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Add more options for ASC and SWC loaders #431

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Add more options for ASC and SWC loaders #431

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18 changes: 13 additions & 5 deletions include/morphio/enums.h
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Expand Up @@ -15,11 +15,15 @@ enum LogLevel { ERROR, WARNING, INFO, DEBUG };
/** The list of modifier flags that can be passed when loading a morphology
* See morphio::mut::modifiers for more information **/
enum Option {
NO_MODIFIER = 0x00, //!< Read morphology as is without any modification
TWO_POINTS_SECTIONS = 0x01, //!< Read sections only with 2 or more points
SOMA_SPHERE = 0x02, //!< Interpret morphology soma as a sphere
NO_DUPLICATES = 0x04, //!< Skip duplicating points
NRN_ORDER = 0x08 //!< Order of neurites will be the same as in NEURON simulator
NO_MODIFIER = 0, //!< Read morphology as is without any modification
TWO_POINTS_SECTIONS = 1 << 0, //!< Keep only the first and last points of sections
SOMA_SPHERE = 1 << 1, //!< Interpret morphology soma as a sphere
NO_DUPLICATES = 1 << 2, //!< Skip duplicating points
NRN_ORDER = 1 << 3, //!< Order of neurites will be the same as in NEURON simulator
ALLOW_ROOT_BIFURCATIONS = 1 << 4, //!< Bifurcations at first point are allowed
ALLOW_SOMA_BIFURCATIONS = 1 << 5, //!< Bifurcations in soma are allowed
ALLOW_MULTIPLE_SOMATA = 1 << 6, //!< Multiple somata are allowed
ALLOW_CUSTOM_ROOT_ID = 1 << 7 //!< Custom root points are allowed
};

/**
Expand All @@ -41,6 +45,10 @@ enum Warning {
ZERO_DIAMETER, //!< Zero section diameter
SOMA_NON_CONTOUR, //!< Soma must be a contour for ASC and H5
SOMA_NON_CYLINDER_OR_POINT, //!< Soma must be stacked cylinders or a point
ROOT_BIFURCATION, //!< Bifurcation at root point
SOMA_BIFURCATION, //!< Bifurcation in soma
MULTIPLE_SOMATA, //!< Multiple somata
CUSTOM_ROOT_ID, //!< Custom root ID
};

enum AnnotationType {
Expand Down
13 changes: 11 additions & 2 deletions include/morphio/errorMessages.h
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Expand Up @@ -232,6 +232,14 @@ class ErrorMessages
std::string WARNING_MITOCHONDRIA_WRITE_NOT_SUPPORTED() const;
/** Writing without soma warning message */
std::string WARNING_WRITE_NO_SOMA() const;
/** Loading soma with a bifurcation */
std::string WARNING_SOMA_BIFURCATION() const;
/** Loading multiple somata */
std::string WARNING_MULTIPLE_SOMATA() const;
/** Loading point with root ID no equal to -1 */
std::string WARNING_CUSTOM_ROOT_ID(const Sample& sample) const;
/** Loading section with only one point */
std::string WARNING_ROOT_BIFURCATION(const Sample& sample) const;
/** Writing empty morphology warning message */
std::string WARNING_WRITE_EMPTY_MORPHOLOGY() const;
/** Soma not found warning message */
Expand All @@ -244,7 +252,8 @@ class ErrorMessages
std::string WARNING_WRONG_DUPLICATE(const std::shared_ptr<morphio::mut::Section>& current,
const std::shared_ptr<morphio::mut::Section>& parent) const;
/** Writing empty section warning message */
std::string WARNING_APPENDING_EMPTY_SECTION(std::shared_ptr<morphio::mut::Section>);
std::string WARNING_APPENDING_EMPTY_SECTION(
const std::shared_ptr<morphio::mut::Section>& section) const;
/** Writing single child section warning message */
std::string WARNING_ONLY_CHILD(const DebugInfo& info,
unsigned int parentId,
Expand All @@ -253,7 +262,7 @@ class ErrorMessages
/** Soma does not conform NeuroMorpho warning message */
std::string WARNING_NEUROMORPHO_SOMA_NON_CONFORM(const Sample& root,
const Sample& child1,
const Sample& child2);
const Sample& child2) const;

