Make sure single point contours have nodes added to groups.

README.rst

@@ -32,17 +32,17 @@ When developing install the required packages for running the tests with::
 
 Then run the tests with::
 
-  nosetests
+  python -m unittest discover -s tests
 
 from the repository root directory.
 
 To see the coverage statistics for the package run::
 
-  nosetests --with-coverage --cover-package=mbfxml2ex
+  coverage run --source=mbfxml2ex -m unittest discover -s tests
 
 For a nice HTML rendering of the coverage statistics run::
 
-  nosetests --with-coverage --cover-package=mbfxml2ex --cover-html
+  coverage html -d cover
 
 To view the HTML coverage output::
 

pyproject.toml

@@ -28,7 +28,7 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-test = ["coverage", "nose", "packaging"]
+test = ["coverage", "packaging"]
 
 [project.scripts]
 mbfxml2exconverter = "mbfxml2ex.app:main"

src/mbfxml2ex/app.py

@@ -34,15 +34,15 @@ def read_xml(file_name):
         relocate_marker_elements = []
         for child in root:
             raw_tag = get_raw_tag(child)
-            if raw_tag in ["tree", "contour"] and child.find('.//{http://www.mbfbioscience.com/2007/neurolucida}marker'):
+            if raw_tag in ["tree", "contour"] and child.find('.//{http://www.mbfbioscience.com/2007/neurolucida}marker') is not None:
                 relocate_marker_elements.append({"owner": child, "ns": "http://www.mbfbioscience.com/2007/neurolucida"})
-            elif raw_tag in ["tree", "contour"] and child.find('.//{}marker'):
+            elif raw_tag in ["tree", "contour"] and child.find('.//{}marker') is not None:
                 relocate_marker_elements.append({"owner": child, "ns": ""})
 
         for marker_root_element in relocate_marker_elements:
             marker_element = marker_root_element["owner"].find(f'.//{{{marker_root_element["ns"]}}}marker')
             marker_element_parent = marker_root_element["owner"].find(f'.//{{{marker_root_element["ns"]}}}marker/..')
-            while marker_element:
+            while marker_element is not None:
                 marker_element_parent.remove(marker_element)
                 root.append(marker_element)
                 marker_element = marker_root_element["owner"].find(f'.//{{{marker_root_element["ns"]}}}marker')

src/mbfxml2ex/zinc.py

@@ -180,10 +180,12 @@ def load(region, data, options):
         merge_fields_with_nodes(field_module, node_identifiers, field_info)
         element_ids = create_elements(field_module, connectivity, field_names=['coordinates', 'radius', 'rgb'])
         create_group_elements(field_module, contour['name'], element_ids)
+        create_group_nodes(field_module, contour['name'], node_identifiers)
 
         text_properties = get_text_properties(contour['properties'])
         for text_property in text_properties:
             create_group_elements(field_module, text_property, element_ids)
+            create_group_nodes(field_module, text_property, node_identifiers)
 
     marker_groups = {}
     for marker in data.get_markers():

tests/resources/contour_with_only_one_point.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<mbf version="4.0" xmlns="https://www.mbfbioscience.com/filespecification"
+ xmlns:nl="https://www.mbfbioscience.com/filespecification"
+ appname="Vesselucida" appversion="2022.1.1" apprrid="SCR_016788" insrrid="SCR_004314">
+<contour name="orientation anterior" color="#A349A4" closed="false" shape="Contour">
+  <property name="GUID"><s>00002042</s></property>
+  <property name="FillDensity"><n>128</n></property>
+  <resolution>9.0</resolution>
+  <property name="TraceAssociation"><s>http://uri.interlex.org/base/ilx_0737829</s></property>
+  <property name="Set"><s>T6L</s></property>
+  <point x="6803.63" y="-11815.62" z="-66570.49" d="10.00"/>
+</contour>
+<contour name="orientation anterior" color="#A349A4" closed="false" shape="Contour">
+  <property name="GUID"><s>00002043</s></property>
+  <property name="FillDensity"><n>128</n></property>
+  <resolution>9.0</resolution>
+  <property name="TraceAssociation"><s>http://uri.interlex.org/base/ilx_0737829</s></property>
+  <property name="Set"><s>T6L</s></property>
+  <point x="5969.44" y="-16499.25" z="-68805.63" d="10.00"/>
+</contour>
+<contour name="orientation anterior" color="#A349A4" closed="false" shape="Contour">
+  <property name="GUID"><s>00002044</s></property>
+  <property name="FillDensity"><n>128</n></property>
+  <resolution>9.0</resolution>
+  <property name="TraceAssociation"><s>http://uri.interlex.org/base/ilx_0737829</s></property>
+  <property name="Set"><s>T6L</s></property>
+  <point x="2601.44" y="-17048.99" z="-14266.61" d="10.00"/>
+  <point x="2601.44" y="-17048.99" z="-14266.61" d="10.00"/>
+</contour>
+</mbf>

tests/test_mbfxml2ex.py

@@ -185,6 +185,19 @@ def test_contour_multiple_properties(self):
         self.assertTrue(_match_line_in_file(ex_file, re.compile(" ?Group name: inner submucosal nerve plexus")))
         self.assertTrue(_match_line_in_file(ex_file, re.compile(" ?Group name: Nerve fiber connecting inner submucosal nerve plexus and outer submucosal nerve plexus")))
 
+    def test_contour_with_one_point(self):
+        ex_file = _resource_path("contour_with_only_one_point.ex")
+        if os.path.exists(ex_file):
+            os.remove(ex_file)
+
+        xml_file = _resource_path("contour_with_only_one_point.xml")
+        neurolucida_data = read_xml(xml_file)
+        self.assertEqual(3, neurolucida_data.contours_count())
+        for i in range(3):
+            contour = neurolucida_data.get_contour(i)
+            self.assertEqual(1 if i != 2 else 2, len(contour['data']))
+        write_ex(ex_file, neurolucida_data)
+
 
 class NeurolucidaXmlReadTreesAndContoursWithMarkersTestCase(unittest.TestCase):