morphio 2.1.3__tar.gz → 2.1.5__tar.gz

{MorphIO-2.1.3 → MorphIO-2.1.5}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: MorphIO
-Version: 2.1.3
+Version: 2.1.5
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: NSE Team - Blue Brain Project

{MorphIO-2.1.3 → MorphIO-2.1.5}/MorphIO.egg-info/SOURCES.txt

@@ -420,6 +420,7 @@ MorphIO.egg-info/not-zip-safe
 MorphIO.egg-info/requires.txt
 MorphIO.egg-info/top_level.txt
 binds/python/CMakeLists.txt
+binds/python/bind_enums.h
 binds/python/bind_immutable.cpp
 binds/python/bind_misc.cpp
 binds/python/bind_mutable.cpp
@@ -524,6 +525,7 @@ tests/data/disconnected_neurite.swc
 tests/data/iterators.asc
 tests/data/multiple_point_section.asc
 tests/data/multiple_soma.swc
+tests/data/nested_single_children.asc
 tests/data/neurite_wrong_root_point.swc
 tests/data/nrn_ordering.swc
 tests/data/reversed_NRN_neurite_order.swc

{MorphIO-2.1.3 → MorphIO-2.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: MorphIO
-Version: 2.1.3
+Version: 2.1.5
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: NSE Team - Blue Brain Project

MorphIO-2.1.5/binds/python/bind_enums.h

@@ -0,0 +1,11 @@
+/**
+   A place for enums that are only used in the bindings
+**/
+#pragma once
+
+enum IterType
+{
+    DEPTH_FIRST,
+    BREADTH_FIRST,
+    UPSTREAM
+};

{MorphIO-2.1.3 → MorphIO-2.1.5}/binds/python/bind_immutable.cpp

@@ -9,6 +9,8 @@
 #include <morphio/enums.h>
 #include <morphio/mut/morphology.h>
 
+#include "bind_enums.h"
+
 namespace py = pybind11;
 
 static void bind_immutable_module(py::module &m) {
@@ -39,7 +41,6 @@ static void bind_immutable_module(py::module &m) {
 
         .def("as_mutable", [](const morphio::Morphology* morph) { return morphio::mut::Morphology(*morph); })
 
-
         // Cell sub-parts accessors
         .def_property_readonly("soma", &morphio::Morphology::soma,
                                "Returns the soma object")
@@ -90,13 +91,13 @@ static void bind_immutable_module(py::module &m) {
                                "Returns the version")
 
         // Iterators
-        .def("iter", [](morphio::Morphology* morpho, morphio::IterType type) {
+        .def("iter", [](morphio::Morphology* morpho, IterType type) {
                 switch (type) {
-                case morphio::IterType::DEPTH_FIRST:
+                case IterType::DEPTH_FIRST:
                     return py::make_iterator(morpho->depth_begin(), morpho->depth_end());
-                case morphio::IterType::BREADTH_FIRST:
+                case IterType::BREADTH_FIRST:
                     return py::make_iterator(morpho->breadth_begin(), morpho->breadth_end());
-                case morphio::IterType::UPSTREAM:
+                case IterType::UPSTREAM:
                 default:
                     LBTHROW(morphio::MorphioError("Only iteration types depth_first and breadth_first are supported"));
                 }
@@ -106,7 +107,7 @@ static void bind_immutable_module(py::module &m) {
             "iter_type controls the order of iteration on sections of a given neurite. 2 values can be passed:\n"
             "- morphio.IterType.depth_first (default)\n"
             "- morphio.IterType.breadth_first (default)\n"
-            "iter_type"_a=morphio::IterType::DEPTH_FIRST);
+            "iter_type"_a=IterType::DEPTH_FIRST);
 
 
 
@@ -151,6 +152,11 @@ static void bind_immutable_module(py::module &m) {
         .def("__ne__", [](const morphio::Section& a, const morphio::Section& b) {
                 return a.operator!=(b);
             }, py::is_operator())
+        .def("__str__", [](const morphio::Section& section) {
+                std::stringstream ss;
+                ss << section;
+                return ss.str();
+            })
 
