diff --git a/ATTRIBUTIONS.md b/ATTRIBUTIONS.md
index 60ad7d0608ee45c0ffb513494000abe67795d038..9b6d3636471a03aa304b209d8d98a01a52a8a6a4 100644
--- a/ATTRIBUTIONS.md
+++ b/ATTRIBUTIONS.md
@@ -46,8 +46,25 @@ Custom license (as it appears in the original `readme` from the project's page):
>What you see here may be used freely but it comes with no support or
>guarantee.
+## Example SWC morphology
+
+The complex SWC file 'pyramidal.swc' used for testing is taken from NeuroMorpho.org,
+with NeuroMorpho ID NMO_49821. The morphology comes from the paper:
+
+> Hönigsperger, C., Marosi, M., Murphy, R., and Storm, J. F. (2015).
+> Dorsoventral differences in Kv7/M-current and its impact on resonance,
+> temporal summation and excitability in rat hippocampal pyramidal cells.
+> _The Journal of Physiology_, 593(7), 1551–1580. doi:10.1113/jphysiol.2014.280826
+
+NeuroMorpho.org is described in:
+
+> Ascoli, G. A., Donohue, D. E., and Halavi, M. (2007).
+> NeuroMorpho.Org: a central resource for neuronal morphologies.
+> _Journal of Neuroscience_ 27(35), 9247–9251. doi:10.1523/JNEUROSCI.2055-07.2007
+
## Acknowledgements
+
This open source software code was developed in part or in whole in the Human
Brain Project, funded from the European Union’s Horizon 2020 Framework
Programme for Research and Innovation under the Specific Grant Agreement
-No. 720270 (Human Brain Project SGA1) and No. 785907 (Human Brain Project SGA2).
\ No newline at end of file
+No. 720270 (Human Brain Project SGA1) and No. 785907 (Human Brain Project SGA2).
diff --git a/arbor/include/arbor/cable_cell.hpp b/arbor/include/arbor/cable_cell.hpp
index 70b42e0e8bf16c526267e3d18de0d3ddfb184b10..21a85c222f6c6e984bdcd548c0545e37f6ce0875 100644
--- a/arbor/include/arbor/cable_cell.hpp
+++ b/arbor/include/arbor/cable_cell.hpp
@@ -228,7 +228,6 @@ public:
using index_type = cell_lid_type;
using size_type = cell_local_size_type;
using value_type = double;
- using point_type = point<value_type>;
using gap_junction_instance = mlocation;
diff --git a/arbor/include/arbor/cable_cell_param.hpp b/arbor/include/arbor/cable_cell_param.hpp
index 958cf2a7de8e4a79bdadb8fddf75b3e90c357c9c..e118b495257d7078f604487fe47d132a6a85e6d9 100644
--- a/arbor/include/arbor/cable_cell_param.hpp
+++ b/arbor/include/arbor/cable_cell_param.hpp
@@ -1,5 +1,6 @@
#pragma once
+#include <cmath>
#include <memory>
#include <optional>
#include <unordered_map>
diff --git a/arbor/include/arbor/morph/segment_tree.hpp b/arbor/include/arbor/morph/segment_tree.hpp
index f3686965d9f992abad2aa63b20091c45f67e0eab..4ce5a19ce2f92e946cc42f2dfb6e18b10c56399d 100644
--- a/arbor/include/arbor/morph/segment_tree.hpp
+++ b/arbor/include/arbor/morph/segment_tree.hpp
@@ -5,7 +5,6 @@
#include <vector>
#include <string>
-#include <arbor/swcio.hpp>
#include <arbor/morph/primitives.hpp>
namespace arb {
@@ -54,9 +53,6 @@ public:
friend std::ostream& operator<<(std::ostream&, const segment_tree&);
};
-/// Build a sample tree from a sequence of swc records.
-segment_tree swc_as_segment_tree(const std::vector<swc_record>& swc_records);
-
} // namesapce arb
diff --git a/arbor/include/arbor/point.hpp b/arbor/include/arbor/point.hpp
deleted file mode 100644
index aa4c71062ad5e0fd21c171207b0e2e3ec683a928..0000000000000000000000000000000000000000
--- a/arbor/include/arbor/point.hpp
+++ /dev/null
@@ -1,76 +0,0 @@
-#pragma once
-
-#include <cmath>
-#include <limits>
-#include <ostream>
-
-namespace arb {
-
-template <typename T>
-struct point {
- using value_type = T;
- value_type x;
- value_type y;
- value_type z;
-
- constexpr point(T a, T b, T c) :
- x{a}, y{b}, z{c}
- {}
-
- // initialize to NaN by default
- constexpr point() :
- x(std::numeric_limits<T>::quiet_NaN()),
- y(std::numeric_limits<T>::quiet_NaN()),
- z(std::numeric_limits<T>::quiet_NaN())
- {}
-
- constexpr bool is_set() const {
- return (x==x && y==y && z==z);
- }
-};
-
-template <typename T>
-constexpr point<T>
-operator+(point<T> const& lhs, point<T> const& rhs) {
- return point<T>(lhs.x + rhs.x, lhs.y + rhs.y, lhs.z + rhs.z);
-}
-
-template <typename T>
-constexpr point<T>
-operator-(point<T> const& lhs, point<T> const& rhs) {
- return point<T>(lhs.x - rhs.x, lhs.y - rhs.y, lhs.z - rhs.z);
-}
-
-template <typename T>
-constexpr point<T>
-operator*(T alpha, point<T> const& p) {
- return point<T>(alpha*p.x, alpha*p.y, alpha*p.z);
-}
-
-template <typename T>
-T norm(point<T> const& p) {
- return std::sqrt(p.x*p.x + p.y*p.y + p.z*p.z);
-}
-
-template <typename T>
-constexpr T
-dot(point<T> const& lhs, point<T> const& rhs) {
- return lhs.x*rhs.x + lhs.y*rhs.y + lhs.z*rhs.z;
-}
-
-template<typename T>
-bool operator==(const point<T> &rhs, const point<T> &lhs) {
- return (rhs.x==lhs.x) && (rhs.y==lhs.y) && (rhs.z==lhs.z);
-}
-
-template<typename T>
-bool operator!=(const point<T> &rhs, const point<T> &lhs) {
- return !(rhs == lhs);
-}
-
-} // namespace arb
-
-template <typename T>
-std::ostream& operator << (std::ostream& o, arb::point<T> const& p) {
- return o << "[" << p.x << ", " << p.y << ", " << p.z << "]";
-}
diff --git a/arbor/include/arbor/swcio.hpp b/arbor/include/arbor/swcio.hpp
index 368a44653e85229fb39bd25308657fc745435365..efcd17fa0a97e3591bbf0389cd84e068002b7872 100644
--- a/arbor/include/arbor/swcio.hpp
+++ b/arbor/include/arbor/swcio.hpp
@@ -1,52 +1,66 @@
#pragma once
-#include <exception>
#include <iostream>
-#include <iterator>
-#include <map>
#include <string>
-#include <unordered_set>
#include <vector>
-#include <arbor/assert.hpp>
#include <arbor/arbexcept.hpp>
-#include <arbor/point.hpp>
+#include <arbor/morph/segment_tree.hpp>
namespace arb {
+// SWC exceptions are thrown by `parse_swc`, and correspond
+// to inconsistent, or in `strict` mode, dubious SWC data.
+
struct swc_error: public arbor_exception {
- explicit swc_error(const std::string& msg, unsigned line_number = 0):
- arbor_exception(msg), line_number(line_number)
- {}
- unsigned line_number;
+ swc_error(const std::string& msg, int record_id);
+ int record_id;
};
-class swc_record {
-public:
- static constexpr int undefined_tag = 0;
-
- using tag_type = int;
- using id_type = int;
- using coord_type = double;
-
- tag_type tag = undefined_tag; // record type
- id_type id = 0; // record id
- coord_type x = 0; // record coordinates
- coord_type y = 0;
- coord_type z = 0;
- coord_type r = 0; // record radius
- id_type parent_id= -1; // record parent's id
-
- // swc records assume zero-based indexing; root's parent remains -1
- swc_record(int tag, int id,
- coord_type x, coord_type y, coord_type z, coord_type r,
- int parent_id):
- tag(tag), id(id), x(x), y(y), z(z), r(r), parent_id(parent_id)
- {}
+// Parent id in record has no corresponding SWC record,
+// nor is the record the root record with parent id -1.
+struct swc_no_such_parent: swc_error {
+ explicit swc_no_such_parent(int record_id);
+};
+
+// Parent id is greater than or equal to record id.
+struct swc_record_precedes_parent: swc_error {
+ explicit swc_record_precedes_parent(int record_id);
+};
+
+// Multiple records cannot have the same id.
+struct swc_duplicate_record_id: swc_error {
+ explicit swc_duplicate_record_id(int record_id);
+};
+
+// Irregular record ordering.
+struct swc_irregular_id: swc_error {
+ explicit swc_irregular_id(int record_id);
+};
+
+// Smells like a spherical soma.
+struct swc_spherical_soma: swc_error {
+ explicit swc_spherical_soma(int record_id);
+};
+
+// Bad or inconsistent SWC data was fed to an `swc_data` consumer.
+struct bad_swc_data: swc_error {
+ explicit bad_swc_data(int record_id);
+};
+
+struct swc_record {
+ int id = 0; // sample number
+ int tag = 0; // structure identifier (tag)
+ double x = 0; // sample coordinates
+ double y = 0;
+ double z = 0;
+ double r = 0; // sample adius
+ int parent_id= -1; // record parent's sample number
swc_record() = default;
- swc_record(const swc_record& other) = default;
- swc_record& operator=(const swc_record& other) = default;
+ swc_record(int id, int tag, double x, double y, double z, double r, int parent_id):
+ id(id), tag(tag), x(x), y(y), z(z), r(r), parent_id(parent_id)
+ {}
bool operator==(const swc_record& other) const {
return id == other.id &&
@@ -57,37 +71,59 @@ public:
parent_id == other.parent_id;
}
- friend bool operator!=(const swc_record& lhs, const swc_record& rhs) {
- return !(lhs == rhs);
+ bool operator!=(const swc_record& other) const {
+ return !(*this == other);
}
- friend std::ostream& operator<<(std::ostream& os, const swc_record& record);
-
- coord_type diameter() const {
- return 2*r;
- }
-
- arb::point<coord_type> coord() const {
- return arb::point<coord_type>(x, y, z);
- }
-
- // validity checks
- bool is_consistent() const;
- void assert_consistent() const; // throw swc_error if inconsistent.
+ friend std::ostream& operator<<(std::ostream&, const swc_record&);
+ friend std::istream& operator>>(std::istream&, swc_record&);
};
+struct swc_data {
+ std::string metadata;
+ std::vector<swc_record> records;
+};
-// Parse one record, skipping comments and blank lines.
-std::istream& operator>>(std::istream& is, swc_record& record);
-
-// Parse and canonicalize an EOF-terminated sequence of records.
-// Throw on parsing failure.
-std::vector<swc_record> parse_swc_file(std::istream& is);
+// Read SWC records from stream, collecting any initial metadata represented
+// in comments (stripping initial '#' and subsequent whitespace).
+// Stops at EOF or after reading the first line that does not parse as SWC.
+//
+// Note that 'one-point soma' SWC files are explicitly not supported.
+//
+// In `relaxed` mode, it will check that:
+// * There are no duplicate record ids.
+// * All record ids are positive.
+// * There are no records whose parent id is not less than the record id.
+// * Only one record has parent id -1; all other parent ids correspond to records.
+// * There are at least two records.
+//
+// In `strict` mode, it will additionally check:
+// * Record ids are numbered contiguously from 1.
+// * The data cannot be interpreted as a 'spherical soma' SWC file.
+// Specifically, the root record shares its tag with at least one other
+// record with has the root as parent.
+//
+// Throws a corresponding exception of type derived from `swc_error` if any of the
+// conditions above are encountered.
+//
+// SWC records are stored in id order.
+
+enum class swc_mode { relaxed, strict };
+
+swc_data parse_swc(std::istream&, swc_mode = swc_mode::strict);
+swc_data parse_swc(const std::string& text, swc_mode mode = swc_mode::strict);
+
+// Parse a series of existing SWC records.
+
+swc_data parse_swc(std::vector<swc_record>, swc_mode = swc_mode::strict);
+
+// Convert a valid, ordered sequence of SWC records to a morphological segment tree.
+
+segment_tree as_segment_tree(const std::vector<swc_record>&);
+
+inline segment_tree as_segment_tree(const swc_data& data) {
+ return as_segment_tree(data.records);
+}
-// Given a vector of random-access mutable sequence of `swc_record` describing
-// a single morphology, check for consistency and renumber records
-// so that ids are contiguous within branches, have no gaps, and
-// are ordered with repect to parent indices.
-void swc_canonicalize(std::vector<swc_record>& swc_records);
} // namespace arb
diff --git a/arbor/io/save_ios.hpp b/arbor/io/save_ios.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..adfcda2475bee2d0fcca3db58323d088bef33c7c
--- /dev/null
+++ b/arbor/io/save_ios.hpp
@@ -0,0 +1,24 @@
+#pragma once
+
+// RAII save-and-restore ios formatting flags.
