Skip to content

Commit

Permalink
WIP Template Morphology in order to Create GlialCell with their own S…
Browse files Browse the repository at this point in the history 
…ection Type: GlialSectionType
  • Loading branch information
@jacquemi-bbp
jacquemi-bbp committed Mar 17, 2021
1 parent 8e61eaf commit f300d9f
Show file tree
Hide file tree
Showing 16 changed files with 333 additions and 95 deletions.
6 changes: 0 additions & 6 deletions binds/python/bind_immutable.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -124,9 +124,6 @@ void bind_immutable_module(py::module& m) {
"Return the graph connectivity of the morphology "
"where each section is seen as a node\nNote: -1 is the soma node")
.def_property_readonly("soma_type", &morphio::Morphology::somaType, "Returns the soma type")
// .def_property_readonly("cell_family",
// &morphio::Morphology::cellFamily,
// "Returns the cell family (neuron or glia)")
.def_property_readonly("version", &morphio::Morphology::version, "Returns the version")

// Iterators
Expand Down Expand Up @@ -252,9 +249,6 @@ void bind_immutable_module(py::module& m) {
"Return the graph connectivity of the GlialCell "
"where each section is seen as a node\nNote: -1 is the soma node")
.def_property_readonly("soma_type", &morphio::GlialCell::somaType, "Returns the soma type")
// .def_property_readonly("cell_family",
// &morphio::GlialCell::cellFamily,
// "Returns the cell family (neuron or glia)")
.def_property_readonly("version", &morphio::GlialCell::version, "Returns the version")

// Iterators
Expand Down
3 changes: 0 additions & 3 deletions binds/python/bind_misc.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -200,9 +200,6 @@ void bind_misc(py::module& m) {
"CellLevel",
"Container class for information available at the "
"cell level (cell type, file version, soma type)")
// .def_readwrite("cell_family",
// &morphio::Property::CellLevel::_cellFamily,
// "Returns the cell family (neuron or glia)")
.def_readwrite("soma_type",
&morphio::Property::CellLevel::_somaType,
"Returns the soma type")
Expand Down
273 changes: 269 additions & 4 deletions binds/python/bind_mutable.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
#include <morphio/mut/mitochondria.h>
#include <morphio/mut/morphology.h>
#include <morphio/morphology.h>
#include <morphio/glial_cell.h>

#include <array>

Expand Down Expand Up @@ -42,6 +43,7 @@ void bind_mutable_module(py::module& m) {
"Additional Ctor that accepts as filename any python "
"object that implements __repr__ or __str__")


// Cell sub-part accessors
.def_property_readonly("sections",
&morphio::mut::Morphology::sections,
Expand Down Expand Up @@ -122,10 +124,6 @@ void bind_mutable_module(py::module& m) {
"Return the graph connectivity of the morphology "
"where each section is seen as a node\nNote: -1 is the soma node")

// .def_property_readonly("cell_family",
// &morphio::mut::Morphology::cellFamily,
// "Returns the cell family (neuron or glia)")

.def_property_readonly("soma_type",
&morphio::mut::Morphology::somaType,
"Returns the soma type")
Expand Down Expand Up @@ -178,6 +176,161 @@ void bind_mutable_module(py::module& m) {
"If recursive == true, all descendent will be appended as well",
"mutable_section"_a,
"recursive"_a = false);

py::class_<morphio::mut::GlialCell>(m, "GlialCell")
.def(py::init<>())
.def(py::init<const std::string&, unsigned int>(),
"filename"_a,
"options"_a = morphio::enums::Option::NO_MODIFIER)
.def(py::init<const morphio::GlialCell&, unsigned int>(),
"morphology"_a,
"options"_a = morphio::enums::Option::NO_MODIFIER)
.def(py::init<const morphio::mut::GlialCell&, unsigned int>(),
"morphology"_a,
"options"_a = morphio::enums::Option::NO_MODIFIER)
.def(py::init([](py::object arg, unsigned int options) {
return std::unique_ptr<morphio::mut::GlialCell>(
new morphio::mut::GlialCell(py::str(arg), options));
}),
"filename"_a,
"options"_a = morphio::enums::Option::NO_MODIFIER,
"Additional Ctor that accepts as filename any python "
"object that implements __repr__ or __str__")


