From 6f06ea41c34a20af80005a1bf00e7920cf97f6d5 Mon Sep 17 00:00:00 2001
From: bcumming <bcumming@cscs.ch>
Date: Wed, 25 May 2016 11:58:19 +0200
Subject: [PATCH] add extra validation test for swc from file
---
src/cell.cpp | 36 ++++++++++++++++++++++++++++++++++++
src/cell.hpp | 6 ++++++
src/segment.hpp | 20 ++++++++++++++++++++
src/util.hpp | 15 +++++++++++++++
tests/test_swcio.cpp | 28 ++++++++++++++++++++++++++++
5 files changed, 105 insertions(+)
diff --git a/src/cell.cpp b/src/cell.cpp
index a6986f06..8fdd1bb6 100644
--- a/src/cell.cpp
+++ b/src/cell.cpp
@@ -195,5 +195,41 @@ std::vector<int> const& cell::segment_parents() const
return parents_;
}
+// Rough and ready comparison of two cells.
+// We don't use an operator== because equality of two cells is open to
+// interpretation. For example, it is possible to have two viable representations
+// of a cell: with and without location information for the cables.
+//
+// Checks that two cells have the same
+// - number and type of segments
+// - volume and area properties of each segment
+// - number of compartments in each segment
+bool cell_basic_equality(cell const& lhs, cell const& rhs)
+{
+ if(lhs.num_segments() != rhs.num_segments()) {
+ return false;
+ }
+ if(lhs.segment_parents() != rhs.segment_parents()) {
+ return false;
+ }
+ for(auto i=0; i<lhs.num_segments(); ++i) {
+ // a quick and dirty test
+ auto& l = *lhs.segment(i);
+ auto& r = *rhs.segment(i);
+
+ if(l.kind() != r.kind()) return false;
+ if(l.area() != r.area()) return false;
+ if(l.volume() != r.volume()) return false;
+ if(l.as_cable()) {
+ if( l.as_cable()->num_compartments()
+ != r.as_cable()->num_compartments())
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+}
+
} // namespace mc
} // namespace nest
diff --git a/src/cell.hpp b/src/cell.hpp
index ba5f9b6b..fece1349 100644
--- a/src/cell.hpp
+++ b/src/cell.hpp
@@ -123,6 +123,12 @@ class cell {
std::vector<std::pair<segment_location, i_clamp>> stimulii_;
};
+// Checks that two cells have the same
+// - number and type of segments
+// - volume and area properties of each segment
+// - number of compartments in each segment
+bool cell_basic_equality(cell const& lhs, cell const& rhs);
+
// create a cable by forwarding cable construction parameters provided by the user
template <typename... Args>
cable_segment* cell::add_cable(cell::index_type parent, Args ...args)
diff --git a/src/segment.hpp b/src/segment.hpp
index fd1d8ded..decb0cdd 100644
--- a/src/segment.hpp
+++ b/src/segment.hpp
@@ -76,6 +76,16 @@ class segment {
return nullptr;
}
+ virtual const cable_segment* as_cable() const
+ {
+ return nullptr;
+ }
+
+ virtual const soma_segment* as_soma() const
+ {
+ return nullptr;
+ }
+
virtual bool is_placeholder() const
{
return false;
@@ -230,6 +240,11 @@ class soma_segment : public segment
return this;
}
+ const soma_segment* as_soma() const override
+ {
+ return this;
+ }
+
/// soma has one and one only compartments
int num_compartments() const override
{
@@ -359,6 +374,11 @@ class cable_segment : public segment
return this;
}
+ const cable_segment* as_cable() const override
+ {
+ return this;
+ }
+
int num_compartments() const override
{
return num_compartments_;
diff --git a/src/util.hpp b/src/util.hpp
index 706ab7da..afa029ff 100644
--- a/src/util.hpp
+++ b/src/util.hpp
@@ -45,6 +45,21 @@ std::ostream& print(std::ostream &o, std::vector<T>const& v)
return o;
}
+template <typename T>
+bool operator ==(const std::vector<T>& lhs, const std::vector<T>& rhs)
+{
+ if(lhs.size() != rhs.size()) {
+ return false;
+ }
+ return std::equal(lhs.begin(), lhs.end(), rhs.begin());
+}
+
+template <typename T>
+bool operator !=(const std::vector<T>& lhs, const std::vector<T>& rhs)
+{
+ return !(lhs==rhs);
+}
+
namespace nest {
namespace mc {
namespace util {
diff --git a/tests/test_swcio.cpp b/tests/test_swcio.cpp
index 679260d6..6968fd43 100644
--- a/tests/test_swcio.cpp
+++ b/tests/test_swcio.cpp
@@ -487,3 +487,31 @@ TEST(swc_io, cell_construction)
cell.cable(3)->radius(0));
}
}
+
+// check that simple ball and stick model with one dendrite attached to a soma
+// which is used in the validation tests can be loaded from file and matches
+// the one generated with the C++ interface
+TEST(swc_parser, from_file_ball_and_stick)
+{
+ auto fname = "../data/ball_and_stick.swc";
+ std::ifstream fid(fname);
+ if(!fid.is_open()) {
+ std::cerr << "unable to open file " << fname << "... skipping test\n";
+ return;
+ }
+
+ // read the file into a cell object
+ auto cell = nest::mc::io::swc_read_cell(fid);
+
+ // verify that the correct number of nodes was read
+ EXPECT_EQ(cell.num_segments(), 2);
+ EXPECT_EQ(cell.num_compartments(), 2u);
+
+ // make an equivalent cell via C++ interface
+ nest::mc::cell local_cell;
+ local_cell.add_soma(6.30785);
+ local_cell.add_cable(0, nest::mc::segmentKind::dendrite, 0.5, 0.5, 200);
+
+ EXPECT_TRUE(nest::mc::cell_basic_equality(local_cell, cell));
+}
+
--
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