+
+#include <ios>
+
+namespace arb {
+namespace io {
+
+struct save_ios_flags {
+ std::ios_base& ios;
+ std::ios_base::fmtflags flags;
+
+ save_ios_flags(std::ios_base& ios):
+ ios(ios), flags(ios.flags()) {}
+
+ save_ios_flags(const save_ios_flags&) = delete;
+
+ ~save_ios_flags() { ios.flags(flags); }
+};
+
+
+} // namespace io
+} // namespace arb
diff --git a/arbor/morph/morphology.cpp b/arbor/morph/morphology.cpp
index ee861e749461f1bb49961e5216a62d1ee5410ae9..ff126d7372fa91c771a6412041979722c7f3f6a9 100644
--- a/arbor/morph/morphology.cpp
+++ b/arbor/morph/morphology.cpp
@@ -1,6 +1,7 @@
#include <iostream>
#include <stack>
#include <unordered_map>
+#include <unordered_set>
#include <utility>
#include <arbor/morph/morphexcept.hpp>
diff --git a/arbor/morph/region.cpp b/arbor/morph/region.cpp
index 5e7c8a5afa243a49d0d9d56e0b5d7716b67399bd..487360fdc6bec2aa70063cd27b6b107b4a5e61d5 100644
--- a/arbor/morph/region.cpp
+++ b/arbor/morph/region.cpp
@@ -1,6 +1,7 @@
#include <optional>
#include <stack>
#include <string>
+#include <unordered_set>
#include <vector>
#include <arbor/morph/label_parse.hpp>
diff --git a/arbor/morph/segment_tree.cpp b/arbor/morph/segment_tree.cpp
index d8fca989248cb7c91b120aeb55ef5d56c970400c..955307cb10c793de62371847cae8f80da84fac0f 100644
--- a/arbor/morph/segment_tree.cpp
+++ b/arbor/morph/segment_tree.cpp
@@ -87,40 +87,5 @@ std::ostream& operator<<(std::ostream& o, const segment_tree& m) {
<< io::sepval(tstr, ' ') << "))";
}
-segment_tree swc_as_segment_tree(const std::vector<swc_record>& swc_records) {
- if (swc_records.size()<2) {
- throw "At least two swc records are required to construct a segment tree.";
- }
-
- auto point = [&swc_records] (msize_t i) {
- auto& r = swc_records[i];
- return mpoint{r.x, r.y, r.z, r.r};
- };
- auto tag = [&swc_records] (msize_t i) {
- return swc_records[i].tag;
- };
-
- segment_tree tree;
- tree.reserve(swc_records.size());
-
- std::unordered_map<msize_t, msize_t> segmap;
-
- tree.append(mnpos, point(0), point(1), tag(1));
- segmap[0] = mnpos;
- segmap[1] = 0;
- for (unsigned i=2; i<swc_records.size(); ++i) {
- msize_t p = segmap[swc_records[i].parent_id];
- if (p==mnpos) {
- tree.append(p, point(0), point(i), tag(i));
- }
- else {
- tree.append(p, point(i), tag(i));
- }
- segmap[i] = i-1;
- }
-
- return tree;
-}
-
} // namespace arb
diff --git a/arbor/swcio.cpp b/arbor/swcio.cpp
index 8c0b14b5d4a075c4b318ec88b753069e7faeff9c..59577b0628bb4c169ce231867c34a6b8fdcbfec8 100644
--- a/arbor/swcio.cpp
+++ b/arbor/swcio.cpp
@@ -1,213 +1,201 @@
-#include <algorithm>
-#include <functional>
-#include <iomanip>
-#include <map>
+#include <iostream>
+#include <limits>
+#include <string>
#include <sstream>
+#include <unordered_map>
#include <unordered_set>
+#include <vector>
-#include <arbor/assert.hpp>
-#include <arbor/point.hpp>
+#include <arbor/morph/segment_tree.hpp>
#include <arbor/swcio.hpp>
-#include "algorithms.hpp"
-#include "util/span.hpp"
+#include "io/save_ios.hpp"
+#include "util/rangeutil.hpp"
namespace arb {
-// swc_record implementation
+// SWC exceptions:
-// helper function: return error message if inconsistent, or nullptr if ok.
-const char* swc_record_error(const swc_record& r) {
- if (r.tag<0) {
- return "unknown record tag";
- }
+swc_error::swc_error(const std::string& msg, int record_id):
+ arbor_exception(msg+": sample id "+std::to_string(record_id)),
+ record_id(record_id)
+{}
- if (r.id < 0) {
- return "negative ids not allowed";
- }
+swc_no_such_parent::swc_no_such_parent(int record_id):
+ swc_error("missing SWC parent record", record_id)
+{}
- if (r.parent_id < -1) {
- return "parent_id < -1 not allowed";
- }
+swc_record_precedes_parent::swc_record_precedes_parent(int record_id):
+ swc_error("SWC parent id is not less than sample id", record_id)
+{}
- if (r.parent_id >= r.id) {
- return "parent_id >= id is not allowed";
- }
+swc_duplicate_record_id::swc_duplicate_record_id(int record_id):
+ swc_error("duplicate SWC sample id", record_id)
+{}
- if (r.r < 0) {
- return "negative radii are not allowed";
- }
+swc_irregular_id::swc_irregular_id(int record_id):
+ swc_error("SWC record id not numbered consecutively from 1", record_id)
+{}
- return nullptr;
-}
+swc_spherical_soma::swc_spherical_soma(int record_id):
+ swc_error("SWC with spherical somata are not supported", record_id)
+{}
+bad_swc_data::bad_swc_data(int record_id):
+ swc_error("Cannot interpret bad SWC data", record_id)
+{}
-bool swc_record::is_consistent() const {
- return swc_record_error(*this)==nullptr;
-}
+// Record I/O
-void swc_record::assert_consistent() const {
- const char* error = swc_record_error(*this);
- if (error) {
- throw swc_error(error);
- }
+std::ostream& operator<<(std::ostream& out, const swc_record& record) {
+ io::save_ios_flags save(out);
+
+ out.precision(std::numeric_limits<double>::digits10+2);
+ return out << record.id << ' ' << record.tag << ' '
+ << record.x << ' ' << record.y << ' ' << record.z << ' ' << record.r
+ << record.parent_id << '\n';
}
-static bool parse_record(const std::string& line, swc_record& record) {
- std::istringstream is(line);
- swc_record r;
+std::istream& operator>>(std::istream& in, swc_record& record) {
+ std::string line;
+ if (!getline(in, line, '\n')) return in;
- is >> r.id >> r.tag >> r.x >> r.y >> r.z >> r.r >> r.parent_id;
- if (is) {
- // Convert to zero-based, leaving parent_id as-is if -1
- --r.id;
- if (r.parent_id>=0) {
- --r.parent_id;
- }
+ swc_record r;
+ std::istringstream s(line);
+ s >> r.id >> r.tag >> r.x >> r.y >> r.z >> r.r >> r.parent_id;
+ if (s) {
record = r;
- return true;
}
- return false;
-}
+ else {
+ in.setstate(std::ios_base::failbit);
+ }
-static bool is_comment(const std::string& line) {
- auto pos = line.find_first_not_of(" \f\n\r\t\v");
- return pos==std::string::npos || line[pos]=='#';
+ return in;
}
-std::istream& operator>>(std::istream& is, swc_record& record) {
- std::string line;
+// Parse SWC format data (comments and sequence of SWC records).
- while (is) {
- std::getline(is, line);
- if (!is) {
- break;
+static std::vector<swc_record> sort_and_validate_swc(std::vector<swc_record> records, swc_mode mode) {
+ if (records.empty()) return {};
+
+ std::unordered_set<int> seen;
+ std::size_t n_rec = records.size();
+ int first_id = records[0].id;
+ int first_tag = records[0].tag;
+
+ if (records.size()<2) {
+ throw swc_spherical_soma(first_id);
+ }
+
+ for (std::size_t i = 0; i<n_rec; ++i) {
+ swc_record& r = records[i];
+
+ if (r.parent_id>=r.id) {
+ throw swc_record_precedes_parent(r.id);
}
- if (is_comment(line)) {
- continue;
+ if (mode==swc_mode::strict && r.id != (int)i+1) {
+ throw swc_irregular_id(r.id);
}
- bool ok = parse_record(line, record);
- if (!ok) {
- is.setstate(std::ios::failbit);
+ if (!seen.insert(r.id).second) {
+ throw swc_duplicate_record_id(r.id);
}
- break;
}
- return is;
-}
-std::ostream& operator<<(std::ostream& os, const swc_record& record) {
- // output in one-based indexing
- os << record.id+1 << " "
- << record.tag << " "
- << std::setprecision(7) << record.x << " "
- << std::setprecision(7) << record.y << " "
- << std::setprecision(7) << record.z << " "
- << std::setprecision(7) << record.r << " "
- << ((record.parent_id == -1) ? record.parent_id : record.parent_id+1);
-
- return os;
+ util::sort_by(records, [](auto& r) { return r.id; });
+ bool first_tag_match = false;
+
+ for (std::size_t i = 0; i<n_rec; ++i) {
+ const swc_record& r = records[i];
+ first_tag_match |= r.parent_id==first_id && r.tag==first_tag;
+
+ if ((i==0 && r.parent_id!=-1) || (i>0 && !seen.count(r.parent_id))) {
+ throw swc_no_such_parent(r.id);
+ }
+ }
+
+ if (mode==swc_mode::strict && !first_tag_match) {
+ throw swc_spherical_soma(first_id);
+ }
+
+ return records;
}
-std::vector<swc_record> parse_swc_file(std::istream& is) {
- constexpr auto eof = std::char_traits<char>::eof();
- std::vector<swc_record> records;
- std::size_t line_number = 1;
- std::string line;
+swc_data parse_swc(std::istream& in, swc_mode mode) {
+ // Collect any initial comments (lines beginning with '#').
- try {
- while (is && is.peek()!=eof) {
- std::getline(is, line);
- if (is_comment(line)) {
- continue;
- }
+ swc_data data;
+ std::string line;
- swc_record record;
- bool ok = parse_record(line, record);
- if (!ok) {
- is.setstate(std::ios::failbit);
- }
- else {
- record.assert_consistent();
- records.push_back(std::move(record));
+ while (in) {
+ auto c = in.get();
+ if (c=='#') {
+ getline(in, line, '\n');
+ auto from = line.find_first_not_of(" \t");
+ if (from != std::string::npos) {
+ data.metadata.append(line, from);
}
- ++line_number;
+ data.metadata += '\n';
+ }
+ else {
+ in.unget();
+ break;
}
- }
- catch (swc_error& e) {
- e.line_number = line_number; // rethrow with saved line number
- throw e;
}
- if (!is.eof()) {
- // parse error, so throw exception
- throw swc_error("SWC parse error", line_number);
+ swc_record r;
+ while (in && in >> r) {
+ data.records.push_back(r);
}
- swc_canonicalize(records);
- return records;
+ data.records = sort_and_validate_swc(std::move(data.records), mode);
+ return data;
}
-void swc_canonicalize(std::vector<swc_record>& swc_records) {
- std::unordered_set<swc_record::id_type> ids;
+swc_data parse_swc(const std::string& text, swc_mode mode) {
+ std::istringstream is(text);
+ return parse_swc(is, mode);
+}
- std::size_t num_trees = 0;
- swc_record::id_type last_id = -1;
- bool needsort = false;
+swc_data parse_swc(std::vector<swc_record> records, swc_mode mode) {
+ swc_data data;
+ data.records = sort_and_validate_swc(std::move(records), mode);
+ return data;
+}
- for (const auto& r: swc_records) {
- r.assert_consistent();
+segment_tree as_segment_tree(const std::vector<swc_record>& records) {
+ if (records.empty()) return {};
+ if (records.size()<2) throw bad_swc_data{records.front().id};
- if (r.parent_id == -1 && ++num_trees > 1) {
- // only a single tree is allowed
- throw swc_error("multiple trees found in SWC record sequence");
- }
- if (ids.count(r.id)) {
- throw swc_error("records with duplicated ids in SWC record sequence");
- }
+ segment_tree tree;
+ std::size_t n_seg = records.size()-1;
+ tree.reserve(n_seg);
- if (!needsort && r.id < last_id) {
- needsort = true;
- }
+ std::unordered_map<int, std::size_t> id_to_index;
+ id_to_index[records[0].id] = 0;
- last_id = r.id;
- ids.insert(r.id);
- }
+ // ith segment is built from i+1th SWC record and its parent.
+ for (std::size_t i = 1; i<n_seg+1; ++i) {
+ const auto& dist = records[i];
- if (needsort) {
- std::sort(swc_records.begin(), swc_records.end(),
- [](const swc_record& a, const swc_record& b) { return a.id<b.id; });
- }
+ auto iter = id_to_index.find(dist.parent_id);
+ if (iter==id_to_index.end()) throw bad_swc_data{dist.id};
+ auto parent_idx = iter->second;
- // Renumber records if necessary.
