morphio 2.6.2__tar.gz → 2.7.0__tar.gz

{MorphIO-2.6.2 → MorphIO-2.7.0}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.2
+Version: 2.7.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL

{MorphIO-2.6.2 → MorphIO-2.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.6.2
+Version: 2.7.0
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL

{MorphIO-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → MorphIO-2.7.0}/morphio/__init__.py

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

{MorphIO-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → MorphIO-2.7.0}/src/readers/morphologyASC.cpp

@@ -353,7 +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-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → 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-2.6.2 → MorphIO-2.7.0}/tests/test_2_neurolucida.py

@@ -705,3 +705,5 @@ 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-2.6.2 → 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)

{MorphIO-2.6.2 → MorphIO-2.7.0}/tests/test_6_writers.py

@@ -1,17 +1,15 @@
 import os
-import numpy as np
-from numpy.testing import assert_array_equal, assert_equal, assert_raises
-from nose.tools import ok_
 from pathlib import Path
 
+import numpy as np
+from morphio import MitochondriaPointLevel
+from morphio import Morphology as ImmutMorphology
+from morphio import PointLevel, SectionBuilderError, SectionType, WriterError, ostream_redirect
 from morphio.mut import Morphology
-from morphio import (SectionBuilderError, set_maximum_warnings, SectionType, PointLevel,
-                     WriterError,
-                     MitochondriaPointLevel, Morphology as ImmutMorphology, ostream_redirect)
-
-from . utils import captured_output, setup_tempdir, assert_string_equal
+from nose.tools import ok_
+from numpy.testing import assert_array_equal, assert_equal, assert_raises
 
-_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "data")
+from .utils import assert_string_equal, captured_output, setup_tempdir
 
 
 def test_write_empty_file():
@@ -20,7 +18,7 @@ def test_write_empty_file():
         with ostream_redirect(stdout=True, stderr=True):
             with setup_tempdir('test_write_empty_file', no_cleanup=True) as tmp_folder:
                 for ext in ['asc', 'swc', 'h5']:
-                    outname = os.path.join(tmp_folder, 'empty.' + ext)
+                    outname = Path(tmp_folder, 'empty.' + ext)
                     Morphology().write(outname)
                     ok_(not os.path.exists(outname))
 
@@ -31,7 +29,7 @@ def test_write_soma_basic():
     morpho.soma.diameters = [2, 3, 3]
 
     with setup_tempdir('test_write_soma_basic') as tmp_folder:
-        morpho.write(os.path.join(tmp_folder, "test_write.swc"))
+        morpho.write(Path(tmp_folder, "test_write.swc"))
         morpho.write(Path(tmp_folder, "test_write_pathlib.swc"))
         assert_equal(len(os.listdir(tmp_folder)), 2)
 
@@ -62,17 +60,19 @@ def test_write_basic():
                                             [2, 4]))
 
     with setup_tempdir('test_write_basic') as tmp_folder:
-        morpho.write(os.path.join(tmp_folder, "test_write.asc"))
-        morpho.write(os.path.join(tmp_folder, "test_write.swc"))
-        h5_out = os.path.join(tmp_folder, "test_write.h5")
+        morpho.write(Path(tmp_folder, "test_write.asc"))
+        morpho.write(Path(tmp_folder, "test_write.swc"))
+        h5_out = Path(tmp_folder, "test_write.h5")
         morpho.write(h5_out)
 
         expected = [[0., 0., 0.], [0., 5., 0.], [0., 5., 0.], [-5., 5., 0.],
                     [0., 5., 0.], [6., 5., 0.], [0., 0., 0.], [0., -4., 0.],
                     [0., -4., 0.], [6., -4., 0.], [0., -4., 0.], [-5., -4., 0.]]
-        assert_array_equal(ImmutMorphology(os.path.join(tmp_folder, "test_write.asc")).points, expected)
-        assert_array_equal(ImmutMorphology(os.path.join(tmp_folder, "test_write.swc")).points, expected)
-        assert_array_equal(ImmutMorphology(os.path.join(tmp_folder, "test_write.h5")).points, expected)
+        assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.asc")).points, expected)
+        assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.swc")).points, expected)
+        h5_morph = ImmutMorphology(Path(tmp_folder, "test_write.h5"))
+        assert_array_equal(h5_morph.points, expected)
+        assert_equal(h5_morph.version, ('h5', 1, 2))
 
         import h5py
         with h5py.File(h5_out, 'r') as h5_file:
@@ -111,7 +111,7 @@ def test_write_merge_only_child():
         for extension in ['swc', 'asc', 'h5']:
             with captured_output() as (_, err):
                 with ostream_redirect(stdout=True, stderr=True):
-                    filename = os.path.join(tmp_folder, 'test.{}'.format(extension))
+                    filename = Path(tmp_folder, 'test.{}'.format(extension))
                     morpho.write(filename)
 
                     assert_equal(err.getvalue().strip(),
@@ -159,7 +159,7 @@ def test_write_perimeter():
                                      [6, 8]))
 
     with setup_tempdir('test_write_perimeter') as tmp_folder:
-        h5_out = os.path.join(tmp_folder, "test_write.h5")
+        h5_out = Path(tmp_folder, "test_write.h5")
         morpho.write(h5_out)
 
         assert_array_equal(ImmutMorphology(h5_out).perimeters,
@@ -167,7 +167,7 @@ def test_write_perimeter():
 
