hdf/rtxi_hdf_matlabize.cpp

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/*
 Copyright (C) 2011 Georgia Institute of Technology, University of Utah, Weill Cornel Medical College

 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */

#include <errno.h>
#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <sstream>
#include <sys/stat.h>
#include <time.h>
#include <hdf5.h>
#include <hdf5_hl.h>

int main(int argc, char *argv[]) {

        // hide HDF5 stack tracks on all error returns
        H5Eset_auto2(H5E_DEFAULT, NULL, NULL);

        if (argc != 2) {
                fprintf(stderr, "Usage: %s <filename>\n", argv[0]);
                return -EINVAL;
        }

        char cmdBuff[200];
        sprintf(cmdBuff, "cp %s %s.old", argv[1], argv[1]);
        system(cmdBuff);
        struct tm* clock;
        struct stat attrib;
        stat(argv[1], &attrib);
        clock = localtime( &(attrib.st_mtime) ); // last modified time

        hid_t fid = H5Fopen(argv[1], H5F_ACC_RDWR, H5P_DEFAULT);
        if (fid < 0) {
                fprintf(stderr, "Failed to open %s.\n", argv[0]);
                return fid;
        }

        // create a temporary file to store the large amount of stream data
        char tempfile_template[] = "rtxi_hdf_matlabize.XXXXXX";
        int tmpfd = mkstemp(tempfile_template);
        if (tmpfd < 0) {
                fprintf(stderr,
                                "Failed to create a temporary file for buffering data.\n");
                return -errno;
        }
        unlink(tempfile_template);

        int trial_num = 1;
        std::stringstream trial_name;
        trial_name << "/Trial1";
        H5G_info_t junk;

        while (H5Gget_info_by_name(fid, trial_name.str().c_str(), &junk,
                        H5P_DEFAULT) >= 0) {

                // determine the dimension of the data
                trial_name << "/Synchronous Data/Channel Data";
                hid_t table = H5Dopen(fid, trial_name.str().c_str(), H5P_DEFAULT);
                if (table >= 0) {

                        hid_t type = H5Dget_type(table);
                        if (H5Tequal(type, H5T_IEEE_F64LE)) {
                                H5Dclose(type);
                                H5Dclose(table);

                                ++trial_num;
                                trial_name.str("");
                                trial_name << "/Trial" << trial_num;
                                continue;
                        }

                        hsize_t cols = H5Tget_size(type) / sizeof(double);
                        H5Dclose(type);
                        H5Dclose(table);

                        hsize_t rows;
                        table = H5PTopen(fid, trial_name.str().c_str());
                        H5PTget_num_packets(table, &rows);

                        lseek(tmpfd, SEEK_SET, 0);
                        for (int i = 0; i < rows; ++i) {
                                double data[cols];

                                H5PTget_next(table, 1, data);
                                write(tmpfd, data, sizeof(data));
                        }

                        H5PTclose(table);
                        H5Ldelete(fid, trial_name.str().c_str(), H5P_DEFAULT);

                        hsize_t dims[] = { rows, cols };
                        hid_t space = H5Screate_simple(2, dims, dims);
                        table = H5Dcreate(fid, trial_name.str().c_str(), H5T_IEEE_F64LE,
                                        space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                        H5Sclose(space);

                        lseek(tmpfd, SEEK_SET, 0);
                        {

                                hid_t data_space = H5Screate_simple(1, &cols, &cols);
                                H5Sselect_all(data_space);

                                double data[cols];
                                hsize_t start[2] = { 0, 0 };
                                hsize_t count[2] = { 1, cols };

                                hid_t select = H5Dget_space(table);

                                for (int i = 0; i < rows; ++i) {

                                        read(tmpfd, data, sizeof(data));

                                        start[0] = i;
                                        H5Sselect_hyperslab(select, H5S_SELECT_SET, start, NULL,
                                                        count, NULL);

                                        H5Dwrite(table, H5T_IEEE_F64LE, data_space, select,
                                                        H5P_DEFAULT, data);
                                }
                                H5Sclose(select);
                                H5Sclose(data_space);
                        }

                        H5Dclose(table);
                }

                trial_name.str("");
                trial_name << "/Trial" << trial_num;
                trial_name << "/Syncronous Data/Channel Data";
            table = H5Dopen(fid, trial_name.str().c_str(), H5P_DEFAULT);
                if (table >= 0) {

                        hid_t type = H5Dget_type(table);
                        if (H5Tequal(type, H5T_IEEE_F64LE)) {
                                H5Dclose(type);
                                H5Dclose(table);

                                ++trial_num;
                                trial_name.str("");
                                trial_name << "/Trial" << trial_num;
                                continue;
                        }

                        hsize_t cols = H5Tget_size(type) / sizeof(double);
                        H5Dclose(type);
                        H5Dclose(table);

                        hsize_t rows;
                        table = H5PTopen(fid, trial_name.str().c_str());
                        H5PTget_num_packets(table, &rows);

                        lseek(tmpfd, SEEK_SET, 0);
                        for (int i = 0; i < rows; ++i) {
                                double data[cols];

                                H5PTget_next(table, 1, data);
                                write(tmpfd, data, sizeof(data));
                        }

                        H5PTclose(table);
                        H5Ldelete(fid, trial_name.str().c_str(), H5P_DEFAULT);

                        hsize_t dims[] = { rows, cols };
                        hid_t space = H5Screate_simple(2, dims, dims);
                        table = H5Dcreate(fid, trial_name.str().c_str(), H5T_IEEE_F64LE,
                                        space, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
                        H5Sclose(space);

                        lseek(tmpfd, SEEK_SET, 0);
                        {

                                hid_t data_space = H5Screate_simple(1, &cols, &cols);
                                H5Sselect_all(data_space);

                                double data[cols];
                                hsize_t start[2] = { 0, 0 };
                                hsize_t count[2] = { 1, cols };

                                hid_t select = H5Dget_space(table);

                                for (int i = 0; i < rows; ++i) {

                                        read(tmpfd, data, sizeof(data));

                                        start[0] = i;
                                        H5Sselect_hyperslab(select, H5S_SELECT_SET, start, NULL,
                                                        count, NULL);

                                        H5Dwrite(table, H5T_IEEE_F64LE, data_space, select,
                                                        H5P_DEFAULT, data);
                                }
                                H5Sclose(select);
                                H5Sclose(data_space);
                        }

                        H5Dclose(table);
                }

                ++trial_num;
                trial_name.str("");
                trial_name << "/Trial" << trial_num;
        }

        H5Fclose(fid);
        close(tmpfd);
        sprintf(cmdBuff, "touch -m --date=\"%s\" %s", asctime(clock), argv[1]);
        sprintf(cmdBuff, "touch -m --date=\"%s\" %s.old", asctime(clock), argv[1]);
        printf("%s\n",asctime(clock));
        system(cmdBuff);

        return 0;

}