morphio 2.5.0__tar.gz → 2.5.2__tar.gz

{MorphIO-2.5.0 → MorphIO-2.5.2}/CMakeLists.txt

@@ -6,7 +6,7 @@ set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 set(CMAKE_VERBOSE_MAKEFILE ON)
 
 option(BUILD_BINDINGS "Build the python bindings" ON)
-option(${PROJECT_NAME}_CXX_WARNINGS "Compile C++ with warnings" ON)
+option(MorphIO_CXX_WARNINGS "Compile C++ with warnings" ON)
 option(EXTERNAL_HIGHFIVE "Use HighFive from external source" OFF)
 option(MORPHIO_USE_DOUBLE "Use doubles instead of floats" OFF)
 

{MorphIO-2.5.0 → MorphIO-2.5.2}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.0
+Version: 2.5.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -495,6 +495,25 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         # Specification
         See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
         
+        
+        # H5v2
+        
+        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them with:
+        
+        ```bash
+        pip install morphio==2.5.1 morph-tool==2.3.0
+        ```
+        
+        and then:
+        ```python
+        # single file, OUTPUT must end with `.h5`
+        morph-tool convert file INPUTFILE OUTPUT
+        
+        # bulk conversion
+        morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+        ```
+        
         # Contributing
         If you want to improve the project or you see any issue, every contribution is welcome.
         Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.0 → MorphIO-2.5.2}/MorphIO.egg-info/SOURCES.txt

@@ -144,7 +144,11 @@ tests/data/nested_single_children.asc
 tests/data/neurite_wrong_root_point.swc
 tests/data/nrn-order-already-sorted.h5
 tests/data/nrn_ordering.swc
+tests/data/pia.asc
 tests/data/reversed_NRN_neurite_order.swc
+tests/data/sections-block.asc
+tests/data/simple-with-font.asc
+tests/data/simple-with-image-coord.asc
 tests/data/simple.asc
 tests/data/simple.swc
 tests/data/simple2.asc
@@ -167,4 +171,5 @@ tests/data/h5/v1/simple-negative-section-type.h5
 tests/data/h5/v1/simple.h5
 tests/data/h5/v1/soma_no_neurites.h5
 tests/data/h5/v1/two_child_unmerged.h5
-tests/data/h5/v2/Neuron.h5
+tests/data/h5/v2/Neuron.h5
+tests/data/h5/v2/no-metadata.h5

{MorphIO-2.5.0 → MorphIO-2.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.0
+Version: 2.5.2
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -495,6 +495,25 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         # Specification
         See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
         
+        
+        # H5v2
+        
+        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them with:
+        
+        ```bash
+        pip install morphio==2.5.1 morph-tool==2.3.0
+        ```
+        
+        and then:
+        ```python
+        # single file, OUTPUT must end with `.h5`
+        morph-tool convert file INPUTFILE OUTPUT
+        
+        # bulk conversion
+        morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+        ```
+        
         # Contributing
         If you want to improve the project or you see any issue, every contribution is welcome.
         Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.0 → MorphIO-2.5.2}/README.md

@@ -488,6 +488,25 @@ morphio.set_maximum_warnings(0)
 # Specification
 See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
 
+
+# H5v2
+
+Starting at version 2.5.2, the file format `h5v2` is no longer supported.
+If you have morphologies in this format, you can convert them with:
+
+```bash
+pip install morphio==2.5.1 morph-tool==2.3.0
+```
+
+and then:
+```python
+# single file, OUTPUT must end with `.h5`
+morph-tool convert file INPUTFILE OUTPUT
+
+# bulk conversion
+morph-tool convert folder -ext h5 INPUTDIR OUTPUTDIR
+```
+
 # Contributing
 If you want to improve the project or you see any issue, every contribution is welcome.
 Please check the [contribution guidelines](CONTRIBUTING.md) for more information.

