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        "author": "NSE Team - Blue Brain Project",
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        "description": "# MorphIO [![Build Status](https://travis-ci.com/wizmer/morpho-tool.svg?token=KRP9rHiV52PC6mX3ACXp&branch=master)](https://travis-ci.com/wizmer/morpho-tool)\n\n## Table of content\n\n* [Installation](#installation)\n   * [Dependencies](#dependencies)\n   * [Installation instructions](#installation-instructions)\n      * [Install as a c++ library](#install-as-a-c-library)\n      * [Install as a Python package](#install-as-a-python-package)\n* [Introduction](#introduction)\n   * [Quick summary](#quick-summary)\n   * [Read-only API](#read-only-api)\n      * [C++](#c)\n      * [Python](#python)\n   * [Mutable (read/write) API](#mutable-readwrite-api)\n      * [C++](#c-1)\n      * [Python](#python-1)\n* [Converter](#converter)\n* [Usage](#usage)\n   * [Immutable C++](#immutable-c)\n   * [Immutable Python](#immutable-python)\n   * [Mutable C++](#mutable-c)\n      * [Reading morphologies](#reading-morphologies)\n      * [Creating morphologies](#creating-morphologies)\n   * [Mutable Python](#mutable-python)\n      * [Reading morphologies](#reading-morphologies-1)\n      * [Creating morphologies](#creating-morphologies-1)\n   * [Mitochondria](#mitochondria)\n* [Specification](#specification)\n\n\n\n## Installation\n\n### Dependencies\nTo build MorphIO from sources, the following dependencies are required:\n- cmake >= 3.2\n- libhdf5-dev\n- A C++11 compiler\n\nDebian:\n```shell\nsudo apt install cmake libhdf5-dev\n```\nRed Hat:\n```shell\nsudo yum install cmake3.x86_64 hdf5-devel.x86_64\n```\nMax OS:\n```shell\nbrew install hdf5 cmake\n```\n\nBB5\n```shell\nsource /opt/rh/rh-python36/enable\nmodule load gcc/5.4.0 nix/cmake/3.9.6\n```\n\n### Installation instructions\n\n#### Install as a c++ library\n\nFor manual installation:\n```shell\ngit clone git@github.com:bluebrain/morphio.git --recursive\ncd morphio\nmkdir build && cd build\ncmake ..\nmake\n```\n\nTo use the installed library:\n```CMake\nfind_package(MorphIO REQUIRED)\n\ntarget_link_libraries(mylib MorphIO::morphio)\n```\n\n#### Install as a Python package\n\nThe python binding can directly be installed using pip:\n```shell\npip install morphio\n```\n\n## Introduction\n\nMorphIO is a library for reading and writing neuron morphology files.\nIt supports the following formats:\n- SWC\n- ASC (aka. neurolucida)\n- H5 v1\n- H5 v2\n\nIt provides 3 classes that are the starting point of every morphology analysis:\n- Soma: contains the information related to the soma\n\n- Section: a section is the succession of points between two bifurcation. To the bare minimum\nthe Section object will contain the section type, the position and diameter of each point.\n\n- Morphology: the morphology object will contain general information about the loaded cell\nbut will also provide accessors to the different section.\n\nOne important concept is that MorphIO is splitted into a *read-only* part and a *read/write* one.\n\n### Quick summary\n*C++ vs Python*:\n- c++ accessors become python properties\n- style: c++ functions are camel case while python ones are snake case\n\n### Include/imports\n\n- C++ mutable\n```C++\n#include <morphio/morphology.h>\n#include <morphio/section.h>\n#include <morphio/soma.h>\n```\n\n- Python mutable\n```python\nfrom morphio import Morphology, Section, Soma\n```\n\n- C++ immutable\n```C++\n#include <morphio/mut/morphology.h>\n#include <morphio/mut/section.h>\n#include <morphio/mut/soma.h>\n```\n\n- Python immutable\n```python\nfrom morphio.mut import Morphology, Section, Soma\n```\n\n### Read-only API\nThe read-only API aims at providing better performances as its internal data\nrepresentation is contiguous in memory. All accessors return immutable objects.\n\nInternally, in this API the morphology object is in fact where all data are stored. The\nSoma and Section classes are lightweight classes that provide views on the Morphology data.