// Cell sub-part accessors
.def_property_readonly("sections",
&morphio::mut::GlialCell::sections,
"Returns a list containing IDs of all sections. "
"The first section of the vector is the soma section")
.def_property_readonly("root_sections",
&morphio::mut::GlialCell::rootSections,
"Returns a list of all root sections IDs "
"(sections whose parent ID are -1)",
py::return_value_policy::reference)
.def_property_readonly(
"soma",
static_cast<std::shared_ptr<morphio::mut::Soma>& (morphio::mut::GlialCell::*) ()>(
&morphio::mut::GlialCell::soma),
"Returns a reference to the soma object\n\n"
"Note: multiple morphologies can share the same Soma "
"instance")
.def_property_readonly(
"mitochondria",
static_cast<morphio::mut::Mitochondria& (morphio::mut::GlialCell::*) ()>(
&morphio::mut::GlialCell::mitochondria),
"Returns a reference to the mitochondria container class")
.def_property_readonly(
"endoplasmic_reticulum",
static_cast<morphio::mut::EndoplasmicReticulum& (morphio::mut::GlialCell::*) ()>(
&morphio::mut::GlialCell::endoplasmicReticulum),
"Returns a reference to the endoplasmic reticulum container class")
.def_property_readonly("annotations",
&morphio::mut::GlialCell::annotations,
"Returns a list of annotations")
.def_property_readonly("markers",
&morphio::mut::GlialCell::markers,
"Returns the list of NeuroLucida markers")
.def("section",
&morphio::mut::GlialCell::section,
"Returns the section with the given id\n\n"
"Note: multiple morphologies can share the same Section "
"instances",
"section_id"_a)
.def("build_read_only",
&morphio::mut::GlialCell::buildReadOnly,
"Returns the data structure used to create read-only "
"morphologies")
.def("append_root_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (morphio::mut::GlialCell::*)(
const morphio::Property::PointLevel&, morphio::GlialSectionType)>(
&morphio::mut::GlialCell::appendRootSection),
"Append a root Section\n",
"point_level_properties"_a,
"section_type"_a)
.def("append_root_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (morphio::mut::GlialCell::*)(
const morphio::GlialSection&, bool)>(&morphio::mut::GlialCell::appendRootSection),
"Append the existing immutable Section as a root section\n"
"If recursive == true, all descendent will be appended as "
"well",
"immutable_section"_a,
"recursive"_a = false)

.def("delete_section",
&morphio::mut::GlialCell::deleteSection,
"Delete the given section\n"
"\n"
"Will silently fail if the section is not part of the "
"tree\n"
"\n"
"If recursive == true, all descendent sections will be "
"deleted as well\n"
"Else, children will be re-attached to their grand-parent",
"section"_a,
"recursive"_a = true)

.def("as_immutable",
[](const morphio::mut::GlialCell* morph) { return morphio::GlialCell(*morph); })

.def_property_readonly("connectivity",
&morphio::mut::GlialCell::connectivity,
"Return the graph connectivity of the morphology "
"where each section is seen as a node\nNote: -1 is the soma node")

.def_property_readonly("soma_type",
&morphio::mut::GlialCell::somaType,
"Returns the soma type")

.def_property_readonly("version", &morphio::mut::GlialCell::version, "Returns the version")

.def("sanitize",
static_cast<void (morphio::mut::GlialCell::*) ()>(
&morphio::mut::GlialCell::sanitize),
"Fixes the morphology single child sections and issues warnings"
"if the section starts and ends are inconsistent")

.def(
"write",
[](morphio::mut::GlialCell* morph, py::object arg) { morph->write(py::str(arg)); },
"Write file to H5, SWC, ASC format depending on filename "
"extension",
"filename"_a)

// Iterators
.def(
"iter",
[](morphio::mut::GlialCell* morph, IterType type) {
switch (type) {
case IterType::DEPTH_FIRST:
return py::make_iterator(morph->depth_begin(), morph->depth_end());
case IterType::BREADTH_FIRST:
return py::make_iterator(morph->breadth_begin(), morph->breadth_end());
case IterType::UPSTREAM:
default:
throw morphio::MorphioError("Only iteration types depth_first and "
"breadth_first are supported");
}
},
py::keep_alive<0, 1>() /* Essential: keep object alive
while iterator exists */
,
"Section iterator that runs successively on every "
"neurite\n"
"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 = IterType::DEPTH_FIRST)
.def("append_root_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (
morphio::mut::GlialCell::*)(const std::shared_ptr<morphio::mut::GlialSection>&, bool)>(
&morphio::mut::GlialCell::appendRootSection),
"Append the existing mutable Section as a root section\n"
"If recursive == true, all descendent will be appended as well",
"mutable_section"_a,
"recursive"_a = false);


py::class_<morphio::mut::Mitochondria>(m, "Mitochondria")
.def(py::init<>())
Expand Down Expand Up @@ -476,6 +629,118 @@ void bind_mutable_module(py::module& m) {
"center",
[](morphio::mut::Soma* soma) { return py::array(3, soma->center().data()); },
"Returns the center of gravity of the soma points");

py::class_<morphio::mut::GlialSection, std::shared_ptr<morphio::mut::GlialSection>>(m, "GlialSection")
.def("__str__",
[](const morphio::mut::GlialSection& section) {
std::stringstream ss;
ss << section;
return ss.str();
})