{MorphIO-2.5.0 → MorphIO-2.5.2}/binds/python/bind_immutable.cpp

@@ -46,6 +46,9 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly("annotations",
                                &morphio::Morphology::annotations,
                                "Returns a list of annotations")
+        .def_property_readonly("markers",
+                               &morphio::Morphology::markers,
+                               "Returns the list of NeuroLucida markers")
         .def_property_readonly("endoplasmic_reticulum",
                                &morphio::Morphology::endoplasmicReticulum,
                                "Returns the endoplasmic reticulum object")

{MorphIO-2.5.0 → MorphIO-2.5.2}/binds/python/bind_misc.cpp

@@ -252,6 +252,21 @@ void bind_misc(py::module& m) {
             [](morphio::Property::Annotation* a) { return a->_points._perimeters; },
             "Returns the list of perimeters of annotated points");
 
+    py::class_<morphio::Property::Marker>(m,
+                                          "Marker",
+                                          "Container class for NeuroLucida extra Markers ")
+        .def_property_readonly(
+            "label",
+            [](morphio::Property::Marker* marker) { return marker->_label; },
+            "Returns the label")
+        .def_property_readonly(
+            "points",
+            [](morphio::Property::Marker* marker) { return marker->_pointLevel._points; },
+            "Returns the list of coordinates of the marker points")
+        .def_property_readonly(
+            "diameters",
+            [](morphio::Property::Marker* marker) { return marker->_pointLevel._diameters; },
+            "Returns the list of diameters of the marker points");
 
     py::class_<morphio::Property::MitochondriaPointLevel>(
         m,

{MorphIO-2.5.0 → MorphIO-2.5.2}/binds/python/bind_mutable.cpp

@@ -71,6 +71,9 @@ void bind_mutable_module(py::module& m) {
         .def_property_readonly("annotations",
                                &morphio::mut::Morphology::annotations,
                                "Returns a list of annotations")
+        .def_property_readonly("markers",
+                               &morphio::mut::Morphology::markers,
+                               "Returns the list of NeuroLucida markers")
         .def("section",
              &morphio::mut::Morphology::section,
              "Returns the section with the given id\n\n"

{MorphIO-2.5.0 → MorphIO-2.5.2}/include/morphio/morphology.h

@@ -61,6 +61,11 @@ class Morphology
      **/
     const std::vector<Property::Annotation>& annotations() const;
 
+    /**
+     * Return the markers
+     **/
+    const std::vector<Property::Marker>& markers() const;
+
     /**
      * Return a vector of all root sections
      * (sections whose parent ID are -1)

{MorphIO-2.5.0 → MorphIO-2.5.2}/include/morphio/mut/morphology.h

@@ -102,6 +102,11 @@ class Morphology
      **/
     inline const std::vector<Property::Annotation>& annotations() const noexcept;
 
+    /**
+     * Return the markers from the ASC file
+     **/
+    inline const std::vector<Property::Marker>& markers() const noexcept;
+
     /**
        Get the shared pointer for the given section
 
@@ -186,6 +191,7 @@ class Morphology
     void write(const std::string& filename);
 
     inline void addAnnotation(const morphio::Property::Annotation& annotation);
+    inline void addMarker(const morphio::Property::Marker& marker);
 
     /**
        Return the data structure used to create read-only morphologies
@@ -222,7 +228,6 @@ class Morphology
     std::shared_ptr<morphio::Property::CellLevel> _cellProperties;
     std::vector<std::shared_ptr<Section>> _rootSections;
     std::map<uint32_t, std::shared_ptr<Section>> _sections;
-    std::vector<morphio::Property::Annotation> _annotations;
     Mitochondria _mitochondria;
     EndoplasmicReticulum _endoplasmicReticulum;
 
@@ -262,10 +267,6 @@ inline const EndoplasmicReticulum& Morphology::endoplasmicReticulum() const noex
     return _endoplasmicReticulum;
 }
 
-inline const std::vector<Property::Annotation>& Morphology::annotations() const noexcept {
-    return _annotations;
-}
-
 inline const std::shared_ptr<Section>& Morphology::section(uint32_t id) const {
     return _sections.at(id);
 }
@@ -274,6 +275,14 @@ inline SomaType Morphology::somaType() const noexcept {
     return _soma->type();
 }
 
