Merge pull request #80 from eth-cscs/exporter_fixes

Exporter fixes

.gitignore

@@ -65,6 +65,7 @@ external/tmp
 mechanisms/*.hpp
 
 # build path
-build
+build*
 
 commit.msg
+

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();
     }

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_;
 };

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;