         // Topology-related member functions
         .def_property_readonly("parent", &morphio::Section::parent,
@@ -176,13 +182,13 @@ static void bind_immutable_module(py::module &m) {
                                "Returns list of section's point perimeters")
 
         // Iterators
-        .def("iter", [](morphio::Section* section, morphio::IterType type) {
+        .def("iter", [](morphio::Section* section, IterType type) {
                 switch (type) {
-                case morphio::IterType::DEPTH_FIRST:
+                case IterType::DEPTH_FIRST:
                     return py::make_iterator(section->depth_begin(), section->depth_end());
-                case morphio::IterType::BREADTH_FIRST:
+                case IterType::BREADTH_FIRST:
                     return py::make_iterator(section->breadth_begin(), section->breadth_end());
-                case morphio::IterType::UPSTREAM:
+                case IterType::UPSTREAM:
                     return py::make_iterator(section->upstream_begin(), section->upstream_end());
                 default:
                     LBTHROW(morphio::MorphioError("Only iteration types depth_first, breadth_first and upstream are supported"));
@@ -195,7 +201,7 @@ static void bind_immutable_module(py::module &m) {
             "- morphio.IterType.depth_first (default)\n"
             "- morphio.IterType.breadth_first\n"
             "- morphio.IterType.upstream\n",
-            "iter_type"_a=morphio::IterType::DEPTH_FIRST);
+            "iter_type"_a=IterType::DEPTH_FIRST);
 
 
     py::class_<morphio::MitoSection>(m, "MitoSection")
@@ -226,13 +232,13 @@ static void bind_immutable_module(py::module &m) {
                                "end of the neuronal section\n")
 
         // Iterators
-        .def("iter", [](morphio::MitoSection* section, morphio::IterType type) {
+        .def("iter", [](morphio::MitoSection* section, IterType type) {
                 switch (type) {
-                case morphio::IterType::DEPTH_FIRST:
+                case IterType::DEPTH_FIRST:
                     return py::make_iterator(section->depth_begin(), section->depth_end());
-                case morphio::IterType::BREADTH_FIRST:
+                case IterType::BREADTH_FIRST:
                     return py::make_iterator(section->breadth_begin(), section->breadth_end());
-                case morphio::IterType::UPSTREAM:
+                case IterType::UPSTREAM:
                     return py::make_iterator(section->upstream_begin(), section->upstream_end());
                 default:
                     LBTHROW(morphio::MorphioError("Only iteration types depth_first, breadth_first and upstream are supported"));
@@ -243,6 +249,6 @@ static void bind_immutable_module(py::module &m) {
             "\n"
             "If id == -1, the iteration will be successively performed starting\n"
             "at each root section",
-            "iter_type"_a=morphio::IterType::DEPTH_FIRST);
+            "iter_type"_a=IterType::DEPTH_FIRST);
 
 }

{MorphIO-2.1.3 → MorphIO-2.1.5}/binds/python/bind_misc.cpp

@@ -9,6 +9,8 @@
 #include <morphio/enums.h>
 #include <morphio/tools.h>
 
+#include "bind_enums.h"
+
 namespace py = pybind11;
 
 static void bind_misc(py::module &m) {
@@ -27,10 +29,10 @@ static void bind_misc(py::module &m) {
         .value("single_child", morphio::enums::AnnotationType::SINGLE_CHILD,
             "Indicates that a section has only one child");
 