+inline const std::vector<Property::Annotation>& Morphology::annotations() const noexcept {
+    return _cellProperties->_annotations;
+}
+
+inline const std::vector<Property::Marker>& Morphology::markers() const noexcept {
+    return _cellProperties->_markers;
+}
+
 inline CellFamily Morphology::cellFamily() const noexcept {
     return _cellProperties->_cellFamily;
 }
@@ -283,7 +292,11 @@ inline MorphologyVersion Morphology::version() const noexcept {
 }
 
 inline void Morphology::addAnnotation(const morphio::Property::Annotation& annotation) {
-    _annotations.push_back(annotation);
+    _cellProperties->_annotations.push_back(annotation);
+}
+
+inline void Morphology::addMarker(const morphio::Property::Marker& marker) {
+    _cellProperties->_markers.push_back(marker);
 }
 
 }  // namespace mut

{MorphIO-2.5.0 → MorphIO-2.5.2}/include/morphio/properties.h

@@ -145,11 +145,17 @@ struct Annotation {
     std::string _details;
 };
 
+struct Marker {
+    PointLevel _pointLevel;
+    std::string _label;
+};
+
 struct CellLevel {
     morphio::CellFamily _cellFamily;
     SomaType _somaType;
     MorphologyVersion _version;
-    std::vector<Annotation> annotation;
+    std::vector<Annotation> _annotations;
+    std::vector<Marker> _markers;
 
     bool diff(const CellLevel& other, LogLevel logLevel) const;
     bool operator==(const CellLevel& other) const;
@@ -172,8 +178,6 @@ struct Properties {
 
     EndoplasmicReticulumLevel _endoplasmicReticulumLevel;
 
-    std::vector<Annotation> _annotations;
-
     ////////////////////////////////////////////////////////////////////////////////
     // Functions
     ////////////////////////////////////////////////////////////////////////////////

{MorphIO-2.5.0 → MorphIO-2.5.2}/src/morphology.cpp

@@ -74,7 +74,11 @@ const EndoplasmicReticulum Morphology::endoplasmicReticulum() const {
 }
 
 const std::vector<Property::Annotation>& Morphology::annotations() const {
-    return _properties->_annotations;
+    return _properties->_cellLevel._annotations;
+}
+
+const std::vector<Property::Marker>& Morphology::markers() const {
+    return _properties->_cellLevel._markers;
 }
 
 Section Morphology::section(uint32_t id) const {

{MorphIO-2.5.0 → MorphIO-2.5.2}/src/mut/morphology.cpp

@@ -46,7 +46,6 @@ Morphology::Morphology(const morphio::Morphology& morphology, unsigned int optio
     _cellProperties = std::make_shared<morphio::Property::CellLevel>(
         morphology._properties->_cellLevel);
 
-    _annotations = morphology.annotations();
     for (const morphio::Section& root : morphology.rootSections()) {
         appendRootSection(root, true);
     }
@@ -262,10 +261,8 @@ Property::Properties Morphology::buildReadOnly() const {
     std::map<uint32_t, int32_t> newIds;
     Property::Properties properties{};
 
-    if (_cellProperties) {
-        properties._cellLevel = *_cellProperties;
-        properties._cellLevel._somaType = _soma->type();
-    }
+    properties._cellLevel = *_cellProperties;
+    properties._cellLevel._somaType = _soma->type();
     _appendProperties(properties._somaLevel, _soma->_pointProperties);
 
     for (auto it = depth_begin(); it != depth_end(); ++it) {
@@ -281,7 +278,6 @@ Property::Properties Morphology::buildReadOnly() const {
     }
 
     mitochondria()._buildMitochondria(properties);
-    properties._annotations = annotations();
     properties._endoplasmicReticulumLevel = endoplasmicReticulum().buildReadOnly();
     return properties;
 }

{MorphIO-2.5.0 → MorphIO-2.5.2}/src/readers/lex.cpp

@@ -32,6 +32,8 @@ enum class Token {
 
     // Special WORDS
     COLOR = 101,
+    FONT,
+    MARKER,
     RGB,
 
     // end of branch weirdness
@@ -77,6 +79,8 @@ inline std::string to_string(Token t) {
         T(DENDRITE)
         T(CELLBODY)
         T(COLOR)
+        T(FONT)
+        T(MARKER)
         T(RGB)
         T(GENERATED)
         T(HIGH)
@@ -151,13 +155,24 @@ class NeurolucidaLexer
         rules_.push("\\|", +Token::PIPE);
 
         rules_.push("Color", +Token::COLOR);
+        rules_.push("Font", +Token::FONT);
 
         rules_.push("Axon", +Token::AXON);
         rules_.push("Apical", +Token::APICAL);
         rules_.push("Dendrite", +Token::DENDRITE);
-        // rules_.push("\\\"CellBody\\\"", +Token::CELLBODY);
         rules_.push("CellBody", +Token::CELLBODY);
 
