Loading src/include/file_io.h +73 −5 Original line number Diff line number Diff line Loading @@ -19,6 +19,8 @@ class FileSchema { protected: //! \brief Number of records conained in the file. int num_records; //! \brief Array of record names. std::string *record_names; //! \brief Array of record descriptors. std::string *record_types; Loading @@ -28,11 +30,28 @@ class FileSchema { * \param num_rec: `int` Number of records in the file. * \param rec_types: `string *` Description of the records in the file. */ FileSchema(int num_rec, std::string *rec_types); FileSchema(int num_rec, std::string *rec_types, std::string *rec_names=NULL); /*! \brief FileSchema instance destroyer. */ ~FileSchema(); /*! \brief Get the number of records in file. * * \return num_records: `int` The number of records contained in the file. */ int get_record_number() { return num_records; } /*! \brief Get a copy of the record types. * * \return rec_types: `string *` A new vector of strings with description of records. */ std::string *get_record_names(); /*! \brief Get a copy of the record names. * * \return rec_names: `string *` A new vector of strings with record names. */ std::string *get_record_types(); }; /*! \class HDFFile Loading @@ -43,28 +62,56 @@ class FileSchema { */ class HDFFile { protected: //! \brief Identifier list. List<hid_t> *id_list; //! \brief Name of the file. std::string file_name; //! \brief Flag for the open file status. bool file_open_flag; //! File identifier handle. hid_t file_id; //! Return status of the last operation. herr_t status; public: /*! \brief HDFFile instance constructor. * * \param name: `string` Name of the file. * \param flags: `unsigned int` File access flags. * \param fcpl_id: `hid_t` File creation property list identifier. * \param fapl_id: `hid_t` File access property list identifier. * \param flags: `unsigned int` File access flags (default is `H5F_ACC_EXCL`). * \param fcpl_id: `hid_t` File creation property list identifier (default is `H5P_DEFAULT`). * \param fapl_id: `hid_t` File access property list identifier (default is `H5P_DEFAULT`). */ HDFFile( std::string name, unsigned int flags = H5F_ACC_EXCL, hid_t fcpl_id = H5P_DEFAULT, hid_t fapl_id = H5P_DEFAULT ); /*! \brief HDFFile instance destroyer. */ ~HDFFile(); /*! \brief Close the current file. */ herr_t close(); /*! \brief Create an empty file from a `FileSchema` instance. * * \param schema: `FileSchema &` Reference to `FileSchema` instance. * \param name: `string` Name of the file. * \param flags: `unsigned int` File access flags (default is `H5F_ACC_EXCL`). * \param fcpl_id: `hid_t` File creation property list identifier (default is `H5P_DEFAULT`). * \param fapl_id: `hid_t` File access property list identifier (default is `H5P_DEFAULT`). * \return hdf_file: `HDFFile *` Pointer to a new, open HDF5 file. */ static HDFFile* from_schema( FileSchema &schema, std::string name, unsigned int flags = H5F_ACC_EXCL, hid_t fcpl_id = H5P_DEFAULT, hid_t fapl_id = H5P_DEFAULT ); /*! \brief Get current status. */ hid_t get_file_id() { return file_id; } /*! \brief Get current status. */ herr_t get_status() { return status; } Loading @@ -72,5 +119,26 @@ class HDFFile { /*! \brief Check whether the attached file is currently open. */ bool is_open() { return file_open_flag; } /* ! \brief Read data from attached file. */ // herr_t read(); /*! \brief Write data to attached file. * * \param dataset_name: `string` Name of the dataset to write to. * \param data_type: `string` Memory data type identifier. * \param buffer: `hid_t` Starting