- std::map<swc_record::id_type, swc_record::id_type> idmap;
- swc_record::id_type next_id = 0;
- for (auto& r: swc_records) {
- if (r.id != next_id) {
- auto old_id = r.id;
- r.id = next_id;
-
- auto new_parent_id = idmap.find(r.parent_id);
- if (new_parent_id != idmap.end()) {
- r.parent_id = new_parent_id->second;
- }
+ const auto& prox = records[parent_idx];
+ msize_t seg_parent = parent_idx? parent_idx-1: mnpos;
- r.assert_consistent();
- idmap.insert(std::make_pair(old_id, next_id));
- }
- ++next_id;
- }
+ tree.append(seg_parent,
+ mpoint{prox.x, prox.y, prox.z, prox.r},
+ mpoint{dist.x, dist.y, dist.z, dist.r},
+ dist.tag);
- // Reject if branches are not contiguously numbered.
- std::vector<swc_record::id_type> parent_list = { 0 };
- for (std::size_t i = 1; i < swc_records.size(); ++i) {
- parent_list.push_back(swc_records[i].parent_id);
+ id_to_index[dist.id] = i;
}
- if (!arb::algorithms::has_contiguous_compartments(parent_list)) {
- throw swc_error("branches are not contiguously numbered", 0);
- }
+ return tree;
}
} // namespace arb
+
diff --git a/example/single/example.swc b/example/single/example.swc
deleted file mode 100644
index 84addf0852529b983cdaeb4076b9ed629c1349f8..0000000000000000000000000000000000000000
--- a/example/single/example.swc
+++ /dev/null
@@ -1,1062 +0,0 @@
-#example swc file from the Allen DB
-#name C:/neuron tracing and reconstruction/vaa3d/vaa3d_bin_msvc_64bit_v2921_a/vaa3d_bin_msvc_64bit_v2921_a/Sst-IRES-Cre;Ai14(IVSCC)-173191.06.01.01.DS.swc_resampled.swc_sorted.swc_pruned.swc_pruned.swc
-#comment
-##n,type,x,y,z,radius,parent
-1 1 345.8312 346.9752 50.96 2.9744 -1
-2 3 347.2486 344.4641 52.04 0.1252 1
-3 3 347.6033 343.3762 52.0789 0.1487 2
-4 3 347.8641 342.2642 52.071 0.1853 3
-5 3 348.1409 341.1534 52.0246 0.2235 4
-6 3 348.4269 340.0551 51.688 0.262 5
-7 3 348.5734 338.942 51.1722 0.3007 6
-8 3 348.6409 337.8312 51.6947 0.3165 7
-9 3 348.9108 336.7387 52.1489 0.3178 8
-10 3 349.031 335.605 52.3401 0.2943 9
-11 3 349.0584 334.4667 52.0985 0.2805 10
-12 3 349.1797 333.3296 52.0738 0.256 11
-13 3 349.6785 332.3057 52.045 0.2305 12
-14 3 350.3752 331.4019 51.9201 0.2051 13
-15 3 351.049 330.5108 51.3243 0.1795 14
-16 3 351.8441 329.7122 50.8623 0.1658 15
-17 3 352.8199 329.1723 50.2564 0.1407 16
-18 3 353.6379 328.622 48.8471 0.1523 17
-19 3 354.4101 327.7835 48.666 0.1903 18
-20 3 355.0015 326.8088 48.4406 0.3432 19
-21 3 355.2406 326.0858 48.0054 0.2905 20
-22 3 355.5586 325.0047 48.0833 0.2134 21
-23 3 355.6399 323.9442 47.4054 0.1627 22
-24 3 355.7966 323.2361 45.3768 0.1525 23
-25 3 356.5951 322.7373 44.0163 0.1742 24
-26 3 357.1213 321.8038 44.4405 0.178 25
-27 3 357.7906 320.8931 44.8554 0.1525 26
-28 3 357.9885 320.5099 44.812 0.2397 27
-29 3 358.2047 319.5203 46.1068 0.2924 28
-30 3 358.3832 318.4873 47.1971 0.2839 29
-31 3 358.9346 317.5389 47.591 0.2536 30
-32 3 359.4311 316.5208 47.6991 0.2415 31
-33 3 359.7079 315.4294 48.1057 0.2592 32
-34 3 360.4023 314.6972 47.546 0.2781 33
-35 3 361.4617 314.4776 46.6984 0.2796 34
-36 3 362.5851 314.3495 46.9686 0.2678 35
-37 3 363.5952 313.8312 46.8367 0.2791 36
-38 3 364.1524 312.8531 46.4405 0.3049 37
-39 3 364.4258 311.7457 46.2462 0.3051 38
-40 3 364.547 311.0547 45.8128 0.1722 39
-41 3 364.5036 310.0549 44.485 0.1761 40
-42 3 364.0139 309.166 43.2284 0.1905 41
-43 3 363.6684 308.0792 43.3289 0.2288 42
-44 3 363.6501 307.4317 43.7506 0.1431 43
-45 3 363.5071 306.3152 43.2762 0.1524 44
-46 3 362.9043 305.3473 43.0903 0.1525 45
-47 3 362.8002 305.0762 41.0407 0.1518 46
-48 3 363.061 305.2192 38.3914 0.1388 47
-49 3 363.7634 304.7948 36.4557 0.1258 48
-50 3 364.4864 304.1301 35.0616 0.1144 49
-51 3 365.3067 303.4277 34.8012 0.1144 50
-52 3 365.9519 303.0101 36.7332 0.1144 51
-53 3 366.1349 302.8271 39.41 0.1144 52
-54 3 366.0468 302.5651 42.1162 0.1241 53
-55 3 365.9553 302.0126 44.0028 0.1562 54
-56 3 366.5708 301.6705 45.638 0.1848 55
-57 3 367.3407 301.4566 47.6333 0.1703 56
-58 3 368.2422 301.0047 48.862 0.1439 57
-59 3 369.2523 300.7587 50.0007 0.1181 58
-60 3 370.1504 300.4064 51.4822 0.1144 59
-61 3 371.1525 300.0334 50.6584 0.1144 60
-62 3 371.9144 300.3 48.72 0.1271 61
-63 3 362.2407 304.6163 42.6549 0.1525 46
-64 3 361.4846 303.7823 42.1585 0.1525 63
-65 3 360.749 302.9484 41.5696 0.1634 64
-66 3 360.5053 301.9382 40.88 0.2127 65
-67 3 360.3234 301.1649 42.0109 0.1525 66
-68 3 360.1312 300.1467 42.0591 0.1977 67
-69 3 360.2856 299.0267 41.8816 0.1652 68
-70 3 360.3085 297.9193 41.3322 0.1679 69
-71 3 360.2284 296.7879 40.9721 0.1722 70
-72 3 360.1484 295.6554 40.6118 0.1764 71
-73 3 359.6896 294.7173 40.8979 0.178 72
-74 3 359.4471 293.8192 40.0518 0.2634 73
-75 3 359.3773 292.7885 39.2188 0.2594 74
-76 3 358.8328 292.2886 40.4404 0.2093 75
-77 3 357.9324 291.8104 40.4524 0.2463 76
-78 3 357.5549 291.148 40.7067 0.178 77
-79 3 357.7929 290.4044 41.778 0.1509 78
-80 3 357.6052 290.2225 39.3299 0.1271 79
-81 3 357.2437 289.2375 39.1308 0.1558 80
-82 3 356.8044 288.5168 39.1642 0.115 81
-83 3 356.0128 288.1027 39.48 0.3209 82
-84 3 355.736 287.2893 38.4395 0.2196 83
-85 3 355.4339 286.6555 39.76 0.1478 84
-86 3 355.3367 285.674 38.9138 0.2157 85
-87 3 354.9832 284.753 38.18 0.2016 86
-88 3 354.3826 283.8722 38.6277 0.122 87
-89 3 353.3919 283.5164 39.3621 0.2288 88
-90 3 352.6586 283.1434 39.5105 0.1801 89
-91 3 351.9768 282.3838 38.3928 0.178 90
-92 3 351.1359 281.845 37.1064 0.1531 91
-93 3 350.1349 281.6906 37.4791 0.1555 92
-94 3 349.5858 281.1792 39.3308 0.2404 93
-95 3 348.872 280.6815 40.5969 0.2284 94
-96 3 348.3514 280.2388 39.1154 0.1628 95
-97 3 347.4042 279.7606 39.0009 0.1305 96
-98 3 346.9615 279.374 40.4776 0.2131 97
-99 3 346.1378 279.184 39.867 0.186 98
-100 3 345.1402 278.9781 40.5045 0.2239 99
-101 3 344.1003 279.128 40.4074 0.1746 100
-102 3 343.4242 278.461 39.0852 0.2288 101
-103 3 342.3283 278.4141 39.5388 0.1792 102
-104 3 341.5401 278.008 40.6 0.2003 103
-105 3 340.7141 277.4006 41.0668 0.178 104
-106 3 339.8641 276.8777 40.7912 0.2248 105
-107 3 338.8265 276.4945 40.32 0.1838 106
-108 3 338.3769 275.6148 39.7911 0.2136 107
-109 3 337.8541 274.7716 40.8598 0.1818 108
-110 3 337.8404 273.9777 39.8051 0.2612 109
-111 3 337.2775 273.2147 39.8112 0.1411 110
-112 3 336.8977 272.8737 41.4341 0.1295 111
-113 3 336.0454 272.4825 41.4882 0.1209 112
-114 3 335.4116 271.9059 41.2969 0.175 113
-115 3 334.5079 271.3396 41.1723 0.1924 114
-116 3 333.9187 270.4107 41.1289 0.1839 115
-117 3 333.4611 269.6339 40.32 0.1626 116
-118 3 333.0562 268.7107 41.0533 0.167 117
-119 3 332.5494 267.8012 40.7145 0.2142 118
-120 3 332.0334 266.8449 40.3763 0.1575 119
-121 3 331.2727 266.02 40.32 0.1652 120
-122 3 330.37 265.3302 40.32 0.1525 121
-123 3 329.4045 264.7491 40.32 0.1464 122
-124 3 328.7856 263.8739 40.32 0.1162 123
-125 3 328.7742 262.7379 40.0663 0.1756 124
-126 3 328.5007 261.6454 39.8079 0.2128 125
-127 3 328.0763 260.586 39.76 0.2415 126
-128 3 327.5867 259.5622 39.76 0.2158 127
-129 3 326.7561 258.7831 39.76 0.1597 128
-130 3 326.3489 257.789 39.9283 0.1144 129
-131 3 325.5858 257.1437 40.04 0.2602 130
-132 3 325.0344 256.1942 40.32 0.1525 131
-133 3 324.046 255.6565 40.3785 0.1557 132
-134 3 323.4523 254.7036 40.6 0.1695 133
-135 3 322.568 253.9829 40.6056 0.2288 134
-136 3 321.7168 253.2519 40.88 0.1885 135
-137 3 321.0933 252.3172 40.88 0.1241 136
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-140 3 319.9871 249.1746 40.88 0.1282 139
-141 3 319.788 248.113 41.4607 0.2398 140
-142 3 319.2526 247.2161 42.0 0.2024 141
-143 3 318.5537 246.3192 42.1347 0.2415 142
-144 3 317.8249 245.4566 42.4766 0.2199 143
-145 3 316.9852 244.6879 42.56 0.1938 144
-146 3 316.0163 244.1376 43.0962 0.2034 145
-147 3 315.204 243.4947 43.6257 0.2013 146
-148 3 314.3266 242.7968 43.68 0.2078 147
-149 3 313.6573 241.9754 44.24 0.1849 148
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-155 3 307.4683 239.7824 43.6892 0.1284 154
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-157 3 305.2993 239.3648 42.84 0.1144 156
-158 3 304.2274 239.0056 42.84 0.1144 157
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-165 3 297.4228 236.2326 42.84 0.1271 164
-166 3 296.4893 235.8928 43.6498 0.1241 165
-167 3 295.4243 235.8928 44.24 0.1144 166
-168 3 294.2803 235.8928 44.24 0.1144 167
-169 3 293.1546 235.6949 44.24 0.122 168
-170 3 292.133 235.211 44.24 0.1459 169
-171 3 291.0302 234.9238 44.24 0.1398 170
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-182 3 370.0748 301.4429 38.64 0.2056 181
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-206 3 382.9346 284.8228 28.3332 0.1865 205
-207 3 382.9574 284.2897 26.4147 0.2317 206
-208 3 382.3534 283.7875 25.1253 0.1863 207
-209 3 381.4805 283.3677 24.3115 0.1144 208
-210 3 381.1659 282.4227 25.2 0.1966 209
-211 3 380.4944 282.3392 25.2 0.1271 210
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-214 3 367.1336 310.1132 44.2781 0.178 213
-215 3 368.1415 309.5904 44.2394 0.178 214
-216 3 369.1093 308.9818 44.2361 0.1907 215
-217 3 369.9616 308.2245 44.2145 0.1805 216
-218 3 370.4558 307.2132 44.0653 0.178 217
-219 3 370.6606 306.1436 43.2916 0.1674 218
-220 3 371.3653 305.4491 42.1047 0.1652 219
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-242 3 389.143 296.9561 34.3484 0.2261 241
-243 3 389.9907 296.701 34.4235 0.1704 242
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-245 3 391.4036 295.6359 32.4764 0.235 244
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-250 3 395.4957 294.111 31.08 0.1328 249
-251 3 396.4212 293.7243 31.535 0.1694 250
-252 3 397.1762 293.4726 31.4401 0.2107 251
-253 3 397.7665 293.3685 32.48 0.1542 252
-254 3 398.6096 292.9761 32.849 0.2149 253
-255 3 399.2549 292.4087 31.6495 0.1144 254
