diff --git a/main.cpp b/main.cpp
index 88517ede7fcd3678bb98d0a2bda8052cb82c6700..ee24b1273b1f334b452defcaa3d6472fefb40cb4 100644
--- a/main.cpp
+++ b/main.cpp
@@ -1,6 +1,8 @@
+#include <array>
#include <iostream>
#include <fstream>
#include <numeric>
+#include <vector>
#include "gtest/gtest.h"
@@ -252,6 +254,18 @@ TEST(cell_tree, json_load) {
}
// SWC tests
+void expect_cell_equals(const neuron::io::cell_record &expected,
+ const neuron::io::cell_record &actual)
+{
+ EXPECT_EQ(expected.id(), actual.id());
+ EXPECT_EQ(expected.type(), actual.type());
+ 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.radius(), actual.radius());
+ EXPECT_EQ(expected.parent(), actual.parent());
+}
+
TEST(cell_record, construction)
{
using namespace neuron::io;
@@ -308,21 +322,14 @@ TEST(cell_record, construction)
EXPECT_EQ(cell.z(), 1.);
EXPECT_EQ(cell.radius(), 1.);
EXPECT_EQ(cell.diameter(), 2*1.);
- EXPECT_EQ(cell.parent_id(), -1);
+ EXPECT_EQ(cell.parent(), -1);
}
{
// check copy constructor
- cell_record proto_cell(cell_record::custom, 0, 1., 1., 1., 1., -1);
- cell_record cell(proto_cell);
- EXPECT_EQ(cell.id(), 0);
- EXPECT_EQ(cell.type(), cell_record::custom);
- EXPECT_EQ(cell.x(), 1.);
- EXPECT_EQ(cell.y(), 1.);
- EXPECT_EQ(cell.z(), 1.);
- EXPECT_EQ(cell.radius(), 1.);
- EXPECT_EQ(cell.diameter(), 2*1.);
- EXPECT_EQ(cell.parent_id(), -1);
+ cell_record cell_orig(cell_record::custom, 0, 1., 1., 1., 1., -1);
+ cell_record cell(cell_orig);
+ expect_cell_equals(cell_orig, cell);
}
}
@@ -330,20 +337,6 @@ TEST(swc_parser, invalid_input)
{
using namespace neuron::io;
- {
- // check empty file
- cell_record cell;
- std::istringstream is("");
- EXPECT_THROW(is >> cell, std::runtime_error);
- }
-
- {
- // check comment-only file
- cell_record cell;
- std::istringstream is("#comment\n#comment\n");
- EXPECT_THROW(is >> cell, std::runtime_error);
- }
-
{
// check incomplete lines; missing parent
std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830\n");
@@ -351,14 +344,6 @@ TEST(swc_parser, invalid_input)
EXPECT_THROW(is >> cell, std::logic_error);
}
- {
- // check incomplete lines; missing newline
- // FIXME: we should probably accept such files
- std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830 -1");
- cell_record cell;
- EXPECT_THROW(is >> cell, std::runtime_error);
- }
-
{
// Check long lines
std::istringstream is(std::string(256, 'a') + "\n");
@@ -387,31 +372,65 @@ TEST(swc_parser, valid_input)
using namespace neuron::io;
{
- // check valid input
- std::istringstream is("\
-# this is a comment\n\
-# this is a comment\n\
-1 1 14.566132 34.873772 7.857000 0.717830 -1 # end-of-line comment\n\
-");
- cell_record cell;
+ // check empty file; no cell may be parsed
+ cell_record cell, cell_orig;
+ std::istringstream is("");
EXPECT_NO_THROW(is >> cell);
- EXPECT_EQ(cell.id(), 0); // zero-based indexing
- EXPECT_EQ(cell.type(), cell_record::soma);
- EXPECT_FLOAT_EQ(cell.x(), 14.566132);
- EXPECT_FLOAT_EQ(cell.y(), 34.873772);
- EXPECT_FLOAT_EQ(cell.z(), 7.857000);
- EXPECT_FLOAT_EQ(cell.radius(), 0.717830);
- EXPECT_FLOAT_EQ(cell.parent_id(), -1);
+ expect_cell_equals(cell_orig, cell);
}
{
- // Test multiple records
+ // check comment-only file not ending with a newline;
+ // no cell may be parsed
+ cell_record cell, cell_orig;
+ std::istringstream is("#comment\n#comment");
+ EXPECT_NO_THROW(is >> cell);
+ expect_cell_equals(cell_orig, cell);
}
+
{
- // Test input ending with comments
+ // check last line case (no newline at the end)
+ std::istringstream is("1 1 14.566132 34.873772 7.857000 0.717830 -1");
+ cell_record cell;
+ EXPECT_NO_THROW(is >> cell);
+ EXPECT_EQ(0, cell.id()); // zero-based indexing
+ EXPECT_EQ(cell_record::soma, cell.type());
+ EXPECT_FLOAT_EQ(14.566132, cell.x());
+ EXPECT_FLOAT_EQ(34.873772, cell.y());
+ EXPECT_FLOAT_EQ( 7.857000, cell.z());
+ EXPECT_FLOAT_EQ( 0.717830, cell.radius());
+ EXPECT_FLOAT_EQ( -1, cell.parent());
}
+ {
+ // check valid input with a series of records
