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don't use exceptions when non-exceptional methods are available
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@mgeplf
mgeplf committed Mar 1, 2022
1 parent efd94ab commit a86eeb4
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Showing 6 changed files with 94 additions and 100 deletions.
2 changes: 1 addition & 1 deletion include/morphio/mut/mitochondria.h
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ class Mitochondria
/**
Append a new root MitoSection
**/
MitoSectionP appendRootSection(const Property::MitochondriaPointLevel& points);
MitoSectionP appendRootSection(const Property::MitochondriaPointLevel& pointProperties);

/**
Append a root MitoSection
Expand Down
156 changes: 80 additions & 76 deletions src/morphology.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,75 @@
#include "readers/morphologyHDF5.h"
#include "readers/morphologySWC.h"

namespace {

void buildChildren(const std::shared_ptr<morphio::Property::Properties> properties) {
{
const auto& sections = properties->get<morphio::Property::Section>();
auto& children = properties->_sectionLevel._children;

for (unsigned int i = 0; i < sections.size(); ++i) {
const int32_t parent = sections[i][1];
children[parent].push_back(i);
}
}

{
const auto& sections = properties->get<morphio::Property::MitoSection>();
auto& children = properties->_mitochondriaSectionLevel._children;

for (unsigned int i = 0; i < sections.size(); ++i) {
const int32_t parent = sections[i][1];
children[parent].push_back(i);
}
}
}

morphio::SomaType getSomaType(long unsigned int num_soma_points) {
switch(num_soma_points){
case 0:
return morphio::SOMA_UNDEFINED;
case 1:
return morphio::SOMA_SINGLE_POINT;
case 2:
return morphio::SOMA_UNDEFINED;
default:
;
}
return morphio::SOMA_SIMPLE_CONTOUR;
}

morphio::Property::Properties loadURI(const std::string& source, unsigned int options) {
const size_t pos = source.find_last_of('.');
if (pos == std::string::npos) {
throw(morphio::UnknownFileType("File has no extension"));
}

// Cross-platform check of file existance
std::ifstream file(source.c_str());
if (!file) {
throw(morphio::RawDataError("File: " + source + " does not exist."));
}

std::string extension = source.substr(pos);

if (extension == ".h5" || extension == ".H5") {
return morphio::readers::h5::load(source);
}
else if (extension == ".asc" || extension == ".ASC") {
return morphio::readers::asc::load(source, options);
}
else if (extension == ".swc" || extension == ".SWC") {
return morphio::readers::swc::load(source, options);
}

throw(morphio::UnknownFileType("Unhandled file type: only SWC, ASC and H5 are supported"));
}


} // namespace

namespace morphio {
void buildChildren(std::shared_ptr<Property::Properties> properties);
SomaType getSomaType(long unsigned int num_soma_point);
Property::Properties loadURI(const std::string& source, unsigned int options);

Morphology::Morphology(const Property::Properties& properties, unsigned int options)
: properties_(std::make_shared<Property::Properties>(properties)) {
Expand Down Expand Up @@ -74,19 +139,21 @@ Section Morphology::section(uint32_t id) const {
}

std::vector<Section> Morphology::rootSections() const {
const auto sections = properties_->children<morphio::Property::Section>();

if(sections.empty()){
return {};
}

std::vector<Section> result;
try {
const std::vector<uint32_t>& children =
properties_->children<morphio::Property::Section>().at(-1);
result.reserve(children.size());
for (auto id : children) {
result.push_back(section(id));
}

return result;
} catch (const std::out_of_range&) {
return result;
const std::vector<uint32_t>& children = sections.at(-1);
result.reserve(children.size());
for (auto id : children) {
result.push_back(section(id));
}

return result;
}

std::vector<Section> Morphology::sections() const {
Expand Down Expand Up @@ -165,67 +232,4 @@ breadth_iterator Morphology::breadth_end() const {
return breadth_iterator();
}

SomaType getSomaType(long unsigned int num_soma_points) {
try {
return std::map<long unsigned int, SomaType>{{0, SOMA_UNDEFINED},
{1, SOMA_SINGLE_POINT},
{2, SOMA_UNDEFINED}}
.at(num_soma_points);
} catch (const std::out_of_range&) {
return SOMA_SIMPLE_CONTOUR;
}
}

void buildChildren(std::shared_ptr<Property::Properties> properties) {
{
const auto& sections = properties->get<Property::Section>();
auto& children = properties->_sectionLevel._children;

for (unsigned int i = 0; i < sections.size(); ++i) {
const int32_t parent = sections[i][1];
children[parent].push_back(i);
}
}

{
const auto& sections = properties->get<Property::MitoSection>();
auto& children = properties->_mitochondriaSectionLevel._children;

for (unsigned int i = 0; i < sections.size(); ++i) {
const int32_t parent = sections[i][1];
children[parent].push_back(i);
}
}
}

Property::Properties loadURI(const std::string& source, unsigned int options) {
const size_t pos = source.find_last_of(".");
if (pos == std::string::npos) {
throw(UnknownFileType("File has no extension"));
}