-256 3 399.9401 291.8882 31.3869 0.1433 255
-257 3 400.4927 290.9981 31.2021 0.2555 256
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-270 3 404.3823 280.0981 26.9817 0.1969 269
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-275 3 408.5224 277.5344 26.32 0.1271 274
-276 3 358.4083 321.2638 42.5488 0.1543 27
-277 3 359.4105 321.4137 42.0297 0.1191 276
-278 3 360.4618 321.0121 42.2167 0.1252 277
-279 3 361.5829 320.9709 41.9863 0.1387 278
-280 3 362.2384 321.0693 39.8014 0.177 279
-281 3 363.1971 320.7296 38.5496 0.203 280
-282 3 364.038 320.1736 37.2288 0.2415 281
-283 3 355.466 326.2985 48.792 0.3253 20
-284 3 356.2199 325.4703 49.3626 0.2961 283
-285 3 356.9738 324.642 49.9332 0.267 284
-286 3 357.7277 323.8138 50.5039 0.2378 285
-287 3 358.4816 322.9855 51.0745 0.2087 286
-288 3 359.2354 322.1573 51.6452 0.1795 287
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-1026 3 330.7293 320.5374 57.4535 0.176 1025
-1027 3 330.2579 319.8658 59.2088 0.165 1026
-1028 3 329.7122 319.176 59.0167 0.1144 1027
-1029 3 328.8828 319.1566 57.8206 0.1715 1028
-1030 3 327.764 319.1302 57.4392 0.2188 1029
-1031 3 326.8225 318.7184 58.24 0.1894 1030
-1032 3 325.6785 318.7184 58.24 0.2154 1031
-1033 3 325.2392 319.0616 58.8 0.2288 1032
-1034 2 346.1607 344.6334 49.8854 0.123 1
-1035 2 346.3174 343.5192 49.3741 0.1211 1034
-1036 2 346.4741 342.4061 48.8631 0.1192 1035
-1037 2 346.6309 341.2918 48.3518 0.1172 1036
-1038 2 346.7876 340.1776 47.8408 0.1153 1037
-1039 2 346.9729 339.1788 47.7985 0.1927 1038
-1040 2 347.0896 338.5496 49.3716 0.1528 1039
-1041 2 347.1971 337.8827 48.72 0.193 1040
-1042 2 347.093 336.7787 48.3546 0.126 1041
-1043 2 347.4534 335.9722 47.5096 0.2025 1042
-1044 2 347.5472 334.9003 47.4533 0.178 1043
-1045 2 347.4328 333.8501 48.3232 0.1477 1044
-1046 2 347.3573 332.9166 49.8243 0.1144 1045
-1047 2 347.3642 332.1238 51.0507 0.1402 1046
-1048 2 347.8996 331.1697 50.9404 0.2872 1047
-1049 2 348.253 330.1813 50.9463 0.1271 1048
-1050 2 348.3663 329.1322 51.0308 0.1968 1049
-1051 2 348.8239 328.7764 49.0297 0.1774 1050
-1052 2 349.1328 327.8338 49.4637 0.1833 1051
-1053 2 349.1488 326.7676 48.7676 0.2731 1052
-1054 2 349.6156 326.0583 49.28 0.1144 1053
-1055 2 350.064 325.0573 48.9135 0.1144 1054
-1056 2 350.5937 324.324 48.72 0.1144 1055
-1057 2 351.3533 323.7428 49.2282 0.2034 1056
-1058 2 351.7159 322.8746 49.3111 0.1907 1057
diff --git a/example/single/single.cpp b/example/single/single.cpp
index e36740d580d50667ff5429e4afa98320af31a7ad..f280096269998f2b8d977e96dfa152da77e446a3 100644
--- a/example/single/single.cpp
+++ b/example/single/single.cpp
@@ -157,5 +157,5 @@ arb::morphology read_swc(const std::string& path) {
std::ifstream f(path);
if (!f) throw std::runtime_error("unable to open SWC file: "+path);
- return arb::morphology(arb::swc_as_segment_tree(arb::parse_swc_file(f)));
+ return arb::morphology(arb::as_segment_tree(arb::parse_swc(f)));
}
diff --git a/python/morphology.cpp b/python/morphology.cpp
index 30be0372bea136e8eec2f7783e67bd529503aea8..1153ced76d195fa52ae3f07bbf87107119481a95 100644
--- a/python/morphology.cpp
+++ b/python/morphology.cpp
@@ -20,7 +20,7 @@ arb::segment_tree load_swc_allen(const std::string& fname, bool no_gaps=false) {
}
try {
using namespace arb;
- auto records = parse_swc_file(fid);
+ auto records = parse_swc(fid, swc_mode::relaxed).records;
// Assert that the file contains at least one sample.
if (records.empty()) {
@@ -104,8 +104,7 @@ arb::segment_tree load_swc_allen(const std::string& fname, bool no_gaps=false) {
catch (arb::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
throw pyarb_error(
- util::pprintf("Allen SWC: error parsing line {} of '{}': {}",
- e.line_number, fname, e.what()));
+ util::pprintf("Allen SWC: error parsing {}: {}", fname, e.what()));
}
}
@@ -237,14 +236,13 @@ void register_morphology(pybind11::module& m) {
throw pyarb_error(util::pprintf("can't open file '{}'", fname));
}
try {
- auto records = arb::parse_swc_file(fid);
- return arb::swc_as_segment_tree(records);
+ auto records = arb::parse_swc(fid).records;
+ return arb::as_segment_tree(records);
}
catch (arb::swc_error& e) {
// Try to produce helpful error messages for SWC parsing errors.
throw pyarb_error(
- util::pprintf("error parsing line {} of '{}': {}.",
- e.line_number, fname, e.what()));
+ util::pprintf("error parsing {}: {}", fname, e.what()));
}
},
"Load an swc file and as a segment_tree.");
diff --git a/test/ubench/fvm_discretize.cpp b/test/ubench/fvm_discretize.cpp
index 3546e8a093b7f3afbaf57141d4cc54083d2329b0..8c353b5ca5b3dd59f38f34cc19f2eea94b810f19 100644
--- a/test/ubench/fvm_discretize.cpp
+++ b/test/ubench/fvm_discretize.cpp
@@ -26,7 +26,7 @@ arb::morphology from_swc(const std::string& path) {
std::ifstream in(path);
if (!in) throw std::runtime_error("could not open "+path);
- return morphology(swc_as_sample_tree(parse_swc_file(in)));
+ return morphology(arb::as_segment_tree(parse_swc(in)));
}
void run_cv_geom(benchmark::State& state) {
@@ -41,11 +41,11 @@ void run_cv_geom(benchmark::State& state) {
}
}
-void run_cv_geom_every_sample(benchmark::State& state) {
+void run_cv_geom_every_segment(benchmark::State& state) {
auto gdflt = neuron_parameter_defaults;
cable_cell c(from_swc(SWCFILE));
- auto ends = cv_policy_every_sample().cv_boundary_points(c);
+ auto ends = cv_policy_every_segment().cv_boundary_points(c);
while (state.KeepRunning()) {
benchmark::DoNotOptimize(cv_geometry_from_ends(c, ends));
@@ -58,7 +58,7 @@ void run_cv_geom_explicit(benchmark::State& state) {
cable_cell c(from_swc(SWCFILE));
while (state.KeepRunning()) {
- auto ends = cv_policy_every_sample().cv_boundary_points(c);
+ auto ends = cv_policy_every_segment().cv_boundary_points(c);
auto ends2 = cv_policy_explicit(std::move(ends)).cv_boundary_points(c);
benchmark::DoNotOptimize(cv_geometry_from_ends(c, ends2));
@@ -77,11 +77,11 @@ void run_discretize(benchmark::State& state) {
}
}
-void run_discretize_every_sample(benchmark::State& state) {
+void run_discretize_every_segment(benchmark::State& state) {
auto gdflt = neuron_parameter_defaults;
cable_cell c(from_swc(SWCFILE));
- c.default_parameters.discretization = cv_policy_every_sample();
+ c.default_parameters.discretization = cv_policy_every_segment();
while (state.KeepRunning()) {
benchmark::DoNotOptimize(fvm_cv_discretize(c, gdflt));
@@ -94,7 +94,7 @@ void run_discretize_explicit(benchmark::State& state) {
cable_cell c(from_swc(SWCFILE));
while (state.KeepRunning()) {
- auto ends = cv_policy_every_sample().cv_boundary_points(c);
+ auto ends = cv_policy_every_segment().cv_boundary_points(c);
c.default_parameters.discretization = cv_policy_explicit(std::move(ends));
benchmark::DoNotOptimize(fvm_cv_discretize(c, gdflt));
@@ -104,8 +104,8 @@ void run_discretize_explicit(benchmark::State& state) {
BENCHMARK(run_cv_geom)->RangeMultiplier(2)->Range(1,32)->Unit(benchmark::kMicrosecond);
BENCHMARK(run_discretize)->RangeMultiplier(2)->Range(1,32)->Unit(benchmark::kMicrosecond);
-BENCHMARK(run_cv_geom_every_sample)->Unit(benchmark::kMillisecond);
-BENCHMARK(run_discretize_every_sample)->Unit(benchmark::kMillisecond);
+BENCHMARK(run_cv_geom_every_segment)->Unit(benchmark::kMillisecond);
+BENCHMARK(run_discretize_every_segment)->Unit(benchmark::kMillisecond);
BENCHMARK(run_cv_geom_explicit)->Unit(benchmark::kMillisecond);
BENCHMARK(run_discretize_explicit)->Unit(benchmark::kMillisecond);
diff --git a/test/ubench/mech_vec.cpp b/test/ubench/mech_vec.cpp
index ed45e38f5c50d342b81678d9f5af1975b2611d9a..6a531779b670503bacc436dcc8c7b8fb9b838a93 100644
--- a/test/ubench/mech_vec.cpp
+++ b/test/ubench/mech_vec.cpp
@@ -9,6 +9,7 @@
#include <fstream>
#include <arbor/cable_cell.hpp>
+#include <arbor/morph/segment_tree.hpp>
#include "backends/multicore/fvm.hpp"
#include "benchmark/benchmark.h"
@@ -48,22 +49,22 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::sample_tree tree;
+ arb::segment_tree tree;
double soma_radius = 12.6157/2.0;
double dend_radius = 1.0/2;
double dend_length = 200;
// Add soma.
- tree.append(arb::mnpos, {{0,0,0,soma_radius}, 1});
+ auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
// Add dendrite
- tree.append(0, {{0,0,soma_radius, dend_radius}, 3});
- tree.append(1, {{0,0,soma_radius+dend_length, dend_radius}, 3});
+ auto s1 = tree.append(s0, {0,0,soma_radius,dend_radius}, 3);
+ tree.append(s1, {0,0,soma_radius+dend_length,dend_radius}, 3);
arb::label_dict d;
d.set("soma", arb::reg::tagged(1));
- arb::cable_cell cell(arb::morphology(tree, true), d);
+ arb::cable_cell cell{arb::morphology(tree), d};
cell.paint("soma", "pas");
auto distribution = std::uniform_real_distribution<float>(0.f, 1.0f);
@@ -99,20 +100,20 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::sample_tree tree;
+ arb::segment_tree tree;
double soma_radius = 12.6157/2.0;
double dend_radius = 1.0/2;
double dend_length = 200;
// Add soma.
- tree.append(arb::mnpos, {{0,0,0,soma_radius}, 1});
+ auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
// Add dendrite
- tree.append(0, {{0,0,soma_radius, dend_radius}, 3});
- tree.append(1, {{0,0,soma_radius+dend_length, dend_radius}, 3});
+ auto s1 = tree.append(s0, {0,0,soma_radius,dend_radius}, 3);
+ tree.append(s1, {0,0,soma_radius+dend_length,dend_radius}, 3);
- arb::cable_cell cell(arb::morphology(tree, true));
+ arb::cable_cell cell{arb::morphology(tree)};
cell.paint(arb::reg::all(), "pas");
cell.default_parameters = arb::neuron_parameter_defaults;
@@ -142,22 +143,22 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::sample_tree tree;
+ arb::segment_tree tree;
double soma_radius = 12.6157/2.0;
double dend_radius = 1.0/2;
double dend_length = 200;
// Add soma.
