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Support NeuroLucida soma stacks #39

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Support NeuroLucida soma stacks #39

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3 changes: 1 addition & 2 deletions include/morphio/errorMessages.h
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Original file line number Diff line number Diff line change
Expand Up @@ -141,8 +141,7 @@ class ErrorMessages {
////////////////////////////////////////////////////////////////////////////////
// NEUROLUCIDA
////////////////////////////////////////////////////////////////////////////////
const std::string ERROR_SOMA_ALREADY_DEFINED(int lineNumber) const;

const std::string ERROR_MULTIPLE_SOMA_STACKS_WITH_SAME_Z(int line1, int line2, float z) const;

const std::string ERROR_PARSING_POINT(int lineNumber,
const std::string& point) const;
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12 changes: 9 additions & 3 deletions src/errorMessages.cpp
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Expand Up @@ -143,9 +143,15 @@ const std::string _col(float val1, float val2) {
////////////////////////////////////////////////////////////////////////////////
// NEUROLUCIDA
////////////////////////////////////////////////////////////////////////////////
const std::string ErrorMessages::ERROR_SOMA_ALREADY_DEFINED(int lineNumber) const {
return errorMsg(lineNumber, ErrorLevel::ERROR,
"A soma is already defined");
const std::string ErrorMessages::ERROR_MULTIPLE_SOMA_STACKS_WITH_SAME_Z(int line1, int line2, float z) const {
std::string msg = errorMsg(line1, ErrorLevel::ERROR,
"\nThere is already a soma stack for Z == "+std::to_string(z) + " at line:");
msg += errorMsg(line2, ErrorLevel::INFO, "");
msg += "\nNote: Multiple blocks of type CellBody means the soma is represented as a soma stack.\n"
"(More info on soma stacks: https://www.neuron.yale.edu/phpBB/viewtopic.php?t=3833)\n"
"In this case, each CellBody block is the soma contour for a given Z position\n"
" and each block must have a different Z value";
return msg;
}


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52 changes: 46 additions & 6 deletions src/plugin/morphologyASC.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
#include <fstream>
#include <unordered_map>
#include <unordered_set>

#include <morphio/mut/morphology.h>
#include <morphio/mut/section.h>
Expand Down Expand Up @@ -71,12 +73,44 @@ class NeurolucidaParser

parse_block();

create_soma();

return nb_;

}


void create_soma() {
if(somaStacks.size() == 1) {
nb_.soma() -> properties() = somaStacks[0];
} else if(somaStacks.size() > 1) {
_raiseIfEachStackHasMultipleZ();
for (const auto& stack: somaStacks) {
morphio::Property::_appendVector(nb_.soma() -> properties()._points, stack._points, 0);
morphio::Property::_appendVector(nb_.soma() -> properties()._diameters, stack._diameters, 0);
}
}
}

private:

void _raiseIfEachStackHasMultipleZ() {
for (const auto& stack: somaStacks) {
std::unordered_set<float> level;
for(const Point& point: stack._points) {
level.insert(point[2]);
}

if (level.size() > 1) {
std::string msg("Soma stack has multiple Z levels:\n");
for (float z: level)
msg += " * " + std::to_string(z) + "\n";

throw RawDataError(msg);
}
}
}

std::tuple<Point, float> parse_point(NeurolucidaLexer& lex)
{
lex.expect(Token::LPAREN, "Point should start in LPAREN");
Expand Down Expand Up @@ -125,16 +159,19 @@ class NeurolucidaParser
int32_t _create_soma_or_section(Token token, int32_t parent_id,
std::vector<Point> &points, std::vector<float> &diameters)
{
lex_.current_section_start_ = lex_.line_num();
int32_t return_id;
morphio::Property::PointLevel properties;
properties._points = points;
properties._diameters = diameters;
if(token == Token::CELLBODY){
if(nb_.soma()->points().size() != 0)
throw SomaError(err_.ERROR_SOMA_ALREADY_DEFINED(lex_.line_num()));
nb_.soma() -> properties() = properties;

float z = points[0][2];
if (soma_z_levels.count(z))
throw RawDataError(err_.ERROR_MULTIPLE_SOMA_STACKS_WITH_SAME_Z(lex_.current_section_start_,
soma_z_levels[z],
z));
soma_z_levels[z] = lex_.current_section_start_;

somaStacks.push_back(properties);
return_id = -1;
} else {
SectionType section_type = TokenSectionTypeMap.at(token);
Expand Down Expand Up @@ -199,6 +236,8 @@ class NeurolucidaParser
Points points;
std::vector<float> diameters;
uint32_t section_id = nb_.sections().size();
lex_.current_section_start_ = lex_.line_num();


while (true)
{
Expand Down Expand Up @@ -297,7 +336,8 @@ class NeurolucidaParser
DebugInfo debugInfo_;
private:
ErrorMessages err_;

std::vector<morphio::Property::PointLevel> somaStacks;
std::unordered_map<float, uint32_t> soma_z_levels;
};

