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Commit 7a11d761 authored by Vasileios Karakasis's avatar Vasileios Karakasis
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Refactoring: Implementation details in separate files. 

Moved SWC parser's and cell record's implementation details to a
separate file. Also added braces around single-line control/loop blocks.
parent e8bfa5b7
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CMakeLists.txt
+ 3
− 3
View file @ 7a11d761
......@@ -11,11 +11,11 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -pthread -Wall")
set(CMAKE_EXPORT_COMPILE_COMMANDS "YES")
# generated .a and .so go into /lib
#set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
#set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
include_directories(${CMAKE_SOURCE_DIR}/src)
include_directories(${CMAKE_SOURCE_DIR})
add_subdirectory(src)
add_subdirectory(tests)
src/CMakeLists.txt 0 → 100644
+ 8
− 0
View file @ 7a11d761
set(HEADERS
swcio.hpp
)
set(BASE_SOURCES
swcio.cpp
)
add_library(cellalgo ${BASE_SOURCES} ${HEADERS})
src/swcio.cpp 0 → 100644
+ 214
− 0
View file @ 7a11d761
#include <iomanip>
#include <map>
#include <sstream>
#include <unordered_set>
#include <swcio.hpp>
namespace nestmc
{
namespace io
{
//
// cell_record implementation
//
void cell_record::renumber(id_type new_id, std::map<id_type, id_type> &idmap)
{
auto old_id = id_;
id_ = new_id;
// Obtain parent_id from the map
auto new_parent_id = idmap.find(parent_id_);
if (new_parent_id != idmap.end()) {
parent_id_ = new_parent_id->second;
}
check_consistency();
idmap.insert(std::make_pair(old_id, new_id));
}
void cell_record::check_consistency() const
{
// Check cell type as well; enum's do not offer complete type safety,
// since you can cast anything that fits to its underlying type
if (type_ < 0 || type_ > custom) {
throw std::invalid_argument("unknown cell type");
}
if (id_ < 0) {
throw std::invalid_argument("negative ids not allowed");
}
if (parent_id_ < -1) {
throw std::invalid_argument("parent_id < -1 not allowed");
}
if (parent_id_ >= id_) {
throw std::invalid_argument("parent_id >= id is not allowed");
}
if (r_ < 0) {
throw std::invalid_argument("negative radii are not allowed");
}
}
std::istream &operator>>(std::istream &is, cell_record &cell)
{
swc_parser parser;
parser.parse_record(is, cell);
return is;
}
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;
}
//
// Utility functions
//
bool starts_with(const std::string &str, const std::string &prefix)
{
return (str.find(prefix) == 0);
}
void check_parse_status(const std::istream &is)
{
if (is.fail())
// If we try to read past the eof; fail bit will also be set
throw swc_parse_error("could not parse value");
}
template<typename T>
T parse_value_strict(std::istream &is)
{
T val;
check_parse_status(is >> val);
// everything's fine
return val;
}
// specialize parsing for cell types
template<>
cell_record::kind parse_value_strict(std::istream &is)
{
cell_record::id_type val;
check_parse_status(is >> val);
// Let cell_record's constructor check for the type validity
return static_cast<cell_record::kind>(val);
}
//
// swc_parser implementation
//
std::istream &swc_parser::parse_record(std::istream &is, cell_record &cell)
{
while (!is.eof() && !is.bad()) {
// consume empty and comment lines first
std::getline(is, linebuff_);
if (!linebuff_.empty() && !starts_with(linebuff_, comment_prefix_))
break;
}
if (is.bad()) {
// let the caller check for such events
return is;
}
if (is.eof() &&
(linebuff_.empty() || starts_with(linebuff_, comment_prefix_))) {
// last line is either empty or a comment; don't parse anything
return is;
}
if (is.fail()) {
throw swc_parse_error("too long line detected");
}
std::istringstream line(linebuff_);
cell = parse_record(line);
return is;
}
cell_record swc_parser::parse_record(std::istringstream &is)
{
auto id = parse_value_strict<int>(is);