- tree.append(arb::mnpos, {{0,0,0,soma_radius}, 1});
+ auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
// Add dendrite
- tree.append(0, {{0 ,0 ,soma_radius, dend_radius}, 3});
- tree.append(1, {{0 ,0 ,soma_radius+dend_length, dend_radius}, 3});
- tree.append(2, {{0 ,dend_length,soma_radius+dend_length, dend_radius}, 3});
- tree.append(2, {{dend_length,0 ,soma_radius+dend_length, dend_radius}, 3});
+ auto s1 = tree.append(s0, {0 ,0 ,soma_radius, dend_radius}, 3);
+ auto s2 = tree.append(s1, {0 ,0 ,soma_radius+dend_length, dend_radius}, 3);
+ tree.append(s2, {0 ,dend_length,soma_radius+dend_length, dend_radius}, 3);
+ tree.append(s2, {dend_length,0 ,soma_radius+dend_length, dend_radius}, 3);
- arb::cable_cell cell(arb::morphology(tree, true));
+ arb::cable_cell cell{arb::morphology(tree)};
cell.paint(arb::reg::all(), "pas");
cell.default_parameters = arb::neuron_parameter_defaults;
@@ -187,20 +188,20 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::sample_tree tree;
+ arb::segment_tree tree;
double soma_radius = 12.6157/2.0;
double dend_radius = 1.0/2;
double dend_length = 200;
// Add soma.
- tree.append(arb::mnpos, {{0,0,0,soma_radius}, 1});
+ auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
// Add dendrite
- tree.append(0, {{0,0,soma_radius, dend_radius}, 3});
- tree.append(1, {{0,0,soma_radius+dend_length, dend_radius}, 3});
+ auto s1 = tree.append(s0, {0 ,0 ,soma_radius, dend_radius}, 3);
+ tree.append(s1, {0 ,0 ,soma_radius+dend_length, dend_radius}, 3);
- arb::cable_cell cell(arb::morphology(tree, true));
+ arb::cable_cell cell{arb::morphology(tree)};
cell.paint(arb::reg::all(), "hh");
cell.default_parameters = arb::neuron_parameter_defaults;
@@ -230,22 +231,22 @@ public:
}
virtual util::unique_any get_cell_description(cell_gid_type gid) const override {
- arb::sample_tree tree;
+ arb::segment_tree tree;
double soma_radius = 12.6157/2.0;
double dend_radius = 1.0/2;
double dend_length = 200;
// Add soma.
- tree.append(arb::mnpos, {{0,0,0,soma_radius}, 1});
+ auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
// Add dendrite
- tree.append(0, {{0 ,0 ,soma_radius, dend_radius}, 3});
- tree.append(1, {{0 ,0 ,soma_radius+dend_length, dend_radius}, 3});
- tree.append(2, {{0 ,dend_length,soma_radius+dend_length, dend_radius}, 3});
- tree.append(2, {{dend_length,0 ,soma_radius+dend_length, dend_radius}, 3});
+ auto s1 = tree.append(s0, {0 ,0 ,soma_radius, dend_radius}, 3);
+ auto s2 = tree.append(s1, {0 ,0 ,soma_radius+dend_length, dend_radius}, 3);
+ tree.append( s2, {0 ,dend_length,soma_radius+dend_length, dend_radius}, 3);
+ tree.append( s2, {dend_length,0 ,soma_radius+dend_length, dend_radius}, 3);
- arb::cable_cell cell(arb::morphology(tree, true));
+ arb::cable_cell cell{arb::morphology(tree)};
cell.paint(arb::reg::all(), "hh");
cell.default_parameters = arb::neuron_parameter_defaults;
diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt
index ba08e6c53ae8a867058b594f8c1f3da8aaa0b5d7..33b43cabd681e7986804a0feed8e82afccbd2908 100644
--- a/test/unit/CMakeLists.txt
+++ b/test/unit/CMakeLists.txt
@@ -134,7 +134,6 @@ set(unit_sources
test_partition_by_constraint.cpp
test_path.cpp
test_piecewise.cpp
- test_point.cpp
test_pp_util.cpp
test_probe.cpp
test_range.cpp
diff --git a/test/unit/swc/example.swc b/test/unit/swc/example.swc
deleted file mode 100644
index 84addf0852529b983cdaeb4076b9ed629c1349f8..0000000000000000000000000000000000000000
--- a/test/unit/swc/example.swc
+++ /dev/null
@@ -1,1062 +0,0 @@
-#example swc file from the Allen DB
-#name C:/neuron tracing and reconstruction/vaa3d/vaa3d_bin_msvc_64bit_v2921_a/vaa3d_bin_msvc_64bit_v2921_a/Sst-IRES-Cre;Ai14(IVSCC)-173191.06.01.01.DS.swc_resampled.swc_sorted.swc_pruned.swc_pruned.swc
-#comment
-##n,type,x,y,z,radius,parent
-1 1 345.8312 346.9752 50.96 2.9744 -1
-2 3 347.2486 344.4641 52.04 0.1252 1
-3 3 347.6033 343.3762 52.0789 0.1487 2
-4 3 347.8641 342.2642 52.071 0.1853 3
-5 3 348.1409 341.1534 52.0246 0.2235 4
-6 3 348.4269 340.0551 51.688 0.262 5
-7 3 348.5734 338.942 51.1722 0.3007 6
-8 3 348.6409 337.8312 51.6947 0.3165 7
-9 3 348.9108 336.7387 52.1489 0.3178 8
-10 3 349.031 335.605 52.3401 0.2943 9
-11 3 349.0584 334.4667 52.0985 0.2805 10
-12 3 349.1797 333.3296 52.0738 0.256 11
-13 3 349.6785 332.3057 52.045 0.2305 12
-14 3 350.3752 331.4019 51.9201 0.2051 13
-15 3 351.049 330.5108 51.3243 0.1795 14
-16 3 351.8441 329.7122 50.8623 0.1658 15
-17 3 352.8199 329.1723 50.2564 0.1407 16
-18 3 353.6379 328.622 48.8471 0.1523 17
-19 3 354.4101 327.7835 48.666 0.1903 18
-20 3 355.0015 326.8088 48.4406 0.3432 19
-21 3 355.2406 326.0858 48.0054 0.2905 20
-22 3 355.5586 325.0047 48.0833 0.2134 21
-23 3 355.6399 323.9442 47.4054 0.1627 22
-24 3 355.7966 323.2361 45.3768 0.1525 23
-25 3 356.5951 322.7373 44.0163 0.1742 24
-26 3 357.1213 321.8038 44.4405 0.178 25
-27 3 357.7906 320.8931 44.8554 0.1525 26
-28 3 357.9885 320.5099 44.812 0.2397 27
-29 3 358.2047 319.5203 46.1068 0.2924 28
-30 3 358.3832 318.4873 47.1971 0.2839 29
-31 3 358.9346 317.5389 47.591 0.2536 30
-32 3 359.4311 316.5208 47.6991 0.2415 31
-33 3 359.7079 315.4294 48.1057 0.2592 32
-34 3 360.4023 314.6972 47.546 0.2781 33
-35 3 361.4617 314.4776 46.6984 0.2796 34
-36 3 362.5851 314.3495 46.9686 0.2678 35
-37 3 363.5952 313.8312 46.8367 0.2791 36
-38 3 364.1524 312.8531 46.4405 0.3049 37
-39 3 364.4258 311.7457 46.2462 0.3051 38
-40 3 364.547 311.0547 45.8128 0.1722 39
-41 3 364.5036 310.0549 44.485 0.1761 40
-42 3 364.0139 309.166 43.2284 0.1905 41
-43 3 363.6684 308.0792 43.3289 0.2288 42
-44 3 363.6501 307.4317 43.7506 0.1431 43
-45 3 363.5071 306.3152 43.2762 0.1524 44
-46 3 362.9043 305.3473 43.0903 0.1525 45
-47 3 362.8002 305.0762 41.0407 0.1518 46
-48 3 363.061 305.2192 38.3914 0.1388 47
-49 3 363.7634 304.7948 36.4557 0.1258 48
-50 3 364.4864 304.1301 35.0616 0.1144 49
-51 3 365.3067 303.4277 34.8012 0.1144 50
-52 3 365.9519 303.0101 36.7332 0.1144 51
-53 3 366.1349 302.8271 39.41 0.1144 52
-54 3 366.0468 302.5651 42.1162 0.1241 53
-55 3 365.9553 302.0126 44.0028 0.1562 54
-56 3 366.5708 301.6705 45.638 0.1848 55
-57 3 367.3407 301.4566 47.6333 0.1703 56
-58 3 368.2422 301.0047 48.862 0.1439 57
-59 3 369.2523 300.7587 50.0007 0.1181 58
-60 3 370.1504 300.4064 51.4822 0.1144 59
-61 3 371.1525 300.0334 50.6584 0.1144 60
-62 3 371.9144 300.3 48.72 0.1271 61
-63 3 362.2407 304.6163 42.6549 0.1525 46
-64 3 361.4846 303.7823 42.1585 0.1525 63
-65 3 360.749 302.9484 41.5696 0.1634 64
-66 3 360.5053 301.9382 40.88 0.2127 65
-67 3 360.3234 301.1649 42.0109 0.1525 66
-68 3 360.1312 300.1467 42.0591 0.1977 67
-69 3 360.2856 299.0267 41.8816 0.1652 68
-70 3 360.3085 297.9193 41.3322 0.1679 69
-71 3 360.2284 296.7879 40.9721 0.1722 70
-72 3 360.1484 295.6554 40.6118 0.1764 71
-73 3 359.6896 294.7173 40.8979 0.178 72
-74 3 359.4471 293.8192 40.0518 0.2634 73
-75 3 359.3773 292.7885 39.2188 0.2594 74
-76 3 358.8328 292.2886 40.4404 0.2093 75
-77 3 357.9324 291.8104 40.4524 0.2463 76
-78 3 357.5549 291.148 40.7067 0.178 77
-79 3 357.7929 290.4044 41.778 0.1509 78
-80 3 357.6052 290.2225 39.3299 0.1271 79
-81 3 357.2437 289.2375 39.1308 0.1558 80
-82 3 356.8044 288.5168 39.1642 0.115 81
-83 3 356.0128 288.1027 39.48 0.3209 82
-84 3 355.736 287.2893 38.4395 0.2196 83
-85 3 355.4339 286.6555 39.76 0.1478 84
-86 3 355.3367 285.674 38.9138 0.2157 85
-87 3 354.9832 284.753 38.18 0.2016 86
-88 3 354.3826 283.8722 38.6277 0.122 87
-89 3 353.3919 283.5164 39.3621 0.2288 88
-90 3 352.6586 283.1434 39.5105 0.1801 89
-91 3 351.9768 282.3838 38.3928 0.178 90
-92 3 351.1359 281.845 37.1064 0.1531 91
-93 3 350.1349 281.6906 37.4791 0.1555 92
-94 3 349.5858 281.1792 39.3308 0.2404 93
-95 3 348.872 280.6815 40.5969 0.2284 94
-96 3 348.3514 280.2388 39.1154 0.1628 95
-97 3 347.4042 279.7606 39.0009 0.1305 96
-98 3 346.9615 279.374 40.4776 0.2131 97
-99 3 346.1378 279.184 39.867 0.186 98
-100 3 345.1402 278.9781 40.5045 0.2239 99
-101 3 344.1003 279.128 40.4074 0.1746 100
-102 3 343.4242 278.461 39.0852 0.2288 101
-103 3 342.3283 278.4141 39.5388 0.1792 102
-104 3 341.5401 278.008 40.6 0.2003 103
-105 3 340.7141 277.4006 41.0668 0.178 104
-106 3 339.8641 276.8777 40.7912 0.2248 105
-107 3 338.8265 276.4945 40.32 0.1838 106
-108 3 338.3769 275.6148 39.7911 0.2136 107
-109 3 337.8541 274.7716 40.8598 0.1818 108
-110 3 337.8404 273.9777 39.8051 0.2612 109
-111 3 337.2775 273.2147 39.8112 0.1411 110
-112 3 336.8977 272.8737 41.4341 0.1295 111
-113 3 336.0454 272.4825 41.4882 0.1209 112
-114 3 335.4116 271.9059 41.2969 0.175 113
-115 3 334.5079 271.3396 41.1723 0.1924 114
-116 3 333.9187 270.4107 41.1289 0.1839 115
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diff --git a/test/unit/swc/pyramidal.swc b/test/unit/swc/pyramidal.swc
new file mode 100644
index 0000000000000000000000000000000000000000..79a3ca3fdcc80e6bee13a88deed3135641de0923
--- /dev/null
+++ b/test/unit/swc/pyramidal.swc
@@ -0,0 +1,5813 @@
+# Standardized morphology of a rat hippocampal pyramidal cell.
+# Source: NeuroMorpho.org ID: NMO_49821
+#
+# References:
+#
+# Hönigsperger, C., Marosi, M., Murphy, R., and Storm, J. F. (2015).
+# Dorsoventral differences in Kv7/M-current and its impact on resonance,
+# temporal summation and excitability in rat hippocampal pyramidal cells.
