morphio 2.6.1__tar.gz → 2.7.0__tar.gz

{MorphIO-2.6.1 → MorphIO-2.7.0}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.1
+Version: 2.7.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -580,6 +580,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
           )  ;  End of markers
           ```
         
+        ℹ️ Markers can may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.
+        
         ##### Usage
         
         ```python

{MorphIO-2.6.1 → MorphIO-2.7.0}/MorphIO.egg-info/SOURCES.txt

@@ -137,6 +137,7 @@ tests/data/circle_contour.asc
 tests/data/complexe.swc
 tests/data/disconnected_neurite.swc
 tests/data/iterators.asc
+tests/data/marker-with-string.asc
 tests/data/mono-type.asc
 tests/data/multiple_point_section.asc
 tests/data/multiple_soma.swc

{MorphIO-2.6.1 → MorphIO-2.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.1
+Version: 2.7.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -580,6 +580,8 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
           )  ;  End of markers
           ```
         
+        ℹ️ Markers can may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.
+        
         ##### Usage
         
         ```python

{MorphIO-2.6.1 → MorphIO-2.7.0}/README.md

@@ -573,6 +573,8 @@ The following s-expressions are parsed:
   )  ;  End of markers
   ```
 
+ℹ️ Markers can may have only `(X Y Z)` specified instead of the more common `(X Y Z D)`. In this case, diameters are set to 0.
+
 ##### Usage
 
 ```python

{MorphIO-2.6.1 → MorphIO-2.7.0}/binds/python/bind_misc.cpp

@@ -80,23 +80,6 @@ void bind_misc(py::module& m) {
         .export_values();
 
 
-    py::enum_<morphio::enums::MorphologyVersion>(m, "MorphologyVersion")
-        .value("MORPHOLOGY_VERSION_H5_1",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_1)
-        .value("MORPHOLOGY_VERSION_H5_2",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_2)
-        .value("MORPHOLOGY_VERSION_H5_1_1",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_1_1)
-        .value("MORPHOLOGY_VERSION_H5_1_2",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_1_2)
-        .value("MORPHOLOGY_VERSION_SWC_1",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_SWC_1)
-        .value("MORPHOLOGY_VERSION_UNDEFINED",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_UNDEFINED)
-        .value("MORPHOLOGY_VERSION_ASC_1",
-               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_ASC_1)
-        .export_values();
-
     py::enum_<morphio::enums::CellFamily>(m, "CellFamily")
         .value("NEURON", morphio::enums::CellFamily::NEURON)
         .value("GLIA", morphio::enums::CellFamily::GLIA)

{MorphIO-2.6.1 → MorphIO-2.7.0}/include/morphio/enums.h

@@ -35,19 +35,6 @@ enum Warning {
     WRITE_EMPTY_MORPHOLOGY
 };
 
-/** The supported versions for morphology files. */
-enum MorphologyVersion {
-    MORPHOLOGY_VERSION_H5_1 = 1,
-    MORPHOLOGY_VERSION_H5_2 = 2,
-    MORPHOLOGY_VERSION_H5_1_1 = 3,
-    MORPHOLOGY_VERSION_ASC_1 = 4,
-    MORPHOLOGY_VERSION_SWC_1 = 101,
-    MORPHOLOGY_VERSION_H5_1_2 = 5,
-    MORPHOLOGY_VERSION_UNDEFINED
-};
-std::ostream& operator<<(std::ostream& os, MorphologyVersion v);
-
-
 enum AnnotationType {
     SINGLE_CHILD,
 };

{MorphIO-2.6.1 → MorphIO-2.7.0}/include/morphio/properties.h

@@ -152,7 +152,9 @@ struct Marker {
 
 struct CellLevel {
     CellLevel()
-        : _version(MORPHOLOGY_VERSION_UNDEFINED) {}
+        : _version({"undefined", 0, 0}) {}
+
+    // A tuple (file format (std::string), major version, minor version)
     MorphologyVersion _version;
     morphio::CellFamily _cellFamily;
     SomaType _somaType;
@@ -162,6 +164,9 @@ struct CellLevel {
     bool diff(const CellLevel& other, LogLevel logLevel) const;
     bool operator==(const CellLevel& other) const;
     bool operator!=(const CellLevel& other) const;
+    std::string fileFormat() const;
+    uint32_t majorVersion();
+    uint32_t minorVersion();
 };
 