         # Cannot right a morph with perimeter data to ASC and SWC
         for ext in ['swc', 'asc']:
-            out_path = os.path.join(tmp_folder, "test_write_perimeter." + ext)
+            out_path = Path(tmp_folder, "test_write_perimeter." + ext)
             assert_raises(WriterError, morpho.write, out_path)
 
 
@@ -188,7 +188,7 @@ def test_write_no_soma():
         for ext in ['asc', 'h5', 'swc']:
             with captured_output() as (_, err):
                 with ostream_redirect(stdout=True, stderr=True):
-                    outfile = os.path.join(tmp_folder, 'tmp.' + ext)
+                    outfile = Path(tmp_folder, 'tmp.' + ext)
                     morpho.write(outfile)
                     assert_equal(err.getvalue().strip(),
                                  'Warning: writing file without a soma')
@@ -219,23 +219,23 @@ def test_mitochondria():
                                         [0.6, 0.7, 0.8, 0.9],
                                         [20, 30, 40, 50]))
     with setup_tempdir('test_mitochondria') as tmp_folder:
-        morpho.write(os.path.join(tmp_folder, "test.h5"))
+        morpho.write(Path(tmp_folder, "test.h5"))
 
         with captured_output() as (_, err):
             with ostream_redirect(stdout=True, stderr=True):
-                morpho.write(os.path.join(tmp_folder, "test.swc"))
+                morpho.write(Path(tmp_folder, "test.swc"))
                 assert_string_equal(err.getvalue(),
                                     "Warning: this cell has mitochondria, they cannot be saved in "
                                     " ASC or SWC format. Please use H5 if you want to save them.")
 
         with captured_output() as (_, err):
             with ostream_redirect(stdout=True, stderr=True):
-                morpho.write(os.path.join(tmp_folder, "test.asc"))
+                morpho.write(Path(tmp_folder, "test.asc"))
                 assert_string_equal(err.getvalue(),
                                     "Warning: this cell has mitochondria, they cannot be saved in "
                                     " ASC or SWC format. Please use H5 if you want to save them.")
 
-        mito = ImmutMorphology(os.path.join(tmp_folder, 'test.h5')).mitochondria
+        mito = ImmutMorphology(Path(tmp_folder, 'test.h5')).mitochondria
         assert_array_equal(mito.root_sections[0].diameters,
                            diameters)
         assert_array_equal(mito.root_sections[0].neurite_section_ids,
@@ -245,7 +245,7 @@ def test_mitochondria():
 
         assert_equal(len(mito.root_sections), 1)
 
-        mito = Morphology(os.path.join(tmp_folder, 'test.h5')).mitochondria
+        mito = Morphology(Path(tmp_folder, 'test.h5')).mitochondria
         assert_equal(len(mito.root_sections), 1)
         assert_equal(mito.root_sections[0].neurite_section_ids, neuronal_section_ids)
         assert_array_equal(mito.section(0).diameters,
@@ -273,7 +273,7 @@ def test_duplicate_different_diameter():
         for ext in ['asc', 'h5', 'swc']:
             with captured_output() as (_, err):
                 with ostream_redirect(stdout=True, stderr=True):
-                    outfile = os.path.join(tmp_folder, 'tmp.' + ext)
+                    outfile = Path(tmp_folder, 'tmp.' + ext)
                     morpho.write(outfile)
 
                     read = Morphology(outfile)
@@ -297,7 +297,7 @@ def test_single_point_root_section():
             m.append_root_section(PointLevel(points, diameters), SectionType(2))
 
             with setup_tempdir('test_single_point_root_section', no_cleanup=True) as tmp_folder:
-                assert_raises(SectionBuilderError, m.write, os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
+                assert_raises(SectionBuilderError, m.write, Path(tmp_folder, "h5/empty_vasculature.h5"))
 
     m = Morphology()
     points = [[1., 1., 1.]]
@@ -305,4 +305,4 @@ def test_single_point_root_section():
     m.append_root_section(PointLevel(points, diameters), SectionType(2))
 
     with setup_tempdir('test_single_point_root_section', no_cleanup=True) as tmp_folder:
-        assert_raises(SectionBuilderError, m.write, os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
+        assert_raises(SectionBuilderError, m.write, Path(tmp_folder, "h5/empty_vasculature.h5"))