diff --git a/.gitignore b/.gitignore
index b710bef2b72c6b9f6eea87de726bf180c4f3a107..c1833bba173b6133b0970eb5dcd6cae4a4c69791 100644
--- a/.gitignore
+++ b/.gitignore
@@ -65,6 +65,7 @@ external/tmp
mechanisms/*.hpp
# build path
-build
+build*
commit.msg
+
diff --git a/miniapp/io.cpp b/miniapp/io.cpp
index fbc70ef823a660c4a14cb4610f1dd011251e4f2b..0ee643bfa29ef9164a27c8caaff9f5c4a50e053d 100644
--- a/miniapp/io.cpp
+++ b/miniapp/io.cpp
@@ -181,6 +181,8 @@ cl_options read_options(int argc, char** argv) {
TCLAP::ValueArg<util::optional<unsigned>> trace_max_gid_arg(
"T", "trace-max-gid", "only trace probes on cells up to and including <gid>",
false, defopts.trace_max_gid, "gid", cmd);
+ TCLAP::SwitchArg spike_output_arg(
+ "f","spike_file_output","save spikes to file", cmd, false);
cmd.reorder_arguments();
cmd.parse(argc, argv);
@@ -241,6 +243,7 @@ cl_options read_options(int argc, char** argv) {
update_option(options.probe_soma_only, probe_soma_only_arg);
update_option(options.trace_prefix, trace_prefix_arg);
update_option(options.trace_max_gid, trace_max_gid_arg);
+ update_option(options.spike_file_output, spike_output_arg);
save_file = ofile_arg.getValue();
}
diff --git a/src/io/exporter_spike_file.hpp b/src/io/exporter_spike_file.hpp
index e74169d19f17090c3ca16781a5f380fc0d29cc89..67c714209becbe140d2244a8a7e28552c41d7b8c 100644
--- a/src/io/exporter_spike_file.hpp
+++ b/src/io/exporter_spike_file.hpp
@@ -21,7 +21,6 @@ namespace io {
template <typename Time, typename CommunicationPolicy>
class exporter_spike_file : public exporter<Time, CommunicationPolicy> {
-
public:
using time_type = Time;
using spike_type = spike<cell_member_type, time_type>;
@@ -31,64 +30,69 @@ public:
// over_write if true will overwrite the specified output file (default = true)
// output_path relative or absolute path
// file_name will be appended with "_x" with x the rank number
- // file_extention a seperator will be added automatically
+ // file_extension a seperator will be added automatically
exporter_spike_file(
- const std::string& file_name, const std::string& path,
- const std::string& file_extention, bool over_write=true)
+ const std::string& file_name,
+ const std::string& path,
+ const std::string& file_extension,
+ bool over_write=true)
{
- auto file_path =
- create_output_file_path(file_name, path, file_extention,
- communication_policy_.id());
+ file_path_ =
+ create_output_file_path(
+ file_name, path, file_extension, communication_policy_.id());
//test if the file exist and depending on over_write throw or delete
- if (!over_write && file_exists(file_path)) {
- throw std::runtime_error("Tried opening file for writing but it exists and over_write is false: " +
- file_path);
+ if (!over_write && file_exists(file_path_)) {
+ throw std::runtime_error(
+ "Tried opening file for writing but it exists and over_write is false: " + file_path_);
}
- file_handle_.open(file_path);
+ file_handle_.open(file_path_);
}
// Performs the a export of the spikes to file
// one id and spike time with 4 decimals after the comma on a
// line space separated
void output(const std::vector<spike_type>& spikes) override {
-
for (auto spike : spikes) {
char linebuf[45];
- auto n = std::snprintf(linebuf, sizeof(linebuf), "%u %.4f\n",
- unsigned{spike.source.gid}, float(spike.time));
+ auto n =
+ std::snprintf(
+ linebuf, sizeof(linebuf), "%u %.4f\n",
+ unsigned{spike.source.gid}, float(spike.time));
file_handle_.write(linebuf, n);
}
}
bool good() const override {
-
return file_handle_.good();
}
// Creates an indexed filename
static std::string create_output_file_path(
- const std::string& file_name, const std::string& path,
- const std::string& file_extention, unsigned index)
+ const std::string& file_name,
+ const std::string& path,
+ const std::string& file_extension,
+ unsigned index)
{
- // Nest does not produce the indexing for nrank == 0
- // I have the feeling this disrupts consistent output. Id rather
- // always put the zero in. it allows a simpler regex when opening
- // files
- return path + file_name + "_" + std::to_string(index) + "." +
- file_extention;
+ return path + file_name + "_" + std::to_string(index) + "." + file_extension;
+ }
+
+ // The name of the output path and file name.
+ // May be either relative or absolute path.
+ const std::string& file_path() const {
+ return file_path_;
}
private:
bool file_exists(const std::string& file_path) {
-
std::ifstream fid(file_path);
return fid.good();
}
// Handle to opened file handle
std::ofstream file_handle_;
+ std::string file_path_;
communication_policy_type communication_policy_;
};
diff --git a/tests/global_communication/test_exporter_spike_file.cpp b/tests/global_communication/test_exporter_spike_file.cpp
index f7ba93571ad39fd6578ccc21949b073faebb93c2..4a85b0784801df6f91c72db70b44b69b36337f2b 100644
--- a/tests/global_communication/test_exporter_spike_file.cpp
+++ b/tests/global_communication/test_exporter_spike_file.cpp
@@ -19,21 +19,20 @@ protected:
nest::mc::io::exporter_spike_file<time_type, communicator_type>;
using spike_type = exporter_type::spike_type;
- std::string file_name;
- std::string path;
- std::string extention;
- unsigned index;
+ std::string file_name_;
+ std::string path_;
+ std::string extension_;
+ unsigned index_;
exporter_spike_file_fixture() :
- file_name("spikes_exporter_spike_file_fixture"),
- path("./"),
- extention("gdf"),
- index(0)
+ file_name_("spikes_exporter_spike_file_fixture"),
+ path_("./"),
+ extension_("gdf"),
+ index_(communicator_type::id())
{}
std::string get_standard_file_name() {
- return exporter_type::create_output_file_path(
- file_name, path, extention, 0);
+ return exporter_type::create_output_file_path(file_name_, path_, extension_, index_);
}
void SetUp() {
@@ -50,7 +49,7 @@ protected:
};
TEST_F(exporter_spike_file_fixture, constructor) {
- exporter_type exporter(file_name, path, extention, true);
+ exporter_type exporter(file_name_, path_, extension_, true);
//test if the file exist and depending on over_write throw or delete
std::ifstream f(get_standard_file_name());
@@ -58,14 +57,14 @@ TEST_F(exporter_spike_file_fixture, constructor) {
// We now know the file exists, so create a new exporter with overwrite false
try {
- exporter_type exporter1(file_name, path, extention, false);
+ exporter_type exporter1(file_name_, path_, extension_, false);
FAIL() << "expected a file already exists error";
}
- catch (std::runtime_error const & err) {
+ catch (const std::runtime_error& err) {
EXPECT_EQ(
err.what(),
- std::string("Tried opening file for writing but it exists and over_write is false: " +
- get_standard_file_name())
+ "Tried opening file for writing but it exists and over_write is false: " +
+ get_standard_file_name()
);
}
catch (...) {
@@ -86,7 +85,7 @@ TEST_F(exporter_spike_file_fixture, create_output_file_path) {
TEST_F(exporter_spike_file_fixture, do_export) {
{
- exporter_type exporter(file_name, path, extention);
+ exporter_type exporter(file_name_, path_, extension_);
// Create some spikes
std::vector<spike_type> spikes;