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increase allowed section type to 19
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* #432
* #456 (type 18 seen in the wild)
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@mgeplf
mgeplf committed Jun 22, 2023
1 parent d6e9733 commit 4a22167
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Showing 8 changed files with 130 additions and 20 deletions.
9 changes: 9 additions & 0 deletions binds/python/bind_misc.cpp
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Expand Up @@ -64,6 +64,15 @@ void bind_misc(py::module& m) {
.value("custom8", morphio::enums::SectionType::SECTION_CUSTOM_8)
.value("custom9", morphio::enums::SectionType::SECTION_CUSTOM_9)
.value("custom10", morphio::enums::SectionType::SECTION_CUSTOM_10)
.value("custom11", morphio::enums::SectionType::SECTION_CUSTOM_11)
.value("custom12", morphio::enums::SectionType::SECTION_CUSTOM_12)
.value("custom13", morphio::enums::SectionType::SECTION_CUSTOM_13)
.value("custom14", morphio::enums::SectionType::SECTION_CUSTOM_14)
.value("custom15", morphio::enums::SectionType::SECTION_CUSTOM_15)
.value("custom16", morphio::enums::SectionType::SECTION_CUSTOM_16)
.value("custom17", morphio::enums::SectionType::SECTION_CUSTOM_17)
.value("custom18", morphio::enums::SectionType::SECTION_CUSTOM_18)
.value("custom19", morphio::enums::SectionType::SECTION_CUSTOM_19)
.value("glia_perivascular_process",
morphio::enums::SectionType::SECTION_GLIA_PERIVASCULAR_PROCESS)
.value("glia_process", morphio::enums::SectionType::SECTION_GLIA_PROCESS)
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30 changes: 24 additions & 6 deletions binds/python/generated/docstrings.h
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Expand Up @@ -831,17 +831,35 @@ static const char *__doc_morphio_enums_SectionType_SECTION_AXON = R"doc(Axon sec

static const char *__doc_morphio_enums_SectionType_SECTION_CNIC_CUSTOM_START = R"doc()doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_10 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_10 = R"doc(Custom section type 10)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_5 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_11 = R"doc(Custom section type 11)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_6 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_12 = R"doc(Custom section type 12)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_7 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_13 = R"doc(Custom section type 13)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_8 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_14 = R"doc(Custom section type 14)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_9 = R"doc(Custom section type)doc";
static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_15 = R"doc(Custom section type 15)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_16 = R"doc(Custom section type 16)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_17 = R"doc(Custom section type 17)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_18 = R"doc(Custom section type 18)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_19 = R"doc(Custom section type 19)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_5 = R"doc(Custom section type 5)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_6 = R"doc(Custom section type 6)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_7 = R"doc(Custom section type 7)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_8 = R"doc(Custom section type 8)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_CUSTOM_9 = R"doc(Custom section type 9)doc";

static const char *__doc_morphio_enums_SectionType_SECTION_DENDRITE = R"doc(General or basal dendrite (near to soma))doc";

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33 changes: 24 additions & 9 deletions include/morphio/enums.h
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Expand Up @@ -75,15 +75,30 @@ enum SectionType {
SECTION_SPINE_HEAD = 3, // Note: overlaps with SECTION_DENDRITE

// unnamed custom section types
SECTION_CUSTOM_5 = 5, //!< Custom section type
SECTION_CUSTOM_6 = 6, //!< Custom section type
SECTION_CUSTOM_7 = 7, //!< Custom section type
SECTION_CUSTOM_8 = 8, //!< Custom section type
SECTION_CUSTOM_9 = 9, //!< Custom section type
SECTION_CUSTOM_10 = 10, //!< Custom section type
// All section types equal or above this number are invalid custom types according
// to neuromorpho.org standard (http://neuromorpho.org/StdSwc1.21.jsp)
SECTION_OUT_OF_RANGE_START = 11,
SECTION_CUSTOM_5 = 5, //!< Custom section type 5
SECTION_CUSTOM_6 = 6, //!< Custom section type 6
SECTION_CUSTOM_7 = 7, //!< Custom section type 7
SECTION_CUSTOM_8 = 8, //!< Custom section type 8
SECTION_CUSTOM_9 = 9, //!< Custom section type 9
SECTION_CUSTOM_10 = 10, //!< Custom section type 10
// according to neuromorpho.org standard (http://neuromorpho.org/StdSwc1.21.jsp)
// `Codes 5-10 signify custom tags, typically defined in the header of the swc file when used.`

// ... but; we are a bit relaxed, since more is better:
// https://github.com/BlueBrain/MorphIO/issues/432
// https://github.com/BlueBrain/MorphIO/issues/456 (type 18 seen in the wild)
SECTION_CUSTOM_11 = 11, //!< Custom section type 11
SECTION_CUSTOM_12 = 12, //!< Custom section type 12
SECTION_CUSTOM_13 = 13, //!< Custom section type 13
SECTION_CUSTOM_14 = 14, //!< Custom section type 14
SECTION_CUSTOM_15 = 15, //!< Custom section type 15
SECTION_CUSTOM_16 = 16, //!< Custom section type 16
SECTION_CUSTOM_17 = 17, //!< Custom section type 17
SECTION_CUSTOM_18 = 18, //!< Custom section type 18
SECTION_CUSTOM_19 = 19, //!< Custom section type 19

// All section types equal or above this number are invalid custom types
SECTION_OUT_OF_RANGE_START = 20,