+        rules_.push("Dot", +Token::MARKER);
+        rules_.push("FilledCircle", +Token::MARKER);
+        rules_.push("SnowFlake", +Token::MARKER);
+        rules_.push("Asterisk", +Token::MARKER);
+        rules_.push("OpenCircle", +Token::MARKER);
+        rules_.push("OpenStar", +Token::MARKER);
+        rules_.push("Flower", +Token::MARKER);
+        rules_.push("OpenSquare", +Token::MARKER);
+        rules_.push("FilledStar", +Token::MARKER);
+        rules_.push("DoubleCircle", +Token::MARKER);
+
         rules_.push("Generated", +Token::GENERATED);
         rules_.push("High", +Token::HIGH);
         rules_.push("Incomplete", +Token::INCOMPLETE);
@@ -254,9 +269,13 @@ class NeurolucidaLexer
         }
     }
 
+    void consume_until(Token endpoint) {
+        while (consume()->id != +endpoint)
+            ;
+    }
+
     // advance iterator until sexp is consumed, including final paren
     void consume_until_balanced_paren() {
-        expect(Token::LPAREN, "consume_until_balanced_paren should start in LPAREN");
         size_t opening_count = 1;
         while (opening_count != 0) {
             size_t id = consume()->id;

{MorphIO-2.5.0 → MorphIO-2.5.2}/src/readers/morphologyASC.cpp

@@ -13,6 +13,18 @@ namespace readers {
 namespace asc {
 namespace {
 
+/**
+   Contain header info about the root S-exps
+**/
+struct Header {
+    Header()
+        : token(static_cast<Token>(+Token::STRING))
+        , parent_id(-1) {}
+    Token token;
+    std::string label;
+    int32_t parent_id;
+};
+
 bool is_eof(Token type) {
     return type == Token::EOF_;
 }
@@ -33,9 +45,9 @@ bool is_end_of_section(Token id) {
 }
 
 bool skip_sexp(size_t id) {
-    return (id == +Token::WORD || id == +Token::STRING || id == +Token::COLOR ||
-            id == +Token::GENERATED || id == +Token::HIGH || id == +Token::INCOMPLETE ||
-            id == +Token::LOW || id == +Token::NORMAL);
+    return (id == +Token::WORD || id == +Token::COLOR || id == +Token::GENERATED ||
+            id == +Token::HIGH || id == +Token::INCOMPLETE || id == +Token::LOW ||
+            id == +Token::NORMAL || id == +Token::FONT);
 }
 }  // namespace
 
@@ -44,7 +56,7 @@ class NeurolucidaParser
   public:
     explicit NeurolucidaParser(const std::string& uri)
         : uri_(uri)
-        , lex_(uri)
+        , lex_(uri, false)
         , debugInfo_(uri)
         , err_(uri) {}
 
@@ -58,7 +70,7 @@ class NeurolucidaParser
 
         lex_.start_parse(input);
 
-        parse_block();
+        parse_root_sexps();
 
         return nb_;
     }
@@ -90,12 +102,12 @@ class NeurolucidaParser
         return std::tuple<Point, floatType>({point[0], point[1], point[2]}, point[3]);
     }
 
-    bool parse_neurite_branch(int32_t parent_id, Token token) {
+    bool parse_neurite_branch(Header& header) {
         lex_.consume(Token::LPAREN, "New branch should start with LPAREN");
 
         bool ret = true;
         while (true) {
-            ret &= parse_neurite_section(parent_id, token);
+            ret &= parse_neurite_section(header);
             if (lex_.ended() ||
                 (lex_.current()->id != +Token::PIPE && lex_.current()->id != +Token::LPAREN)) {
                 break;
@@ -106,8 +118,7 @@ class NeurolucidaParser
         return ret;
     }
 