// Cross-platform check of file existance
std::ifstream file(source.c_str());
if (!file) {
throw(RawDataError("File: " + source + " does not exist."));
}

std::string extension = source.substr(pos);

auto loader = [&source, &options, &extension]() {
if (extension == ".h5" || extension == ".H5") {
return readers::h5::load(source);
}
if (extension == ".asc" || extension == ".ASC") {
return readers::asc::load(source, options);
}
if (extension == ".swc" || extension == ".SWC") {
return readers::swc::load(source, options);
}
throw(UnknownFileType("Unhandled file type: only SWC, ASC and H5 are supported"));
};

return loader();
}

} // namespace morphio
8 changes: 2 additions & 6 deletions src/mut/mito_section.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -82,12 +82,8 @@ std::shared_ptr<MitoSection> MitoSection::parent() const {
}

bool MitoSection::isRoot() const {
try {
parent();
return false;
} catch (const std::out_of_range&) {
return true;
}
return mitochondria_->parent_.count(id()) == 0;

}

bool MitoSection::hasSameShape(const MitoSection& other) const noexcept {
Expand Down
22 changes: 8 additions & 14 deletions src/mut/mitochondria.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ namespace mut {

Mitochondria::MitoSectionP Mitochondria::appendRootSection(const morphio::MitoSection& section_,
bool recursive) {
const auto ptr = std::make_shared<MitoSection>(this, _counter, section_);
auto ptr = std::make_shared<MitoSection>(this, _counter, section_);
_register(ptr);
root_sections_.push_back(ptr);

Expand All @@ -25,7 +25,7 @@ Mitochondria::MitoSectionP Mitochondria::appendRootSection(const morphio::MitoSe

Mitochondria::MitoSectionP Mitochondria::appendRootSection(const MitoSectionP& section_,
bool recursive) {
const auto section_copy = std::make_shared<MitoSection>(this, _counter, *section_);
auto section_copy = std::make_shared<MitoSection>(this, _counter, *section_);
_register(section_copy);
root_sections_.push_back(section_copy);

Expand All @@ -40,7 +40,7 @@ Mitochondria::MitoSectionP Mitochondria::appendRootSection(const MitoSectionP& s

Mitochondria::MitoSectionP Mitochondria::appendRootSection(
const Property::MitochondriaPointLevel& pointProperties) {
const auto ptr = std::make_shared<MitoSection>(this, _counter, pointProperties);
auto ptr = std::make_shared<MitoSection>(this, _counter, pointProperties);
_register(ptr);
root_sections_.push_back(ptr);

Expand Down Expand Up @@ -70,12 +70,7 @@ const Mitochondria::MitoSectionP& Mitochondria::parent(const MitoSectionP& paren
}

bool Mitochondria::isRoot(const MitoSectionP& section_) const {
try {
parent(section_);
return false;
} catch (const std::out_of_range&) {
return true;
}
return parent_.count(section_->id()) == 0;
}

const Mitochondria::MitoSectionP& Mitochondria::section(uint32_t id) const {
Expand All @@ -86,14 +81,13 @@ void Mitochondria::_buildMitochondria(Property::Properties& properties) const {
int32_t counter = 0;
std::map<uint32_t, int32_t> newIds;

for (std::shared_ptr<MitoSection> mitoStart : root_sections_) {
for (const std::shared_ptr<MitoSection>& mitoStart : root_sections_) {
std::queue<std::shared_ptr<MitoSection>> q;
q.push(mitoStart);
while (!q.empty()) {
std::shared_ptr<MitoSection> section_ = q.front();
q.pop();
bool root = isRoot(section_);
int32_t parentOnDisk = root ? -1 : newIds[parent(section_)->id()];
int32_t parentOnDisk = isRoot(section_) ? -1 : newIds[parent(section_)->id()];

properties._mitochondriaSectionLevel._sections.push_back(
{static_cast<int>(properties._mitochondriaPointLevel._diameters.size()),
Expand All @@ -102,7 +96,7 @@ void Mitochondria::_buildMitochondria(Property::Properties& properties) const {

newIds[section_->id()] = counter++;

for (auto child : children(section_)) {
for (const auto& child : children(section_)) {
q.push(child);
}
}
Expand Down Expand Up @@ -138,7 +132,7 @@ mito_upstream_iterator Mitochondria::upstream_end() const {
}

uint32_t Mitochondria::_register(const MitoSectionP& section) {
if (sections_.count(section->id())) {
if (sections_.count(section->id()) > 0) {
throw SectionBuilderError("Section already exists");
}
_counter = std::max(_counter, section->id()) + 1;
Expand Down
2 changes: 1 addition & 1 deletion tests/test_3_h5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ def test_soma_no_neurite():
[ 1., 0., 0.],
[ 0., 25., 0.]])
assert_array_equal(n.soma.diameters,
[6,6,15])
[6, 6, 15])

assert len(n.root_sections) == 0

Expand Down
4 changes: 2 additions & 2 deletions tests/test_morphology_readers.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -111,8 +111,8 @@ TEST_CASE("LoadH5Glia", "[morphology]") {
{
const morphio::Morphology m("data/h5/v1/glia_soma_only.h5");
REQUIRE(m.soma().points().size() == 1);
REQUIRE(m.points().size() == 0);
REQUIRE(m.perimeters().size() == 0);
REQUIRE(m.points().empty());
REQUIRE(m.perimeters().empty());
}

{ // empty perimeters
Expand Down

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