auto type = parse_value_strict<cell_record::kind>(is);
auto x = parse_value_strict<float>(is);
auto y = parse_value_strict<float>(is);
auto z = parse_value_strict<float>(is);
auto r = parse_value_strict<float>(is);
auto parent_id = parse_value_strict<cell_record::id_type>(is);
// Convert to zero-based, leaving parent_id as-is if -1
if (parent_id != -1) {
parent_id--;
}
return cell_record(type, id-1, x, y, z, r, parent_id);
}
std::vector<cell_record> swc_read_cells(std::istream &is)
{
std::vector<cell_record> cells;
std::unordered_set<cell_record::id_type> ids;
std::size_t num_trees = 0;
cell_record::id_type last_id = -1;
bool needsort = false;
cell_record curr_cell;
while ( !(is >> curr_cell).eof()) {
if (curr_cell.parent() == -1 && ++num_trees > 1) {
// only a single tree is allowed
break;
}
auto inserted = ids.insert(curr_cell.id());
if (inserted.second) {
// not a duplicate; insert cell
cells.push_back(curr_cell);
if (!needsort && curr_cell.id() < last_id) {
needsort = true;
}
last_id = curr_cell.id();
}
}
if (needsort) {
std::sort(cells.begin(), cells.end());
}
// Renumber cells if necessary
std::map<cell_record::id_type, cell_record::id_type> idmap;
cell_record::id_type next_id = 0;
for (auto &c : cells) {
if (c.id() != next_id) {
c.renumber(next_id, idmap);
}
++next_id;
}
return std::move(cells);
}
} // end of nestmc::io
} // end of nestmc
src/swcio.hpp
+ 6
− 175
View file @ 7a11d761
......@@ -2,10 +2,7 @@
#include <exception>
#include <iostream>
#include <map>
#include <sstream>
#include <type_traits>
#include <unordered_set>
#include <string>
#include <vector>
namespace nestmc
......@@ -15,11 +12,6 @@ namespace io
{
static bool starts_with(const std::string &str, const std::string &prefix)
{
return (str.find(prefix) == 0);
}
class cell_record
{
public:
......@@ -147,41 +139,10 @@ public:
return 2*r_;
}
void renumber(id_type new_id, std::map<id_type, id_type> &idmap)
{
auto old_id = id_;
id_ = new_id;
// Obtain parent_id from the map
auto new_parent_id = idmap.find(parent_id_);
if (new_parent_id != idmap.end()) {
parent_id_ = new_parent_id->second;
}
check_consistency();
idmap.insert(std::make_pair(old_id, new_id));
}
void renumber(id_type new_id, std::map<id_type, id_type> &idmap);
private:
void check_consistency() const
{
// Check cell type as well; enum's do not offer complete type safety,
// since you can cast anything that fits to its underlying type
if (type_ < 0 || type_ > custom)
throw std::invalid_argument("unknown cell type");
if (id_ < 0)
throw std::invalid_argument("negative ids not allowed");
if (parent_id_ < -1)
throw std::invalid_argument("parent_id < -1 not allowed");
if (parent_id_ >= id_)
throw std::invalid_argument("parent_id >= id is not allowed");
if (r_ < 0)
throw std::invalid_argument("negative radii are not allowed");
}
void check_consistency() const;
kind type_; // cell type
id_type id_; // cell id
......@@ -216,50 +177,9 @@ public:
, comment_prefix_("#")
{ }
std::istream &parse_record(std::istream &is, cell_record &cell)
{
while (!is.eof() && !is.bad()) {
// consume empty and comment lines first
std::getline(is, linebuff_);
if (!linebuff_.empty() && !starts_with(linebuff_, comment_prefix_))
break;
}
if (is.bad())
// let the caller check for such events
return is;
if (is.eof() &&
(linebuff_.empty() || starts_with(linebuff_, comment_prefix_)))
// last line is either empty or a comment; don't parse anything
return is;
if (is.fail())
throw swc_parse_error("too long line detected");
std::istringstream line(linebuff_);
cell = parse_record(line);
return is;
}
std::istream &parse_record(std::istream &is, cell_record &cell);
private:
void check_parse_status(const std::istream &is)
{
if (is.fail())
// If we try to read past the eof; fail bit will also be set
throw swc_parse_error("could not parse value");
}
template<typename T>
T parse_value_strict(std::istream &is)
{
T val;