/** Wrong root point warning message */
std::string WARNING_WRONG_ROOT_POINT(const std::vector<Sample>& children) const;
Expand Down
26 changes: 24 additions & 2 deletions src/errorMessages.cpp
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Expand Up @@ -284,6 +284,14 @@ std::string ErrorMessages::WARNING_WRITE_NO_SOMA() const {
return errorMsg(0, ErrorLevel::WARNING, "Warning: writing file without a soma");
}

std::string ErrorMessages::WARNING_SOMA_BIFURCATION() const {
return errorMsg(0, ErrorLevel::WARNING, "Warning: found soma bifurcation");
}

std::string ErrorMessages::WARNING_MULTIPLE_SOMATA() const {
return errorMsg(0, ErrorLevel::WARNING, "Warning: found multiple somata");
}

std::string ErrorMessages::WARNING_WRITE_EMPTY_MORPHOLOGY() const {
return errorMsg(0,
ErrorLevel::WARNING,
Expand All @@ -307,12 +315,26 @@ std::string ErrorMessages::WARNING_DISCONNECTED_NEURITE(const Sample& sample) co
}

std::string ErrorMessages::WARNING_APPENDING_EMPTY_SECTION(
std::shared_ptr<morphio::mut::Section> section) {
const std::shared_ptr<morphio::mut::Section>& section) const {
return errorMsg(0,
ErrorLevel::WARNING,
"Warning: appending empty section with id: " + std::to_string(section->id()));
}

std::string ErrorMessages::WARNING_CUSTOM_ROOT_ID(const Sample& sample) const {
return errorMsg(sample.lineNumber,
ErrorLevel::WARNING,
"Warning: root id changed from " + std::to_string(sample.parentId) +
" to -1 for point with id: " + std::to_string(sample.id));
}

std::string ErrorMessages::WARNING_ROOT_BIFURCATION(const Sample& sample) const {
return errorMsg(sample.lineNumber,
ErrorLevel::WARNING,
"Warning: root bifurcation kept for point with id: " +
std::to_string(sample.id));
}

std::string ErrorMessages::WARNING_WRONG_DUPLICATE(
const std::shared_ptr<morphio::mut::Section>& current,
const std::shared_ptr<morphio::mut::Section>& parent) const {
Expand Down Expand Up @@ -374,7 +396,7 @@ std::string ErrorMessages::WARNING_ONLY_CHILD(const DebugInfo& info,

std::string ErrorMessages::WARNING_NEUROMORPHO_SOMA_NON_CONFORM(const Sample& root,
const Sample& child1,
const Sample& child2) {
const Sample& child2) const {
floatType x = root.point[0], y = root.point[1], z = root.point[2], r = root.diameter / 2;
std::stringstream ss;
ss << "Warning: the soma does not conform the three point soma spec\n"
Expand Down
48 changes: 32 additions & 16 deletions src/readers/morphologyASC.cpp
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Expand Up @@ -72,9 +72,9 @@ class NeurolucidaParser
NeurolucidaParser(NeurolucidaParser const&) = delete;
NeurolucidaParser& operator=(NeurolucidaParser const&) = delete;

morphio::mut::Morphology& parse(const std::string& input) {
morphio::mut::Morphology& parse(const std::string& input, unsigned int& options) {
lex_.start_parse(input);
parse_root_sexps();
parse_root_sexps(options);
return nb_;
}

Expand Down Expand Up @@ -112,12 +112,12 @@ class NeurolucidaParser
return {{point[0], point[1], point[2]}, point[3]};
}

bool parse_neurite_branch(Header& header) {
bool parse_neurite_branch(Header& header, unsigned int& options) {
lex_.consume(Token::LPAREN, "New branch should start with LPAREN");

bool ret = true;
while (true) {
ret &= parse_neurite_section(header);
ret &= parse_neurite_section(header, options);
if (lex_.ended() ||
(lex_.current()->id != +Token::PIPE && lex_.current()->id != +Token::LPAREN)) {
break;
Expand All @@ -130,7 +130,8 @@ class NeurolucidaParser