-    py::enum_<morphio::enums::IterType>(m, "IterType")
-        .value("depth_first", morphio::enums::IterType::DEPTH_FIRST)
-        .value("breadth_first", morphio::enums::IterType::BREADTH_FIRST)
-        .value("upstream", morphio::enums::IterType::UPSTREAM)
+    py::enum_<IterType>(m, "IterType")
+        .value("depth_first", IterType::DEPTH_FIRST)
+        .value("breadth_first", IterType::BREADTH_FIRST)
+        .value("upstream", IterType::UPSTREAM)
         .export_values();
 
     py::enum_<morphio::enums::LogLevel>(m, "LogLevel")
@@ -218,13 +220,13 @@ static void bind_misc(py::module &m) {
 
 
   m.def("diff", static_cast<bool (*)(const morphio::Morphology& left, const morphio::Morphology& right, morphio::enums::LogLevel logLevel)>(&morphio::diff),
-        "Perform a diff on 2 morphologies", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
+        "Perform a diff on 2 morphologies, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
   m.def("diff", static_cast<bool (*)(const morphio::Section& left, const morphio::Section& right, morphio::enums::LogLevel logLevel)>(&morphio::diff),
-        "Perform a diff on 2 sections", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
+        "Perform a diff on 2 sections, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
 
   m.def("diff", static_cast<bool (*)(const morphio::mut::Morphology& left, const morphio::mut::Morphology& right, morphio::enums::LogLevel logLevel)>(&morphio::mut::diff),
-        "Perform a diff on 2 morphologies", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
+        "Perform a diff on 2 morphologies, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
   m.def("diff", static_cast<bool (*)(const morphio::mut::Section& left, const morphio::mut::Section& right, morphio::enums::LogLevel logLevel)>(&morphio::mut::diff),
-        "Perform a diff on 2 sections", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
+        "Perform a diff on 2 sections, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
 
 }

{MorphIO-2.1.3 → MorphIO-2.1.5}/binds/python/bind_mutable.cpp

@@ -4,6 +4,8 @@
 #include <morphio/mut/section.h>
 #include <morphio/mut/soma.h>
 
+#include "bind_enums.h"
+
 namespace py = pybind11;
 
 static void bind_mutable_module(py::module &m) {
@@ -88,13 +90,13 @@ static void bind_mutable_module(py::module &m) {
              "Write file to H5, SWC, ASC format depending on filename extension", "filename"_a)
 
         // Iterators
-        .def("iter", [](morphio::mut::Morphology* morph, morphio::IterType type) {
+        .def("iter", [](morphio::mut::Morphology* morph, IterType type) {
                 switch (type) {
-                case morphio::IterType::DEPTH_FIRST:
+                case IterType::DEPTH_FIRST:
                     return py::make_iterator(morph->depth_begin(), morph->depth_end());
-                case morphio::IterType::BREADTH_FIRST:
+                case IterType::BREADTH_FIRST:
                     return py::make_iterator(morph->breadth_begin(), morph->breadth_end());
-                case morphio::IterType::UPSTREAM:
+                case IterType::UPSTREAM:
                 default:
                 LBTHROW(morphio::MorphioError("Only iteration types depth_first and breadth_first are supported"));
                 }
@@ -104,7 +106,7 @@ static void bind_mutable_module(py::module &m) {
             "iter_type controls the order of iteration on sections of a given neurite. 2 values can be passed:\n"
             "- morphio.IterType.depth_first (default)\n"
             "- morphio.IterType.breadth_first",
-            "iter_type"_a=morphio::IterType::DEPTH_FIRST);
+            "iter_type"_a=IterType::DEPTH_FIRST);
 
 
     mutable_morphology.def("append_root_section", static_cast<std::shared_ptr<morphio::mut::Section> (morphio::mut::Morphology::*)
@@ -230,6 +232,11 @@ static void bind_mutable_module(py::module &m) {
         .def("__ne__", [](const morphio::mut::Section& a, const morphio::mut::Section& b) {
                 return a.operator!=(b);
                 }, py::is_operator())
+        .def("__str__", [](const morphio::mut::Section& section) {
+                std::stringstream ss;
+                ss << section;
+                return ss.str();
+            })
 