 // The lowest level data blob
@@ -188,9 +193,6 @@ struct Properties {
     template <typename T>
     const std::vector<typename T::Type>& get() const noexcept;
 
-    morphio::MorphologyVersion& version() noexcept {
-        return _cellLevel._version;
-    }
     const morphio::MorphologyVersion& version() const noexcept {
         return _cellLevel._version;
     }

{MorphIO-2.6.1 → MorphIO-2.7.0}/include/morphio/types.h

@@ -47,6 +47,7 @@ class Soma;
 }  // namespace mut
 
 using SectionRange = std::pair<size_t, size_t>;
+using MorphologyVersion = std::tuple<std::string, uint32_t, uint32_t>;
 
 template <typename T>
 using range = gsl::span<T>;

{MorphIO-2.6.1 → MorphIO-2.7.0}/morphio/__init__.py

@@ -15,7 +15,6 @@ from ._morphio import (
     MitochondriaPointLevel,
     MorphioError,
     Morphology,
-    MorphologyVersion,
     MultipleTrees,
     Option,
     PointLevel,

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/enums.cpp

@@ -4,27 +4,6 @@
 namespace morphio {
 namespace enums {
 
-/** Output stream formatter for MorphologyVersion */
-std::ostream& operator<<(std::ostream& os, const MorphologyVersion v) {
-    switch (v) {
-    case MORPHOLOGY_VERSION_H5_1:
-        return os << "h5v1";
-    case MORPHOLOGY_VERSION_H5_1_1:
-        return os << "h5v1.1";
-    case MORPHOLOGY_VERSION_H5_1_2:
-        return os << "h5v1.2";
-    case MORPHOLOGY_VERSION_H5_2:
-        return os << "h5v2";
-    case MORPHOLOGY_VERSION_SWC_1:
-        return os << "swcv1";
-    case MORPHOLOGY_VERSION_ASC_1:
-        return os << "ascv1";
-    default:
-    case MORPHOLOGY_VERSION_UNDEFINED:
-        return os << "UNDEFINED";
-    }
-}
-
 /** Output stream formatter for MorphologyVersion */
 std::ostream& operator<<(std::ostream& os, const SomaType v) {
     switch (v) {

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/morphology.cpp

@@ -27,13 +27,12 @@ Morphology::Morphology(const Property::Properties& properties, unsigned int opti
     : _properties(std::make_shared<Property::Properties>(properties)) {
     buildChildren(_properties);
 
-    if (version() != MORPHOLOGY_VERSION_SWC_1)
+    if (_properties->_cellLevel.fileFormat() != "swc")
         _properties->_cellLevel._somaType = getSomaType(soma().points().size());
 
     // For SWC and ASC, sanitization and modifier application are already taken care of by
     // their respective loaders
-    if ((version() == MORPHOLOGY_VERSION_H5_1 || version() == MORPHOLOGY_VERSION_H5_1_1 ||
-         version() == MORPHOLOGY_VERSION_H5_2)) {
+    if (properties._cellLevel.fileFormat() == "h5") {
         mut::Morphology mutable_morph(*this);
         mutable_morph.sanitize();
         if (options) {

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/mut/writers.cpp

@@ -374,7 +374,7 @@ void h5(const Morphology& morpho, const std::string& filename) {
 
     HighFive::Group g_metadata = h5_file.createGroup("metadata");
 
-    write_attribute(g_metadata, "version", std::vector<uint32_t>{1, 1});
+    write_attribute(g_metadata, "version", std::vector<uint32_t>{1, 2});
     write_attribute(g_metadata, "cell_family", std::vector<uint32_t>{morpho.cellFamily()});
     write_attribute(h5_file, "comment", std::vector<std::string>{version_string()});
 

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/properties.cpp

@@ -217,6 +217,18 @@ bool CellLevel::operator!=(const CellLevel& other) const {
     return diff(other, LogLevel::ERROR);
 }
 
+std::string CellLevel::fileFormat() const {
+    return std::get<0>(_version);
+}
+
+uint32_t CellLevel::majorVersion() {
+    return std::get<1>(_version);
+}
+
+uint32_t CellLevel::minorVersion() {
+    return std::get<2>(_version);
+}
+
 