+# The Journal of Physiology, 593(7), 1551–1580. doi:10.1113/jphysiol.2014.280826
+#
+# Ascoli, G. A., Donohue, D. E., and Halavi, M. (2007).
+# NeuroMorpho.Org: a central resource for neuronal morphologies.
+# Journal of Neuroscience 27(35), 9247–9251. doi:10.1523/JNEUROSCI.2055-07.2007
+#
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+5560 4 -30.12 51.16 1.35 0.275 5559
+5561 4 -30.56 52.93 1.35 0.275 5560
+5562 4 -31.62 53.52 1.35 0.275 5561
+5563 4 -31.37 54.29 1.35 0.365 5562
+5564 4 -31.73 55.53 0.13 0.365 5563
+5565 4 -31.76 55.71 0.13 0.365 5564
+5566 4 -31.69 56.45 0.13 0.365 5565
+5567 4 -31.05 57.1 0.13 0.275 5566
+5568 4 -30.9 57.31 0.13 0.275 5567
+5569 4 -30.07 57.99 0.13 0.275 5568
+5570 4 -30.32 59.61 0.13 0.275 5569
+5571 4 -29.99 61.13 0.13 0.275 5570
+5572 4 -29.99 61.13 0.0 0.275 5571
+5573 4 -29.25 62.34 0.0 0.275 5572
+5574 4 -28.98 64.22 0.0 0.275 5573
+5575 4 -29.0 64.4 0.0 0.275 5574
+5576 4 -29.43 65.99 0.0 0.275 5575
+5577 4 -29.64 66.14 0.0 0.275 5576
+5578 4 -30.84 68.0 0.0 0.275 5577
+5579 4 -30.69 68.2 0.0 0.275 5578
+5580 4 -29.43 69.67 0.0 0.275 5579
+5581 4 -27.55 71.98 0.0 0.185 5580
+5582 4 -27.58 72.16 0.0 0.185 5581
+5583 4 -25.85 75.37 0.0 0.185 5582
+5584 4 -25.67 75.4 0.0 0.185 5583
+5585 4 -24.13 77.47 0.0 0.185 5584
+5586 4 -24.19 77.82 0.0 0.185 5585
+5587 4 -24.95 79.18 0.0 0.185 5586
+5588 4 -24.79 79.39 0.0 0.185 5587
+5589 4 -24.06 79.5 0.0 0.185 5588
+5590 4 -23.71 79.55 0.0 0.185 5589
+5591 4 -22.91 80.4 0.0 0.185 5590
+5592 4 -22.76 80.62 0.0 0.185 5591
+5593 4 -22.61 80.82 0.0 0.185 5592
+5594 4 -21.56 82.45 0.0 0.185 5593
+5595 4 -32.17 53.79 1.35 0.275 5562
+5596 4 -33.58 55.79 1.35 0.275 5595
+5597 4 -33.61 55.97 1.35 0.275 5596
+5598 4 -34.58 57.48 1.35 0.275 5597
+5599 4 -36.34 63.1 4.67 0.275 5598
+5600 4 -37.33 67.19 6.87 0.275 5599
+5601 4 -37.66 69.35 6.87 0.275 5600
+5602 4 -37.53 69.73 6.87 0.275 5601
+5603 4 -37.37 69.94 6.87 0.275 5602
+5604 4 -37.56 71.2 6.87 0.275 5603
+5605 4 -37.73 73.56 6.87 0.275 5604
+5606 4 -38.18 77.73 6.87 0.275 5605
+5607 4 -38.21 77.91 6.87 0.275 5606
+5608 4 -38.74 80.23 6.87 0.275 5607
+5609 4 -38.76 80.4 6.87 0.275 5608
+5610 4 -40.08 84.25 6.87 0.275 5609
+5611 4 -40.56 86.2 6.87 0.275 5610
+5612 4 -40.96 88.9 6.87 0.275 5611
+5613 4 -42.71 94.33 10.43 0.275 5612
+5614 4 -43.53 97.33 10.43 0.275 5613
+5615 4 -44.99 99.69 10.43 0.275 5614
+5616 4 -45.23 100.03 10.43 0.275 5615
+5617 4 -45.97 102.32 10.43 0.275 5616
+5618 4 -46.34 103.55 10.43 0.365 5617
+5619 4 -46.4 105.19 10.43 0.365 5618
+5620 4 -47.25 108.38 10.43 0.365 5619
+5621 4 -47.3 108.74 10.43 0.365 5620
+5622 4 -48.52 111.87 10.43 0.365 5621
+5623 4 -48.58 112.23 10.43 0.365 5622
+5624 4 -49.12 115.83 10.43 0.365 5623
+5625 4 -49.17 116.18 10.43 0.365 5624
+5626 4 -50.22 121.92 8.58 0.365 5625
+5627 4 -50.83 124.77 8.58 0.365 5626
+5628 4 -51.03 124.92 8.58 0.365 5627
+5629 4 -51.25 125.07 8.58 0.365 5628
+5630 4 -53.0 129.41 7.36 0.365 5629
+5631 4 -53.03 129.59 7.36 0.365 5630
+5632 4 -54.75 132.46 7.36 0.365 5631
+5633 4 -55.0 132.79 7.36 0.365 5632
+5634 4 -56.57 137.16 6.01 0.275 5633
+5635 4 -57.96 140.25 6.01 0.275 5634
+5636 4 -57.99 140.44 6.01 0.275 5635
+5637 4 -59.29 141.71 6.01 0.275 5636
+5638 4 -59.14 141.92 6.01 0.275 5637
+5639 4 -61.44 142.49 6.01 0.275 5638
+5640 4 -64.21 147.41 6.01 0.275 5639
+5641 4 -45.59 103.48 10.43 0.365 5617
+5642 4 -45.37 104.43 10.43 0.365 5641
+5643 4 -45.18 104.46 10.43 0.365 5642
+5644 4 -44.24 105.52 10.43 0.365 5643
+5645 4 -42.92 106.64 10.43 0.365 5644
+5646 4 -42.74 106.66 10.43 0.365 5645
+5647 4 -42.6 108.16 10.43 0.365 5646
+5648 4 -42.78 108.14 10.43 0.365 5647
+5649 4 -43.54 109.49 10.43 0.365 5648
+5650 4 -43.75 109.65 10.43 0.365 5649
+5651 4 -43.77 109.83 10.43 0.365 5650
+5652 4 -45.2 110.71 10.43 0.365 5651
+5653 4 -45.38 110.69 10.43 0.365 5652
+5654 4 -47.2 111.7 10.43 0.365 5653
+5655 4 -47.38 111.67 10.43 0.365 5654
+5656 4 -47.77 113.09 10.43 0.365 5655
+5657 4 -47.62 113.29 10.43 0.365 5656
+5658 4 -47.5 113.68 10.43 0.365 5657
+5659 4 -47.5 114.97 10.43 0.365 5658
+5660 4 -47.61 115.69 10.43 0.365 5659
+5661 4 -47.65 117.15 10.43 0.365 5660
+5662 4 -47.52 117.54 10.43 0.365 5661
+5663 4 -47.76 117.87 10.43 0.365 5662
+5664 4 -48.07 118.75 10.43 0.365 5663
+5665 4 -49.04 120.26 10.43 0.365 5664
+5666 4 -49.25 120.41 10.43 0.365 5665
+5667 4 -52.14 119.98 8.46 0.365 5666
+5668 4 -52.11 119.8 8.46 0.365 5667
+5669 4 -52.67 118.61 8.46 0.365 5668
+5670 4 -52.86 118.58 8.58 0.365 5669
+5671 4 -54.18 118.75 8.58 0.365 5670
+5672 4 -54.23 119.1 8.58 0.365 5671
+5673 4 -54.44 119.27 8.95 0.365 5672
+5674 4 -55.42 119.66 11.04 0.365 5673
+5675 4 -55.81 119.79 11.04 0.365 5674
+5676 4 -58.29 120.33 11.04 0.365 5675
+5677 4 -58.5 120.48 11.04 0.365 5676
+5678 4 -60.13 120.24 11.04 0.275 5677
+5679 4 -60.33 120.4 11.04 0.275 5678
+5680 4 -61.25 121.55 11.41 0.275 5679
+5681 4 -62.21 121.77 12.75 0.275 5680
+5682 4 -62.21 121.77 13.38 0.275 5681
+5683 4 -63.32 121.79 13.38 0.275 5682
+5684 4 -64.21 122.76 15.09 0.275 5683
+5685 4 -64.05 122.97 15.09 0.275 5684
+5686 4 -64.07 123.15 15.09 0.275 5685
+5687 4 -64.03 124.07 15.46 0.275 5686
+5688 4 -64.23 124.22 15.46 0.275 5687
+5689 4 -64.45 124.38 15.46 0.275 5688
+5690 4 -64.65 124.53 15.46 0.275 5689
+5691 4 -64.86 124.69 15.46 0.275 5690
+5692 4 -65.16 125.38 15.46 0.275 5691
+5693 4 -65.36 125.53 15.46 0.275 5692
+5694 4 -65.62 126.04 15.46 0.275 5693
+5695 4 -66.53 127.19 15.46 0.275 5694
+5696 4 -66.67 128.09 15.46 0.275 5695
+5697 4 -66.42 128.87 15.46 0.275 5696
+5698 4 -66.26 129.08 15.46 0.275 5697
+5699 4 -65.47 129.93 15.46 0.275 5698
+5700 4 -65.32 130.14 15.46 0.275 5699
+5701 4 -64.95 130.19 15.46 0.275 5700
+5702 4 -64.75 130.04 15.46 0.275 5701
+5703 4 -64.54 129.88 15.46 0.275 5702
+5704 4 -64.51 129.7 15.46 0.275 5703
+5705 4 -64.27 129.38 15.46 0.275 5704
+5706 4 -18.81 33.72 1.35 0.365 5546
+5707 4 -22.36 36.51 0.87 0.185 5706
+5708 4 -22.98 36.96 0.87 0.365 5707
+5709 4 -24.32 38.42 0.87 0.365 5708
+5710 4 -25.87 38.92 0.87 0.365 5709
+5711 4 -27.54 37.75 0.87 0.365 5710
+5712 4 -29.57 36.52 0.87 0.365 5711
+5713 4 -31.1 36.84 0.87 0.365 5712
+5714 4 -32.84 37.32 0.87 0.365 5713
+5715 4 -34.32 36.17 0.87 0.365 5714
+5716 4 -33.72 34.6 3.09 0.365 5715
+5717 4 -33.28 32.83 3.09 0.365 5716
+5718 4 -34.33 32.49 3.09 0.365 5717
+5719 4 -34.35 32.67 3.09 0.365 5718
+5720 4 -34.78 34.26 3.09 0.365 5719
+5721 4 -34.8 34.44 3.09 0.365 5720
+5722 4 -35.88 35.39 3.09 0.365 5721
+5723 4 -37.68 35.12 3.09 0.365 5722
+5724 4 -38.9 34.56 3.09 0.275 5723
+5725 4 -40.67 32.83 3.09 0.275 5724
+5726 4 -42.74 30.68 3.09 0.275 5725
+5727 4 -43.84 29.4 3.09 0.275 5726
+5728 4 -44.39 29.32 3.09 0.275 5727
+5729 4 -45.18 27.18 -0.22 0.275 5728
+5730 4 -47.3 25.39 -0.22 0.275 5729
+5731 4 -47.47 25.19 -0.22 0.275 5730
+5732 4 -48.92 23.85 -0.22 0.275 5731
+5733 4 -50.94 23.74 -0.22 0.275 5732
+5734 4 -52.65 24.03 -0.22 0.275 5733
+5735 4 -53.01 23.98 -0.22 0.275 5734
+5736 4 -54.12 23.99 -0.22 0.275 5735
+5737 4 -55.77 22.64 1.0 0.275 5736
+5738 4 -55.87 19.68 1.0 0.275 5737
+5739 4 -57.6 18.88 1.0 0.275 5738
+5740 4 -57.97 18.82 1.0 0.275 5739
+5741 4 -58.51 18.74 1.0 0.275 5740
+5742 4 -58.48 18.55 1.0 0.275 5741
+5743 4 -60.1 18.31 1.0 0.275 5742
+5744 4 -60.08 18.13 1.0 0.275 5743
+5745 4 -60.74 16.37 1.0 0.275 5744
+5746 4 -60.92 16.35 1.0 0.275 5745
+5747 4 -62.02 15.08 1.0 0.275 5746
+5748 4 -62.84 14.41 1.0 0.275 5747
+5749 4 -63.02 14.38 1.0 0.275 5748
+5750 4 -64.39 13.62 1.0 0.275 5749
+5751 4 -38.0 35.99 3.09 0.185 5723
+5752 4 -38.03 36.17 3.09 0.185 5751
+5753 4 -38.8 36.42 3.09 0.185 5752
+5754 4 -40.04 36.05 3.09 0.185 5753
+5755 4 -41.66 35.81 3.09 0.185 5754
+5756 4 -42.65 36.21 3.09 0.185 5755
+5757 4 -43.54 37.18 3.09 0.185 5756
+5758 4 -44.44 37.05 3.09 0.185 5757
+5759 4 -45.13 36.75 3.09 0.185 5758
+5760 4 -45.29 36.55 3.09 0.185 5759
+5761 4 -45.44 36.34 3.09 0.185 5760
+5762 4 -46.32 36.03 3.09 0.185 5761
+5763 4 -46.34 36.21 3.09 0.185 5762
+5764 4 -47.82 36.16 3.09 0.185 5763
+5765 4 -48.28 35.55 3.09 0.185 5764
+5766 4 -48.25 35.37 3.09 0.185 5765
+5767 4 -49.08 34.69 3.09 0.185 5766
+5768 4 -50.63 35.2 3.09 0.185 5767
+5769 4 -51.16 36.22 3.09 0.185 5768
+5770 4 -51.53 37.45 3.09 0.185 5769
+5771 4 -51.7 37.42 3.09 0.185 5770
+5772 4 -52.61 37.28 3.09 0.185 5771
+5773 4 -53.0 37.41 3.09 0.185 5772
+5774 4 -53.88 37.09 3.09 0.185 5773
+5775 4 -54.08 37.25 3.09 0.185 5774
+5776 4 -54.87 38.79 3.09 0.185 5775
+5777 4 -54.9 38.96 3.09 0.185 5776
+5778 4 -54.31 39.97 3.09 0.185 5777
+5779 4 -55.68 40.5 4.69 0.185 5778
+5780 4 -55.7 40.68 4.69 0.185 5779
+5781 4 -56.79 40.52 4.69 0.185 5780
+5782 4 -57.16 40.46 4.69 0.185 5781
+5783 4 -50.11 34.17 3.09 0.185 5768
+5784 4 -49.76 33.11 3.09 0.185 5783
+5785 4 -35.6 37.27 0.87 0.275 5715
+5786 4 -36.46 38.06 0.87 0.275 5785
+5787 4 -36.62 39.14 0.87 0.275 5786
+5788 4 -36.09 40.51 0.87 0.275 5787
+5789 4 -35.6 40.95 0.87 0.275 5788
+5790 4 -34.41 40.4 0.87 0.275 5789