\n\nFor more convenience, all section data are accessed through properties, such as:\n```python\npoints = section.points\ndiameters = section.diameters\n```\n\n\n#### C++\nIn C++ the API is available under the `morphio/mut` namespace:\n```C++\n#include <morphio/mut/morphology.h>\n#include <morphio/mut/section.h>\n#include <morphio/mut/soma.h>\n```\n\n#### Python\nIn Python the API is available under the `morphio.mut` module:\n\n```Python\nfrom morphio.mut import Morphology, Section, Soma\n```\n\n\n### C++\n\n```cpp\n#include <morphio/morphology.h>\n#include <morphio/section.h>\n\nint main()\n{\n    auto m = morphio::Morphology(\"sample.asc\");\n\n    auto roots = m.rootSections();\n\n    auto first_root = roots[0];\n\n    // iterate on sections starting at first_root\n    for(auto it = first_root.depth_begin(); it != first_root.depth_end(); ++it) {\n        const morphio::Section &section = (*it);\n\n        std::cout << \"Section type: \" << section.type() << std::endl;\n        std::cout << \"Section id: \" << section.id() << std::endl;\n        std::cout << \"Parent section id: \" << section.parent().id() << std::endl;\n        std::cout << \"Number of child sections: \" << section.children().size() << std::endl;\n        std::cout << \"X - Y - Z - Diameter\" << std::endl;\n        for(int i = 0; i<section.points().size(); ++i) {\n            std::cout <<\n                section.points()[i][0] << ' ' <<\n                section.points()[i][1] << ' ' <<\n                section.points()[i][2] << ' ' <<\n                section.diameters()[i] << std::endl;\n        }\n\n        std::cout << std::endl;\n    }\n}\n```\n\n### Python\n\n```python\nfrom morphio import Morphology\n\nm = Morphology(\"sample.asc\")\nroots = m.rootSections\nfirst_root = roots[0]\n\n# iterate on sections starting at first_root\nfor section in first_root.iter():\n    print(\"Section type: {}\".format(section.type))\n    print(\"Section id: {}\".format(section.id))\n    print(\"Parent section id: {}\".format(section.parent.id))\n    print(\"Number of child sections: {}\".format(len(section.children)))\n    print(\"X - Y - Z - Diameter\")\n\n    for point, diameter in zip(section.points, section.diameters):\n        print('{} - {}'.format(point, diameter))\n```\n\n\n\n\n#### Creating morphologies with the mutable API\n\nHere is a simple example to create a morphology from scratch and writing it to disk\n\n```C++\n#include <morphio/mut/morphology.h>\n\nint main()\n{\n    morphio::mut::Morphology morpho;\n    morpho.soma()->points() = {{0, 0, 0}, {1, 1, 1}};\n    morpho.soma()->diameters() = {1, 1};\n\n    std::shared_ptr<morphio::mut::Section> section = morpho.appendRootSection(\n        morphio::Property::PointLevel(\n            {{2, 2, 2}, {3, 3, 3}}, // x,y,z coordinates of each point\n            {4, 4}, // diameter of each point\n            {5, 5}),\n        morphio::SectionType::SECTION_AXON); // (optional) perimeter of each point\n\n    std::shared_ptr<morphio::mut::Section> childSection = section.appendSection(\n        morphio::Property::PointLevel(\n            {{3, 3, 3}, {4, 4, 4}},\n            {4, 4},\n            {5, 5}),\n        morphio::SectionType::SECTION_AXON);\n\n    // Writing the file in the 3 formats\n    morpho.write(\"outfile.asc\");\n    morpho.write(\"outfile.swc\");\n    morpho.write(\"outfile.h5\");\n}\n```\n\n### Mutable Python\n\n#### Reading morphologies\n\n```python\nfrom morphio.mut import Morphology\n\nm = Morphology(\"sample.asc\")\nroots = m.root_sections\nfirst_root = roots[0]\n\n# iterate on sections starting at first_root\nfor section in m.iter(first_root):\n    print(\"Section type: {}\".format(section.type))\n    print(\"Section id: {}\".format(section.id))\n    if not m.is_root(section):\n        print(\"Parent section id: {}\".format(m.parent(section)))\n    print(\"Number of child sections: {}\".format(len(m.children(section))))\n    print(\"X - Y - Z - Diameter\")\n\n    for point, diameter in zip(section.points, section.diameters):\n        print('{} - {}'.format(point, diameter))\n```\n\n#### Creating morphologies\n\nHere is a simple example to create a morphology from scratch and writing it to disk\n\n```python\nfrom morphio.mut import Morphology\nfrom morphio import SectionType, PointLevel\n\nmorpho = Morphology()\nmorpho.soma.points = [[0, 0, 0], [1, 1, 1]]\nmorpho.soma.diameters = [1, 1]\n\nsection = morpho.append_root_section(\n    PointLevel(\n        [[2, 2, 2], [3, 3, 3]],  # x, y, z coordinates of each point\n        [4, 4],  # diameter of each point\n        [5, 5]),\n    SectionType.axon)  # (optional) perimeter of each point\n\nchild_section = section.append_section(\n    PointLevel(\n        [[3, 3, 3], [4, 4, 4]],\n        [4, 4],\n        [5, 5])) # section type is omitted -> parent section type will be used\n\nmorpho.write(\"outfile.asc\")\nmorpho.write(\"outfile.swc\")\nmorpho.write(\"outfile.h5\")\n```\n### Opening flags\nWhen opening the file, modifier flags can be passed to alter the morphology representation.