 MitochondriaPointLevel::MitochondriaPointLevel(const MitochondriaPointLevel& data,
                                                const SectionRange& range) {

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/readers/morphologyASC.cpp

@@ -76,23 +76,30 @@ class NeurolucidaParser
     }
 
   private:
-    std::tuple<Point, floatType> parse_point(NeurolucidaLexer& lex) {
+    std::tuple<Point, floatType> parse_point(NeurolucidaLexer& lex, bool is_marker) {
         lex.expect(Token::LPAREN, "Point should start in LPAREN");
-        std::array<morphio::floatType, 4> point{};  // X,Y,Z,R
-        for (auto& p : point) {
+        std::array<morphio::floatType, 4> point{};  // X,Y,Z,D
+        for (unsigned int i = 0; i < 4; i++) {
             try {
 #ifdef MORPHIO_USE_DOUBLE
-                p = std::stod(lex.consume()->str());
+                point[i] = std::stod(lex.consume()->str());
 #else
-                p = std::stof(lex.consume()->str());
+                point[i] = std::stof(lex.consume()->str());
 #endif
             } catch (const std::invalid_argument&) {
                 throw RawDataError(err_.ERROR_PARSING_POINT(lex.line_num(), lex.current()->str()));
             }
+
+            // Markers can have an s-exp (X Y Z) without diameter
+            if (is_marker && i == 2 && (lex_.peek()->str() == ")")) {
+                point[3] = 0;
+                break;
+            }
         }
 
         lex.consume();
 
+        // case where the s-exp is (X Y Z R WORD). For example: (1 1 0 1 S1)
         if (lex.current()->id == +Token::WORD) {
             lex.consume(Token::WORD);
         }
@@ -231,13 +238,14 @@ class NeurolucidaParser
             } else if (id == Token::RPAREN) {
                 return header;
             } else if (id == Token::LPAREN) {
+                const auto next_token = static_cast<Token>(peek_id);
                 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);
+                } else if (is_neurite_type(next_token)) {
+                    header.token = next_token;
                     lex_.consume();  // Advance to NeuriteType
                     lex_.consume();
                     lex_.consume(Token::RPAREN, "New Neurite should end in RPAREN");
@@ -286,7 +294,7 @@ class NeurolucidaParser
                 } else if (peek_id == +Token::NUMBER) {
                     Point point;
                     floatType radius;
-                    std::tie(point, radius) = parse_point(lex_);
+                    std::tie(point, radius) = parse_point(lex_, (header.token == Token::STRING));
                     points.push_back(point);
                     diameters.push_back(radius);
                 } else if (peek_id == +Token::LPAREN) {
@@ -300,6 +308,8 @@ class NeurolucidaParser
                     throw RawDataError(
                         err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
                 }
+            } else if (id == Token::STRING) {
+                lex_.consume();
             } else {
                 throw RawDataError(err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
             }
@@ -343,7 +353,7 @@ Property::Properties load(const std::string& uri, unsigned int options) {
 
     Property::Properties properties = nb_.buildReadOnly();
     properties._cellLevel._cellFamily = NEURON;
-    properties._cellLevel._version = MORPHOLOGY_VERSION_ASC_1;
+    properties._cellLevel._version = {"asc", 1, 0};
     return properties;
 }
 

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/readers/morphologyHDF5.cpp

@@ -75,6 +75,7 @@ Property::Properties MorphologyHDF5::load() {
     _readPerimeters(firstSectionOffset);
     _readMitochondria();
     _readEndoplasmicReticulum();
+    std::get<0>(_properties._cellLevel._version) = "h5";
 
     return _properties;
 }
@@ -114,21 +115,21 @@ void MorphologyHDF5::_readMetadata(const std::string& source) {
         const auto metadata = _group.getGroup(_g_metadata);
         const auto attr = metadata.getAttribute(_a_version);
 
