inpd):
-
+
+        def _read_location(_inpd):
+            _flag_location = True
+
+            _inpd.GetLines().InitTraversal()
+            for lidx in range(0, _inpd.GetNumberOfLines()):
+                ptids = vtk.vtkIdList()
+                _inpd.GetLines().GetNextCell(ptids)
+                for pidx in range(0, ptids.GetNumberOfIds()):
+                    mask_location[lidx] = array.GetTuple(ptids.GetId(pidx))[0]
+
+            return _flag_location
+
         mask_location = numpy.zeros(pd.GetNumberOfLines())
 
         inpointdata = inpd.GetPointData()
@@ -117,15 +136,13 @@ def read_mask_location_from_vtk(inpd):
             for idx in point_data_array_indices:
                 array = inpointdata.GetArray(idx)
                 if array.GetName() == 'HemisphereLocataion':
-                    flag_location = True
-
-                    inpd.GetLines().InitTraversal()
-                    for lidx in range(0, inpd.GetNumberOfLines()):
-                        ptids = vtk.vtkIdList()
-                        inpd.GetLines().GetNextCell(ptids)
-                        for pidx in range(0, ptids.GetNumberOfIds()):
-                            mask_location[lidx] = array.GetTuple(ptids.GetId(pidx))[0]
-
+                    warnings.warn(
+                        wma.utils.hemisphere_loc_name_typo_warn_msg,
+                        PendingDeprecationWarning)
+                    flag_location = _read_location(inpd)
+                    break
+                elif array.GetName() == 'HemisphereLocation':
+                    flag_location = _read_location(inpd)
                     break
 
         return flag_location, mask_location
@@ -160,7 +177,7 @@ def read_mask_location_from_vtk(inpd):
 
         flag_location, mask_location = read_mask_location_from_vtk(pd)
 
-         # If HemisphereLocataion is not defined in the input vtk file, the location of each fiber in the cluster is decided.
+         # If HemisphereLocation is not defined in the input vtk file, the location of each fiber in the cluster is decided.
         if not flag_location:
             print("Error:", fname, "has no hemisphere location information")
             exit()

utilities/tests/test_wm_fix_hemisphere_loc_name_in_tractogram.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+def test_help_option(script_runner):
+    ret = script_runner.run(
+        ["wm_fix_hemisphere_loc_name_in_tractogram.py", "--help"])
+    assert ret.success

utilities/wm_fix_hemisphere_loc_name_in_tractogram.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Fix hemisphere location property name in tractogram: older versions of WMA
+contain a typo in the hemisphere location VTK array scalar property. Change
+`HemisphereLocataion` to `HemisphereLocation`.
+"""
+
+import os
+import argparse
+
+import vtk
+
+import whitematteranalysis as wma
+
+
+def fix_hemisphere_location_property_name(polydata):
+
+    out_polydata = vtk.vtkPolyData()
+    point_data = polydata.GetPointData()
+
+    if point_data.GetNumberOfArrays():
+        point_data_array_indices = list(range(point_data.GetNumberOfArrays()))
+
+        for idx in point_data_array_indices:
+            array = point_data.GetArray(idx)
+
+            if array.GetName() == "HemisphereLocataion":
+                print("HemisphereLocataion is in the input data: re-writing to HemisphereLocation.")
+            elif array.GetName() == "HemisphereLocation":
+                print("HemisphereLocation is in the input data: no re-write needed.")
+            else:
+                print("Hemisphere location property is not in the input data: no re-write needed.")
+
+    vtk_array = vtk.vtkDoubleArray()
+    vtk_array.SetName("HemisphereLocation")
+
+    polydata.GetLines().InitTraversal()
+
+    for l_idx in range(polydata.GetNumberOfLines()):
+        point_ids = vtk.vtkIdList()
+        polydata.GetLines().GetNextCell(point_ids)
+
+        for p_idx in range(point_ids.GetNumberOfIds()):
+            vtk_array.InsertNextTuple1(l_idx)
+
+    out_polydata.GetPointData().AddArray(vtk_array)
+
+    return out_polydata
+
+
+def _build_arg_parser():
+
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter
+    )
+    parser.add_argument('in_fname', help='Input filename (.*vtk|.*vtp).')
+    parser.add_argument('out_fname', help='Output filename (.*vtk|.*vtp).')
+
+    return parser
+
+
+def _parse_args(parser):
+
+    args = parser.parse_args()
+    return args
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
+
+    out_fname = args.outputFilename
+    if os.path.exists(out_fname):
+        msg = f"Output file {out_fname} exists. Remove or rename the output file."
+        parser.error(msg)
+
+    print(f"{os.path.basename(__file__)}. Starting.")
+    print("")
+    print("=====input filename======\n", args.in_fname)
+    print("=====output filename=====\n", args.out_fname)
+    print("==========================")
+
+    polydata = wma.io.read_polydata(args.in_fname)
+    out_polydata = fix_hemisphere_location_property_name(polydata)
+    wma.io.write_polydata(out_polydata, args.out_fname)
+
+
+if __name__ == "__main__":
+    main()

whitematteranalysis/__init__.py

@@ -1,3 +1,3 @@
 print("Importing whitematteranalysis package.")
-from . import io, similarity, fibers, filter, laterality, render, cluster, relative_distance, mrml, congeal_multisubject, register_two_subjects, register_two_subjects_nonrigid, register_two_subjects_nonrigid_bsplines, congeal_to_atlas, tract_measurement
+from . import io, similarity, fibers, filter, laterality, render, cluster, relative_distance, mrml, congeal_multisubject, register_two_subjects, register_two_subjects_nonrigid, register_two_subjects_nonrigid_bsplines, congeal_to_atlas, tract_measurement, utils
 

whitematteranalysis/utils.py

@@ -0,0 +1,8 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+hemisphere_loc_name_typo_warn_msg = (
+    'Hemisphere location scalar is described by the HemisphereLocataion name, '
+    'which contains a typo. Reading files that contain the typo will not be '
+    'supported in future releases. Use whitematteranalysis to re-write such '
+    'files.')