Add option for root point not equal to -1 in SWC files

include/morphio/enums.h

@@ -18,7 +18,8 @@ enum Option {
     NRN_ORDER = 1 << 3,            //!< Order of neurites will be the same as in NEURON simulator
     ALLOW_ROOT_BIFURCATIONS = 1 << 4,  //!< Bifurcations at first point are allowed
     ALLOW_SOMA_BIFURCATIONS = 1 << 5,  //!< Bifurcations in soma are allowed
-    ALLOW_MULTIPLE_SOMATA = 1 << 6     //!< Multiple somata are allowed
+    ALLOW_MULTIPLE_SOMATA = 1 << 6,    //!< Multiple somata are allowed
+    ALLOW_CUSTOM_ROOT_ID = 1 << 7      //!< Custom root points are allowed
 };
 
 /**
@@ -40,7 +41,8 @@ enum Warning {
     ZERO_DIAMETER,            //!< Zero section diameter
     ROOT_BIFURCATION,         //!< Bifurcation at root point
     SOMA_BIFURCATION,         //!< Bifurcation in soma
-    MULTIPLE_SOMATA           //!< Multiple somata
+    MULTIPLE_SOMATA,          //!< Multiple somata
+    CUSTOM_ROOT_ID            //!< Custom root ID
 };
 
 enum AnnotationType {

include/morphio/errorMessages.h

@@ -222,6 +222,8 @@ class ErrorMessages
     std::string WARNING_SOMA_BIFURCATION() const;
     /** Loading multiple somata */
     std::string WARNING_MULTIPLE_SOMATA() const;
+    /** Loading point with root ID no equal to -1 */
+    std::string WARNING_CUSTOM_ROOT_ID(const Sample& sample) const;
     /** Loading section with only one point */
     std::string WARNING_ROOT_BIFURCATION(const Sample& sample) const;
     /** Writing empty morphology warning message */

src/errorMessages.cpp

@@ -298,6 +298,13 @@ std::string ErrorMessages::WARNING_APPENDING_EMPTY_SECTION(
                     "Warning: appending empty section with id: " + std::to_string(section->id()));
 }
 
+std::string ErrorMessages::WARNING_CUSTOM_ROOT_ID(const Sample& sample) const {
+    return errorMsg(sample.lineNumber,
+                    ErrorLevel::WARNING,
+                    "Warning: root id changed from " + std::to_string(sample.parentId) +
+                        " to -1 for point with id: " + std::to_string(sample.id));
+}
+
 std::string ErrorMessages::WARNING_ROOT_BIFURCATION(const Sample& sample) const {
     return errorMsg(sample.lineNumber,
                     ErrorLevel::WARNING,

src/readers/morphologySWC.cpp

@@ -317,6 +317,24 @@ class SWCBuilder
     Property::Properties buildProperties(const std::string& contents, unsigned int options) {
         _readSamples(contents);
 
+        if (options & ALLOW_CUSTOM_ROOT_ID) {
+            for (auto& sample_pair : samples) {
+                auto& sample = sample_pair.second;
+                if (sample.parentId > -1 &&
+                    samples.count(static_cast<unsigned int>(sample.parentId)) == 0) {
+                    printError(Warning::CUSTOM_ROOT_ID, err.WARNING_CUSTOM_ROOT_ID(sample));
+                    // Remove the sample from the children
+                    children[sample.parentId].erase(std::remove(children[sample.parentId].begin(),
+                                                                children[sample.parentId].end(),
+                                                                sample.id),
+                                                    children[sample.parentId].end());
+                    // Update the sample and add it to the proper children
+                    sample.parentId = -1;
+                    children[-1].push_back(sample.id);
+                }
+            }
+        }
+
         for (const auto& sample_pair : samples) {
             const auto& sample = sample_pair.second;
             raiseIfNonConform(sample, options);

tests/data/edge_cases/bad_root_point.swc

@@ -0,0 +1,7 @@
+# The root point is not -1
+1 2 0 0 0 6 0
+2 2 0 0 1 6 1
+3 2 0 0 2 6 2
+4 2 1 0 0 6 0
+5 2 1 0 1 6 1
+6 2 1 0 2 6 2

tests/test_reader_options.cpp

@@ -146,3 +146,22 @@ TEST_CASE("multiple somata", "[loader_edge_cases]") {
                                            morphio::enums::Option::ALLOW_MULTIPLE_SOMATA));
     }
 }
+
+
+TEST_CASE("bad root point", "[loader_edge_cases]") {
+    std::vector<std::string> exts{"swc"};
+    for (auto&& ext : exts) {
+        SECTION("testing mutable morphology with " + ext + " extension") {
+            // By default, root points not equal to -1 are considered as errors in SWC files
+            REQUIRE_THROWS(morphio::mut::Morphology("data/edge_cases/bad_root_point." + ext));
+
+            // Bad root points can optionaly be loaded from SWC files
+            auto mutable_morph =
+                morphio::mut::Morphology("data/edge_cases/bad_root_point." + ext,
+                                         morphio::enums::Option::ALLOW_CUSTOM_ROOT_ID);
+
+            REQUIRE(mutable_morph.soma()->points().size() == 0);
+            REQUIRE(mutable_morph.rootSections().size() == 2);
+        }
+    }
+}