-        uint32_t version[2];
-        attr.read(version);
-        if (version[0] == 1 && (version[1] == 1 || version[1] == 2)) {
+        uint32_t versions[2];
+        attr.read(&versions);
+        std::get<1>(_properties._cellLevel._version) = versions[0];
+        std::get<2>(_properties._cellLevel._version) = versions[1];
+        const auto majorVersion = _properties._cellLevel.majorVersion();
+        const auto minorVersion = _properties._cellLevel.minorVersion();
+        if (majorVersion == 1 && (minorVersion == 1 || minorVersion == 2)) {
             uint32_t family;
             const auto familyAttr = metadata.getAttribute(_a_family);
             familyAttr.read(family);
-            if (version[1] == 1)
-                _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_1_1;
-            else
-                _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_1_2;
             _properties._cellLevel._cellFamily = static_cast<CellFamily>(family);
         } else {
             throw morphio::RawDataError(
-                "Error in " + source + "\nUnsupported h5 version: " + std::to_string(version[0]) +
-                "." + std::to_string(version[1]) +
+                "Error in " + source + "\nUnsupported h5 version: " + std::to_string(majorVersion) +
+                "." + std::to_string(minorVersion) +
                 "See "
                 "https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/"
                 "index.html for the list of supported versions.");
@@ -139,9 +140,11 @@ void MorphologyHDF5::_readMetadata(const std::string& source) {
     try {
         _resolveV1();
 
-        // The fact that the resolution passes and _version is not set yet tells us it is h5v1.0
-        if (_properties._cellLevel._version == MORPHOLOGY_VERSION_UNDEFINED) {
-            _properties._cellLevel._version = MORPHOLOGY_VERSION_H5_1;
+        // The fact that the resolution passes and majorVersion is still uninitialized tells us
+        // it is h5v1.0
+        if (_properties._cellLevel.majorVersion() == 0) {
+            std::get<1>(_properties._cellLevel._version) = 1;  // major version
+            std::get<2>(_properties._cellLevel._version) = 0;  // minor version
             // Version 1.0 only support NEURON has a CellFamily.
             // Other CellFamily have been added in version 1.1:
             // https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
@@ -274,7 +277,9 @@ int MorphologyHDF5::_readSections() {
 }
 
 void MorphologyHDF5::_readPerimeters(int firstSectionOffset) {
-    if (_properties.version() != MORPHOLOGY_VERSION_H5_1_1 || !HasNeurites(firstSectionOffset))
+    // Perimeter information is available starting at v1.1
+    if (!(_properties._cellLevel.majorVersion() == 1 && _properties._cellLevel.minorVersion() > 0 &&
+          HasNeurites(firstSectionOffset)))
         return;
 
     try {
@@ -301,10 +306,9 @@ void MorphologyHDF5::_readPerimeters(int firstSectionOffset) {
 template <typename T>
 void MorphologyHDF5::_read(const std::string& groupName,
                            const std::string& _dataset,
-                           MorphologyVersion version,
                            unsigned int expectedDimension,
                            T& data) {
-    if (_properties.version() != version)
+    if (_properties._cellLevel.majorVersion() != 1 || _properties._cellLevel.minorVersion() < 1)
         return;
     try {
         const auto group = _group.getGroup(groupName);
@@ -339,22 +343,18 @@ void MorphologyHDF5::_readEndoplasmicReticulum() {
 
     _read(_g_endoplasmic_reticulum,
           _d_section_index,
-          MORPHOLOGY_VERSION_H5_1_1,
           1,
           _properties._endoplasmicReticulumLevel._sectionIndices);
     _read(_g_endoplasmic_reticulum,
           _d_volume,
-          MORPHOLOGY_VERSION_H5_1_1,
           1,
           _properties._endoplasmicReticulumLevel._volumes);
     _read(_g_endoplasmic_reticulum,
           _d_surface_area,
-          MORPHOLOGY_VERSION_H5_1_1,
           1,
           _properties._endoplasmicReticulumLevel._surfaceAreas);
     _read(_g_endoplasmic_reticulum,
           _d_filament_count,
-          MORPHOLOGY_VERSION_H5_1_1,
           1,
           _properties._endoplasmicReticulumLevel._filamentCounts);
 }
@@ -371,7 +371,7 @@ void MorphologyHDF5::_readMitochondria() {
     }
 
     std::vector<std::vector<morphio::floatType>> points;
-    _read(_g_mitochondria, _d_points, MORPHOLOGY_VERSION_H5_1_1, 2, points);
+    _read(_g_mitochondria, _d_points, 2, points);
 
     auto& mitoSectionId = _properties.get<Property::MitoNeuriteSectionId>();
     auto& pathlength = _properties.get<Property::MitoPathLength>();
@@ -386,7 +386,7 @@ void MorphologyHDF5::_readMitochondria() {
     }
 
     std::vector<std::vector<int32_t>> structure;
-    _read(_g_mitochondria, "structure", MORPHOLOGY_VERSION_H5_1_1, 2, structure);
+    _read(_g_mitochondria, "structure", 2, structure);
 
     auto& mitoSection = _properties.get<Property::MitoSection>();
     mitoSection.reserve(mitoSection.size() + structure.size());

