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Bring back morphology types as enum array in HTTP API #271

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Jan 11, 2018
Merged

Bring back morphology types as enum array in HTTP API #271

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11 changes: 10 additions & 1 deletion brayns/common/types.h
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Original file line number Diff line number Diff line change
Expand Up @@ -256,13 +256,22 @@ enum class GeometryQuality
/** Morphology element types */
enum class MorphologySectionType
{
undefined = 0x00,
soma = 0x01,
axon = 0x02,
dendrite = 0x04,
apical_dendrite = 0x08,
all = 0xff
};
using MorphologySectionTypes = std::vector<MorphologySectionType>;

template <typename T>
size_t enumsToBitmask(const std::vector<T> enums)
{
size_t bit{0};
for (auto& val : enums)
bit |= size_t(val);
return bit;
}

/**
* @brief The Histogram struct contains the range as well as the values of the
Expand Down
6 changes: 3 additions & 3 deletions brayns/io/MorphologyLoader.cpp
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Expand Up @@ -496,7 +496,7 @@ class MorphologyLoader::Impl
try
{
const size_t morphologySectionTypes =
_geometryParameters.getMorphologySectionTypes();
enumsToBitmask(_geometryParameters.getMorphologySectionTypes());

brain::neuron::Morphology morphology(uri, transformation);
const auto sectionTypes = _getSectionTypes(morphologySectionTypes);
Expand Down Expand Up @@ -590,7 +590,7 @@ class MorphologyLoader::Impl
Vector3f translation;

const size_t morphologySectionTypes =
_geometryParameters.getMorphologySectionTypes();
enumsToBitmask(_geometryParameters.getMorphologySectionTypes());

brain::neuron::Morphology morphology(uri, transformation);
brain::neuron::SectionTypes sectionTypes;
Expand Down Expand Up @@ -871,7 +871,7 @@ class MorphologyLoader::Impl
{
bool returnValue = true;
const size_t morphologySectionTypes =
_geometryParameters.getMorphologySectionTypes();
enumsToBitmask(_geometryParameters.getMorphologySectionTypes());
if (morphologySectionTypes ==
static_cast<size_t>(MorphologySectionType::soma))
return _importMorphologyAsPoint(index, material, transformation,
Expand Down
22 changes: 17 additions & 5 deletions brayns/parameters/GeometryParameters.cpp
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Expand Up @@ -112,7 +112,7 @@ GeometryParameters::GeometryParameters()
, _radiusCorrection(0.f)
, _colorScheme(ColorScheme::none)
, _geometryQuality(GeometryQuality::high)
, _morphologySectionTypes(size_t(MorphologySectionType::all))
, _morphologySectionTypes{MorphologySectionType::all}
, _metaballsGridSize(0)
, _metaballsThreshold(1.f)
, _metaballsSamplesFromSoma(3)
Expand Down Expand Up @@ -297,8 +297,20 @@ bool GeometryParameters::_parse(const po::variables_map& vm)
_circuitConfiguration._circuitMeshFolder =
vm[PARAM_CIRCUIT_MESH_FOLDER].as<std::string>();
if (vm.count(PARAM_MORPHOLOGY_SECTION_TYPES))
_morphologySectionTypes =
vm[PARAM_MORPHOLOGY_SECTION_TYPES].as<size_t>();
{
_morphologySectionTypes.clear();
const auto bits = vm[PARAM_MORPHOLOGY_SECTION_TYPES].as<size_t>();
if (bits & size_t(MorphologySectionType::soma))
_morphologySectionTypes.push_back(MorphologySectionType::soma);
if (bits & size_t(MorphologySectionType::axon))
_morphologySectionTypes.push_back(MorphologySectionType::axon);
if (bits & size_t(MorphologySectionType::dendrite))
_morphologySectionTypes.push_back(MorphologySectionType::dendrite);
if (bits & size_t(MorphologySectionType::apical_dendrite))
_morphologySectionTypes.push_back(
MorphologySectionType::apical_dendrite);
}

if (vm.count(PARAM_MORPHOLOGY_LAYOUT))
{
size_ts values = vm[PARAM_MORPHOLOGY_LAYOUT].as<size_ts>();
Expand Down Expand Up @@ -473,8 +485,8 @@ void GeometryParameters::print()
<< (_circuitConfiguration._circuitMeshTransformation ? "Yes"
: "No")
<< std::endl;
BRAYNS_INFO << "Morphology section types : " << _morphologySectionTypes
<< std::endl;
BRAYNS_INFO << "Morphology section types : "
<< enumsToBitmask(_morphologySectionTypes) << std::endl;
BRAYNS_INFO << "Morphology Layout : " << std::endl;
BRAYNS_INFO << " - Columns : "
<< _morphologyLayout.nbColumns << std::endl;
Expand Down
7 changes: 5 additions & 2 deletions brayns/parameters/GeometryParameters.h
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Expand Up @@ -207,7 +207,10 @@ class GeometryParameters : public AbstractParameters
const GeometryQuality value) const;

/** Morphology section types*/
size_t getMorphologySectionTypes() const { return _morphologySectionTypes; }
const MorphologySectionTypes& getMorphologySectionTypes() const
{
return _morphologySectionTypes;
}
/** Morphology layout */
const MorphologyLayout& getMorphologyLayout() const
{
Expand Down Expand Up @@ -341,7 +344,7 @@ class GeometryParameters : public AbstractParameters
float _radiusCorrection;
ColorScheme _colorScheme;
GeometryQuality _geometryQuality;
size_t _morphologySectionTypes;
MorphologySectionTypes _morphologySectionTypes;
MorphologyLayout _morphologyLayout;
bool _generateMultipleModels;
std::string _molecularSystemConfig;
Expand Down
1 change: 0 additions & 1 deletion plugins/extensions/plugins/SDK.h
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,6 @@ STATICJSON_DECLARE_ENUM(brayns::GeometryQuality,
{"high", brayns::GeometryQuality::high});

STATICJSON_DECLARE_ENUM(brayns::MorphologySectionType,
{"undefined", brayns::MorphologySectionType::undefined},
{"soma", brayns::MorphologySectionType::soma},
{"axon", brayns::MorphologySectionType::axon},
{"dendrite", brayns::MorphologySectionType::dendrite},
Expand Down
6 changes: 4 additions & 2 deletions tests/brayns.cpp
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Expand Up @@ -111,8 +111,10 @@ BOOST_AUTO_TEST_CASE(defaults)
brayns::SceneEnvironment::none);
BOOST_CHECK(geomParams.getGeometryQuality() ==
brayns::GeometryQuality::high);
BOOST_CHECK_EQUAL(geomParams.getMorphologySectionTypes(),
size_t(brayns::MorphologySectionType::all));
BOOST_CHECK_EQUAL(
brayns::enumsToBitmask(geomParams.getMorphologySectionTypes()),
brayns::enumsToBitmask(std::vector<brayns::MorphologySectionType>{
brayns::MorphologySectionType::all}));
BOOST_CHECK_EQUAL(geomParams.getMorphologyLayout().nbColumns, 0);
BOOST_CHECK_EQUAL(geomParams.getCircuitStartSimulationTime(), 0.f);
BOOST_CHECK_EQUAL(geomParams.getCircuitEndSimulationTime(),
Expand Down