-    int32_t _create_soma_or_section(Token token,
-                                    int32_t parent_id,
+    int32_t _create_soma_or_section(const Header& header,
                                     std::vector<Point>& points,
                                     std::vector<morphio::floatType>& diameters) {
         lex_.current_section_start_ = lex_.line_num();
@@ -115,24 +126,30 @@ class NeurolucidaParser
         morphio::Property::PointLevel properties;
         properties._points = points;
         properties._diameters = diameters;
-        if (token == Token::CELLBODY) {
+        if (header.token == Token::STRING) {
+            Property::Marker marker;
+            marker._pointLevel = properties;
+            marker._label = header.label;
+            nb_.addMarker(marker);
+            return_id = -1;
+        } else if (header.token == Token::CELLBODY) {
             if (!nb_.soma()->points().empty())
                 throw SomaError(err_.ERROR_SOMA_ALREADY_DEFINED(lex_.line_num()));
             nb_.soma()->properties() = properties;
-
             return_id = -1;
         } else {
-            SectionType section_type = TokenSectionTypeMap.at(token);
-            insertLastPointParentSection(parent_id, properties, diameters);
-
-            // Condition to remove a single point section that is made of only the duplicate point
-            // See test_single_point_section_duplicate_parent for an example
-            if (parent_id > -1 && properties._points.size() == 1) {
-                return_id = parent_id;
+            SectionType section_type = TokenSectionTypeMap.at(header.token);
+            insertLastPointParentSection(header.parent_id, properties, diameters);
+
+            // Condition to remove single point section that duplicate parent
+            // point See test_single_point_section_duplicate_parent for an
+            // example
+            if (header.parent_id > -1 && properties._points.size() == 1) {
+                return_id = header.parent_id;
             } else {
                 std::shared_ptr<morphio::mut::Section> section;
-                if (parent_id > -1)
-                    section = nb_.section(static_cast<unsigned int>(parent_id))
+                if (header.parent_id > -1)
+                    section = nb_.section(static_cast<unsigned int>(header.parent_id))
                                   ->appendSection(properties, section_type);
                 else
                     section = nb_.appendRootSection(properties, section_type);
@@ -189,7 +206,56 @@ class NeurolucidaParser
         properties._diameters.insert(properties._diameters.begin(), childSectionNextDiameter);
     }
 
-    bool parse_neurite_section(int32_t parent_id, Token token) {
+    /**
+       Parse the root sexp until finding the first sexp containing numbers
+    **/
+    Header parse_root_sexp_header() {
+        Header header;
+
+        while (true) {
+            const Token id = static_cast<Token>(lex_.current()->id);
+            const size_t peek_id = lex_.peek()->id;
+
+            if (is_eof(id)) {
+                throw RawDataError(err_.ERROR_EOF_IN_NEURITE(lex_.line_num()));
+            } else if (id == Token::MARKER) {
+                lex_.consume();
+            } else if (id == Token::WORD) {
+                lex_.consume_until_balanced_paren();
+                lex_.consume(Token::LPAREN);
+            } else if (id == Token::STRING) {
+                header.label = lex_.current()->str();
+                // Get rid of quotes
+                header.label = header.label.substr(1, header.label.size() - 2);
+                lex_.consume();
+            } else if (id == Token::RPAREN) {
+                return header;
+            } else if (id == Token::LPAREN) {
+                if (skip_sexp(peek_id)) {
+                    // skip words/strings/markers
+                    lex_.consume_until_balanced_paren();
+                    if (peek_id == +Token::FONT)
+                        lex_.consume_until_balanced_paren();
+                } else if (is_neurite_type(static_cast<Token>(peek_id))) {
+                    header.token = static_cast<Token>(peek_id);
+                    lex_.consume();  // Advance to NeuriteType
+                    lex_.consume();
+                    lex_.consume(Token::RPAREN, "New Neurite should end in RPAREN");
+                } else if (peek_id == +Token::NUMBER) {
+                    return header;
+                } else {
+                    throw RawDataError(
+                        err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
+                }
+            } else {
+                throw RawDataError(
+                    err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.current()->str()));
+            }
+        }
+    }
+
+
+    bool parse_neurite_section(Header header) {
         Points points;
         std::vector<morphio::floatType> diameters;
         auto section_id = static_cast<int>(nb_.sections().size());
@@ -202,7 +268,7 @@ class NeurolucidaParser
                 throw RawDataError(err_.ERROR_EOF_IN_NEURITE(lex_.line_num()));
             } else if (is_end_of_section(id)) {
                 if (!points.empty()) {
-                    _create_soma_or_section(token, parent_id, points, diameters);
+                    _create_soma_or_section(header, points, diameters);
                 }
                 return true;
             } else if (is_end_of_branch(id)) {
@@ -225,9 +291,11 @@ class NeurolucidaParser
                     diameters.push_back(radius);
                 } else if (peek_id == +Token::LPAREN) {
                     if (!points.empty()) {
-                        section_id = _create_soma_or_section(token, parent_id, points, diameters);
+                        section_id = _create_soma_or_section(header, points, diameters);
                     }
-                    parse_neurite_branch(section_id, token);
+                    Header child_header = header;
+                    child_header.parent_id = section_id;
+                    parse_neurite_branch(child_header);
                 } else {
                     throw RawDataError(
                         err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
@@ -238,24 +306,20 @@ class NeurolucidaParser
         }
     }
 
