mirror of
https://git.rwth-aachen.de/acs/public/villas/node/
synced 2025-03-09 00:00:00 +01:00
minor changes
Signed-off-by: Alexandra <alexandra.bach@eonerc.rwth-aachen.de>
This commit is contained in:
Alexandra
parent
33f64ee642
commit
9bf579074a
2 changed files with 82 additions and 100 deletions
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@ -29,16 +29,16 @@ struct Sample;
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class HDF5node : public Node {
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protected:
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Format *formatter;
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FILE *stream_in; // File to read from.
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FILE *stream_out; // File to write to.
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// Format *formatter;
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// FILE *stream_in; // File to read from.
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// FILE *stream_out; // File to write to.
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char *uri_tmpl; // Format string for file name.
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char *uri; // Real file name.
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int flush; // Flush / upload file contents after each write.
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size_t buffer_size_out; // Defines size of output stream buffer. No buffer is created if value is set to zero.
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size_t buffer_size_in; // Defines size of input stream buffer. No buffer is created if value is set to zero.
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// int flush; // Flush / upload file contents after each write.
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// size_t buffer_size_out; // Defines size of output stream buffer. No buffer is created if value is set to zero.
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// size_t buffer_size_in; // Defines size of input stream buffer. No buffer is created if value is set to zero.
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// names
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const char *file_name;
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@ -50,23 +50,13 @@ protected:
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const char *author_name;
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const char *unit;
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// HDF5
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// H5File file(H5std_string(uri), H5F_ACC_TRUNC);
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// DataSet *dataset;
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// DataSpace *dataspace;
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// Attribute *timestamp_attr;
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// Attribute *location_attr;
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// Attribute *description_attr;
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// Attribute *project_attr;
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// Attribute *author_attr;
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struct attributes {
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int *timestamp;
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char *location;
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char *description;
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char *project;
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char *author;
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} attributes;
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hid_t file, dataset, dataspace, filespace, memspace, prop;
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herr_t status;
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int dim_row;
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// virtual int _read(struct Sample *smps[], unsigned cnt);
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@ -79,6 +69,8 @@ public:
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* Have a look at node.hpp/node.cpp for the default behaviour.
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*/
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HDF5node() : dim_row(0) {} // Initalize dim_row to 0
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virtual ~HDF5node();
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// virtual int prepare();
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@ -88,9 +80,9 @@ public:
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// Validate node configuration
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// virtual int check();
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// virtual int start();
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virtual int start();
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// virtual int stop();
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virtual int stop();
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// virtual
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// int pause();
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@ -23,6 +23,7 @@
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#include <villas/super_node.hpp>
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#include <villas/utils.hpp>
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#define RANK 2
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using namespace H5;
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using namespace villas;
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@ -55,6 +56,7 @@ int HDF5node::parse(json_t *json) {
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author_name = "none";
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json_error_t err;
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// TODO: include uri where to store file
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int ret = json_unpack_ex(json, &err, 0, "{ s: s, s: s, s?: s, s?: s, s?: s, s?: s, s: s }",
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"file", &file_name, "dataset", &dataset_name, "location", &location_name,
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"description", &description_name, "project", &project_name, "author", &author_name,
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@ -77,20 +79,43 @@ int HDF5node::parse(json_t *json) {
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// return 0;
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// }
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// int HDF5node::start() {
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// assert(state == State::PREPARED ||
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// state == State::PAUSED);
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// logger->debug("HDF5node::start()");
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// return Node::start();
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// }
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int HDF5node::start() {
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// Create a new empty file which will be extended in _write
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// int HDF5node::stop()
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// {
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// fclose(stream_in);
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// fclose(stream_out);
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hsize_t dims[2] = {0, 0}; /* dataset dimensions at creation time */
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hsize_t maxdims[2] = {H5S_UNLIMITED, H5S_UNLIMITED};
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// return 0;
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// }
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/* TODO: adapt chunk */
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hsize_t chunk_dims[2] = {2, 5};
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/* Create the data space with unlimited dimensions. */
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dataspace = H5Screate_simple(RANK, dims, maxdims);
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/* Create a new file. If file exists its contents will be overwritten. */
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file = H5Fcreate(file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
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/* Modify dataset creation properties, i.e. enable chunking */
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prop = H5Pcreate(H5P_DATASET_CREATE);
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status = H5Pset_chunk(prop, RANK, chunk_dims);
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/* Create a new dataset within the file using chunk
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creation properties. */
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dataset = H5Dcreate2(file, dataset_name, H5T_NATIVE_INT, dataspace, H5P_DEFAULT, prop, H5P_DEFAULT);
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logger->info("HDF5 file is initialized");
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return Node::start();
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}
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int HDF5node::stop()
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{
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status = H5Dclose(dataset);
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status = H5Pclose(prop);
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status = H5Sclose(dataspace);
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status = H5Fclose(file);
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return Node::stop();
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}
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// int HDF5node::pause()
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// {
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@ -145,78 +170,43 @@ int HDF5node::parse(json_t *json) {
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// similar to file node-type: takes the samples and writes them to a HDF5 file
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int HDF5node::_write(struct Sample *smps[], unsigned cnt) {
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// Create a new file using the default property lists.
