Add morphio.mut.Morphology.sanitize() python binding (#185)

As requested in #184
BlueBrain · Apr 23, 2020 · 83d1fb7 · 83d1fb7
1 parent 9e13ca3
commit 83d1fb7
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Showing 5 changed files with 45 additions and 2 deletions.
diff --git a/.github/workflows/clang_format_check.yaml b/.github/workflows/clang_format_check.yaml
@@ -9,6 +9,8 @@ jobs:
     steps:
         - name: Fetch repository
           uses: actions/checkout@v1
+        - name: Install apt
+          run: sudo apt-get update -y
         - name: Install packages
           run: sudo apt-get install python3-venv
         - name: check_clang_format

diff --git a/binds/python/bind_mutable.cpp b/binds/python/bind_mutable.cpp
@@ -127,6 +127,12 @@ void bind_mutable_module(py::module& m) {
 
         .def_property_readonly("version", &morphio::mut::Morphology::version, "Returns the version")
 
+        .def("sanitize",
+             static_cast<void (morphio::mut::Morphology::*) ()>(
+                 &morphio::mut::Morphology::sanitize),
+             "Fixes the morphology single child sections and issues warnings"
+             "if the section starts and ends are inconsistent")
+
         .def(
             "write",
             [](morphio::mut::Morphology* morph, py::object arg) { morph->write(py::str(arg)); },
@@ -316,6 +322,7 @@ void bind_mutable_module(py::module& m) {
              "immutable_section"_a,
              "recursive"_a = false);
 
+
     py::class_<morphio::mut::Section, std::shared_ptr<morphio::mut::Section>>(m, "Section")
         .def("__str__",
              [](const morphio::mut::Section& section) {

diff --git a/include/morphio/mut/morphology.h b/include/morphio/mut/morphology.h
@@ -201,7 +201,8 @@ class Morphology
 
 
     /**
-       Check that the neuron is valid, issue warning and fix unifurcations
+       Fixes the morphology single child sections and issues warnings
+       if the section starts and ends are inconsistent
      **/
     void sanitize();
     void sanitize(const morphio::readers::DebugInfo& debugInfo);

diff --git a/tests/test_0_API.py b/tests/test_0_API.py
@@ -32,7 +32,7 @@ def methods(cls):
 
     only_in_immut = {'section_types', 'diameters', 'perimeters', 'points', 'section_offsets',
                      'as_mutable'}
-    only_in_mut = {'write', 'append_root_section', 'delete_section', 'build_read_only',
+    only_in_mut = {'sanitize', 'write', 'append_root_section', 'delete_section', 'build_read_only',
                    'as_immutable'}
     assert_equal(methods(morphio.Morphology) - only_in_immut,
                  methods(morphio.mut.Morphology) - only_in_mut)

diff --git a/tests/test_5_mut.py b/tests/test_5_mut.py
@@ -429,3 +429,36 @@ def test_endoplasmic_reticulum():
     assert_equal(reticulum.volumes, [2, 2])
     assert_equal(reticulum.surface_areas, [3, 3])
     assert_equal(reticulum.filament_counts, [4, 4])
+
+
+def test_sanitize():
+    m = Morphology()
+    section = m.append_root_section(PointLevel([[1, 0, 0],
+                                                [2, 0, 0]], [2, 2], [20, 20]),
+                                    SectionType.axon)
+    section.append_section(PointLevel([[2, 0, 0],
+                                       [3, 0, 0]], [2, 2], [20, 20]))
+    with captured_output() as (_, err):
+        with ostream_redirect(stdout=True, stderr=True):
+            m.sanitize()
+            assert_equal(len(list(m.iter())), 1)
+            assert_equal(err.getvalue().strip(),
+                         'Warning: section 1 is the only child of section: 0\nIt will be merged '
+                         'with the parent section')
+
+    # Checking that sanitize() issues a warning on missing duplicate
+    m = Morphology()
+    section = m.append_root_section(PointLevel([[1, 0, 0],
+                                                [2, 0, 0]], [2, 2], [20, 20]),
+                                    SectionType.axon)
+    section.append_section(PointLevel([[2, 0, 0],
+                                       [3, 0, 0]], [2, 2], [20, 20]))
+    with captured_output() as (_, err):
+        with ostream_redirect():
+            section.append_section(PointLevel([[2, 1, 0],
+                                               [2, 0, 0]], [2, 2], [20, 20]))
+    with captured_output() as (_, err):
+        with ostream_redirect():
+            m.sanitize()
+            assert_equal(err.getvalue().strip(),
+                         'Warning: while appending section: 2 to parent: 0\nThe section first point should be parent section last point: \n        : X Y Z Diameter\nparent last point :[2.000000, 0.000000, 0.000000, 2.000000]\nchild first point :[2.000000, 1.000000, 0.000000, 2.000000]')