Property::Properties load(const URI& uri, unsigned int options)
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91 changes: 71 additions & 20 deletions tests/test_2_neurolucida.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,26 +55,6 @@ def test_unfinished_point():
':4:error')


def test_multiple_soma():
_test_asc_exception('''
("CellBody"
(Color Red)
(CellBody)
(1 1 0 1 S1)
(-1 1 0 1 S2)
)

("CellBody"
(Color Red)
(CellBody)
(1 1 0 1 S1)
(-1 1 0 1 S2)
)''',
SomaError,
'A soma is already defined',
':14:error')


def test_single_neurite_no_soma():
with tmp_asc_file('''
( (Color Yellow)
Expand Down Expand Up @@ -516,3 +496,74 @@ def test_markers():
[-268.17, -130.62, -24.75],
[-266.79, -131.77, -26.13]],
dtype=np.float32))


def test_multiple_soma_stack():
_test_asc_exception('''
(
(CellBody)
( 5.55 5.05 1.0 2.35)
( 2.86 5.72 1.0 2.35)
)

(
(CellBody)
( 0.84 1.52 2.0 2.35)
( -4.54 2.36 2.0 2.35)
( -6.55 0.17 10.0 2.35) ; Wrong Z
)
''',
RawDataError,
"Soma stack has multiple Z levels:",
''' * 10.000000
* 2.000000'''
)

_test_asc_exception('''
(
(CellBody)
( 5.88 0.84 1.0 2.35)
( 6.05 2.53 1.0 2.35)
( 6.39 4.38 1.0 2.35)
)

(
(CellBody)
( 1.85 0.67 1.0 2.35)
( 0.84 1.52 1.0 2.35)
( -4.54 2.36 1.0 2.35)
)
''',
RawDataError,
':11:error',
'There is already a soma stack for Z == 1.000000 at line:',
':4:info'
)

with tmp_asc_file('''
(
(CellBody)
( 5.88 0.84 1.0 2.35)
( 6.05 2.53 1.0 2.35)
( 6.39 4.38 1.0 2.35)
)

(
(CellBody)
( 1.85 0.67 2.0 2.35)
( 0.84 1.52 2.0 2.35)
( -4.54 2.36 2.0 2.35)
)
''') as tmp_file:
m = Morphology(tmp_file.name)
assert_array_equal(m.soma.points,
np.array([[ 5.88, 0.84, 1. ],
[ 6.05, 2.53, 1. ],
[ 6.39, 4.38, 1. ],
[ 1.85, 0.67, 2. ],
[ 0.84, 1.52, 2. ],
[-4.54, 2.36, 2. ]],
dtype=np.float32))
assert_array_equal(m.soma.diameters,
np.array([2.35] * 6,
dtype=np.float32))
21 changes: 14 additions & 7 deletions tests/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,17 +66,24 @@ def assert_string_equal(str1, str2):
str1.join(sep), str2.join(sep)))


def _test_exception(content, exception, str1, str2, extension):
'''Create tempfile with given content and check that the exception is raised'''
with _tmp_file(content, extension) as tmp_file:
def _test_swc_exception(content, exception, *messages):
'''Create tempfile with given content, check that the exception is raised
and that messages are part of the error message'''
with _tmp_file(content, 'swc') as tmp_file:
with assert_raises(exception) as obj:
Morphology(tmp_file.name)
assert_substring(str1, str(obj.exception))
assert_substring(str2, str(obj.exception))
for msg in messages:
assert_substring(msg, str(obj.exception))

def _test_asc_exception(content, exception, *messages):
'''Create tempfile with given content, check that the exception is raised
and that messages are part of the error message'''
with _tmp_file(content, 'asc') as tmp_file:
with assert_raises(exception) as obj:
Morphology(tmp_file.name)
for msg in messages:
assert_substring(msg, str(obj.exception))

_test_asc_exception = partial(_test_exception, extension='asc')
_test_swc_exception = partial(_test_exception, extension='swc')


@contextmanager
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