diff --git a/arbor/morph/segment_tree.cpp b/arbor/morph/segment_tree.cpp
index 43c353b5bc08058d15b52a9996867473f6bde411..3249ed5fdfab3f63a1b5f08a5c5cd56c375560d1 100644
--- a/arbor/morph/segment_tree.cpp
+++ b/arbor/morph/segment_tree.cpp
@@ -26,7 +26,7 @@ node_p yes = [](node_t) { return true; };
std::map<msize_t, std::vector<msize_t>> tree_to_children(const segment_tree& tree) {
const auto& parents = tree.parents();
std::map<msize_t, std::vector<msize_t>> result;
- for (auto ix = 0; ix < tree.size(); ++ix) result[parents[ix]].push_back(ix);
+ for (msize_t ix = 0; ix < tree.size(); ++ix) result[parents[ix]].push_back(ix);
for (auto& [k, v]: result) std::sort(v.begin(), v.end());
return result;
}
@@ -105,7 +105,7 @@ equivalent(const segment_tree& a,
auto bs = fetch_children(b_cursor, b.segments(), b_children_of);
todo.pop_back();
if (as.size() != bs.size()) return false;
- for (auto ix = 0; ix < as.size(); ++ix) {
+ for (msize_t ix = 0; ix < as.size(); ++ix) {
if ((as[ix].prox != bs[ix].prox) ||
(as[ix].dist != bs[ix].dist) ||
(as[ix].tag != bs[ix].tag)) return false;
diff --git a/arborio/include/arborio/neurolucida.hpp b/arborio/include/arborio/neurolucida.hpp
index 3fd4d1fc8f83e694c46747d46ea7fb88f7ead720..a260c784eac56ad1ace95e232f1f72058b60699b 100644
--- a/arborio/include/arborio/neurolucida.hpp
+++ b/arborio/include/arborio/neurolucida.hpp
@@ -45,8 +45,10 @@ struct asc_morphology {
// Perform the parsing of the input as a string.
ARB_ARBORIO_API asc_morphology parse_asc_string(const char* input);
+ARB_ARBORIO_API arb::segment_tree parse_asc_string_raw(const char* input);
// Load asc morphology from file with name filename.
ARB_ARBORIO_API asc_morphology load_asc(std::string filename);
+ARB_ARBORIO_API arb::segment_tree load_asc_raw(std::string filename);
} // namespace arborio
diff --git a/arborio/neurolucida.cpp b/arborio/neurolucida.cpp
index 832a7d2451f3b3a2a55bc8966c2a4c265076c1a9..4c8d46a1f52ba62cef6e4b00b84859b51c2a703b 100644
--- a/arborio/neurolucida.cpp
+++ b/arborio/neurolucida.cpp
@@ -610,7 +610,7 @@ parse_hopefully<sub_tree> parse_sub_tree(asc::lexer& L) {
// Perform the parsing of the input as a string.
-asc_morphology parse_asc_string(const char* input) {
+ARB_ARBORIO_API arb::segment_tree parse_asc_string_raw(const char* input) {
asc::lexer lexer(input);
std::vector<sub_tree> sub_trees;
@@ -768,6 +768,14 @@ asc_morphology parse_asc_string(const char* input) {
}
}
+ return stree;
+}
+
+
+ARB_ARBORIO_API asc_morphology parse_asc_string(const char* input) {
+ // Parse segment tree
+ arb::segment_tree stree = parse_asc_string_raw(input);
+
// Construct the morphology.
arb::morphology morphology(stree);
@@ -781,7 +789,8 @@ asc_morphology parse_asc_string(const char* input) {
return {stree, std::move(morphology), std::move(labels)};
}
-ARB_ARBORIO_API asc_morphology load_asc(std::string filename) {
+
+inline std::string read_file(std::string filename) {
std::ifstream fid(filename);
if (!fid.good()) {
@@ -796,9 +805,21 @@ ARB_ARBORIO_API asc_morphology load_asc(std::string filename) {
fstr.assign((std::istreambuf_iterator<char>(fid)),
std::istreambuf_iterator<char>());
+ return fstr;
+}
+
+ARB_ARBORIO_API asc_morphology load_asc(std::string filename) {
+ std::string fstr = read_file(filename);
return parse_asc_string(fstr.c_str());
}
+
+ARB_ARBORIO_API arb::segment_tree load_asc_raw(std::string filename) {
+ std::string fstr = read_file(filename);
+ return parse_asc_string_raw(fstr.c_str());
+}
+
+
} // namespace arborio
diff --git a/python/morphology.cpp b/python/morphology.cpp
index 52bf43bba503f55c650531088df0a9c5ef536fd9..d1ca3446855d70cfb46bbe6cf24d8ab0bb11fd5c 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -356,18 +356,25 @@ void register_morphology(py::module& m) {
[](const arborio::asc_morphology& m) {return label_dict_proxy(m.labels);},
"The four canonical regions are labeled 'soma', 'axon', 'dend' and 'apic'.");
+ using asc_morph_or_tree = std::variant<arb::segment_tree, arborio::asc_morphology>;
+
m.def("load_asc",
- [](py::object fn) {
+ [](py::object fn, bool raw) -> asc_morph_or_tree {
try {
auto contents = util::read_file_or_buffer(fn);
- return arborio::load_asc(contents);
+ if (raw) {
+ return arborio::parse_asc_string_raw(contents.c_str());
+ }
+ return arborio::parse_asc_string(contents.c_str());
}
catch (std::exception& e) {
// Try to produce helpful error messages for SWC parsing errors.