.def_property_readonly("id", &morphio::mut::GlialSection::id, "Return the section ID")
.def_property(
"type",
static_cast<const morphio::GlialSectionType& (morphio::mut::GlialSection::*) () const>(
&morphio::mut::GlialSection::type),
[](morphio::mut::GlialSection* section, morphio::GlialSectionType _type) {
section->type() = _type;
},
"Returns the morphological type of this section "
"(dendrite, axon, ...)")
.def_property(
"points",
[](morphio::mut::GlialSection* section) {
return py::array(static_cast<py::ssize_t>(section->points().size()),
section->points().data());
},
[](morphio::mut::GlialSection* section, py::array_t<morphio::floatType> _points) {
section->points() = array_to_points(_points);
},
"Returns the coordinates (x,y,z) of all points of this section")
.def_property(
"diameters",
[](morphio::mut::GlialSection* section) {
return py::array(static_cast<py::ssize_t>(section->diameters().size()),
section->diameters().data());
},
[](morphio::mut::GlialSection* section, py::array_t<morphio::floatType> _diameters) {
section->diameters() = _diameters.cast<std::vector<morphio::floatType>>();
},
"Returns the diameters of all points of this section")
.def_property(
"perimeters",
[](morphio::mut::GlialSection* section) {
return py::array(static_cast<py::ssize_t>(section->perimeters().size()),
section->perimeters().data());
},
[](morphio::mut::GlialSection* section, py::array_t<morphio::floatType> _perimeters) {
section->perimeters() = _perimeters.cast<std::vector<morphio::floatType>>();
},
"Returns the perimeters of all points of this section")
.def_property_readonly("is_root",
&morphio::mut::GlialSection::isRoot,
"Return True if section is a root section")
.def_property_readonly("parent",
&morphio::mut::GlialSection::parent,
"Get the parent ID\n\n"
"Note: Root sections return -1")
.def_property_readonly("children",
&morphio::mut::GlialSection::children,
"Returns a list of children IDs")
// Iterators
.def(
"iter",
[](morphio::mut::GlialSection* section, IterType type) {
switch (type) {
case IterType::DEPTH_FIRST:
return py::make_iterator(section->depth_begin(), section->depth_end());
case IterType::BREADTH_FIRST:
return py::make_iterator(section->breadth_begin(), section->breadth_end());
case IterType::UPSTREAM:
return py::make_iterator(section->upstream_begin(), section->upstream_end());
default:
throw morphio::MorphioError("Only iteration types depth_first, breadth_first and "
"upstream are supported");
}
},
py::keep_alive<0, 1>() /* Essential: keep object alive while iterator exists */,
"GlialSection iterator\n"
"\n"
"iter_type controls the iteration order. 3 values can be passed:\n"
"- morphio.IterType.depth_first (default)\n"
"- morphio.IterType.breadth_first\n"
"- morphio.IterType.upstream\n",
"iter_type"_a = IterType::DEPTH_FIRST)

// Editing
.def("append_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (morphio::mut::GlialSection::*)(
const morphio::GlialSection&, bool)>(&morphio::mut::GlialSection::appendSection),
"Append the existing immutable GlialSection to this section"
"If recursive == true, all descendent will be appended as well",
"immutable_section"_a,
"recursive"_a = false)

.def("append_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (
morphio::mut::GlialSection::*)(const std::shared_ptr<morphio::mut::GlialSection>&, bool)>(
&morphio::mut::GlialSection::appendSection),
"Append the existing mutable GlialSection to this section\n"
"If recursive == true, all descendent will be appended as well",
"mutable_section"_a,
"recursive"_a = false)

.def("append_section",
static_cast<std::shared_ptr<morphio::mut::GlialSection> (morphio::mut::GlialSection::*)(
const morphio::Property::PointLevel&, morphio::GlialSectionType)>(
&morphio::mut::GlialSection::appendSection),
"Append a new GlialSection to this section\n"
" If section_type is omitted or set to 'undefined'"
" the type of the parent section will be used",
"point_level_properties"_a,
"section_type"_a = morphio::GlialSectionType::UNDEFINED);


py::class_<morphio::mut::EndoplasmicReticulum>(m, "EndoplasmicReticulum")
.def(py::init<>())
Expand Down
3 changes: 0 additions & 3 deletions include/morphio/enums.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -41,9 +41,6 @@ enum AnnotationType {
SINGLE_CHILD,
};

/** The cell family represented by morphio::Morphology. */
//enum CellFamily { NEURON = 0, GLIA = 1 };

enum SomaType {
SOMA_UNDEFINED = 0,
SOMA_SINGLE_POINT,
Expand Down
2 changes: 1 addition & 1 deletion include/morphio/mut/glial_cell.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ bool _checkDuplicatePoint(const std::shared_ptr<GlialSection>& parent,
class GlialCell
{
public:
using Family = CellFamily::GLIA;
using CellType = CellFamily::GLIA;

GlialCell()
: _counter(0)
Expand Down
2 changes: 1 addition & 1 deletion include/morphio/mut/morphology.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ bool _checkDuplicatePoint(const std::shared_ptr<Section>& parent,
class Morphology
{
public:
using Family = CellFamily::NEURON;
using CellType = CellFamily::NEURON;

Morphology()
: _counter(0)
Expand Down
Loading

0 comments on commit f300d9f

Please sign in to comment.