+ std::vector<cell_record> cells_orig = {
+ cell_record(cell_record::soma, 0,
+ 14.566132, 34.873772, 7.857000, 0.717830, -1),
+ cell_record(cell_record::dendrite, 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 : cells_orig)
+ swc_input << c << "\n";
+
+ swc_input << "# this is a final comment\n";
+ try {
+ std::size_t nr_records = 0;
+ cell_record cell;
+ while ( !(swc_input >> cell).eof()) {
+ ASSERT_LT(nr_records, cells_orig.size());
+ expect_cell_equals(cells_orig[nr_records], cell);
+ ++nr_records;
+ }
+ } catch (std::exception &e) {
+ ADD_FAILURE();
+ }
+ }
}
int main(int argc, char **argv) {
diff --git a/swcio.hpp b/swcio.hpp
index 7e9725b7e872b37338cad4f0d107688d9af8d0f9..9b2756f811be9366b9c8cb924f3c47924312ba92 100644
--- a/swcio.hpp
+++ b/swcio.hpp
@@ -1,5 +1,6 @@
#pragma once
+#include <cmath>
#include <exception>
#include <iostream>
#include <sstream>
@@ -68,48 +69,62 @@ public:
, y_(0)
, z_(0)
, r_(0)
- , parent_id_(0)
+ , parent_id_(-1)
{ }
cell_record(const cell_record &other) = default;
cell_record &operator=(const cell_record &other) = default;
- kind type()
+ friend bool operator==(const cell_record &lhs,
+ const cell_record &rhs)
+ {
+ return lhs.id_ == rhs.id_;
+ }
+
+ friend bool operator!=(const cell_record &lhs,
+ const cell_record &rhs)
+ {
+ return !(lhs == rhs);
+ }
+
+ friend std::ostream &operator<<(std::ostream &os, const cell_record &cell);
+
+ kind type() const
{
return type_;
}
- int id()
+ int id() const
{
return id_;
}
- int parent_id()
+ int parent() const
{
return parent_id_;
}
- float x()
+ float x() const
{
return x_;
}
- float y()
+ float y() const
{
return y_;
}
- float z()
+ float z() const
{
return z_;
}
- float radius()
+ float radius() const
{
return r_;
}
- float diameter()
+ float diameter() const
{
return 2*r_;
}
@@ -136,7 +151,6 @@ public:
{
init_linebuff();
}
-
swc_parser()
: delim_(" ")
@@ -152,7 +166,7 @@ public:
delete[] linebuff_;
}
- cell_record parse_record(std::istream &is)
+ std::istream &parse_record(std::istream &is, cell_record &cell)
{
while (!is.eof() && !is.bad()) {
// consume empty and comment lines first
@@ -161,17 +175,21 @@ public:
break;
}
- if (is.eof())
- throw std::runtime_error("unexpected eof found");
-
if (is.bad())
- throw std::runtime_error("i/o error");
+ // let the caller check for such events
+ return is;
+
+ if (is.eof() &&
+ (linebuff_[0] == 0 || linebuff_[0] == comment_prefix_))
+ // last line is either empty or a comment; don't parse anything
+ return is;
if (is.fail() && is.gcount() == max_line_ - 1)
throw std::runtime_error("too long line detected");
std::istringstream line(linebuff_);
- return parse_record(line);
+ cell = parse_record(line);
+ return is;
}
private:
@@ -186,16 +204,15 @@ private:
// If we try to read past the eof; fail bit will also be set
// FIXME: better throw a custom parse_error exception
throw std::logic_error("could not parse value");
-
- if (is.bad())
- throw std::runtime_error("i/o error");
}
+ // FIXME: need not to be a member function
template<typename T>
T parse_value_strict(std::istream &is)
{
T val;
is >> val;
+ // std::cout << val << "\n";
check_parse_status(is);
// everything's fine
@@ -246,12 +263,23 @@ cell_record swc_parser::parse_record(std::istringstream &is)
std::istream &operator>>(std::istream &is, cell_record &cell)
{
swc_parser parser;
- cell = parser.parse_record(is);
+ parser.parse_record(is, cell);
return is;
}
-std::ostream &operator<<(std::ostream &os, const cell_record &cell);
-
+std::ostream &operator<<(std::ostream &os, const cell_record &cell)
+{
+ // output in one-based indexing
+ os << cell.id_+1 << " "
+ << cell.type_ << " "
+ << std::setprecision(7) << cell.x_ << " "
+ << std::setprecision(7) << cell.y_ << " "
+ << std::setprecision(7) << cell.z_ << " "
+ << std::setprecision(7) << cell.r_ << " "
+ << ((cell.parent_id_ == -1) ? cell.parent_id_ : cell.parent_id_+1);
+
+ return os;
+}
} // end of neuron::io
} // end of neuron