Create a warning if the section type changes without a bifurcation

BlueBrain · Sep 11, 2024 · f58f391 · f58f391
1 parent 7bdb495
commit f58f391
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Showing 5 changed files with 28 additions and 4 deletions.
diff --git a/binds/python/bind_enums.cpp b/binds/python/bind_enums.cpp
@@ -97,7 +97,8 @@ void bind_enums(py::module& m) {
         .value("write_empty_morphology", morphio::enums::WRITE_EMPTY_MORPHOLOGY)
         .value("zero_diameter", morphio::enums::Warning::ZERO_DIAMETER)
         .value("soma_non_contour", morphio::enums::Warning::SOMA_NON_CONTOUR)
-        .value("soma_non_cylinder_or_point", morphio::enums::Warning::SOMA_NON_CYLINDER_OR_POINT);
+        .value("soma_non_cylinder_or_point", morphio::enums::Warning::SOMA_NON_CYLINDER_OR_POINT)
+        .value("type_changed_within_section", morphio::enums::Warning::SECTION_TYPE_CHANGED);
 
     py::enum_<morphio::enums::SomaType>(m, "SomaType", py::arithmetic())
         .value("SOMA_UNDEFINED", morphio::enums::SomaType::SOMA_UNDEFINED)

diff --git a/include/morphio/enums.h b/include/morphio/enums.h
@@ -42,6 +42,7 @@ enum Warning {
     ZERO_DIAMETER,               //!< Zero section diameter
     SOMA_NON_CONTOUR,            //!< Soma must be a contour for ASC and H5
     SOMA_NON_CYLINDER_OR_POINT,  //!< Soma must be stacked cylinders or a point
+    SECTION_TYPE_CHANGED,  //!< In SWC, the type changed within a section, not post bifurcation
 };
 
 enum AnnotationType {

diff --git a/include/morphio/warning_handling.h b/include/morphio/warning_handling.h
@@ -54,6 +54,22 @@ struct ZeroDiameter: public WarningMessage {
     uint64_t lineNumber;
 };
 
+struct SectionTypeChanged: public WarningMessage {
+    SectionTypeChanged(std::string uri_, uint64_t lineNumber_)
+        : WarningMessage(std::move(uri_))
+        , lineNumber(lineNumber_) {}
+    morphio::enums::Warning warning() const final {
+        return Warning::SECTION_TYPE_CHANGED;
+    }
+    morphio::readers::ErrorLevel errorLevel = morphio::readers::ErrorLevel::WARNING;
+    std::string msg() const final {
+        static const char* description = "Warning: Type changed within section, without bifurcation";
+        return "\n" + details::errorLink(uri, lineNumber, errorLevel) + description;
+    }
+
+    uint64_t lineNumber;
+};
+
 struct DisconnectedNeurite: public WarningMessage {
     DisconnectedNeurite(std::string uri_, uint64_t lineNumber_)
         : WarningMessage(std::move(uri_))

diff --git a/src/readers/morphologySWC.cpp b/src/readers/morphologySWC.cpp
@@ -467,8 +467,7 @@ class SWCBuilder
         const SWCSample* sample = &samples_.at(id);
 
         // create duplicate point if needed
-        if (!is_root && sample->point != start_point /*|| sample->diameter != start_diameter */) {
-        //if (!(is_root && sample->type == SECTION_SOMA) && sample->point != start_point /*|| sample->diameter != start_diameter */) {
+        if (!is_root && sample->point != start_point) {
             points.push_back(start_point);
             diameters.push_back(start_diameter);
         }
@@ -478,6 +477,8 @@ class SWCBuilder
         while (children_count == 1) {
             sample = &samples_.at(id);
             if(sample->type != samples_.at(children_.at(id)[0]).type){
+                warning_handler_->emit(std::make_unique<SectionTypeChanged>(
+                    path_, sample->lineNumber));
                 break;
             }
             points.push_back(sample->point);

diff --git a/tests/test_1_swc.py b/tests/test_1_swc.py
@@ -574,7 +574,8 @@ def test_multi_type_section():
                   3 7 0 0 3 0.5 2        # <- type 7
                   4 8 0 0 4 0.5 3        # <- type 8
                   5 9 0 0 5 0.5 4''')    # <- type 9
-    n = Morphology(contents, "swc")
+    warnings = morphio.WarningHandlerCollector()
+    n = Morphology(contents, "swc", warning_handler=warnings)
     assert_array_equal(n.soma.points, [[0, 4, 0]])
     assert_array_equal(n.soma.diameters, [6.0])
     assert len(n.root_sections) == 1
@@ -583,6 +584,10 @@ def test_multi_type_section():
                        np.array([[0, 0, 2], ]))
     assert len(n.sections) == 4
     assert_array_equal(n.section_offsets, [0, 1, 3, 5, 7])
+    warnings = [f.warning for f in warnings.get_all()]
+    assert len(warnings) == 3  # type 7, 8, and 9
+    for warning in warnings:
+        assert warning.warning() == Warning.type_changed_within_section
 
 
 def test_missing_parent():