address of the memory sector to be written. * \param mem_space_id: `hid_t` Memory data space identifier (defaults to `H5S_ALL`). * \param file_space_id: `hid_t` File space identifier (defaults to `H5S_ALL`). * \param dapl_id: `hid_t` Data access property list identifier (defaults to `H5P_DEFAULT`). * \param dxpl_id: `hid_t` Data transfer property list identifier (defaults to `H5P_DEFAULT`). * \return status: `herr_t` Exit status of the operation. */ herr_t write( std::string dataset_name, std::string data_type, const void *buffer, hid_t mem_space_id=H5S_ALL, hid_t file_space_id=H5S_ALL, hid_t dapl_id=H5P_DEFAULT, hid_t dxpl_id=H5P_DEFAULT ); }; #endif src/libnptm/file_io.cpp +143 −4 Original line number Diff line number Diff line Loading @@ -2,32 +2,171 @@ * * \brief Implementation of file I/O operations. */ #include <stdexcept> #include <regex> #include <string> #include "hdf5.h" #ifndef INCLUDE_LIST_H_ #include "List.h" #endif #ifndef INCLUDE_FILE_IO_H_ #include "../include/file_io.h" #include "file_io.h" #endif using namespace std; FileSchema::FileSchema(int num_rec, string *rec_types) { FileSchema::FileSchema(int num_rec, string *rec_types, string *rec_names) { num_records = num_rec; record_types = new string[num_rec]; for (int i = 0; i < num_rec; i++) record_types[i] = rec_types[i]; record_names = new string[num_rec]; for (int i = 0; i < num_rec; i++) { record_types[i] = rec_types[i]; if (rec_names != NULL) record_names[i] = rec_names[i]; else record_names[i] = "/dset" + to_string(i); } } FileSchema::~FileSchema() { delete[] record_types; } FileSchema::~FileSchema() { delete[] record_names; delete[] record_types; } string* FileSchema::get_record_names() { string *rec_names = new string[num_records]; for (int i = 0; i < num_records; i++) rec_names[i] = record_names[i]; return rec_names; } string* FileSchema::get_record_types() { string *rec_types = new string[num_records]; for (int i = 0; i < num_records; i++) rec_types[i] = record_types[i]; return rec_types; } HDFFile::HDFFile(string name, unsigned int flags, hid_t fcpl_id, hid_t fapl_id) { file_name = name; file_id = H5Fcreate(name.c_str(), flags, fcpl_id, fapl_id); id_list = new List<hid_t>(1); id_list->set(0, file_id); if (file_id != H5I_INVALID_HID) file_open_flag = true; status = (herr_t)0; } HDFFile::~HDFFile() { if (H5Iis_valid(file_id) > 0) status = H5Fclose(file_id); delete id_list; } herr_t HDFFile::close() { status = H5Fclose(file_id); if (status == 0) file_open_flag = false; return status; } HDFFile* HDFFile::from_schema( FileSchema &schema, string name, unsigned int flags, hid_t fcpl_id, hid_t fapl_id ) { HDFFile *hdf_file = new HDFFile(name, flags, fcpl_id, fapl_id); hid_t file_id = hdf_file->get_file_id(); herr_t status; string *rec_types = schema.get_record_types(); string *rec_names = schema.get_record_names(); string known_types[] = {"INT32", "FLOAT64"}; int rec_num = schema.get_record_number(); regex re; smatch m; for (int ri = 0; ri < rec_num; ri++) { int rank = 0; hsize_t *dims, *max_dims; hid_t data_type; string str_target = rec_types[ri]; int type_index = 0; bool found_type = false; while (!found_type) { re = regex(known_types[type_index++]); if (regex_search(str_target, m, re)) { found_type = true; str_target = m.suffix().str(); if (type_index == 1) data_type = H5Tcopy(H5T_NATIVE_INT); else if (type_index == 2) data_type = H5Tcopy(H5T_NATIVE_DOUBLE); } if (type_index == 2) break; } if (found_type) { re = regex("[0-9]+"); string old_target = str_target; while (regex_search(str_target, m, re)) { rank++; str_target = m.suffix().str(); } dims = new hsize_t[rank](); max_dims = new hsize_t[rank](); str_target = old_target; for (int ti = 0; ti < rank; ti++) { regex_search(str_target, m, re); hsize_t dim = (hsize_t)stoi(m.str()); dims[ti] = dim; max_dims[ti] = dim; str_target = m.suffix().str(); } hid_t dataspace_id = H5Screate_simple(rank, dims, max_dims); hid_t dataset_id = H5Dcreate( file_id, rec_names[ri].c_str(), data_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT ); status = H5Sclose(dataspace_id); status = H5Dclose(dataset_id); delete[] dims; delete[] max_dims; } else { string message = "unrecognized type \"" + rec_types[ri] + "\"\n"; throw runtime_error(message); } } delete[] rec_types; delete[] rec_names; return hdf_file; } herr_t HDFFile::write( string dataset_name, string data_type, const void *buffer, hid_t mem_space_id, hid_t file_space_id, hid_t dapl_id, hid_t dxpl_id ) { string known_types[] = {"INT32", "FLOAT64"}; regex re; smatch m; bool found_type = false; int type_index = 0; while (!found_type) { re = regex(known_types[type_index++]); found_type = regex_search(data_type, m, re); if (type_index == 2) break; } if (found_type) { hid_t dataset_id = H5Dopen2(file_id, dataset_name.c_str(), dapl_id); hid_t mem_type_id; switch (type_index) { case 1: mem_type_id = H5T_NATIVE_INT; break; case 2: mem_type_id = H5T_NATIVE_DOUBLE; break; default: throw runtime_error("Unrecognized data type \"" + data_type + "\""); } if (dataset_id != H5I_INVALID_HID) { status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buffer); if (status == 0) status = H5Dclose(dataset_id); else status = (herr_t)-2; } else { status = (herr_t)-1; } } else { throw runtime_error("Unrecognized data type \"" + data_type + "\""); } return status; } Loading
src/include/file_io.h +73 −5 Original line number Diff line number Diff line Loading @@ -19,6 +19,8 @@ class FileSchema { protected: //! \brief Number of records conained in the file. int num_records; //! \brief Array of record names. std::string *record_names; //! \brief Array of record descriptors. std::string *record_types; Loading @@ -28,11 +30,28 @@ class FileSchema { * \param num_rec: `int` Number of records in the file. * \param rec_types: `string *` Description of the records in the file. */ FileSchema(int num_rec, std::string *rec_types); FileSchema(int num_rec, std::string *rec_types, std::string *rec_names=NULL); /*! \brief FileSchema instance destroyer. */ ~FileSchema(); /*! \brief Get the number of records in file. * * \return num_records: `int` The number of records contained in the file. */ int get_record_number() { return num_records; } /*! \brief Get a copy of the record types. * * \return rec_types: `string *` A new vector of strings with description of records. */ std::string *get_record_names(); /*! \brief Get a copy of the record names. * * \return rec_names: `string *` A new vector of strings with record names. */ std::string *get_record_types(); }; /*! \class HDFFile Loading @@ -43,28 +62,56 @@ class FileSchema { */ class HDFFile { protected: //! \brief Identifier list. List<hid_t> *id_list; //! \brief Name of the file. std::string file_name; //! \brief Flag for the open file status. bool file_open_flag; //! File identifier handle. hid_t file_id; //! Return status of the last operation. herr_t status; public: /*! \brief HDFFile instance constructor. * * \param name: `string` Name of the file. * \param flags: `unsigned int` File access flags. * \param fcpl_id: `hid_t` File creation property list identifier. * \param fapl_id: `hid_t` File access property list identifier. * \param flags: `unsigned int` File access flags (default is `H5F_ACC_EXCL`). * \param fcpl_id: `hid_t` File creation property list identifier (default is `H5P_DEFAULT`). * \param fapl_id: `hid_t` File access property list identifier (default is `H5P_DEFAULT`). */ HDFFile( std::string name, unsigned int flags = H5F_ACC_EXCL, hid_t fcpl_id = H5P_DEFAULT, hid_t fapl_id = H5P_DEFAULT ); /*! \brief HDFFile instance destroyer. */ ~HDFFile(); /*! \brief Close the current file. */ herr_t close(); /*! \brief Create an empty file from a `FileSchema` instance. * * \param schema: `FileSchema &` Reference to `FileSchema` instance. * \param name: `string` Name of the file. * \param flags: `unsigned int` File access flags (default is `H5F_ACC_EXCL`). * \param fcpl_id: `hid_t` File creation property list identifier (default is `H5P_DEFAULT`). * \param fapl_id: `hid_t` File access property list identifier (default is `H5P_DEFAULT`). * \return hdf_file: `HDFFile *` Pointer to a new, open HDF5 file. */ static HDFFile* from_schema( FileSchema &schema, std::string name, unsigned int flags = H5F_ACC_EXCL, hid_t fcpl_id = H5P_DEFAULT, hid_t fapl_id = H5P_DEFAULT ); /*! \brief Get current status. */ hid_t get_file_id() { return file_id; } /*! \brief Get current status. */ herr_t get_status() { return status; } Loading @@ -72,5 +119,26 @@ class HDFFile { /*! \brief Check whether the attached file is currently open. */ bool is_open() { return file_open_flag; } /* ! \brief Read data from attached file. */ // herr_t read(); /*! \brief Write data to attached file. * * \param dataset_name: `string` Name of the dataset to write to. * \param data_type: `string` Memory data type identifier. * \param buffer: `hid_t` Starting address of the memory sector to be written. * \param mem_space_id: `hid_t` Memory data space identifier (defaults to `H5S_ALL`). * \param file_space_id: `hid_t` File space identifier (defaults to `H5S_ALL`). * \param dapl_id: `hid_t` Data access property list identifier (defaults to `H5P_DEFAULT`). * \param dxpl_id: `hid_t` Data transfer property list identifier (defaults to `H5P_DEFAULT`). * \return status: `herr_t` Exit status of the operation. */ herr_t write( std::string dataset_name, std::string data_type, const void *buffer, hid_t mem_space_id=H5S_ALL, hid_t file_space_id=H5S_ALL, hid_t dapl_id=H5P_DEFAULT, hid_t dxpl_id=H5P_DEFAULT ); }; #endif
src/libnptm/file_io.cpp +143 −4 Original line number Diff line number Diff line Loading @@ -2,32 +2,171 @@ * * \brief Implementation of file I/O operations. */ #include <stdexcept> #include <regex> #include <string> #include "hdf5.h" #ifndef INCLUDE_LIST_H_ #include "List.h" #endif #ifndef INCLUDE_FILE_IO_H_ #include "../include/file_io.h" #include "file_io.h" #endif using namespace std; FileSchema::FileSchema(int num_rec, string *rec_types) { FileSchema::FileSchema(int num_rec, string *rec_types, string *rec_names) { num_records = num_rec; record_types = new string[num_rec]; for (int i = 0; i < num_rec; i++) record_types[i] = rec_types[i]; record_names = new string[num_rec]; for (int i = 0; i < num_rec; i++) { record_types[i] = rec_types[i]; if (rec_names != NULL) record_names[i] = rec_names[i]; else record_names[i] = "/dset" + to_string(i); } } FileSchema::~FileSchema() { delete[] record_types; } FileSchema::~FileSchema() { delete[] record_names; delete[] record_types; } string* FileSchema::get_record_names() { string *rec_names = new string[num_records]; for (int i = 0; i < num_records; i++) rec_names[i] = record_names[i]; return rec_names; } string* FileSchema::get_record_types() { string *rec_types = new string[num_records]; for (int i = 0; i < num_records; i++) rec_types[i] = record_types[i]; return rec_types; } HDFFile::HDFFile(string name, unsigned int flags, hid_t fcpl_id, hid_t fapl_id) { file_name = name; file_id = H5Fcreate(name.c_str(), flags, fcpl_id, fapl_id); id_list = new List<hid_t>(1); id_list->set(0, file_id); if (file_id != H5I_INVALID_HID) file_open_flag = true; status = (herr_t)0; } HDFFile::~HDFFile() { if (H5Iis_valid(file_id) > 0) status = H5Fclose(file_id); delete id_list; } herr_t HDFFile::close() { status = H5Fclose(file_id); if (status == 0) file_open_flag = false; return status; } HDFFile* HDFFile::from_schema( FileSchema &schema, string name, unsigned int flags, hid_t fcpl_id, hid_t fapl_id ) { HDFFile *hdf_file = new HDFFile(name, flags, fcpl_id, fapl_id); hid_t file_id = hdf_file->get_file_id(); herr_t status; string *rec_types = schema.get_record_types(); string *rec_names = schema.get_record_names(); string known_types[] = {"INT32", "FLOAT64"}; int rec_num = schema.get_record_number(); regex re; smatch m; for (int ri = 0; ri < rec_num; ri++) { int rank = 0; hsize_t *dims, *max_dims; hid_t data_type; string str_target = rec_types[ri]; int type_index = 0; bool found_type = false; while (!found_type) { re = regex(known_types[type_index++]); if (regex_search(str_target, m, re)) { found_type = true; str_target = m.suffix().str(); if (type_index == 1) data_type = H5Tcopy(H5T_NATIVE_INT); else if (type_index == 2) data_type = H5Tcopy(H5T_NATIVE_DOUBLE); } if (type_index == 2) break; } if (found_type) { re = regex("[0-9]+"); string old_target = str_target; while (regex_search(str_target, m, re)) { rank++; str_target = m.suffix().str(); } dims = new hsize_t[rank](); max_dims = new hsize_t[rank](); str_target = old_target; for (int ti = 0; ti < rank; ti++) { regex_search(str_target, m, re); hsize_t dim = (hsize_t)stoi(m.str()); dims[ti] = dim; max_dims[ti] = dim; str_target = m.suffix().str(); } hid_t dataspace_id = H5Screate_simple(rank, dims, max_dims); hid_t dataset_id = H5Dcreate( file_id, rec_names[ri].c_str(), data_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT ); status = H5Sclose(dataspace_id); status = H5Dclose(dataset_id); delete[] dims; delete[] max_dims; } else { string message = "unrecognized type \"" + rec_types[ri] + "\"\n"; throw runtime_error(message); } } delete[] rec_types; delete[] rec_names; return hdf_file; } herr_t HDFFile::write( string dataset_name, string data_type, const void *buffer, hid_t mem_space_id, hid_t file_space_id, hid_t dapl_id, hid_t dxpl_id ) { string known_types[] = {"INT32", "FLOAT64"}; regex re; smatch m; bool found_type = false; int type_index = 0; while (!found_type) { re = regex(known_types[type_index++]); found_type = regex_search(data_type, m, re); if (type_index == 2) break; } if (found_type) { hid_t dataset_id = H5Dopen2(file_id, dataset_name.c_str(), dapl_id); hid_t mem_type_id; switch (type_index) { case 1: mem_type_id = H5T_NATIVE_INT; break; case 2: mem_type_id = H5T_NATIVE_DOUBLE; break; default: throw runtime_error("Unrecognized data type \"" + data_type + "\""); } if (dataset_id != H5I_INVALID_HID) { status = H5Dwrite(dataset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buffer); if (status == 0) status = H5Dclose(dataset_id); else status = (herr_t)-2; } else { status = (herr_t)-1; } } else { throw runtime_error("Unrecognized data type \"" + data_type + "\""); } return status; }