\nThe following flags are supported:\n\n- morphio::NO\\_MODIFIER:\nThis is the default flag, it will do nothing.\n- morphio::TWO\\_POINTS\\_SECTIONS:\nEach section gets reduce to a line made of the first and last point.\n- morphio::SOMA\\_SPHERE:\nThe soma is reduced to a sphere which is the center of gravity of the real soma.\n- morphio::NO\\_DUPLICATES:\nThe duplicate point are not present. It means the first point of each section\nis no longer the last point of the parent section.\n- morphio::NRN\\_ORDER:\nNeurite are reordered according to the\n[NEURON simulator ordering](https://github.com/neuronsimulator/nrn/blob/2dbf2ebf95f1f8e5a9f0565272c18b1c87b2e54c/share/lib/hoc/import3d/import3d_gui.hoc#L874)\n\nMultiple flags can be passed by using the standard bit flag manipulation (works the same way in C++ and Python):\nC++:\n```C++\n#include <morphio/Morphology.h>\nMorphology(\"myfile.asc\", options=morphio::NO_DUPLICATES|morphio::NRN_ORDER)\n```\n\nPython:\n```python\nfrom morphio import Morphology, Option\nMorphology(\"myfile.asc\", options=Option.no_duplicates|Option.nrn_order)\n```\n\n### Mitochondria\n\nIt is also possible to read and write mitochondria from/to the h5 files (*SWC and ASC are not supported*).\nAs mitochondria can be represented as trees, one can define the concept of *mitochondrial section*\nsimilar to neuronal section and end up with a similar API. The morphology object has a\n*mitochondria* handle method that exposes the basic methods:\n\n- root_sections: returns the section ID of the starting mitochondrial section\nof each mitochondrion.\n- section(id): returns a given mitochondrial section\n- append_section: creates a new mitochondrial section\n_ depth_begin: a depth first iterator\n_ breadth_begin: a breadth first iterator\n_ upstream_begin: an upstream iterator\n\n```python\nfrom morphio.mut import Morphology\nfrom morphio import MitochondriaPointLevel, PointLevel, SectionType\n\nmorpho = Morphology()\n\n# A neuronal section that will store mitochondria\nsection = morpho.append_root_section(\n    PointLevel([[2, 2, 2], [3, 3, 3]], [4, 4], [5, 5]),\n    SectionType.axon)\n\n# Creating a new mitochondrion\nmito_id = morpho.mitochondria.append_section(\n    -1,\n    MitochondriaPointLevel([section.id, section.id], # section id hosting the mitochondria point\n                           [0.5, 0.6], # relative distance between the start of the section and the point\n                           [10, 20] # mitochondria diameters\n                           ))\n\n# Appending a new mitochondrial section to the previous one\nmorpho.mitochondria.append_section(\n    mito_id, MitochondriaPointLevel([0, 0, 0, 0],\n                                    [0.6, 0.7, 0.8, 0.9],\n                                    [20, 30, 40, 50]))\n\n# Iteration works the same as iteration on neuronal sections\nfirst_root = morpho.mitochondria.root_sections[0]\nfor section_id in morpho.mitochondria.depth_begin(first_root):\n    section = morpho.mitochondria.section(section_id)\n    print('relative_path_length - diameter')\n    for relative_path_length, diameter in zip(section.diameters,\n                                              section.relative_path_lengths):\n        print(\"{} - {}\".format(relative_path_length, diameter))\n```\n\nReading mithochondria from H5 files:\n\n```python\nfrom morphio import Morphology\n\nmorpho = Morphology(\"file_with_mithochondria.h5\")\n\nfor mitochondrial_section in morpho.mitochondria.root_sections:\n    print('{neurite_id}, {relative_path_lengths}, {diameters}'.format(\n          neurite_id=mitochondrial_section.neurite_section_ids,\n          relative_path_lengths=mitochondrial_section.relative_path_lengths,\n          diameters=mitochondrial_section.diameters))\n\n    print(\"Number of children: {}\".format(len(mitochondrial_section.children)))\n```\n\n### Tips\n#### Maximum number of warnings\nOn can control the maximum number of warnings using the command:\n```python\n\n# Will stop displaying warnings after 100 warnings\nmorphio.set_maximum_warnings(100)\n\n# Will never stop displaying warnings\nmorphio.set_maximum_warnings(-1)\n\n# Warnings won't be displayed\nmorphio.set_maximum_warnings(0)\n```\n\n# Specification\nSee https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md\n\n\n",
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