throw pyarb_error(util::pprintf("error loading neurolucida asc file: {}", e.what()));
}
},
- "filename"_a, "Load a morphology and meta data from a Neurolucida ASCII .asc file.");
+ "filename_or_stream"_a,
+ pybind11::arg_v("raw", false, "Return a segment tree instead of a fully formed morphology"),
+ "Load a morphology or segment_tree and meta data from a Neurolucida ASCII .asc file.");
#ifdef ARB_NEUROML_ENABLED
diff --git a/python/test/unit/test_io.py b/python/test/unit/test_io.py
index b3eda93b99f6ca19d937c951f08882538376215a..3c2eea72688e2cc06d689a4ac187996ffb2a8864 100644
--- a/python/test/unit/test_io.py
+++ b/python/test/unit/test_io.py
@@ -5,6 +5,8 @@ import arbor as A
from pathlib import Path
from tempfile import TemporaryDirectory as TD
from io import StringIO
+from functools import partial
+
acc = """(arbor-component
(meta-data
@@ -62,32 +64,141 @@ acc = """(arbor-component
"""
-class TestAccIo(unittest.TestCase):
- def test_stringio(self):
- sio = StringIO(acc)
- A.load_component(sio)
+swc_arbor = """1 1 -5.0 0.0 0.0 5.0 -1
+2 1 0.0 0.0 0.0 5.0 1
+3 1 5.0 0.0 0.0 5.0 2
+"""
- def test_fileio(self):
- fn = "test.acc"
+
+swc_neuron = """1 1 0.1 0.2 0.3 0.4 -1
+"""
+
+
+asc = """((CellBody)\
+ (0 0 0 4)\
+)\
+((Dendrite)\
+ (0 2 0 2)\
+ (0 5 0 2)\
+ (\
+ (-5 5 0 2)\
+ |\
+ (6 5 0 2)\
+ )\
+)\
+((Axon)\
+ (0 -2 0 2)\
+ (0 -5 0 2)\
+ (\
+ (-5 -5 0 2)\
+ |\
+ (6 -5 0 2)\
+ )\
+)
+"""
+
+
+def load_string(loaders, morph_str):
+ for loader in loaders:
+ sio = StringIO(morph_str)
+ loader(sio)
+
+
+def load_file(loaders, morph_str, morph_fn):
+ for loader in loaders:
with TD() as tmp:
tmp = Path(tmp)
- with open(tmp / fn, "w") as fd:
- fd.write(acc)
- with open(tmp / fn) as fd:
- A.load_component(fd)
+ with open(tmp / morph_fn, "w") as fd:
+ fd.write(morph_str)
+ with open(tmp / morph_fn) as fd:
+ loader(fd)
- def test_nameio(self):
- fn = "test.acc"
+
+def load_name(loaders, morph_str, morph_fn):
+ for loader in loaders:
with TD() as tmp:
tmp = Path(tmp)
- with open(tmp / fn, "w") as fd:
- fd.write(acc)
- A.load_component(str(tmp / fn))
+ with open(tmp / morph_fn, "w") as fd:
+ fd.write(morph_str)
+ loader(str(tmp / morph_fn))
- def test_pathio(self):
- fn = "test.acc"
+
+def load_pathio(loaders, morph_str, morph_fn):
+ for loader in loaders:
with TD() as tmp:
tmp = Path(tmp)
- with open(tmp / fn, "w") as fd:
- fd.write(acc)
- A.load_component(tmp / fn)
+ with open(tmp / morph_fn, "w") as fd:
+ fd.write(morph_str)
+ loader(tmp / morph_fn)
+
+
+class TestAccIo(unittest.TestCase):
+ @staticmethod
+ def loaders():
+ return (A.load_component,)
+
+ def test_stringio(self):
+ load_string(self.loaders(), acc)
+
+ def test_fileio(self):
+ load_file(self.loaders(), acc, "test.acc")
+
+ def test_nameio(self):
+ load_name(self.loaders(), acc, "test.acc")
+
+ def test_pathio(self):
+ load_pathio(self.loaders(), acc, "test.acc")
+
+
+class TestSwcArborIo(unittest.TestCase):
+ @staticmethod
+ def loaders():
+ return (A.load_swc_arbor, partial(A.load_swc_arbor, raw=True))
+
+ def test_stringio(self):
+ load_string(self.loaders(), swc_arbor)
+
+ def test_fileio(self):
+ load_file(self.loaders(), swc_arbor, "test.swc")
+
+ def test_nameio(self):
+ load_name(self.loaders(), swc_arbor, "test.swc")
+
+ def test_pathio(self):
+ load_pathio(self.loaders(), swc_arbor, "test.swc")
+
+
+class TestSwcNeuronIo(unittest.TestCase):
+ @staticmethod
+ def loaders():
+ return (A.load_swc_neuron, partial(A.load_swc_neuron, raw=True))
+
+ def test_stringio(self):
+ load_string(self.loaders(), swc_neuron)
+
+ def test_fileio(self):
+ load_file(self.loaders(), swc_neuron, "test.swc")
+
+ def test_nameio(self):
+ load_name(self.loaders(), swc_neuron, "test.swc")
+
+ def test_pathio(self):
+ load_pathio(self.loaders(), swc_neuron, "test.swc")
+
+
+class TestAscIo(unittest.TestCase):
+ @staticmethod
+ def loaders():
+ return (A.load_asc, partial(A.load_asc, raw=True))
+
+ def test_stringio(self):
+ load_string(self.loaders(), asc)
+
+ def test_fileio(self):
+ load_file(self.loaders(), asc, "test.asc")
+
+ def test_nameio(self):
+ load_name(self.loaders(), asc, "test.asc")
+
+ def test_pathio(self):
+ load_pathio(self.loaders(), asc, "test.asc")