-    bool parse_block() {
+    void parse_root_sexps() {
         // parse the top level blocks, and if they are a neurite, otherwise skip
         while (!lex_.ended()) {
-            const auto peek_id = static_cast<Token>(lex_.peek()->id);
-            if (is_neurite_type(peek_id)) {
-                lex_.consume();  // Advance to NeuriteType
-                const auto current_id = static_cast<Token>(lex_.current()->id);
-
+            if (static_cast<Token>(lex_.current()->id) == Token::LPAREN) {
                 lex_.consume();
-                lex_.consume(Token::RPAREN, "New Neurite should end in RPAREN");
-                parse_neurite_section(-1, current_id);
+                Header header = parse_root_sexp_header();
+                if (lex_.current()->id != +Token::RPAREN) {
+                    parse_neurite_section(header);
+                }
             }
 
             if (!lex_.ended())
                 lex_.consume();
         }
-
-        return true;
     }
 
     morphio::mut::Morphology nb_;

{MorphIO-2.5.0 → MorphIO-2.5.2}/src/readers/morphologyHDF5.cpp

@@ -141,6 +141,8 @@ void MorphologyHDF5::_resolveV1() {
 }
 
 bool MorphologyHDF5::_readV11Metadata() {
+    uint32_t family;
+
     try {
         HighFive::SilenceHDF5 silence;
         const auto metadata = _group.getGroup(_g_metadata);
@@ -151,12 +153,8 @@ bool MorphologyHDF5::_readV11Metadata() {
         if (version[0] != 1 || version[1] != 1)
             return false;
 
-        _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_1_1;
-
         const auto familyAttr = metadata.getAttribute(_a_family);
-        uint32_t family;
         familyAttr.read(family);
-        _properties._cellLevel._cellFamily = static_cast<CellFamily>(family);
     } catch (const HighFive::GroupException&) {
         return false;
     } catch (const HighFive::Exception& e) {
@@ -166,6 +164,8 @@ bool MorphologyHDF5::_readV11Metadata() {
         throw morphio::RawDataError("Error reading morphology " + _uri + "  metadata." + e.what());
     }
 
+    _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_1_1;
+    _properties._cellLevel._cellFamily = static_cast<CellFamily>(family);
     _resolveV1();
     return true;
 }
@@ -176,8 +176,10 @@ bool MorphologyHDF5::_readV2Metadata() {
         const auto root = _group.getGroup(_g_root);
         const auto attr = root.getAttribute(_a_version);
         attr.read(_properties._cellLevel._version);
-        if (_properties.version() == MORPHOLOGY_VERSION_H5_2)
+        if (_properties.version() == MORPHOLOGY_VERSION_H5_2) {
+            _properties._cellLevel._cellFamily = CellFamily::NEURON;
             return true;
+        }
     } catch (const HighFive::Exception&) {
     }
 
@@ -185,6 +187,7 @@ bool MorphologyHDF5::_readV2Metadata() {
         HighFive::SilenceHDF5 silence;
         _group.getGroup(_g_root);
         _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_2;
+        _properties._cellLevel._cellFamily = CellFamily::NEURON;
         return true;
     } catch (const HighFive::Exception&) {
         return false;