// CNIC defined types
// It defines too extra types SWC_SECTION_FORK_POINT and
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Binary file modified tests/data/h5/v1/simple-broken-section-type.h5
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47 changes: 47 additions & 0 deletions tests/data/simple-all-types.swc
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@@ -0,0 +1,47 @@
# index, type, x, y, z, radius, parent
1 1 0. 0. 0. .1 -1

2 5 0. 0. 0. .5 1
3 5 4.06736643 9.13545458 0. .5 2

4 6 0. 0. 0. .6 1
5 6 7.43144825 6.69130606 0. .6 4

6 7 0. 0. 0. .7 1
7 7 9.51056516 3.09016994 0. .7 6

8 8 0. 0. 0. .8 1
9 8 9.94521895 -1.04528463 0. .8 8

10 9 0. 0. 0. .9 1
11 9 8.66025404 -5. 0. .9 10

12 10 0. 0. 0. 1.0 1
13 10 5.87785252 -8.09016994 0. 1.0 12

14 11 0. 0. 0. 1.1 1
15 11 2.07911691 -9.78147601 0. 1.1 14

16 12 0. 0. 0. 1.1 1
17 12 -2.07911691 -9.78147601 0. 1.2 16

18 13 0. 0. 0. 1.1 1
19 13 -5.87785252 -8.09016994 0. 1.3 18

20 14 0. 0. 0. 1.1 1
21 14 -8.66025404 -5. 0. 1.4 20

22 15 0. 0. 0. 1.1 1
23 15 -9.94521895 -1.04528463 0. 1.5 22

24 16 0. 0. 0. 1.1 1
25 16 -9.51056516 3.09016994 0. 1.6 24

26 17 0. 0. 0. 1.1 1
27 17 -7.43144825 6.69130606 0. 1.7 26

28 18 0. 0. 0. 1.1 1
29 18 -4.06736643 9.13545458 0. 1.8 28

30 19 0. 0. 0. 1.1 1
31 19 0. 10. 0. 1.9 30
4 changes: 2 additions & 2 deletions tests/test_1_swc.py
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Expand Up @@ -437,12 +437,12 @@ def test_unsupported_section_type():

content = ('''1 1 0 4 0 3.0 -1
2 3 0 0 2 0.5 1
3 11 0 0 3 0.5 2 # <-- 11 is unsupported section type
3 20 0 0 3 0.5 2 # <-- 20 is unsupported section type
''')

with pytest.raises(RawDataError, match=':3:error') as obj:
Morphology(content, extension='swc')
assert obj.match('Unsupported section type: 11')
assert obj.match('Unsupported section type: 20')


def test_root_node_split():
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2 changes: 1 addition & 1 deletion tests/test_3_h5.py
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Expand Up @@ -46,7 +46,7 @@ def test_v1():


def test_wrong_section_type():
with pytest.raises(RawDataError, match='Unsupported section type: 12'):
with pytest.raises(RawDataError, match='Unsupported section type: 20'):
Morphology(H5V1_PATH / 'simple-broken-section-type.h5')

with pytest.raises(RawDataError, match='Unsupported section type: -2'):
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25 changes: 23 additions & 2 deletions tests/test_morphology_readers.cpp
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Expand Up @@ -158,9 +158,30 @@ TEST_CASE("LoadH5MorphologySingleNeurite", "[morphology]") {
}

TEST_CASE("LoadSWCMorphology", "[morphology]") {
const morphio::Morphology m("data/simple.swc");
{
const morphio::Morphology m("data/simple.swc");
REQUIRE(m.diameters().size() == 12);
}

REQUIRE(m.diameters().size() == 12);
{
const morphio::Morphology all_types("data/simple-all-types.swc");
REQUIRE(all_types.diameters().size() == 30);
REQUIRE(all_types.rootSections()[0].type() == morphio::SECTION_CUSTOM_5);
REQUIRE(all_types.rootSections()[1].type() == morphio::SECTION_CUSTOM_6);
REQUIRE(all_types.rootSections()[2].type() == morphio::SECTION_CUSTOM_7);
REQUIRE(all_types.rootSections()[3].type() == morphio::SECTION_CUSTOM_8);
REQUIRE(all_types.rootSections()[4].type() == morphio::SECTION_CUSTOM_9);
REQUIRE(all_types.rootSections()[5].type() == morphio::SECTION_CUSTOM_10);
REQUIRE(all_types.rootSections()[6].type() == morphio::SECTION_CUSTOM_11);
REQUIRE(all_types.rootSections()[7].type() == morphio::SECTION_CUSTOM_12);
REQUIRE(all_types.rootSections()[8].type() == morphio::SECTION_CUSTOM_13);
REQUIRE(all_types.rootSections()[9].type() == morphio::SECTION_CUSTOM_14);
REQUIRE(all_types.rootSections()[10].type() == morphio::SECTION_CUSTOM_15);
REQUIRE(all_types.rootSections()[11].type() == morphio::SECTION_CUSTOM_16);
REQUIRE(all_types.rootSections()[12].type() == morphio::SECTION_CUSTOM_17);
REQUIRE(all_types.rootSections()[13].type() == morphio::SECTION_CUSTOM_18);
REQUIRE(all_types.rootSections()[14].type() == morphio::SECTION_CUSTOM_19);
}
}

TEST_CASE("LoadNeurolucidaMorphology", "[morphology]") {
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