         .def_property_readonly("id", &morphio::mut::Section::id,
                                "Return the section ID")
@@ -280,13 +287,13 @@ static void bind_mutable_module(py::module &m) {
         .def_property_readonly("children", &morphio::mut::Section::children,
              "Returns a list of children IDs")
         // Iterators
-        .def("iter", [](morphio::mut::Section* section, morphio::IterType type) {
+        .def("iter", [](morphio::mut::Section* section, IterType type) {
                          switch (type) {
-                         case morphio::IterType::DEPTH_FIRST:
+                         case IterType::DEPTH_FIRST:
                              return py::make_iterator(section->depth_begin(), section->depth_end());
-                         case morphio::IterType::BREADTH_FIRST:
+                         case IterType::BREADTH_FIRST:
                              return py::make_iterator(section->breadth_begin(), section->breadth_end());
-                         case morphio::IterType::UPSTREAM:
+                         case IterType::UPSTREAM:
                              return py::make_iterator(section->upstream_begin(), section->upstream_end());
                          default:
                              LBTHROW(morphio::MorphioError("Only iteration types depth_first, breadth_first and upstream are supported"));
@@ -299,7 +306,7 @@ static void bind_mutable_module(py::module &m) {
             "- morphio.IterType.depth_first (default)\n"
             "- morphio.IterType.breadth_first\n"
             "- morphio.IterType.upstream\n",
-            "iter_type"_a=morphio::IterType::DEPTH_FIRST)
+            "iter_type"_a=IterType::DEPTH_FIRST)
 
         // Editing
         .def("append_section", static_cast<std::shared_ptr<morphio::mut::Section> (morphio::mut::Section::*) (const morphio::Section&, bool)>(&morphio::mut::Section::appendSection),

{MorphIO-2.1.3 → MorphIO-2.1.5}/binds/python/bindings_utils.cpp

@@ -4,7 +4,6 @@
 
 namespace py = pybind11;
 
-
 static py::array_t<float> span_array_to_ndarray(const morphio::range<const std::array<float, 3> > &span)
 {
     const void* ptr = static_cast<const void*>(span.data());

{MorphIO-2.1.3 → MorphIO-2.1.5}/include/morphio/enums.h

@@ -87,13 +87,6 @@ inline std::ostream& operator<<(std::ostream& os, const MorphologyVersion v)
     }
 }
 
-enum IterType
-{
-    DEPTH_FIRST,
-    BREADTH_FIRST,
-    UPSTREAM
-};
-
 enum SomaType
 {
     SOMA_UNDEFINED = 0,

{MorphIO-2.1.3 → MorphIO-2.1.5}/include/morphio/iterators.h

@@ -19,9 +19,8 @@ class Iterator
 
     T container;
 
-    Iterator();
-
 public:
+    Iterator();
     Iterator(const Section& section);
     Iterator(const Morphology& morphology);
     bool operator==(Iterator other) const;

{MorphIO-2.1.3 → MorphIO-2.1.5}/include/morphio/mut/section.h

@@ -125,7 +125,6 @@ private:
 
 void friendDtorForSharedPtr(Section* section);
 
-std::ostream& operator<<(std::ostream&, const Section&);
 std::ostream& operator<<(std::ostream&, std::shared_ptr<Section>);
 
 } // namespace mut

{MorphIO-2.1.3 → MorphIO-2.1.5}/include/morphio/section.h

@@ -45,11 +45,6 @@ public:
     bool operator==(const Section& other) const;
     bool operator!=(const Section& other) const;
 
-    /**
-       Euclidian distance between first and last point of the section
-    **/
-    float length() const;
-
     /**
        Depth first search iterator
     **/

{MorphIO-2.1.3 → MorphIO-2.1.5}/include/morphio/tools.h

@@ -4,24 +4,24 @@ namespace morphio
 {
 
 /**
-   Perform a diff on 2 morphologies
+   Perform a diff on 2 morphologies, returns True if items differ
 **/
 bool diff(const Morphology& left, const Morphology& right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO);
 
 /**
-   Perform a diff on 2 sections
+   Perform a diff on 2 sections, returns True if items differ
 **/
 bool diff(const Section& left, const Section& right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO);
 
 namespace mut
 {
 /**
-   Perform a diff on 2 morphologies
+   Perform a diff on 2 morphologies, returns True if items differ
 **/
 bool diff(const Morphology& left, const Morphology& right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO);
 
