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Refactor hdf5 read_points and avoid temp obj (#170)
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Co-authored-by: Matthias Wolf <[email protected]>
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@ferdonline @matz-e
ferdonline and matz-e authored Mar 10, 2020
1 parent 594dcf2 commit 33f69c7
Showing 1 changed file with 43 additions and 67 deletions.
110 changes: 43 additions & 67 deletions src/readers/morphologyHDF5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@ void MorphologyHDF5::_resolveV1() {

if (_pointsDims.size() != 2 || _pointsDims[1] != _pointColumns) {
throw morphio::RawDataError("Opening morphology file '" + _file->getName() +
"': bad number of dimensions in 'points' dataspace");
"': bad number of dimensions in 'points' dataspace");
}

_sections.reset(new HighFive::DataSet(_file->getDataSet(_d_structure)));
Expand Down Expand Up @@ -199,10 +199,10 @@ HighFive::DataSet MorphologyHDF5::_getStructureDataSet(size_t nSections) {


/**
Returns true if the neuron has no neurites
Returns true if the neuron has neurites (for MORPHOLOGY_VERSION_H5_2)
**/
static inline bool noNeurites(int firstSectionOffset) {
return (firstSectionOffset == -1);
static inline bool v2HasNeurites(int firstSectionOffset) {
return (firstSectionOffset > -1);
}


Expand All @@ -213,6 +213,32 @@ void MorphologyHDF5::_readPoints(int firstSectionOffset) {
auto& somaPoints = _properties._somaLevel._points;
auto& somaDiameters = _properties._somaLevel._diameters;

auto loadPoints = [&](const std::vector<std::vector<float>>& hd5fData, bool hasNeurites) {
const std::size_t section_offset = hasNeurites ? std::size_t(firstSectionOffset)
: hd5fData.size();

// points and diameters are PODs. Fastest to resize then assign values
somaPoints.resize(somaPoints.size() + section_offset);
somaDiameters.resize(somaDiameters.size() + section_offset);
for (std::size_t i = 0; i < section_offset; ++i) {
const auto& p = hd5fData[i];
somaPoints[i] = {p[0], p[1], p[2]};
somaDiameters[i] = p[3];
}

if (hasNeurites) {
const size_t size = (points.size() + hd5fData.size() - section_offset);
points.resize(size);
diameters.resize(size);
for (std::size_t i = section_offset; i < hd5fData.size(); ++i) {
const auto& p = hd5fData[i];
const std::size_t section_i = i - section_offset;
points[section_i] = {p[0], p[1], p[2]};
diameters[section_i] = p[3];
}
}
};

if (_properties.version() == MORPHOLOGY_VERSION_H5_2) {
auto dataset = [this]() {
std::string path = "/" + _g_root + "/" + _stage + "/" + _d_points;
Expand All @@ -231,57 +257,11 @@ void MorphologyHDF5::_readPoints(int firstSectionOffset) {
}
std::vector<std::vector<float>> vec(dims[0]);
dataset.read(vec);

std::size_t offset = vec.size();
if (firstSectionOffset >= 0) {
offset = static_cast<size_t>(firstSectionOffset);
}

somaPoints.reserve(somaPoints.size() + offset);
somaDiameters.reserve(somaDiameters.size() + offset);
for (std::size_t i = 0; i < offset; ++i) {
const auto& p = vec[i];
somaPoints.emplace_back(Point{p[0], p[1], p[2]});
somaDiameters.emplace_back(p[3]);
}

if (!noNeurites(firstSectionOffset)) {
size_t size = (points.size() + vec.size() -
static_cast<unsigned int>(firstSectionOffset));
points.reserve(size);
diameters.reserve(size);
for (std::size_t i = offset; i < vec.size(); ++i) {
const auto& p = vec[i];
points.emplace_back(Point{p[0], p[1], p[2]});
diameters.emplace_back(p[3]);
}
}
return;
}

std::vector<std::vector<float>> vec;
vec.resize(_pointsDims[0]);
_points->read(vec);

std::size_t offset = vec.size();
if (firstSectionOffset >= 0) {
offset = static_cast<unsigned int>(firstSectionOffset);
}

somaPoints.reserve(somaPoints.size() + offset);
somaDiameters.reserve(somaDiameters.size() + offset);
for (std::size_t i = 0; i < offset; ++i) {
const auto& p = vec[i];
somaPoints.emplace_back(Point{p[0], p[1], p[2]});
somaDiameters.emplace_back(p[3]);
}

points.reserve(points.size() + vec.size() - offset);
diameters.reserve(diameters.size() + vec.size() - offset);
for (std::size_t i = offset; i < vec.size(); ++i) {
const auto& p = vec[i];
points.emplace_back(Point{p[0], p[1], p[2]});
diameters.emplace_back(p[3]);
loadPoints(vec, v2HasNeurites(firstSectionOffset));
} else {
std::vector<std::vector<float>> vec(_pointsDims[0]);
_points->read(vec);
loadPoints(vec, std::size_t(firstSectionOffset) < _pointsDims[0]);
}
}

Expand All @@ -301,15 +281,13 @@ int MorphologyHDF5::_readSections() {
try {
return _file->getDataSet(raw_path);
} catch (HighFive::DataSetException&) {
throw MorphioError("Could not find unraveled structure neither at " +
path + " or " + raw_path +
" for dataset for morphology file " +
throw MorphioError("Could not find unraveled structure neither at " + path +
" or " + raw_path + " for dataset for morphology file " +
_file->getName() + " repair stage " + _stage);
}
} else {
throw MorphioError("Could not open " + path +
" dataset for morphology file " + _file->getName() +
" repair stage " + _stage);
throw MorphioError("Could not open " + path + " dataset for morphology file " +
_file->getName() + " repair stage " + _stage);
}
}
}();
Expand Down Expand Up @@ -410,7 +388,7 @@ void MorphologyHDF5::_readSectionTypes() {


void MorphologyHDF5::_readPerimeters(int firstSectionOffset) {
if (_properties.version() != MORPHOLOGY_VERSION_H5_1_1 || noNeurites(firstSectionOffset))
if (_properties.version() != MORPHOLOGY_VERSION_H5_1_1 || !v2HasNeurites(firstSectionOffset))
return;

try {
Expand All @@ -430,8 +408,7 @@ void MorphologyHDF5::_readPerimeters(int firstSectionOffset) {
perimeters.end());
} catch (...) {
if (_properties._cellLevel._cellFamily == FAMILY_GLIA)
throw MorphioError("No empty perimeters allowed for glia "
"morphology");
throw MorphioError("No empty perimeters allowed for glia morphology");
}
}

Expand All @@ -451,15 +428,14 @@ void MorphologyHDF5::_read(const std::string& groupName,
auto dims = dataset.getSpace().getDimensions();
if (dims.size() != expectedDimension) {
throw MorphioError("Reading morphology file '" + _file->getName() +
"': bad number of dimensions in 'perimeters' dataspace");
"': bad number of dimensions in 'perimeters' dataspace");
}

data.resize(dims[0]);
dataset.read(data);
} catch (...) {
if (_properties._cellLevel._cellFamily == FAMILY_GLIA)
throw MorphioError("No empty perimeters allowed for glia "
"morphology");
throw MorphioError("No empty perimeters allowed for glia morphology");
}
}

Expand Down

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