+5791 4 -33.57 39.78 0.87 0.185 5790
+5792 4 -7.7 27.49 0.0 0.455 2392
+5793 4 -8.58 28.46 0.0 0.185 5792
+5794 4 -9.16 29.84 0.0 0.185 5793
+5795 4 -9.28 31.85 0.0 0.185 5794
+5796 4 -9.68 33.26 0.0 0.185 5795
+5797 4 -9.88 33.41 0.0 0.185 5796
+5798 4 -9.91 33.6 0.0 0.185 5797
+5799 4 -10.64 34.77 0.0 0.185 5798
diff --git a/test/unit/test_morphology.cpp b/test/unit/test_morphology.cpp
index 5cc929b611b6837b0156fa19c85a8876a2b76858..f35d8217a582049ff709a43b5537150f17a6b1f3 100644
--- a/test/unit/test_morphology.cpp
+++ b/test/unit/test_morphology.cpp
@@ -5,12 +5,13 @@
#include "../test/gtest.h"
+#include <arbor/cable_cell.hpp>
#include <arbor/morph/morphexcept.hpp>
#include <arbor/morph/morphology.hpp>
-#include <arbor/cable_cell.hpp>
+#include <arbor/morph/primitives.hpp>
+#include <arbor/morph/segment_tree.hpp>
+#include <arbor/swcio.hpp>
-#include "arbor/morph/primitives.hpp"
-#include "arbor/morph/segment_tree.hpp"
#include "util/span.hpp"
#include "morph_pred.hpp"
@@ -309,7 +310,7 @@ TEST(morphology, branches) {
#ifndef ARB_HIP
TEST(morphology, swc) {
std::string datadir{DATADIR};
- auto fname = datadir + "/example.swc";
+ auto fname = datadir + "/pyramidal.swc";
std::ifstream fid(fname);
if (!fid.is_open()) {
std::cerr << "unable to open file " << fname << "... skipping test\n";
@@ -317,15 +318,15 @@ TEST(morphology, swc) {
}
// Load swc samples from file.
- auto swc_samples = arb::parse_swc_file(fid);
+ auto swc = arb::parse_swc(fid, arb::swc_mode::strict);
// Build a segmewnt_tree from swc samples.
- auto sm = arb::swc_as_segment_tree(swc_samples);
- EXPECT_EQ(1057u, sm.size()); // file contains 195 samples
+ auto sm = arb::as_segment_tree(swc);
+ EXPECT_EQ(5798u, sm.size()); // SWC data contains 5799 samples.
// Test that the morphology contains the expected number of branches.
auto m = arb::morphology(sm);
- EXPECT_EQ(30u, m.num_branches());
+ EXPECT_EQ(221u, m.num_branches()); // 219 branches + 2 from divided soma.
}
#endif
diff --git a/test/unit/test_point.cpp b/test/unit/test_point.cpp
deleted file mode 100644
index 872ec6dd015cf0bcfda8cd764d2e1745c30a4dc1..0000000000000000000000000000000000000000
--- a/test/unit/test_point.cpp
+++ /dev/null
@@ -1,110 +0,0 @@
-#include <cmath>
-#include <limits>
-
-#include "../gtest.h"
-
-#include <arbor/point.hpp>
-
-using namespace arb;
-
-TEST(point, construction)
-{
- {
- // default constructor
- point<float> p;
-
- EXPECT_FALSE(p.is_set());
-
- // expect NaN, which returns false when comparing for equality
- EXPECT_NE(p.x, p.x);
- EXPECT_NE(p.y, p.y);
- EXPECT_NE(p.z, p.z);
- }
-
- {
- // initializer list
- point<float> p{1, 2, 3};
- EXPECT_EQ(p.x, 1.);
- EXPECT_EQ(p.y, 2.);
- EXPECT_EQ(p.z, 3.);
- }
-
- {
- // explicit call to constructor
- point<double> p1(1, 2, 3);
-
- EXPECT_EQ(p1.x, 1.);
- EXPECT_EQ(p1.y, 2.);
- EXPECT_EQ(p1.z, 3.);
-
- // copy constructor
- auto p2 = p1;
- EXPECT_EQ(p1, p2);
- }
-}
-
-TEST(point, constexpr)
-{
- // perform test using constexpr
- constexpr point<double> p1(1, 2, 3);
- constexpr point<double> p2(1, 2, 3);
-
- constexpr auto p = p1 + p2;
-
- static_assert(p.x == p1.x+p2.x, "failed x-component");
- static_assert(p.y == p1.y+p2.y, "failed y-component");
- static_assert(p.z == p1.z+p2.z, "failed z-component");
-}
-
-TEST(point, addition)
-{
- // perform test using constexpr
- point<double> p1(1, 2, 3);
- point<double> p2(1, 2, 3);
-
- auto p = p1 + p2;
-
- EXPECT_EQ(point<double>(2, 4, 6), p);
-}
-
-TEST(point, subtraction)
-{
- // perform test using constexpr
- point<double> p1(1, 2, 3);
- point<double> p2(1, 2, 3);
-
- auto p = p1 - p2;
-
- EXPECT_EQ(point<double>(0, 0, 0), p);
-}
-
-TEST(point, scalar_prod)
-{
- // perform test using constexpr
- point<double> p1(1, 2, 3);
-
- auto p = 0.5 * p1;
-
- EXPECT_EQ(point<double>(0.5, 1.0, 1.5), p);
-}
-
-TEST(point, norm)
-{
- // don't use constexpr, because the sqrt is not constexpr
- point<double> p1(1, 1, 1);
- point<double> p2(1, 2, 3);
-
- EXPECT_EQ(norm(p1), std::sqrt(3.));
- EXPECT_EQ(norm(p2), std::sqrt(1.+4.+9.));
-}
-
-TEST(point, dot)
-{
- // perform test using constexpr
- constexpr point<double> p1(1, -1, 1);
- constexpr point<double> p2(1, 2, 3);
-
- static_assert(dot(p1,p2)==2., "unable to perform constexpr dot product");
-
- EXPECT_EQ(dot(p1,p2), 2.);
-}
diff --git a/test/unit/test_swcio.cpp b/test/unit/test_swcio.cpp
index ce388d13a4fe4b2c143a39b9aeb6e9bbf8df7ac6..ab890246d7474d7080245d34ba9f40f07152f18b 100644
--- a/test/unit/test_swcio.cpp
+++ b/test/unit/test_swcio.cpp
@@ -1,11 +1,7 @@
#include <array>
-#include <exception>
#include <iostream>
-#include <iterator>
#include <fstream>
-#include <numeric>
-#include <type_traits>
-#include <vector>
+#include <sstream>
#include <arbor/cable_cell.hpp>
#include <arbor/swcio.hpp>
@@ -20,392 +16,202 @@
using namespace arb;
-// SWC tests
-void expect_record_equals(const swc_record& expected,
- const swc_record& actual)
-{
- EXPECT_EQ(expected.id, actual.id);
- EXPECT_EQ(expected.tag, actual.tag);
- EXPECT_FLOAT_EQ(expected.x, actual.x);
- EXPECT_FLOAT_EQ(expected.y, actual.y);
- EXPECT_FLOAT_EQ(expected.z, actual.z);
- EXPECT_FLOAT_EQ(expected.r, actual.r);
- EXPECT_EQ(expected.parent_id, actual.parent_id);
+TEST(swc_record, construction) {
+ swc_record record(1, 7, 1., 2., 3., 4., -1);
+ EXPECT_EQ(record.id, 1);
+ EXPECT_EQ(record.tag, 7);
+ EXPECT_EQ(record.x, 1.);
+ EXPECT_EQ(record.y, 2.);
+ EXPECT_EQ(record.z, 3.);
+ EXPECT_EQ(record.r, 4.);
+ EXPECT_EQ(record.parent_id, -1);
+
+ // Check copy ctor and copy assign.
+ swc_record r2(record);
+ EXPECT_EQ(record, r2);
+
+ swc_record r3;
+ EXPECT_NE(record, r3);
+
+ r3 = record;
+ EXPECT_EQ(record, r3);
}
-TEST(swc_record, construction)
-{
- int soma_tag = 1;
-
+TEST(swc_record, invalid_input) {
+ swc_record dummy{2, 3, 4., 5., 6., 7., 1};
{
- // invalid id
- EXPECT_THROW(swc_record(soma_tag, -3, 1., 1., 1., 1., 5).assert_consistent(),
- swc_error);
- }
+ // Incomplete line: missing parent id.
+ swc_record record(dummy);
+ std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
+ is >> record;
- {
- // invalid parent id
- EXPECT_THROW(swc_record(soma_tag, 0, 1., 1., 1., 1., -5).assert_consistent(),
- swc_error);
+ EXPECT_TRUE(is.fail());
+ EXPECT_EQ(dummy, record);
}
{
- // invalid radius
- EXPECT_THROW(swc_record(soma_tag, 0, 1., 1., 1., -1., -1).assert_consistent(),
- swc_error);
- }
+ // Bad id value.
+ swc_record record(dummy);
+ std::istringstream is("1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
+ is >> record;
- {
- // parent_id > id
- EXPECT_THROW(swc_record(soma_tag, 0, 1., 1., 1., 1., 2).assert_consistent(),
- swc_error);
+ EXPECT_TRUE(is.fail());
+ EXPECT_EQ(dummy, record);
}
+}
+TEST(swc_parser, bad_relaxed) {
{
- // parent_id == id
- EXPECT_THROW(swc_record(soma_tag, 0, 1., 1., 1., 1., 0).assert_consistent(),
- swc_error);
- }
+ std::string bad1 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n"
+ "3 1 0.1 0.2 0.3 0.4 2\n"
+ "5 1 0.1 0.2 0.3 0.4 4\n";
- {
- // check standard construction by value
- swc_record record(soma_tag, 0, 1., 1., 1., 1., -1);
- EXPECT_TRUE(record.is_consistent());
- EXPECT_EQ(record.id, 0);
- EXPECT_EQ(record.tag, soma_tag);
- EXPECT_EQ(record.x, 1.);
- EXPECT_EQ(record.y, 1.);
- EXPECT_EQ(record.z, 1.);
- EXPECT_EQ(record.r, 1.);
- EXPECT_EQ(record.diameter(), 2*1.);
- EXPECT_EQ(record.parent_id, -1);
+ EXPECT_THROW(parse_swc(bad1, swc_mode::relaxed), swc_no_such_parent);
}
{
- // check copy constructor
- swc_record record_orig(soma_tag, 0, 1., 1., 1., 1., -1);
- swc_record record(record_orig);
- expect_record_equals(record_orig, record);
- }
-}
+ std::string bad2 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n"
+ "3 1 0.1 0.2 0.3 0.4 2\n"
+ "4 1 0.1 0.2 0.3 0.4 -1\n";
-
-TEST(swc_parser, invalid_input_istream)
-{
- {
- // check incomplete lines; missing parent
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
- swc_record record;
- is >> record;
- EXPECT_TRUE(is.fail());
+ EXPECT_THROW(parse_swc(bad2, swc_mode::relaxed), swc_no_such_parent);
}
{
- // Check non-parsable values
- std::istringstream is(
- "1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
- swc_record record;
- is >> record;
- EXPECT_TRUE(is.fail());
- }
-}
+ std::string bad3 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 3\n"
+ "3 1 0.1 0.2 0.3 0.4 1\n"
+ "4 1 0.1 0.2 0.3 0.4 3\n";
-TEST(swc_parser, invalid_input_parse)
-{
- {
- // check incomplete lines; missing parent
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
- EXPECT_THROW(parse_swc_file(is), swc_error);
+ EXPECT_THROW(parse_swc(bad3, swc_mode::relaxed), swc_record_precedes_parent);
}
{
- // Check non-parsable values
- std::istringstream is(
- "1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
- EXPECT_THROW(parse_swc_file(is), swc_error);
- }
+ std::string bad4 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "3 1 0.1 0.2 0.3 0.4 1\n"
+ "3 1 0.1 0.2 0.3 0.4 1\n"
+ "4 1 0.1 0.2 0.3 0.4 3\n";
- {
- // Non-contiguous numbering in branches is considered invalid
- // 1
- // / \.