 /**
-   Perform a diff on 2 sections
+   Perform a diff on 2 sections, returns True if items differ
 **/
 bool diff(const Section& left, const Section& right, morphio::enums::LogLevel verbose=morphio::enums::LogLevel::INFO);
 }

{MorphIO-2.1.3 → MorphIO-2.1.5}/src/mut/morphology.cpp

@@ -267,8 +267,12 @@ void Morphology::sanitize(const morphio::plugin::DebugInfo& debugInfo)
 {
     morphio::plugin::ErrorMessages err(debugInfo._filename);
 
-    for (auto it = depth_begin(); it != depth_end(); ++it) {
+    auto it = depth_begin();
+    while (it != depth_end()) {
         std::shared_ptr<Section> section_ = *it;
+
+        // Incrementing iterator here before we potentially delete the section
+        ++it;
         unsigned int sectionId = section_->id();
 
         if (section_->isRoot())

{MorphIO-2.1.3 → MorphIO-2.1.5}/src/section.cpp

@@ -21,16 +21,6 @@ SectionType Section::type() const
     return val;
 }
 
-float Section::length() const
-{
-    auto points_ = this->points();
-    if (points_.size() < 2)
-        return 0;
-
-    size_t last = points_.size() - 1;
-    return distance(points_[0], points_[last]);
-}
-
 depth_iterator Section::depth_begin() const
 {
     return depth_iterator(*this);

{MorphIO-2.1.3 → MorphIO-2.1.5}/src/version.cpp

@@ -3,5 +3,5 @@
 #include <morphio/types.h>
 namespace morphio
 {
-  const std::string VERSION("2.1.3.dev4+g7344642.d20190626");
+  const std::string VERSION("2.1.5.dev2+g6899b1d");
 }

MorphIO-2.1.5/tests/data/nested_single_children.asc

@@ -0,0 +1,19 @@
+("CellBody"
+  (CellBody)
+  (0 0 0 1)
+)
+
+( (Color Blue)
+  (Axon)
+  (0 0 0 1)
+  (0 0 1 1)
+  (
+    (0 0 2 1)
+    (
+      (0 0 3 1)
+      (
+        (0 0 4 1)
+      )
+    )
+  )
+)

{MorphIO-2.1.3 → MorphIO-2.1.5}/tests/test_2_neurolucida.py

@@ -255,6 +255,18 @@ def test_empty_sibling():
     assert_array_equal(annotation.points, [[3, -10, 0], [0, -10, 0], [-3, -10, 0]])
     assert_array_equal(annotation.diameters, [2, 2, 2])
 
+def test_nested_single_child():
+    with captured_output() as (_, err):
+        with ostream_redirect(stdout=True, stderr=True):
+            n = Morphology(os.path.join(_path, 'nested_single_children.asc'))
+    assert_array_equal(n.root_sections[0].points,
+                       [[0., 0., 0.],
+                        [0., 0., 1.],
+                        [0., 0., 2.],
+                        [0., 0., 3.],
+                        [0., 0., 4.]])
+
+
 
 
 def test_section_single_point():

{MorphIO-2.1.3 → MorphIO-2.1.5}/tests/test_4_immut.py

@@ -147,3 +147,7 @@ def test_iterators_vasculature():
     for sec in morphology.iter():
         all_sections.remove(sec.id)
     assert_equal(len(all_sections), 0)
+
+def test_section___str__():
+    assert_equal(str(CELLS['asc'].root_sections[0]),
+                 'Section(id=0, points=[(0 0 0),..., (0 5 0)])')

{MorphIO-2.1.3 → MorphIO-2.1.5}/tests/test_5_mut.py

@@ -448,3 +448,7 @@ def test_annotation():
     assert_equal(len(n.annotations), 1)
     annotation = n.annotations[0]
     assert_equal(annotation.type, morphio.AnnotationType.single_child)
+
+def test_section___str__():
+    assert_equal(str(SIMPLE.root_sections[0]),
+                 'Section(id=0, points=[(0 0 0),..., (0 5 0)])')