int32_t _create_soma_or_section(const Header& header,
std::vector<Point>& points,
std::vector<morphio::floatType>& diameters) {
std::vector<morphio::floatType>& diameters,
unsigned int& options) {
int32_t return_id = -1;
morphio::Property::PointLevel properties;
properties._points = points;
Expand All @@ -144,9 +145,24 @@ class NeurolucidaParser
nb_.addMarker(marker);
return_id = -1;
} else if (header.token == Token::CELLBODY) {
if (!nb_.soma()->points().empty())
throw SomaError(err_.ERROR_SOMA_ALREADY_DEFINED(lex_.line_num()));
nb_.soma()->properties() = properties;
if (!nb_.soma()->points().empty()) {
if (options & ALLOW_SOMA_BIFURCATIONS) {
printError(Warning::SOMA_BIFURCATION, err_.WARNING_SOMA_BIFURCATION());
} else if (options & ALLOW_MULTIPLE_SOMATA) {
printError(Warning::MULTIPLE_SOMATA, err_.WARNING_MULTIPLE_SOMATA());
} else {
throw SomaError(err_.ERROR_SOMA_ALREADY_DEFINED(lex_.line_num()));
}
nb_.soma()->properties()._points.insert(nb_.soma()->properties()._points.end(),
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properties._points.begin(),
properties._points.end());
nb_.soma()->properties()._diameters.insert(
nb_.soma()->properties()._diameters.end(),
properties._diameters.begin(),
properties._diameters.end());
} else {
nb_.soma()->properties() = properties;
}
return_id = -1;
} else {
SectionType section_type = TokenToSectionType(header.token);
Expand Down Expand Up @@ -273,7 +289,7 @@ class NeurolucidaParser
}


bool parse_neurite_section(const Header& header) {
bool parse_neurite_section(const Header& header, unsigned int& options) {
Points points;
std::vector<morphio::floatType> diameters;
auto section_id = static_cast<int>(nb_.sections().size());
Expand All @@ -286,7 +302,7 @@ class NeurolucidaParser
throw RawDataError(err_.ERROR_EOF_IN_NEURITE(lex_.line_num()));
} else if (is_end_of_section(id)) {
if (!points.empty()) {
_create_soma_or_section(header, points, diameters);
_create_soma_or_section(header, points, diameters, options);
}
return true;
} else if (is_end_of_branch(id)) {
Expand Down Expand Up @@ -320,7 +336,7 @@ class NeurolucidaParser
marker_header.token = Token::STRING;
marker_header.label = lex_.peek()->str();
lex_.consume_until(Token::LPAREN);
parse_neurite_section(marker_header);
parse_neurite_section(marker_header, options);
lex_.consume(Token::RPAREN, "Marker should end with RPAREN");
} else if (peek_id == +Token::NUMBER) {
Point point;
Expand All @@ -330,11 +346,11 @@ class NeurolucidaParser
diameters.push_back(radius);
} else if (peek_id == +Token::LPAREN) {
if (!points.empty()) {
section_id = _create_soma_or_section(header, points, diameters);
section_id = _create_soma_or_section(header, points, diameters, options);
}
Header child_header = header;
child_header.parent_id = section_id;
parse_neurite_branch(child_header);
parse_neurite_branch(child_header, options);
} else {
throw RawDataError(
err_.ERROR_UNKNOWN_TOKEN(lex_.line_num(), lex_.peek()->str()));
Expand All @@ -347,14 +363,14 @@ class NeurolucidaParser
}
}

void parse_root_sexps() {
void parse_root_sexps(unsigned int& options) {
// parse the top level blocks, and if they are a neurite, otherwise skip
while (!lex_.ended()) {
if (static_cast<Token>(lex_.current()->id) == Token::LPAREN) {
lex_.consume();
const Header header = parse_root_sexp_header();
if (lex_.current()->id != +Token::RPAREN) {
parse_neurite_section(header);
parse_neurite_section(header, options);
}
}

Expand All @@ -378,7 +394,7 @@ Property::Properties load(const std::string& path,
unsigned int options) {
NeurolucidaParser parser(path);

morphio::mut::Morphology& nb_ = parser.parse(contents);
morphio::mut::Morphology& nb_ = parser.parse(contents, options);
nb_.applyModifiers(options);