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H5File file(H5std_string(file_name), H5F_ACC_TRUNC);
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// Create the data space for the dataset. Defines the size and shape of the dataset.
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logger->info("smps[0]->length {}", smps[0]->length);
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// hsize_t dims[2] = {cnt, 1}; // cnt rowns, smps[0]->length columns
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hsize_t dims[2] = {4, 6};
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DataSpace dataspace(2, dims);
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// TODO: adjust
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// dimension of the data which should be written
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hsize_t dimsext[2] = {4, 3}; /* extend dimensions */
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int dataext[7][3] = {{1, 2, 3}, {1, 2, 3}, {1, 2, 3}, {1, 2, 3}};
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// Create the dataset. Composes a collection of data elements, raw data and metadata.
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DataSet dataset = file.createDataSet(H5std_string(dataset_name), PredType::STD_I32BE, dataspace);
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// update dimension of row
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dim_row = dimsext[0] + dim_row;
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// Write the data to the dataset.
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// for (unsigned j = 0; j < cnt; j++) {
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// struct Sample *smp = smps[j];
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// // ret = formatter->print(stream_out, smp, j+1);
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// dataset.write(smp->data, PredType::NATIVE_DOUBLE);
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// }
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int data[4][6] = { {1, 2, 3, 4, 5, 6}, {7, 8, 9, 10, 11, 12}, {13, 14, 15, 16, 17, 18}, {19, 20, 21, 22, 23, 24}};
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dataset.write(data, H5::PredType::NATIVE_INT);
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/* Extend the dataset. Dataset becomes 10 x 3 */
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hsize_t size[2];
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size[0] = dim_row;
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size[1] = dimsext[1];
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status = H5Dset_extent(dataset, size);
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// Create a dataspace for the attribute
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DataSpace attr_dataspace(H5S_SCALAR);
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/* Select a hyperslab in extended portion of dataset */
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filespace = H5Dget_space(dataset);
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hsize_t offset[2];
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offset[0] = dim_row; // start at the end of the dataset
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offset[1] = 0;
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// Create a string datatype
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StrType strdatatype(PredType::C_S1, H5T_VARIABLE); // for variable-length string
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hsize_t dims[2];
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H5Sget_simple_extent_dims(filespace, dims, NULL);
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if (dim_row + dimsext[0] > dims[0])
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status = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL, dimsext, NULL);
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else
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throw RuntimeError("HDF5node::_write() - dimension of the data which should be written is too large");
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/* Define memory space */
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memspace = H5Screate_simple(RANK, dimsext, NULL);
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// Create the timestamp attribute and write to it
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Attribute timestampAttribute = dataset.createAttribute("timestamp", strdatatype, attr_dataspace);
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/* Write the data to the extended portion of dataset */
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status = H5Dwrite(dataset, H5T_NATIVE_INT, memspace, filespace, H5P_DEFAULT, dataext);
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// Get the current time
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auto now = std::chrono::system_clock::now();
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std::time_t now_c = std::chrono::system_clock::to_time_t(now);
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status = H5Sclose(filespace);
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status = H5Sclose(memspace);
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// Convert the current time to a string
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std::stringstream ss;
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ss << std::put_time(std::localtime(&now_c), "%Y-%m-%dT%H:%M:%S");
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std::string timestamp = ss.str();
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// Write the timestamp to the attribute
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timestampAttribute.write(strdatatype, timestamp);
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// Create the location attribute and write to it
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Attribute locationAttribute = dataset.createAttribute("location", strdatatype, attr_dataspace);
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// convert location_name to sting
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std::string location_name_string = location_name;
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locationAttribute.write(strdatatype, location_name_string);
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// Create the description attribute and write to it
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Attribute descriptionAttribute = dataset.createAttribute("description", strdatatype, attr_dataspace);
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std::string description_name_string = description_name;
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descriptionAttribute.write(strdatatype, description_name_string);
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// Create the project attribute and write to it
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Attribute projectAttribute = dataset.createAttribute("project", strdatatype, attr_dataspace);
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std::string project_name_string = project_name;
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projectAttribute.write(strdatatype, project_name_string);
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// Create the author attribute and write to it
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Attribute authorAttribute = dataset.createAttribute("author", strdatatype, attr_dataspace);
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std::string author_name_string = author_name;
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authorAttribute.write(strdatatype, author_name_string);
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logger->debug("attributes created and written");
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timestampAttribute.close(); // put in extra destroy function?
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locationAttribute.close();
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descriptionAttribute.close();
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projectAttribute.close();
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authorAttribute.close();
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dataset.close();
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file.close();
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logger->debug("HDF5node::_write() cnt: {}", cnt);
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return cnt;
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}
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