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/readers/morphologyHDF5.h

@@ -37,7 +37,6 @@ class MorphologyHDF5
     template <typename T>
     void _read(const std::string& group,
                const std::string& _dataset,
-               MorphologyVersion version,
                unsigned int expectedDimension,
                T& data);
 

{MorphIO-2.6.1 → MorphIO-2.7.0}/src/readers/morphologySWC.cpp

@@ -353,7 +353,7 @@ class SWCBuilder
 Property::Properties load(const std::string& uri, unsigned int options) {
     auto properties = SWCBuilder(uri)._buildProperties(options);
     properties._cellLevel._cellFamily = NEURON;
-    properties._cellLevel._version = MORPHOLOGY_VERSION_SWC_1;
+    properties._cellLevel._version = {"swc", 1, 0};
     return properties;
 }
 

MorphIO-2.7.0/tests/data/marker-with-string.asc

@@ -0,0 +1,12 @@
+; The following annotation has been found in C280999A-I4.asc
+; It is a top-level annotation with a quote inside
+( (Color Red)
+  (   -0.97  -141.17    84.77)
+  "<--4 boutons on a PC soma"
+)  ;  End of text
+
+("CellBody"
+ (Color Red)
+ (CellBody)
+ (0 0 0 2)
+ )

{MorphIO-2.6.1 → MorphIO-2.7.0}/tests/test_1_swc.py

@@ -447,3 +447,7 @@ def test_root_node_split():
 def test_three_point_soma():
     n = Morphology(os.path.join(_path, 'three_point_soma.swc'))
     assert_equal(n.soma_type, SomaType.SOMA_NEUROMORPHO_THREE_POINT_CYLINDERS)
+
+def test_version():
+    assert_array_equal(Morphology(os.path.join(_path, 'simple.swc')).version,
+                       ('swc', 1, 0))

{MorphIO-2.6.1 → MorphIO-2.7.0}/tests/test_2_neurolucida.py

@@ -700,3 +700,10 @@ def test_skip_imagecoord():
 def test_Sections_block():
     assert_array_equal(Morphology(DATA_DIR / 'sections-block.asc').points,
                        Morphology(DATA_DIR / 'simple.asc').points)
+
+def test_marker_with_string():
+    m = Morphology(DATA_DIR / 'marker-with-string.asc')
+    assert_array_equal(m.markers[0].points, np.array([[  -0.97    , -141.169998,   84.769997]],
+                                                     dtype=np.float32))
+def test_version():
+    assert_array_equal(Morphology(DATA_DIR / 'simple.asc').version, ('asc', 1, 0))

{MorphIO-2.6.1 → MorphIO-2.7.0}/tests/test_3_h5.py

@@ -3,7 +3,7 @@ from itertools import chain, repeat
 from pathlib import Path
 
 import requests
-from morphio import (CellFamily, Morphology, MorphologyVersion, RawDataError, SectionType,
+from morphio import (CellFamily, Morphology, RawDataError, SectionType,
                      ostream_redirect)
 from nose.tools import assert_equal, assert_raises, ok_
 from numpy.testing import assert_array_equal
@@ -21,10 +21,10 @@ def test_v1():
     assert_equal(len(n.root_sections), 2)
     assert_equal(n.root_sections[0].type, 3)
     assert_equal(n.root_sections[1].type, 2)
-    assert_equal(n.version, MorphologyVersion.MORPHOLOGY_VERSION_H5_1_1)
+    assert_equal(n.version, ("h5", 1, 1))
 
     n = Morphology(H5V1_PATH / 'Neuron.h5')
-    assert_equal(n.version, MorphologyVersion.MORPHOLOGY_VERSION_H5_1)
+    assert_equal(n.version, ("h5", 1, 0))
 
     assert_equal(len(n.sections), 84)
     assert_equal(len(n.soma.points), 3)