check_parse_status(is >> val);
// everything's fine
return val;
}
// Read the record from a string stream; will be treated like a single line
cell_record parse_record(std::istringstream &is);
......@@ -269,56 +189,7 @@ private:
};
// specialize parsing for cell types
template<>
cell_record::kind swc_parser::parse_value_strict(std::istream &is)
{
cell_record::id_type val;
check_parse_status(is >> val);
// Let cell_record's constructor check for the type validity
return static_cast<cell_record::kind>(val);
}
cell_record swc_parser::parse_record(std::istringstream &is)
{
auto id = parse_value_strict<int>(is);
auto type = parse_value_strict<cell_record::kind>(is);
auto x = parse_value_strict<float>(is);
auto y = parse_value_strict<float>(is);
auto z = parse_value_strict<float>(is);
auto r = parse_value_strict<float>(is);
auto parent_id = parse_value_strict<int>(is);
// Convert to zero-based, leaving parent_id as-is if -1
if (parent_id != -1)
parent_id--;
return cell_record(type, id-1, x, y, z, r, parent_id);
}
std::istream &operator>>(std::istream &is, cell_record &cell)
{
swc_parser parser;
parser.parse_record(is, cell);
return is;
}
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;
}
std::istream &operator>>(std::istream &is, cell_record &cell);
//
// Reads cells from an input stream until an eof is encountered and returns a
......@@ -327,47 +198,7 @@ std::ostream &operator<<(std::ostream &os, const cell_record &cell)
// For more information check here:
// https://github.com/eth-cscs/cell_algorithms/wiki/SWC-file-parsing
//
std::vector<cell_record> swc_read_cells(std::istream &is)
{
std::vector<cell_record> cells;
std::unordered_set<cell_record::id_type> ids;
std::size_t num_trees = 0;
cell_record::id_type last_id = -1;
bool needsort = false;
cell_record curr_cell;
while ( !(is >> curr_cell).eof()) {
if (curr_cell.parent() == -1 && ++num_trees > 1)
// only a single tree is allowed
break;
auto inserted = ids.insert(curr_cell.id());
if (inserted.second) {
// not a duplicate; insert cell
cells.push_back(curr_cell);
if (!needsort && curr_cell.id() < last_id)
needsort = true;
last_id = curr_cell.id();
}
}
if (needsort)
std::sort(cells.begin(), cells.end());
// Renumber cells if necessary
std::map<cell_record::id_type, cell_record::id_type> idmap;
cell_record::id_type next_id = 0;
for (auto &c : cells) {
if (c.id() != next_id)
c.renumber(next_id, idmap);
++next_id;
}
return std::move(cells);
}
std::vector<cell_record> swc_read_cells(std::istream &is);
} // end of nestmc::io
} // end of nestmc
tests/CMakeLists.txt
+ 5
− 6
View file @ 7a11d761
......@@ -18,10 +18,9 @@ set(TEST_SOURCES
add_executable(test.exe ${TEST_SOURCES} ${HEADERS})
#target_link_libraries(test_compiler LINK_PUBLIC compiler gtest)
#set_target_properties( test.exe
# PROPERTIES
# RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests"
#)
target_link_libraries(test.exe LINK_PUBLIC cellalgo)
set_target_properties(test.exe
PROPERTIES
RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/tests"
)
tests/test_swcio.cpp
+ 5
− 2
View file @ 7a11d761
......@@ -117,14 +117,16 @@ TEST(swc_parser, invalid_input)
{
// Check non-parsable values
std::istringstream is("1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
std::istringstream is(
"1a 1 14.566132 34.873772 7.857000 0.717830 -1\n");
cell_record cell;
EXPECT_THROW(is >> cell, swc_parse_error);
}
{
// Check invalid cell type
std::istringstream is("1 10 14.566132 34.873772 7.857000 0.717830 -1\n");
std::istringstream is(
"1 10 14.566132 34.873772 7.857000 0.717830 -1\n");
cell_record cell;
EXPECT_THROW(is >> cell, std::invalid_argument);
}
......@@ -214,6 +216,7 @@ TEST(swc_parser, from_allen_db)
while( !(fid >> node).eof()) {
nodes.push_back(std::move(node));
}
// verify that the correct number of nodes was read
EXPECT_EQ(nodes.size(), 1058u);
}
......
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