- // 2 3
- // /
- // 4
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "2 1 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "3 1 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "4 1 14.566132 34.873772 7.857000 0.717830 2\n";
-
- EXPECT_THROW(parse_swc_file(is), swc_error);
+ EXPECT_THROW(parse_swc(bad4, swc_mode::relaxed), swc_duplicate_record_id);
}
-}
-TEST(swc_parser, valid_input)
-{
{
- // check empty file; no record may be parsed
- swc_record record, record_orig;
- std::istringstream is("");
- is >> record;
+ std::string bad5 =
+ "1 1 0.1 0.2 0.3 0.4 -3\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n"
+ "3 1 0.1 0.2 0.3 0.4 2\n"
+ "4 1 0.1 0.2 0.3 0.4 -1\n";
- EXPECT_TRUE(is.eof());
- EXPECT_TRUE(is.fail());
- EXPECT_FALSE(is.bad());
- expect_record_equals(record_orig, record);
+ EXPECT_THROW(parse_swc(bad5, swc_mode::relaxed), swc_no_such_parent);
}
{
- // check comment-only file not ending with a newline;
- // no record may be parsed
- swc_record record, record_orig;
- std::istringstream is("#comment\n#comment");
- is >> record;
+ std::string bad6 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n";
- EXPECT_TRUE(is.eof());
- EXPECT_TRUE(is.fail());
- EXPECT_FALSE(is.bad());
- expect_record_equals(record_orig, record);
+ EXPECT_THROW(parse_swc(bad6, swc_mode::relaxed), swc_spherical_soma);
}
+}
+TEST(swc_parser, bad_strict) {
{
- // check comment not starting at first character
- swc_record record, record_orig;
- std::istringstream is(" #comment\n");
- is >> record;
+ std::string bad1 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.1 0.2 0.3 0.4 1\n"
+ "3 1 0.1 0.2 0.3 0.4 2\n"
+ "5 1 0.1 0.2 0.3 0.4 3\n"; // non-contiguous
- EXPECT_TRUE(is.eof());
- EXPECT_TRUE(is.fail());
- EXPECT_FALSE(is.bad());
- expect_record_equals(record_orig, record);
+ EXPECT_THROW(parse_swc(bad1, swc_mode::strict), swc_irregular_id);
+ EXPECT_NO_THROW(parse_swc(bad1, swc_mode::relaxed));
}
{
- // check whitespace lines
- swc_record record;
- std::stringstream is;
- is << "#comment\n";
- is << " \t\n";
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
-
- is >> record;
- EXPECT_TRUE(is);
+ std::string bad2 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "3 1 0.1 0.2 0.3 0.4 2\n" // out of order
+ "2 1 0.1 0.2 0.3 0.4 1\n"
+ "4 1 0.1 0.2 0.3 0.4 3\n";
- int soma_tag = 1;
- swc_record record_expected(
- soma_tag,
- 0, 14.566132, 34.873772, 7.857000, 0.717830, -1);
- expect_record_equals(record_expected, record);
+ EXPECT_THROW(parse_swc(bad2, swc_mode::strict), swc_irregular_id);
+ EXPECT_NO_THROW(parse_swc(bad2, swc_mode::relaxed));
}
{
- // check windows eol
- swc_record record;
- std::stringstream is;
- is << "#comment\r\n";
- is << "\r\n";
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\r\n";
+ std::string bad3 =
+ "1 1 0.1 0.2 0.3 0.4 -1\n" // solitary tag
+ "2 0 0.1 0.2 0.3 0.4 1\n"
+ "3 0 0.1 0.2 0.3 0.4 2\n"
+ "4 0 0.1 0.2 0.3 0.4 1\n";
- is >> record;
- EXPECT_TRUE(is);
-
- int soma_tag = 1;
- swc_record record_expected(
- soma_tag,
- 0, 14.566132, 34.873772, 7.857000, 0.717830, -1);
- expect_record_equals(record_expected, record);
+ EXPECT_THROW(parse_swc(bad3, swc_mode::strict), swc_spherical_soma);
+ EXPECT_NO_THROW(parse_swc(bad3, swc_mode::relaxed));
}
+}
+TEST(swc_parser, valid_relaxed) {
+}
+
+TEST(swc_parser, valid_strict) {
{
- // check old-style mac eol; these eol are treated as simple whitespace
- // characters, so should look line a long comment.
- swc_record record;
- std::stringstream is;
- is << "#comment\r";
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\r";
+ std::string valid1 =
+ "# Hello\n"
+ "# world.\n";
- is >> record;
- EXPECT_TRUE(is.eof());
- EXPECT_TRUE(is.fail());
- EXPECT_FALSE(is.bad());
+ swc_data data = parse_swc(valid1, swc_mode::strict);
+ EXPECT_EQ("Hello\nworld.\n", data.metadata);
+ EXPECT_TRUE(data.records.empty());
}
{
- // check last line case (no newline at the end)
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830 -1");
- swc_record record;
- is >> record;
- EXPECT_TRUE(is.eof());
- EXPECT_FALSE(is.fail());
- EXPECT_FALSE(is.bad());
- EXPECT_EQ(0, record.id); // zero-based indexing
- EXPECT_EQ(1, record.tag);
- EXPECT_FLOAT_EQ(14.566132, record.x);
- EXPECT_FLOAT_EQ(34.873772, record.y);
- EXPECT_FLOAT_EQ( 7.857000, record.z);
- EXPECT_FLOAT_EQ( 0.717830, record.r);
- EXPECT_FLOAT_EQ( -1, record.parent_id);
- }
+ std::string valid2 =
+ "# Some people put\n"
+ "# <xml /> in here!\n"
+ "1 1 0.1 0.2 0.3 0.4 -1\n"
+ "2 1 0.3 0.4 0.5 0.3 1\n"
+ "3 2 0.2 0.6 0.8 0.2 2\n"
+ "4 0 0.2 0.8 0.6 0.3 2";
- {
+ swc_data data = parse_swc(valid2, swc_mode::strict);
+ EXPECT_EQ("Some people put\n<xml /> in here!\n", data.metadata);
+ ASSERT_EQ(4u, data.records.size());
+ EXPECT_EQ(swc_record(1, 1, 0.1, 0.2, 0.3, 0.4, -1), data.records[0]);
+ EXPECT_EQ(swc_record(2, 1, 0.3, 0.4, 0.5, 0.3, 1), data.records[1]);
+ EXPECT_EQ(swc_record(3, 2, 0.2, 0.6, 0.8, 0.2, 2), data.records[2]);
+ EXPECT_EQ(swc_record(4, 0, 0.2, 0.8, 0.6, 0.3, 2), data.records[3]);
+
+ // Trailing garbage is ignored in data records.
+ std::string valid3 =
+ "# Some people put\n"
+ "# <xml /> in here!\n"
+ "1 1 0.1 0.2 0.3 0.4 -1 # what is that?\n"
+ "2 1 0.3 0.4 0.5 0.3 1 moooooo\n"
+ "3 2 0.2 0.6 0.8 0.2 2 # it is a cow!\n"
+ "4 0 0.2 0.8 0.6 0.3 2";
- // check valid input with a series of records
- std::vector<swc_record> records_orig = {
- swc_record(1, 0,
- 14.566132, 34.873772, 7.857000, 0.717830, -1),
- swc_record(3, 1,
- 14.566132+1, 34.873772+1, 7.857000+1, 0.717830+1, -1)
- };
-
- std::stringstream swc_input;
- swc_input << "# this is a comment\n";
- swc_input << "# this is a comment\n";
- for (auto c : records_orig)
- swc_input << c << "\n";
-
- swc_input << "# this is a final comment\n";
-
- using swc_iter = std::istream_iterator<swc_record>;
- swc_iter end;
-
- std::size_t nr_records = 0;
- for (swc_iter i = swc_iter(swc_input); i!=end; ++i) {
- ASSERT_LT(nr_records, records_orig.size());
- expect_record_equals(records_orig[nr_records], *i);
- ++nr_records;
- }
- EXPECT_EQ(2u, nr_records);
+ swc_data data2 = parse_swc(valid2, swc_mode::strict);
+ EXPECT_EQ(data.records, data2.records);
}
}
// hipcc bug in reading DATADIR
#ifndef ARB_HIP
-TEST(swc_parser, from_allen_db)
+TEST(swc_parser, from_neuromorpho)
{
std::string datadir{DATADIR};
- auto fname = datadir + "/example.swc";
+ auto fname = datadir + "/pyramidal.swc";
std::ifstream fid(fname);
if (!fid.is_open()) {
std::cerr << "unable to open file " << fname << "... skipping test\n";
return;
}
- // load the record records into a std::vector
- std::vector<swc_record> nodes = parse_swc_file(fid);
-
- // verify that the correct number of nodes was read
- EXPECT_EQ(1058u, nodes.size());
+ auto data = parse_swc(fid, swc_mode::strict);
+ EXPECT_EQ(5799u, data.records.size());
}
#endif
-
-TEST(swc_parser, input_cleaning)
-{
- {
- // Check duplicates
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
-
- EXPECT_THROW(parse_swc_file(is), swc_error);
- }
-
- {
- // Check multiple trees
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "3 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "4 2 14.566132 34.873772 7.857000 0.717830 1\n";
-
- EXPECT_THROW(parse_swc_file(is), swc_error);
- }
-
- {
- // Check unsorted input
- std::stringstream is;
- is << "3 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "4 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
-
- std::array<swc_record::id_type, 4> expected_id_list = {{ 0, 1, 2, 3 }};
-
- auto records = parse_swc_file(is);
- ASSERT_EQ(expected_id_list.size(), records.size());
-
- for (unsigned i = 0; i< expected_id_list.size(); ++i) {
- EXPECT_EQ(expected_id_list[i], records[i].id);
- }
- }
-
- {
- // Check holes in numbering
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "21 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "31 2 14.566132 34.873772 7.857000 0.717830 21\n";
- is << "41 2 14.566132 34.873772 7.857000 0.717830 21\n";
- is << "51 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "61 2 14.566132 34.873772 7.857000 0.717830 51\n";
-
- std::array<swc_record::id_type, 6> expected_id_list =
- {{ 0, 1, 2, 3, 4, 5 }};
- std::array<swc_record::id_type, 6> expected_parent_list =
- {{ -1, 0, 1, 1, 0, 4 }};
-
- auto records = parse_swc_file(is);
- ASSERT_EQ(expected_id_list.size(), records.size());
- for (unsigned i = 0; i< expected_id_list.size(); ++i) {
- EXPECT_EQ(expected_id_list[i], records[i].id);
- EXPECT_EQ(expected_parent_list[i], records[i].parent_id);
- }
- }
-}
-
-TEST(swc_parser, raw)
-{
- {
- // Check valid usage
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "3 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "4 2 14.566132 34.873772 7.857000 0.717830 1\n";
-
- using swc_iter = std::istream_iterator<swc_record>;
- std::vector<swc_record> records{swc_iter(is), swc_iter()};
-
- EXPECT_EQ(4u, records.size());
- EXPECT_EQ(3, records.back().id);
- }
-
- {
- // Check parse error context
- std::stringstream is;
- is << "1 1 14.566132 34.873772 7.857000 0.717830 -1\n";
- is << "2 2 14.566132 34.873772 7.857000 0.717830 1\n";
- is << "-3 2 14.566132 34.873772 7.857000 0.717830 1\n"; // invalid sample identifier -3
- is << "4 2 14.566132 34.873772 7.857000 0.717830 1\n";
-
- try {
- parse_swc_file(is);
- ADD_FAILURE() << "expected an exception\n";
- }
- catch (const swc_error& e) {
- EXPECT_EQ(3u, e.line_number);
- }
- }
-
- {
- // Test empty range
- std::stringstream is("");
- using swc_iter = std::istream_iterator<swc_record>;
- std::vector<swc_record> records{swc_iter(is), swc_iter()};
-
- EXPECT_TRUE(records.empty());
- }
-}
-