Property::Properties properties = nb_.buildReadOnly();
Expand Down
47 changes: 38 additions & 9 deletions src/readers/morphologySWC.cpp
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Expand Up @@ -133,7 +133,7 @@ class SWCBuilder
return somata;
}

void raiseIfBrokenSoma(const Sample& sample) {
void raiseIfBrokenSoma(const Sample& sample, const unsigned int& options) {
if (sample.type != SECTION_SOMA) {
return;
}
Expand All @@ -149,7 +149,11 @@ class SWCBuilder
}

if (soma_bifurcations.size() > 1) {
throw morphio::SomaError(err.ERROR_SOMA_BIFURCATION(sample, soma_bifurcations));
if (options & ALLOW_SOMA_BIFURCATIONS) {
printError(Warning::SOMA_BIFURCATION, err.WARNING_SOMA_BIFURCATION());
} else {
throw morphio::SomaError(err.ERROR_SOMA_BIFURCATION(sample, soma_bifurcations));
}
}
}

Expand All @@ -171,11 +175,15 @@ class SWCBuilder
}
}

void checkSoma() {
void checkSoma(const unsigned int& options) {
auto somata = _potentialSomata();

if (somata.size() > 1) {
throw morphio::SomaError(err.ERROR_MULTIPLE_SOMATA(somata));
if (options & ALLOW_MULTIPLE_SOMATA) {
printError(Warning::MULTIPLE_SOMATA, err.WARNING_MULTIPLE_SOMATA());
} else {
throw morphio::SomaError(err.ERROR_MULTIPLE_SOMATA(somata));
}
}

if (somata.empty()) {
Expand Down Expand Up @@ -241,9 +249,9 @@ class SWCBuilder
return ret;
}

void raiseIfNonConform(const Sample& sample) {
void raiseIfNonConform(const Sample& sample, const unsigned int& options) {
raiseIfSelfParent(sample);
raiseIfBrokenSoma(sample);
raiseIfBrokenSoma(sample, options);
raiseIfNoParent(sample);
warnIfZeroDiameter(sample);
}
Expand Down Expand Up @@ -327,12 +335,29 @@ class SWCBuilder
Property::Properties buildProperties(const std::string& contents, unsigned int options) {
_readSamples(contents);

if (options & ALLOW_CUSTOM_ROOT_ID) {
for (auto& sample_pair : samples) {
auto& sample = sample_pair.second;
if (sample.parentId != SWC_ROOT && samples.count(sample.parentId) == 0) {
printError(Warning::CUSTOM_ROOT_ID, err.WARNING_CUSTOM_ROOT_ID(sample));
// Remove the sample from the children
children[sample.parentId].erase(std::remove(children[sample.parentId].begin(),
children[sample.parentId].end(),
sample.id),
children[sample.parentId].end());
// Update the sample and add it to the proper children
sample.parentId = SWC_ROOT;
children[SWC_ROOT].push_back(sample.id);
}
}
}

for (const auto& sample_pair : samples) {
const auto& sample = sample_pair.second;
raiseIfNonConform(sample);
raiseIfNonConform(sample, options);
}

checkSoma();
checkSoma(options);

// The process might occasionally creates empty section before
// filling them so the warning is ignored
Expand All @@ -345,7 +370,11 @@ class SWCBuilder

// Bifurcation right at the start
if (isRootPoint(sample) && isSectionEnd(sample)) {
continue;
if (options & ALLOW_ROOT_BIFURCATIONS) {
printError(Warning::ROOT_BIFURCATION, err.WARNING_ROOT_BIFURCATION(sample));
} else {
continue;
}
}

if (isSectionStart(sample)) {
Expand Down
11 changes: 6 additions & 5 deletions tests/CMakeLists.txt
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Expand Up @@ -7,6 +7,7 @@ set(TESTS_SRC
test_mutable_morphology.cpp
test_point_utils.cpp
test_properties.cpp
test_reader_options.cpp
test_soma.cpp
test_swc_reader.cpp
test_utilities.cpp
Expand Down Expand Up @@ -53,13 +54,13 @@ target_link_libraries(unittests
${TESTS_LINK_LIBRAIRIES}
)

add_test(NAME unittests
COMMAND unittests
WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
)

if (NOT EXTERNAL_CATCH2)
catch_discover_tests( unittests
WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
)
else()
add_test(NAME unittests
COMMAND unittests
WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
)
endif()
7 changes: 7 additions & 0 deletions tests/data/edge_cases/bad_root_point.swc
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@@ -0,0 +1,7 @@
# The root point is not -1
1 2 0 0 0 6 0
2 2 0 0 1 6 1
3 2 0 0 2 6 2
4 2 1 0 0 6 0
5 2 1 0 1 6 1
6 2 1 0 2 6 2
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